¶ Introduction
This section of the API documentation provides detailed instructions on how to register and display structure residue annotations. These are not to be confused with structure annotations, described here
When a structure chain is mapped to a UniProt sequence, its residues inherit UniProt sequence annotations (e.g., Pfam and PROSITE domains and sites). However, some chains may not have a corresponding UniProt entry—such as internal antibody or nanobody chains. In other cases, internal data (e.g. predicted properties) may be available to enrich the structure.
In both scenarios, users can register custom annotations directly at the structure residue level. These are referred to as structure residue annotations, and they can be added to any user-registered structure.
Common examples of structure residue annotations include:
- CDR regions
- Chemical liability motifs
- Alternative residue numbering schemes
Whether experimental or predicted, these annotations are essential for internal analysis and decision-making.
Unlike biomolecular sequence annotations, structure residue annotations are specific to the structure and are not linked back to the underlying biomolecular sequence. They follow the same privacy settings as the structure itself, meaning only users with access to the structure can view its associated annotations.
Only users that is the owner of a structure, or has the privilege to "manage structure annotations" can add annotations to a structure.
Like UniProt sequence annotations, structure residue annotations are displayed in the Annotation Browser, where they can be highlighted in 3D in a simple click.
¶ Adding Structure Residue Annotations
To register structure residue annotations, follow these steps:
- Verify that you have the privilege to
manage structure annotationson the structure. If this is not the case, ask the owner of the structure, or and admin to grant you this privilege via theMy Structurespanel or the API endpointPOST /structures/{id}/user/email/privileges/{privilegename} - Register the
annotation type labelsyou want to use for the structure residue annotations. These labels are displayed on the left hand side of the Annotation Browser and regroup annotations of the same type in a single line. The annotation type labels are registered via the endpointPOST /annotation-types. More details can be found here. - Register the
structure residue annotationsvia the API endpointPOST /annotations/structure-residues. The payload includes the following parameters:
label: the value of the annotation. It can be a numeric value or a string, e.g. "CDR-H1"typeLabel: the annotation type label (registered in the previous step), e.g. "Antibody"source: the source of the annotation, e.g. "MOE 2024",link: URL to source or reference, e.g. "https://doi.org/10.1128/JVI.00660-20"authResNum: residue number, e.g. 105authChain: chain code of the residue, e.g. "A"insertionCode: isnertion code of the residue, e.g. ""externalCode: 6-digit code that identifies a structure registered by a User, e.g."123abc",
¶ Sequence Mapping and Annotation Independence
Sequence Mapping is one of several post-registration analyses triggered automatically after structure registration. If a structure chain is poorly mapped, any user can relaunch the sequence analysis via the API by providing the correct UniProt code(s). More details on this process can be found here.
Importantly, relaunching the Sequence Mapping analysis does not affect structure residue annotations.
¶ Example 1: Annotate a range of resiudes with CDR labels
In this example, we will add CDR annotations to a range of residue in an antibody structure.
- Register the annotation type label via the API endpoint
POST /annotation-types:
{
"annot_type_label": "Antibody CDR (IMGT definition)"
}
- Register the structure residue annotation via the API endpoint
POST /annotations/structure-residueswith the following payload:
payload
{
"annotations": [
{
"annotation": {
"label": "CDR-H1",
"typeLabel": "Antibody CDR (IMGT definition)",
"source": "MOE",
"link": "",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 26,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 27,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 28,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 29,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 30,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 31,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 32,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 33,
"authChain": "H",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "CDR-H2",
"typeLabel": "Antibody CDR (IMGT definition)",
"source": "MOE",
"link": "",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 51,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 52,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 53,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 54,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 55,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 56,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 57,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 58,
"authChain": "H",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "CDR-H3",
"typeLabel": "Antibody CDR (IMGT definition)",
"source": "MOE",
"link": "",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 97,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 98,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 99,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 100,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 101,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 102,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 103,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 104,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 105,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 106,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 107,
"authChain": "H",
"insertionCode": ""
},
{
"authResNum": 108,
"authChain": "H",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "CDR-L1",
"typeLabel": "Antibody CDR (IMGT definition)",
"source": "MOE",
"link": "",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 27,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 28,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 29,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 30,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 31,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 32,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "CDR-L2",
"typeLabel": "Antibody CDR (IMGT definition)",
"source": "MOE",
"link": "",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 50,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 51,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 52,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "CDR-L3",
"typeLabel": "Antibody CDR (IMGT definition)",
"source": "MOE",
"link": "",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 89,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 90,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 91,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 92,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 93,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 94,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 95,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 96,
"authChain": "L",
"insertionCode": ""
},
{
"authResNum": 97,
"authChain": "L",
"insertionCode": ""
}
]
}
],
"externalCode": "hlt3av",
"commit": true
}
¶ Example 2: Annotate residues with predicted properties
In this example, we will add annotations with numeric values to individual residue in an antibody structure.
- Register all annotation type labels that do not yet exist in the database. Use individual call via API endpoint
POST /annotation-types:
{
"annot_type_label": "SASA"
}
{
"annot_type_label": "pKa"
}
{
"annot_type_label": "Exposure"
}
- Register the structure residue annotation via the API endpoint
POST /annotations/structure-residueswith the following payload:
payload
{
"annotations": [
{
"annotation": {
"label": "187.8",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 1,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "7.72",
"typeLabel": "pKa",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 1,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "94.0",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 1,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "14.1",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 2,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "6.2",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 2,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "99.5",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 3,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "50.9",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 3,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "0.0",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 4,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "0.0",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 4,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "84.9",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 5,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "48.7",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 5,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "2.5",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 6,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "1.2",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 6,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "61.6",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 7,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "42.2",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 7,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "53.2",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 8,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "31.0",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 8,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "78.2",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 9,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "56.9",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 9,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "121.8",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 10,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "54.8",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 10,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "46.9",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 11,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "19.2",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 11,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "46.1",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 12,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "31.6",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 12,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "2.6",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 13,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "1.9",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 13,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "42.2",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 14,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "28.9",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 14,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "87.6",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 15,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "51.0",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 15,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "49.7",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 16,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "49.5",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 16,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "85.7",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 17,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "3.63",
"typeLabel": "pKa",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 17,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "41.3",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 17,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "135.1",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 18,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "10.22",
"typeLabel": "pKa",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 18,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "57.4",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 18,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "5.5",
"typeLabel": "SASA",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 19,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "2.8",
"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 19,
"authChain": "L",
"insertionCode": ""
}
]
},
{
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"typeLabel": "Exposure",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 107,
"authChain": "L",
"insertionCode": ""
}
]
}
],
"externalCode": "qsu7de",
"commit": true
}
¶ Example 3: Annotate individual resiudes with text labels
In this example, we will add oxidation site annotations to individual residue in an antibody structure.
- Register the annotation type label via the API endpoin
POST /annotation-types:
{
"annot_type_label": "Oxidation"
}
- Register the structure residue annotation via the API endpoint
POST /annotations/structure-residueswith the following payload:
payload
{
"annotations": [
{
"annotation": {
"label": "Oxidation",
"typeLabel": "Oxidation",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 11,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "Oxidation",
"typeLabel": "Oxidation",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 47,
"authChain": "L",
"insertionCode": ""
}
]
},
{
"annotation": {
"label": "Oxidation",
"typeLabel": "Oxidation",
"source": "3dpredict",
"link": "https://doi.org/10.1128/JVI.00660-20",
"groups": null,
"data": null
},
"location": [
{
"authResNum": 91,
"authChain": "L",
"insertionCode": ""
}
]
}
],
"externalCode": "i45k8u",
"commit": true
}