2NY0
HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, T257S, V275C, S334A, S375W, A433M) Complexed with CD4 and Antibody 17b
- PDB DOI: https://doi.org/10.2210/pdb2NY0/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Human immunodeficiency virus 1, Homo sapiens
- Expression System: Homo sapiens, Escherichia coli
- Mutation(s): No
- Deposited: 2006-11-20 Released: 2007-02-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.242
- R-Value Work: 0.202
- R-Value Observed: 0.204
This is version 1.5 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ENVELOPE GLYCOPROTEIN GP120 | 317 | Human immunodeficiency virus 1 | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P19551 (Human immunodeficiency virus type 1 group M subtype B (isolate MFA)) Explore P19551 Go to UniProtKB: P19551 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P19551 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| T-cell surface glycoprotein CD4 | 184 | Homo sapiens | Mutation(s): 0 Gene Names: CD4 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01730 (Homo sapiens) Explore P01730 Go to UniProtKB: P01730 | |||||
PHAROS: P01730 GTEx: ENSG00000010610 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01730 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ANTIBODY 17B, LIGHT CHAIN | 214 | Homo sapiens | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for Q6P5S8 (Homo sapiens) Explore Q6P5S8 Go to UniProtKB: Q6P5S8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6P5S8 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ANTIBODY 17B, HEAVY CHAIN | 229 | Homo sapiens | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| HEZ Query on HEZ | Q [auth A] | HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.242
- R-Value Work: 0.202
- R-Value Observed: 0.204
- Space Group: P 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 71.887 | α = 90 |
| b = 87.309 | β = 90 |
| c = 196.459 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2007-02-06 Deposition Author(s): Zhou, T., Xu, L., Dey, B., Hessell, A.J., Van Ryk, D., Xiang, S.H., Yang, X., Zhang, M.Y., Zwick, M.B., Arthos, J., Burton, D.R., Dimitrov, D.S., Sodroski, J., Wyatt, R., Nabel, G.J., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2007-02-06
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.5: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary
