4DQO

Crystal Structure of PG16 Fab in Complex with V1V2 Region from HIV-1 strain ZM109


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 4DQO

Classification: IMMUNE SYSTEM

Total Structure Weight: 66431.14

Macromolecule Entities
Molecule Chains Length Organism Details
PG16 Fab Heavy Chain H 246 Homo sapiens
PG16 Fab Light Chain L 216 Homo sapiens
1FD6-V1V2 scaffold ZM109 HIV-1 strain C 124 Human immunodeficiency virus 1 Gene Name(s): env
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SIA
Query on SIA

C O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

C BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

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

C BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
H L-PEPTIDE LINKING C5 H7 N O3 GLU
TYS
Query on TYS
H L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.201
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 81.05 α = 90.00
b = 207.56 β = 90.00
c = 87.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-16
  • Released Date: 2013-03-06
  • Deposition author(s): Pancera, M., McLellan, J.S., Kwong, P.D.

Revision History

  • Version 1_0: 2013-03-06

    Type: Initial release

  • Version 1_1: 2013-05-08

    Type: Derived calculations, Other

  • Version 1_2: 2013-06-05

    Type: Database references

  • Version 1_3: 2013-07-24

    Type: Database references