2D1K

Ternary complex of the WH2 domain of mim with actin-dnase I

Structural Biology Knowledgebase: 2D1K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.217

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2D1K

Classification: STRUCTURAL PROTEIN

Total Structure Weight: 75778.05

Macromolecule Entities
Molecule Chains Length Organism Details
Actin, alpha skeletal muscle A 375 Oryctolagus cuniculus Mutation: H73X
Gene Name(s): ACTA1 Gene View ACTA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Deoxyribonuclease-1 B 260 Bos taurus EC#: 3.1.21.1 IUBMB
Gene Name(s): DNASE1 Gene View DNL1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metastasis suppressor protein 1 C 32 Homo sapiens Fragment: WH2 Domain (residues 724-755)
Gene Name(s): MTSS1 Gene View KIAA0429 MIM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ATP
Query on ATP

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

B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.217
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.09 α = 90.00
b = 75.49 β = 90.00
c = 228.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-08-26
  • Released Date: 2006-09-12
  • Deposition author(s): Chereau, D., Kerff, F., Dominguez, R.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4