4XMP

Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with HIV-1 clade A strain Q842.d12 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.165

Literature

Macromolecules
Sequence Display for 4XMP

Classification: IMMUNE SYSTEM

Total Structure Weight: 90549.73

Macromolecule Entities
Molecule Chains Length Organism Details
Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160 G 354 Human immunodeficiency virus 1 Fragment: UNP RESIDUES 43-122, 195-297, 319-481
Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HEAVY CHAIN OF ANTIBODY VRC08 H 235 Homo sapiens Gene Name(s): IGHG1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
LIGHT CHAIN OF ANTIBODY VRC08 L 211 Homo sapiens Gene Name(s): IGKC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

G N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BU3
Query on BU3

G (R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
H L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.165
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 69.71 α = 90.00
b = 82.50 β = 90.00
c = 163.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-01-15
  • Released Date: 2015-04-29
  • Deposition author(s): Zhou, T., Srivatsan, S., Kwong, P.D.

Revision History

  • Version 1_0: 2015-04-29

    Type: Initial release

  • Version 1_1: 2015-05-06

    Type: Database references