2HVD

Human nucleoside diphosphate kinase A complexed with ADP

Structural Biology Knowledgebase: 2HVD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.247

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2HVD

Classification: SIGNALING PROTEIN TRANSFERASE

Total Structure Weight: 52794.16

Macromolecule Entities
Molecule Chains Length Organism Details
Nucleoside diphosphate kinase A A, B, C 152 Homo sapiens EC#: 2.7.4.6 IUBMB
Gene Name(s): NME1 Gene View NDPKA NM23

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A, B, C ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.247
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 114.26 α = 90.00
b = 114.26 β = 90.00
c = 89.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-07-28
  • Released Date: 2006-09-19
  • Deposition author(s): Giraud, M.-F., Georgescauld, F., Lascu, I., Dautant, A.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4