1GY3

PCDK2/CYCLIN A IN COMPLEX WITH MGADP, NITRATE AND PEPTIDE SUBSTRATE

Structural Biology Knowledgebase: 1GY3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.313
  • R-Value Work: 0.250

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1GY3

Classification: TRANSFERASE / TRANSFERASE SUBSTRATE

Total Structure Weight: 130579.88

Macromolecule Entities
Molecule Chains Length Organism Details
CELL DIVISION PROTEIN KINASE 2 A, C 299 Homo sapiens EC#: 2.7.11.22 IUBMB
Details: PHOSPHORYLATED ON THR160
Gene Name(s): CDK2 Gene View CDKN2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYCLIN A2 B, D 258 Homo sapiens Fragment: RESIDUES 175-432
Gene Name(s): CCNA2 Gene View CCN1 CCNA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SUBSTRATE PEPTIDE E, F 7 synthetic Details: SEQUENCE HHASPRK

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

A, C ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B, C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A, C NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
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)
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: 2.7 Å
  • R-Value Free: 0.313
  • R-Value Work: 0.250
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 150.71 α = 90.00
b = 164.10 β = 90.00
c = 72.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-04-19
  • Released Date: 2002-04-29
  • Deposition author(s): Cook, A., Lowe, E.D., Chrysina, E.D., Skamnaki, V.T., Oikonomakos, N.G., Johnson, L.N.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry