3U2S

Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain ZM109

Structural Biology Knowledgebase: 3U2S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.178

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3U2S

Classification: IMMUNE SYSTEM

Total Structure Weight: 130614.80

Macromolecule Entities
Molecule Chains Length Organism Details
PG9 heavy chain A, H 248 Homo sapiens Fragment: antigen-binding fragment
PG9 light chain B, L 216 Homo sapiens
Envelope glycoprotein gp120 C, G 124 Human immunodeficiency virus 1 Fragment: V1V2 region
Gene Name(s): env

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

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

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

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

B, H, L SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BU3
Query on BU3

B, L (R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
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: 1.8 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.178
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 89.46 α = 90.00
b = 86.57 β = 92.08
c = 94.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-10-04
  • Released Date: 2011-11-30
  • Deposition author(s): McLellan, J.S., Pancera, M., Kwong, P.D.

Revision History

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