4LSQ

Crystal structure of broadly and potently neutralizing antibody VRC-CH31 in complex with HIV-1 clade A/E gp120 93TH057 with LOOP D and Loop V5 from clade A strain 3415_v1_c1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 4LSQ

Classification: viral protein / immune system

Total Structure Weight: 90449.76

Macromolecule Entities
Molecule Chains Length Organism Details
ENVELOPE GLYCOPROTEIN GP120 WITH LOOP D AND V5 FROM STRAIN 3415_V1_C1 G 352 Human immunodeficiency virus 1 Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HEAVY CHAIN OF ANTIBODY VRC-CH31 H 236 Homo sapiens
LIGHT CHAIN OF ANTIBODY VRC-CH31 WITH N70D MUTATION L 210 Homo sapiens

Small Molecules
Ligands 5 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)
CD
Query on CD

G, H, L CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-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)
CL
Query on CL

G, H CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

G SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.192
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 66.51 α = 90.00
b = 67.62 β = 90.00
c = 221.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-07-23
  • Released Date: 2013-08-21
  • Deposition author(s): Zhou, T., Moquin, S., Kwong, P.D.

Revision History

  • 2013-09-04
    Type: Database references
  • 2013-09-25
    Type: Database references
  • 2014-05-07
    Type: Other