3SE8

Crystal structure of broadly and potently neutralizing antibody VRC03 in complex with HIV-1 gp120

Structural Biology Knowledgebase: 3SE8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 3SE8

Classification: VIRAL PROTEIN / IMMUNE SYSTEM

Total Structure Weight: 91101.46

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 Clade AE strain 93TH057 gp120 G 353 Human immunodeficiency virus 1 Fragment: Core gp120 with truncations
Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Heavy chain of antibody VRC03 H 233 Homo sapiens Fragment: Antigen binding fragement of antibody heavy chain
Light chain of antibody VRC03 L 209 Homo sapiens Fragment: antibody light chain

Small Molecules
Ligands 4 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)
TRS
Query on TRS

H 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

G, H, L SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

H 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.187
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.01 α = 90.00
b = 70.26 β = 90.00
c = 217.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-06-10
  • Released Date: 2011-08-10
  • Deposition author(s): Kwong, P.D., Zhou, T.

Revision History

  • 2012-08-15
    Type: Other | Details: typo
  • 2011-10-05
    Type: Citation | Details: Citation update