1GZF

STRUCTURE OF THE CLOSTRIDIUM BOTULINUM C3 EXOENZYME (WILD-TYPE) IN COMPLEX WITH NAD

Structural Biology Knowledgebase: 1GZF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.234

Literature

Macromolecules
Sequence Display for 1GZF

Classification: TRANSFERASE

Total Structure Weight: 96984.20

Macromolecule Entities
Molecule Chains Length Organism Details
MONO-ADP-RIBOSYLTRANSFERASE C3 A, B, C, D 211 Clostridium botulinum EC#: 2.4.2 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 41-251
Gene Name(s): C3 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADP
Query on ADP

C, D ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NIR
Query on NIR

C 3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY- 5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM
C11 H18 N2 O4
MYKCTORFOIHUSG-LALMQGGXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NAD N/A in BindingDB
Kd: 60000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.234
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 103.95 α = 90.00
b = 74.19 β = 102.10
c = 119.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-05-21
  • Released Date: 2002-08-29
  • Deposition author(s): Menetrey, J., Flatau, G., Stura, E.A., Charbonnier, J.B., Gas, F., Teulon, J.M., Le Du, M.H., Boquet, P., Menez, A.

Revision History

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