4R4H

Crystal structure of non-neutralizing, A32-like antibody 2.2c in complex with HIV-1 Env gp120

• PDB DOI: https://doi.org/10.2210/pdb4R4H/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM/INHIBITOR
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2014-08-19 Released: 2014-09-17 
• Deposition Author(s): Mclellan, J., Acharya, P., Huang, C.-C., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.28 Å
• R-Value Free: 0.320 
• R-Value Work: 0.309 
• R-Value Observed: 0.310 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 117.09 kDa 
• Atom Count: 7,415 
• Modelled Residue Count: 945 
• Deposited Residue Count: 1,041 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Env gp120	A	433	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q73372 (Human immunodeficiency virus type 1 group M subtype B (strain 89.6)) Explore Q73372  Go to UniProtKB:  Q73372

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD4	B	178	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 2.2c, Light chain	C [auth L]	210	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 2.2c, Heavy chain	D [auth H]	220	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.28 Å
• R-Value Free: 0.320 
• R-Value Work: 0.309 
• R-Value Observed: 0.310 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.357	α = 90
b = 69.429	β = 90
c = 328.576	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Mclellan, J., Acharya, P., Huang, C.-C., Kwong, P.D.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2014-10-22
  Changes: Database references
• Version 1.2: 2018-01-31
  Changes: Experimental preparation
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary