Limited breadth of anti-HIV Env glycan hole antibodies is further hindered by strain-specific peptide interactions
Ozorowski, G., Cottrell, C.A., de Val, N., Scaringi, N., Polveroni, T.M., Ward, A.B.To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
BG505 HIV-1 Env gp120 | A, E [auth C], I [auth G] | 516 | Human immunodeficiency virus 1 | Mutation(s): 6  Gene Names: env | ![]() |
UniProt | |||||
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q2N0S6 | ||||
Glycosylation | |||||
Glycosylation Sites: 16 | |||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
BG505 HIV-1 Env gp41 | B, F [auth D], J [auth I] | 153 | Human immunodeficiency virus 1 | Mutation(s): 2  Gene Names: env | ![]() |
UniProt | |||||
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q2N0S6 | ||||
Sequence AnnotationsExpand | |||||
|
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
monoclonal antibody 11B kappa chain | C [auth L], G [auth E], K [auth J] | 237 | Oryctolagus cuniculus | Mutation(s): 0  | ![]() |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
monoclonal antibody 11B fragment antigen binding heavy chain | D [auth H], H [auth F], L [auth K] | 241 | Oryctolagus cuniculus | Mutation(s): 0  | ![]() |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | M, O, P, Q, S M, O, P, Q, S, T, U, W, X | 2 | N/A | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | N, R, V | 4 | N/A | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth A] AB [auth G] BA [auth A] BB [auth G] CA [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Task | Software Package | Version |
---|---|---|
MODEL REFINEMENT | Rosetta | 2020.03.61102 |
RECONSTRUCTION | cryoSPARC | 2 |
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | UM1AI100663 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | UM1 AI144462 |
Bill & Melinda Gates Foundation | United States | OPP1115782 |