2NY7
HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12
- PDB DOI: https://doi.org/10.2210/pdb2NY7/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Human immunodeficiency virus 1, Homo sapiens
- Expression System: Homo sapiens, Cricetulus griseus
- Mutation(s): No 
- Deposited: 2006-11-20 Released: 2007-02-06 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.255 
- R-Value Work: 0.193 
- R-Value Observed: 0.196 
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 | A [auth G] | 317 | Human immunodeficiency virus 1 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04578  Go to UniProtKB:  P04578 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04578 | ||||
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 |
ANTIBODY b12, HEAVY CHAIN | B [auth H] | 230 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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 b12, LIGHT CHAIN | C [auth L] | 215 | Homo sapiens | Mutation(s): 0  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834 | |||||
PHAROS:  P01834 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01834 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | D [auth G] E [auth G] F [auth G] G H [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.255 
- R-Value Work: 0.193 
- R-Value Observed: 0.196 
- Space Group: P 65 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 101.955 | α = 90 |
b = 101.955 | β = 90 |
c = 298.294 | γ = 120 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | 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, Derived calculations, Structure summary - Version 1.5: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary