1UCN

X-ray structure of human nucleoside diphosphate kinase A complexed with ADP at 2 A resolution

Structural Biology Knowledgebase: 1UCN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.237

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1UCN

Classification: transferase

Total Structure Weight: 53275.45

Macromolecule Entities
Molecule Chains Length Organism Details
nucleoside diphosphate kinase A A, B, C 152 Homo sapiens EC#: 2.7.4.6 IUBMB
Mutation: F60W, H118G
Gene Name(s): NME1 Gene View NDPKA NM23
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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)
TRS
Query on TRS

B 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ADP N/A in BindingDB
Kd: 6000 nM  BindingMOAD
Kd: 6000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.237
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 116.07 α = 90.00
b = 116.07 β = 90.00
c = 91.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-16
  • Released Date: 2003-09-30
  • Deposition author(s): Chen, Y., Gallois-Montbrun, S., Schneider, B., Veron, M., Morera, S., Deville-Bonne, D., Janin, J.

Revision History

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