1XQI

Crystal Structure Analysis of an NDP kinase from Pyrobaculum aerophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 1XQI

Classification: TRANSFERASE

Total Structure Weight: 66906.02

Macromolecule Entities
Molecule Chains Length Organism Details
Nucleoside diphosphate kinase A, B, C 195 Pyrobaculum aerophilum EC#: 2.7.4.6 IUBMB
Mutation: M1M, A10D, M13M, G33D, E40K, M51M, R71Q, S107N, M112M, I117N, M120M
Gene Name(s): ndk PAE1561
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

A, B, C 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.187
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 125.02 α = 90.00
b = 72.04 β = 133.30
c = 104.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-10-12
  • Released Date: 2005-09-20
  • Deposition author(s): Pedelacq, J.D., Waldo, G.S., Cabantous, S., Liong, E.C., Berendzen, J., Terwilliger, T.C.

Revision History

  • Version 1_0: 2005-09-20

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance