4JM2

Crystal Structure of PGT 135 Fab in Complex with gp120 Core Protein from HIV-1 Strain JR-FL Bound to CD4 and 17b Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.238

Literature

Macromolecules
Sequence Display for 4JM2

Classification: IMMUNE SYSTEM / VIRAL PROTEIN

Total Structure Weight: 159274.77

Macromolecule Entities
Molecule Chains Length Organism Details
PGT 135 Heavy chain A 236 Homo sapiens Fragment: Fab
PGT 135 Light chain B 214 Homo sapiens Fragment: Fab
17b Light chain C 214 Homo sapiens Fragment: Fab
17b Heavy chain D 229 Homo sapiens Fragment: Fab
gp120 E 321 Human immunodeficiency virus 1 Fragment: core with mini V3 loop
Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
T-cell surface glycoprotein CD4 F 185 Homo sapiens Fragment: Ig-like V-type and C2-type 1 domains (UNP residues 26-208)
Gene Name(s): CD4 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

E N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG4
Query on PG4

C TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

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

E BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.238
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 218.41 α = 90.00
b = 92.15 β = 104.75
c = 88.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-13
  • Released Date: 2013-05-29
  • Deposition author(s): Kong, L., Wilson, I.A.

Revision History

  • Version 1_0: 2013-05-29

    Type: Initial release

  • Version 1_1: 2013-06-12

    Type: Database references

  • Version 1_2: 2013-07-17

    Type: Database references