2NY1
HIV-1 gp120 Envelope Glycoprotein (I109C, T257S, S334A, S375W, Q428C) Complexed with CD4 and Antibody 17b
- PDB DOI: https://doi.org/10.2210/pdb2NY1/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: 1.99 Å
- R-Value Free: 0.250 
- R-Value Work: 0.209 
- R-Value Observed: 0.211 
This is version 2.1 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 Q993A8 (Human immunodeficiency virus 1) Explore Q993A8  Go to UniProtKB:  Q993A8 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q993A8 | ||||
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  | ||
UniProt | |||||
Find proteins for Q6N030 (Homo sapiens) Explore Q6N030  Go to UniProtKB:  Q6N030 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6N030 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900003 Query on PRD_900003 | E | sucrose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.250 
- R-Value Work: 0.209 
- R-Value Observed: 0.211 
- Space Group: P 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 71.113 | α = 90 |
b = 88.156 | β = 90 |
c = 197.672 | 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: 2018-01-24
Changes: Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary