3JWD

Structure of HIV-1 gp120 with gp41-Interactive Region: Layered Architecture and Basis of Conformational Mobility

Structural Biology Knowledgebase: 3JWD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3JWD

Classification: VIRAL PROTEIN

Total Structure Weight: 222998.78

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 GP120 ENVELOPE GLYCOPROTEIN A, B 379 Human immunodeficiency virus 1
T-cell surface glycoprotein CD4 C, D 184 Homo sapiens Gene Name(s): CD4 Gene View
FAB 48D LIGHT CHAIN L, O 213 Homo sapiens
FAB 48D HEAVY CHAIN H, P 220 Homo sapiens

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

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B, P GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
YCM
Query on YCM
L, O L-PEPTIDE LINKING C5 H10 N2 O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.201
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 83.11 α = 90.00
b = 172.95 β = 90.00
c = 193.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-09-18
  • Released Date: 2009-12-29
  • Deposition author(s): Pancera, M., Majeed, S., Ban, Y.A., Chen, L., Huang, C.C., Kong, L., Kwon, Y.D., Stuckey, J., Zhou, T., Robinson, J.E., Schief, W.R., Sodroski, J., Wyatt, 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