2BF1

STRUCTURE OF AN UNLIGANDED AND FULLY-GLYCOSYLATED SIV GP120 ENVELOPE GLYCOPROTEIN

Structural Biology Knowledgebase: 2BF1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.0 Å
  • R-Value Free: 0.388
  • R-Value Work: 0.385

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2BF1

Classification: VIRUS PROTEIN

Total Structure Weight: 46066.67

Macromolecule Entities
Molecule Chains Length Organism Details
EXTERIOR MEMBRANE GLYCOPROTEIN GP120 A 316 Simian immunodeficiency virus Fragment: GP120 CORE, RESIDUES 66-109,209-311,342-502
Gene Name(s): env

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDG
Query on NDG

A 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.0 Å
  • R-Value Free: 0.388
  • R-Value Work: 0.385
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 108.05 α = 90.00
b = 108.05 β = 90.00
c = 117.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-02
  • Released Date: 2005-02-17
  • Deposition author(s): Chen, B., Vogan, E.M., Gong, H., Skehel, J.J., Wiley, D.C., Harrison, S.C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4