3VX3

Crystal structure of [NiFe] hydrogenase maturation protein HypB from Thermococcus kodakarensis KOD1

Structural Biology Knowledgebase: 3VX3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.194

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VX3

Classification: ADP BINDING PROTEIN

Total Structure Weight: 56471.34

Macromolecule Entities
Molecule Chains Length Organism Details
ATPase involved in chromosome partitioning, ParA/MinD family, Mrp homolog A, B 248 Thermococcus kodakarensis Gene Name(s): TK2007

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

A, B ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ADP N/A in BindingDB
N/A in BindingMoad
Kd: 15 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.194
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 66.24 α = 90.00
b = 137.69 β = 90.00
c = 150.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-09
  • Released Date: 2013-02-27
  • Deposition author(s): Sasaki, D., Watanabe, S., Miki, K.

Revision History

  • 2013-06-12
    Type: Citation | Details: Citation update