2AFB

Crystal structure of 2-dehydro-3- deoxygluconokinase (EC 2.7.1.45) (tm0067) from THERMOTOGA MARITIMA at 2.05 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.176

Literature

Macromolecules
Sequence Display for 2AFB

Classification: TRANSFERASE

Total Structure Weight: 79483.80

Macromolecule Entities
Molecule Chains Length Organism Details
2-keto-3-deoxygluconate kinase A, B 351 Thermotoga maritima Mutation: M1M, M10M, M45M, M181M, M185M, M255M, M292M
Gene Name(s): TM_0067 Tmari_0064
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, 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
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 120.99 α = 90.00
b = 120.99 β = 90.00
c = 260.30 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-07-25
  • Released Date: 2006-02-14
  • Deposition author(s): Joint Center for Structural Genomics (JCSG)
  • This entry supercedes: 1J5V

Revision History

  • Version 1_0: 2006-02-14

    Type: Initial release

  • Version 1_1: 2007-12-26

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Derived calculations, Source and taxonomy, Version format compliance

  • Version 1_3: 2017-10-11

    Type: Refinement description