3TV3

Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with Man9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.159

Literature

Macromolecules
Sequence Display for 3TV3

Classification: IMMUNE SYSTEM

Total Structure Weight: 49921.37

Macromolecule Entities
Molecule Chains Length Organism Details
PGT128 light chain, Ig lambda-2 chain C regions L 211 Homo sapiens Fragment: PGT128 light chain
Gene Name(s): IGLC2 IGLC3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PGT128 heavy chain, Ig gamma-1 chain C region H 239 Homo sapiens Fragment: PGT128 heavy chain
Gene Name(s): IGHG1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

H 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

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

H, L GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AML
Query on AML

H AMYLAMINE
C5 H13 N
DPBLXKKOBLCELK-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
H L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.159
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 72.14 α = 90.00
b = 106.02 β = 90.00
c = 145.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-19
  • Released Date: 2011-10-19
  • Deposition author(s): Pejchal, R., Wilson, I.A.

Revision History

  • Version 1_0: 2011-10-19

    Type: Initial release

  • Version 1_1: 2011-10-26

    Type: Database references

  • Version 1_2: 2011-12-07

    Type: Database references

  • Version 1_3: 2017-08-02

    Type: Refinement description, Source and taxonomy