1GA8

CRYSTAL STRUCTURE OF GALACOSYLTRANSFERASE LGTC IN COMPLEX WITH DONOR AND ACCEPTOR SUGAR ANALOGS.

Structural Biology Knowledgebase: 1GA8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 1GA8

Classification: TRANSFERASE

Total Structure Weight: 37060.87

Macromolecule Entities
Molecule Chains Length Organism Details
GALACTOSYL TRANSFERASE LGTC A 311 Neisseria meningitidis EC#: 2.4.1.44 IUBMB
Mutation: M1M, C128S, M145M, M172M, C174S, M184M, M210M, M217M, M238M, S248P, G268A
Gene Name(s): lgtC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE
URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO- GALACTOPYRANOSYL-MONOPHOSPHATE ESTER (Synonym)
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-KBQKSTHMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DEL
Query on DEL

A 4-DEOXYLACTOSE
C12 H22 O10
DSYGIMVFFQCOQZ-KYYLAPRMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
UPF N/A in BindingDB
Ki: 2000 nM  BindingMOAD

DEL N/A in BindingDB
Ki: 16000000 nM  BindingMOAD
Ki: 16000000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.189
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 39.97 α = 90.00
b = 76.16 β = 90.00
c = 87.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-11-29
  • Released Date: 2001-02-14
  • Deposition author(s): Persson, K., Ly, H.D., Diekelmann, M., Wakarchuk, W.W., Withers, S.G., Strynadka, N.C.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4