1GY3 Transferase Transferase Substrate date Apr 19, 2002
title Pcdk2cyclin A In Complex With Mgadp, Nitrate And Peptide Su
authors A.Cook, E.D.Lowe, E.D.Chrysina, V.T.Skamnaki, N.G.Oikonomakos, L.
compound source
Molecule: Cell Division Protein Kinase 2
Chain: A, C
Synonym: P33 Protein Kinase
Engineered: Yes
Other_details: Phosphorylated On Thr160
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834 (De3) Plyss
Expression_system_vector: Pgex
Other_details: Cdk2 Was Co-Expressed With Cak1 - Produce Th Phospho-Cdk2;

Molecule: Cyclin A2
Chain: B, D
Fragment: Residues 175-432
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834 (De3) Plyss
Expression_system_vector: Pet21d

Molecule: Substrate Peptide
Chain: E, F
Engineered: Yes
Other_details: Sequence Hhasprk

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 2
R_factor 0.250 R_Free 0.313
crystal
cell
length a length b length c angle alpha angle beta angle gamma
150.710 164.100 72.430 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand ATP, GOL, MG, NO3, TPO enzyme
related structures by homologous chain: 1G5S, 1GIH, 1H28, 1OGU
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceStructural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism., Cook A, Lowe ED, Chrysina ED, Skamnaki VT, Oikonomakos NG, Johnson LN, Biochemistry 2002 Jun 11;41(23):7301-11. PMID:12044161
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (196 Kb) [Save to disk]
  • Biological Unit Coordinates (1gy3.pdb1.gz) 96 Kb
  • Biological Unit Coordinates (1gy3.pdb2.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 1GY3
  • CSU: Contacts of Structural Units for 1GY3
  • Likely Quarternary Molecular Structure file(s) for 1GY3
  • Structure Factors (631 Kb)
  • Retrieve 1GY3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GY3 from S2C, [Save to disk]
  • Re-refined 1gy3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GY3 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1GY3
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1GY3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gy3a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1gy3b1, region B:175-309 [Jmol] [rasmolscript] [script source]
        - Domain d1gy3b2, region B:310-432 [Jmol] [rasmolscript] [script source]
        - Domain d1gy3c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1gy3d1, region D:175-309 [Jmol] [rasmolscript] [script source]
        - Domain d1gy3d2, region D:310-432 [Jmol] [rasmolscript] [script source]
  • Fold representative 1gy3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1gy3] [1gy3_D] [1gy3_B] [1gy3_F] [1gy3_C] [1gy3_A] [1gy3_E]
  • SWISS-PROT database: [P20248] [P24941]
  • Domain organization of [CCNA2_HUMAN] [CDK2_HUMAN] by SWISSPFAM
  • Domains found in 1GY3: [CYCLIN] [Cyclin_C] [S_TKc ] by SMART
  • Other resources with information on 1GY3
  • Community annotation for 1GY3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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