1GC1

HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY

Structural Biology Knowledgebase: 1GC1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.302
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1GC1

Classification: Viral protein / receptor / Immune system

Total Structure Weight: 106803.38

Macromolecule Entities
Molecule Chains Length Organism Details
ENVELOPE PROTEIN GP120 G 321 Human immunodeficiency virus 1 Fragment: CORE
Mutation: D94N, D346A, L470P
Gene Name(s): env
CD4 C 185 Homo sapiens Fragment: D1D2, N-TERMINAL TWO DOMAIN FRAGMENT
Gene Name(s): CD4 Gene View
ANTIBODY 17B L 213 Homo sapiens Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Details: MONOCLONAL ANTIBODY 17B BINDS TO A CD4-INDUCED SITE ON GP120
ANTIBODY 17B H 229 Homo sapiens Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Details: MONOCLONAL ANTIBODY 17B BINDS TO A CD4-INDUCED SITE ON GP120

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

G 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

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

G 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: 2.5 Å
  • R-Value Free: 0.302
  • R-Value Work: 0.210
  • Space Group: P 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 71.64 α = 90.00
b = 88.13 β = 90.00
c = 196.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-06-15
  • Released Date: 1998-07-08
  • Deposition author(s): Kwong, P.D., Wyatt, R., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A.

Revision History

  • 2013-09-18
    Type: Biological assembly | Details: Update biological assembly based on citation
  • 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