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 
• Deposition Author(s): Joyce, M.G., Mascola, J.R., Kwong, P.D.

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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 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91.53 kDa 
• Atom Count: 6,783 
• Modelled Residue Count: 780 
• Deposited Residue Count: 813 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
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 ID: 2
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 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth G], E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [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 Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Joyce, M.G., Mascola, J.R., Kwong, P.D.

Revision History  

• 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