4XVS
Crystal structure of HIV-1 donor 45 d45-01dG5 coreE gp120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995)
- PDB DOI: https://doi.org/10.2210/pdb4XVS/pdb
- Classification: Viral protein/Immune system
- Organism(s): Homo sapiens, Human immunodeficiency virus 1
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2015-01-27 Released: 2015-05-06 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.214 
- R-Value Work: 0.194 
- R-Value Observed: 0.195 
This is version 1.3 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
VRC07_1995 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 Heavy chain | A [auth H] | 228 | 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: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 Light chain | B [auth L] | 210 | 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 |
Donor 45 01dG5 coreE gp120 | C [auth G] | 375 | Human immunodeficiency virus 1 | Mutation(s): 0  | |
UniProt | |||||
Find proteins for H9DP89 (Human immunodeficiency virus 1) Explore H9DP89  Go to UniProtKB:  H9DP89 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | H9DP89 | ||||
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: 1.90 Å
- R-Value Free: 0.214 
- R-Value Work: 0.194 
- R-Value Observed: 0.195 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 67.641 | α = 90 |
b = 69.334 | β = 90 |
c = 200.546 | γ = 90 |
Software Name | Purpose |
---|---|
BUSTER | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2015-05-06  Deposition Author(s): Joyce, M.G., Mascola, J.R., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2015-05-06
Type: Initial release - Version 1.1: 2016-07-27
Changes: Data collection - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary