4DVS

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557

Structural Biology Knowledgebase: 4DVS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DVS

Classification: viral protein / transcription inhibitor

Total Structure Weight: 84429.19

Macromolecule Entities
Molecule Chains Length Organism Details
glycoprotein gp120 A, B 353 Human immunodeficiency virus 1 Fragment: unp residues 43-122, 201-303, 325-486
Mutation: H375S
Gene Name(s): env

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0LY
Query on 0LY

A, B N-(4-bromophenyl)-N'-(2,2,6,6-tetramethylpiperidin- 4-yl)ethanediamide
NBD-557 (Synonym)
C17 H24 Br N3 O2
QQRFLGRIDNNARB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EPE
Query on EPE

A, B 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.193
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 64.64 α = 90.00
b = 68.22 β = 91.48
c = 94.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-23
  • Released Date: 2013-02-27
  • Deposition author(s): Kwon,Y.D., Kwong, P.D.

Revision History

  • 2014-12-17
    Type: Non-polymer description | Details: --
  • 2014-03-19
    Type: Citation | Details: Citation update