3IDX

Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222

Structural Biology Knowledgebase: 3IDX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 3IDX

Classification: IMMUNE SYSTEM

Total Structure Weight: 88069.80

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 HxBc2 gp120 core G 317 Human immunodeficiency virus 1 Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fab b13 heavy chain H 231 Homo sapiens
Fab b13 light chain L 215 Homo sapiens

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EPE
Query on EPE

G, H 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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)
SO4
Query on SO4

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

G GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.178
  • Space Group: C 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 112.61 α = 90.00
b = 203.96 β = 90.00
c = 109.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-22
  • Released Date: 2009-11-17
  • Deposition author(s): Chen, L., Kwon, Y.D., Zhou, T., Wu, X., O'Dell, S., Cavacini, L., Hessell, A.J., Pancera, M., Tang, M., Xu, L., Yang, Z.Y., Zhang, M.Y., Arthos, J., Burton, D.R., Dimitrov, D.S., Nabel, G.J., Posner, M., Sodroski, J., Wyatt, R., Mascola, J.R., Kwong, P.D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update