4H03

Crystal structure of NAD+-Ia-actin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.216

Literature

Macromolecules
Sequence Display for 4H03

Classification: TOXIN / STRUCTURAL PROTEIN

Total Structure Weight: 94801.28

Macromolecule Entities
Molecule Chains Length Organism Details
Iota toxin component Ia A 418 Clostridium perfringens EC#: 2.4.2.31 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Actin, alpha skeletal muscle B 375 Oryctolagus cuniculus Gene Name(s): ACTA1 Gene View ACTA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAD
Query on NAD

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

B ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LAR
Query on LAR

B LATRUNCULIN A
8, (Synonym)
C22 H31 N O5 S
DDVBPZROPPMBLW-IZGXTMSKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
HIC
Query on HIC
B L-PEPTIDE LINKING C7 H11 N3 O2 HIS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.216
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 53.86 α = 90.00
b = 135.04 β = 90.00
c = 154.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-07
  • Released Date: 2013-02-20
  • Deposition author(s): Tsurumura, T., Oda, M., Nagahama, M., Tsuge, H.

Revision History

  • 2013-07-10
    Type: Database references