5I8H

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3 Loop-targeting Antibody PGT122 Fab and Fusion Peptide-targeting Antibody VRC34.01 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.309
  • R-Value Work: 0.281

Literature

Macromolecules
Sequence Display for 5I8H

Classification: IMMUNE SYSTEM

Total Structure Weight: 356089.38

Macromolecule Entities
Molecule Chains Length Organism Details
BG505 SOSIP.664 gp120 A, C 481 Human immunodeficiency virus 1 Mutation: T332N, A501C, E509R, K510R
Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
BG505 SOSIP.664 gp41 B, D 153 Human immunodeficiency virus 1 Mutation: T605C
Gene Name(s): env
PGT122 Fab light chain J, L 210 Homo sapiens
VRC34.01 Fab heavy chain E, G 223 Homo sapiens
VRC34.01 Fab light chain F, H 212 Homo sapiens
PGT122 Fab heavy chain I, K 235 Homo sapiens

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

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

A, C, I BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.309
  • R-Value Work: 0.281
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 252.30 α = 90.00
b = 252.30 β = 90.00
c = 561.20 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-02-18
  • Released Date: 2016-05-25
  • Deposition author(s): Xu, K., Zhou, T., Kwong, P.D.

Revision History

  • Version 1_0: 2016-05-25

    Type: Initial release

  • Version 1_1: 2016-06-01

    Type: Derived calculations

  • Version 1_2: 2017-09-20

    Type: Author supporting evidence, Derived calculations