4I3Z

Structure of pCDK2/CyclinA bound to ADP and 2 Magnesium ions

Structural Biology Knowledgebase: 4I3Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I3Z

Classification: Transferase / Cell Cycle

Total Structure Weight: 128238.37

Macromolecule Entities
Molecule Chains Length Organism Details
Cyclin-dependent kinase 2 A, C 296 Homo sapiens EC#: 2.7.11.22 IUBMB
Gene Name(s): CDK2 Gene View CDKN2
Cyclin-A2 B, D 257 Mus musculus Fragment: UNP RESIDUES 105-421
Gene Name(s): Ccna2 Ccna Cyca

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

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

A, B, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ADP N/A in BindingDB
Kd: 51300000 nM  BindingMOAD
Kd: 51300 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TPO
Query on TPO
A, C L-PEPTIDE LINKING C4 H10 N O6 P THR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.77 α = 90.00
b = 164.13 β = 107.07
c = 73.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-27
  • Released Date: 2012-12-26
  • Deposition author(s): Jacobsen, D.M., Bao, Z.-Q., O'Brien, P.J., Brooks, C.L., Young, M.A.

Revision History

No revisions since initial release