7L79

Crystal structure of broadly HIV-1-neutralizing antibody VRC40.01

• PDB DOI: https://doi.org/10.2210/pdb7L79/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-12-27 Released: 2021-10-27 
• Deposition Author(s): Zhou, T., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.280 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Literature

Crystal structure of broadly HIV-1-neutralizing antibody

Zhou, T.

(2021) Cell Rep 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.14 kDa 
• Atom Count: 6,885 
• Modelled Residue Count: 886 
• Deposited Residue Count: 888 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of VRC40.01	A [auth H], C [auth A]	230	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of VRC40.01	B [auth L], D [auth B]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth H], F [auth L], G [auth L], H [auth L], I [auth L], J [auth L], K [auth B], L [auth B], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.280 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.792	α = 90
b = 135.95	β = 90
c = 136.908	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-10-27 
Deposition Author(s): Zhou, T., Kwong, P.D.

Revision History  

• Version 1.0: 2021-10-27
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description