3NGB

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120

Structural Biology Knowledgebase: 3NGB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3NGB

Classification: VIRAL PROTEIN / IMMUNE SYSTEM

Total Structure Weight: 363539.16

Macromolecule Entities
Molecule Chains Length Organism Details
Envelope glycoprotein gp160 A, D, G, I 353 Human immunodeficiency virus 1 Fragment: UNP RESIDUES 43-122, 201-303, 325-486
Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Antigen binding fragment of heavy chain: Antibody VRC01 B, E, H, J 224 Homo sapiens
Antigen binding fragment of light chain: Antibody VRC01 C, F, K, L 210 Homo sapiens

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, C, D, F, G, I, K, L N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

C, K, L ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

A, B, C, D, E, G, I, J BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

C, K, L BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A, D, I, J, K 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.197
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 108.63 α = 90.00
b = 98.28 β = 99.68
c = 205.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-06-11
  • Released Date: 2010-07-07
  • Deposition author(s): Zhou, T., Kwong, P.D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4