4NCO

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.7 Å
  • R-Value Free: 0.389
  • R-Value Work: 0.375

Literature

Macromolecules
Sequence Display for 4NCO

Classification: VIRAL PROTEIN / IMMUNE SYSTEM

Total Structure Weight: 352718.28

Macromolecule Entities
Molecule Chains Length Organism Details
BG505 SOSIP gp120 A, E, I 475 Human immunodeficiency virus 1 Fragment: UNP residues 30-504
Mutation: T332N, A501C
Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
BG505 SOSIP gp41 B, F, J 78 Human immunodeficiency virus 1 Fragment: SEE REMARK 999
PGT122 light chain C, G, K 211 Homo sapiens Fragment: Fab
PGT122 heavy chain D, H, L 235 Homo sapiens Fragment: Fab

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

A, E, I N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, C, E, G, I, K ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, E, I BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
B, F, J L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.7 Å
  • R-Value Free: 0.389
  • R-Value Work: 0.375
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 152.20 α = 90.00
b = 260.72 β = 99.56
c = 283.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-24
  • Released Date: 2013-11-13
  • Deposition author(s): Julien, J.-P., Stanfield, R.L., Lyumkis, D., Ward, A.B., Wilson, I.A.

Revision History

  • 2014-01-15
    Type: Database references