5KZC

Crystal structure of an HIV-1 gp120 engineered outer domain with a Man9 glycan at position N276, in complex with broadly neutralizing antibody VRC01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.223

Literature

Macromolecules
Sequence Display for 5KZC

Classification: IMMUNE SYSTEM

Total Structure Weight: 207308.39

Macromolecule Entities
Molecule Chains Length Organism Details
VRC01 Fab heavy chain B, E, H 224 Homo sapiens
Engineered outer domain of gp120 A, C, F 182 Homo sapiens
VRC01 Fab light chain D, G, L 210 Homo sapiens

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

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

A, C, F 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: 3.25 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.223
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 113.51 α = 90.00
b = 113.51 β = 90.00
c = 412.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-07-24
  • Released Date: 2016-08-10
  • Deposition author(s): Julien, J.-P., Jardine, J.G., Diwanji, D., Schief, W.R., Wilson, I.A.

Revision History

  • Version 1_0: 2016-08-10

    Type: Initial release

  • Version 1_1: 2016-09-07

    Type: Database references

  • Version 1_2: 2017-09-06

    Type: Author supporting evidence, Derived calculations