2B4C
Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody
- PDB DOI: https://doi.org/10.2210/pdb2B4C/pdb
- Classification: Viral protein/Immune system
- Organism(s): Human immunodeficiency virus 1, Homo sapiens
- Expression System: Drosophila melanogaster, Cricetulus griseus, Escherichia coli
- Mutation(s): No 
- Deposited: 2005-09-23 Released: 2005-11-15 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.30 Å
- R-Value Free: 0.349 
- R-Value Work: 0.319 
- R-Value Observed: 0.319 
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 | A [auth G] | 344 | Human immunodeficiency virus 1 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q75760 (Human immunodeficiency virus 1) Explore Q75760  Go to UniProtKB:  Q75760 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q75760 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
T-cell surface glycoprotein CD4 | B [auth C] | 181 | 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 | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
anti-HIV-1 gp120 immunoglobulin X5 light chain | C [auth L] | 215 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
anti-HIV-1 gp120 immunoglobulin X5 heavy chain | D [auth H] | 235 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | F [auth G], G, H [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
XYL Query on XYL | K [auth H], L [auth H], M [auth H] | Xylitol C5 H12 O5 HEBKCHPVOIAQTA-SCDXWVJYSA-N | |||
SO4 Query on SO4 | I [auth G], J [auth L], N [auth H], O [auth H], P [auth H] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.30 Å
- R-Value Free: 0.349 
- R-Value Work: 0.319 
- R-Value Observed: 0.319 
- Space Group: P 6 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 225.993 | α = 90 |
b = 225.993 | β = 90 |
c = 97.968 | γ = 120 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
SCALEPACK | data scaling |
CNS | refinement |
HKL-2000 | data reduction |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2005-11-15  Deposition Author(s): Huang, C., Tang, M., Zhang, M.Y., Majeed, S., Montabana, E., Stanfield, R.L., Dimitrov, D.S., Korber, B., Sodroski, J., Wilson, I.A., Wyatt, R., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2005-11-15
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2017-08-16
Changes: Refinement description, Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary