4DVR

Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.228

Literature

Macromolecules
Sequence Display for 4DVR

Classification: IMMUNE SYSTEM / TRANSCRIPTION INHIBITOR

Total Structure Weight: 83328.09

Macromolecule Entities
Molecule Chains Length Organism Details
Envelope glycoprotein gp120 G 313 Human immunodeficiency virus 1 Fragment: unp residues 82-122; 199-297; 319-479
Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Fab 48d Light chain L 212 Homo sapiens
Fab 48d Heavy chain H 219 Homo sapiens

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

G 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.228
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 53.44 α = 90.00
b = 109.74 β = 90.00
c = 130.68 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

  • Version 1_0: 2013-02-27

    Type: Initial release

  • Version 1_1: 2014-03-19

    Type: Database references

  • Version 1_2: 2014-12-17

    Type: Non-polymer description

  • Version 1_3: 2017-05-31

    Type: Structure summary