2XCE

Structure of YncF in complex with dUpNHpp

Structural Biology Knowledgebase: 2XCE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.151

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2XCE

Classification: HYDROLASE

Total Structure Weight: 102267.56

Macromolecule Entities
Molecule Chains Length Organism Details
PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF A, B, C..., D, E, FA, B, C, D, E, F 144 Bacillus subtilis EC#: 3.6.1.23 IUBMB
Gene Name(s): yncF BSU17660

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

A, B, C, D, E, F 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, D, E, F GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D, E CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.151
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 99.12 α = 90.00
b = 99.35 β = 90.00
c = 99.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-04-22
  • Released Date: 2010-08-11
  • Deposition author(s): Garcia-Nafria, J., Burchell, L., Takezawa, M., Rzechorzek, N., Fogg, M., Wilson, K.S.

Revision History

  • 2012-04-11
    Type: Non-polymer description | Details: HETSYN
  • 2012-04-11
    Type: Citation | Details: JRNL
  • 2012-04-11
    Type: Version format compliance | Details: REMARK 4