3U4E

Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain CAP45

Structural Biology Knowledgebase: 3U4E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.182

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3U4E

Classification: IMMUNE SYSTEM

Total Structure Weight: 132968.92

Macromolecule Entities
Molecule Chains Length Organism Details
V1V2 region of HIV-1 on 1FD6 scaffold G, J 124 Human immunodeficiency virus 1 Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PG9 Heavy Chain A, H 248 Homo sapiens
PG9 Light Chain B, L 216 Homo sapiens

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

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

A, G, J BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, G, J ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B, G, L SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
A, H L-PEPTIDE LINKING C5 H7 N O3 GLU
TYS
Query on TYS
A, H L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.182
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 73.03 α = 90.00
b = 103.54 β = 90.00
c = 186.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-10-07
  • Released Date: 2011-11-30
  • Deposition author(s): Gorman, J., McLellan, J., Pancera, M., Kwong, P.D.

Revision History

  • 2011-12-21
    Type: Citation | Details: Citation update