3TYG

Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with a glycosylated engineered gp120 outer domain with miniV3 (eODmV3)

Structural Biology Knowledgebase: 3TYG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.207

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3TYG

Classification: IMMUNE SYSTEM VIRAL PROTEIN

Total Structure Weight: 72745.75

Macromolecule Entities
Molecule Chains Length Organism Details
Envelope glycoprotein gp160 A 199 Human immunodeficiency virus 1 Mutation: L23I, T86S, I88C, K108P, N175D
Gene Name(s): env
PGT128 light chain, Ig lambda-2 chain C regions L 211 Homo sapiens Gene Name(s): IGLC2
PGT128 heavy chain, Ig gamma-1 chain C region H 239 Homo sapiens Gene Name(s): IGHG1

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

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

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

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
H, L L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.207
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 50.79 α = 90.00
b = 73.51 β = 90.00
c = 241.45 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-25
  • Released Date: 2011-10-19
  • Deposition author(s): Pejchal, R., Huang, P.S., Schief, W.R., Stanfield, R.L., Wilson, I.A.

Revision History

  • 2011-12-07
    Type: Citation | Details: Citation update
  • 2011-10-26
    Type: Citation | Details: Citation update