3V0P

Crystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with a novel UDP-Gal derived inhibitor (4GW) and H-antigen acceptor

Structural Biology Knowledgebase: 3V0P SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.159

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3V0P

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 71420.17

Macromolecule Entities
Molecule Chains Length Organism Details
Histo-blood group ABO system transferase A, B 298 Homo sapiens EC#: 2.4.1.37 IUBMB 2.4.1.40 IUBMB
Fragment: Extracellular catalytic domain
Mutation: L266G, G268A
Gene Name(s): ABO Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 5-(5-formylthiophen-2-yl)uridine 5'-(trihydrogen diphosphate)
C14 H16 N2 O13 P2 S
JAVHWQPALRUGBE-UORFTKCHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BHE
Query on BHE

A, B octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)- beta-D-galactopyranoside
2)-Beta- D-Galp-O(CH2)7CH3, (Synonym)
C20 H38 O10
GTTDTLMUWQMDNA-ARNYJBIMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
4GW N/A in BindingDB
N/A in BindingMoad
Ki: 530 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.159
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.30 α = 90.00
b = 153.52 β = 90.00
c = 52.83 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-08
  • Released Date: 2013-01-23
  • Deposition author(s): Palcic, M.M., Jorgensen, R.

Revision History

  • 2014-11-12
    Type: Function and keywords | Details: --
  • 2013-09-25
    Type: Citation | Details: Citation update
  • 2013-08-28
    Type: Citation | Details: Citation update