3TGS

Crystal structure of HIV-1 clade C strain C1086 gp120 core in complex with NBD-556

Structural Biology Knowledgebase: 3TGS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.239

Literature

Macromolecules
Sequence Display for 3TGS

Classification: VIRAL PROTEIN

Total Structure Weight: 83063.44

Macromolecule Entities
Molecule Chains Length Organism Details
HIV-1 clade C1086 gp120 core A, B 358 Human immunodeficiency virus 1 Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
03G
Query on 03G

A, B N-(4-chlorophenyl)-N'-(2,2,6,6-tetramethylpiperidin- 4-yl)ethanediamide
NBD-556 (Synonym)
C17 H24 Cl N3 O2
ZKXLQCIOURANAD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
03G IC50: 73700 nM (90) BindingDB
Kd: 3700 nM (90) BindingDB

N/A in BindingMoad
Kd: 4100 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.295
  • R-Value Work: 0.239
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 66.96 α = 90.00
b = 126.00 β = 90.00
c = 191.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-08-17
  • Released Date: 2012-04-04
  • Deposition author(s): Kwon, Y.D., Kwong, P.D.

Revision History

  • 2014-12-17
    Type: Non-polymer description | Details: --
  • 2012-05-23
    Type: Citation | Details: Citation update