4YC3 Cell Cycle date Feb 19, 2015
title Cdk1cyclinb1cks2 Apo
authors N.R.Brown, S.Korolchuk, M.P.Martin, W.Stanley, R.Moukhametzianov M.E.M.Noble, J.A.Endicott
compound source
Molecule: Cyclin-Dependent Kinase 1
Chain: A
Synonym: Cdk1,Cell Division Control Protein 2 Homolog,Cell Protein Kinase 1,P34 Protein Kinase;
Engineered: Yes
Other_details: Gst-Fusion Protein Cleaved By 3c Protease
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdk1, Cdc2, Cdc28a, Cdkn1, P34cdc2
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9

Molecule: G2mitotic-Specific Cyclin-B1
Chain: B
Fragment: Unp Residues 165-433
Engineered: Yes
Other_details: N-Terminal His Tag Removed By Thrombin Cleav

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ccnb1, Ccnb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Codonplus Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28 A+

Molecule: Cyclin-Dependent Kinases Regulatory Subunit 2
Chain: C
Synonym: Cks-2
Engineered: Yes
Other_details: N-Terminal Gst Tag Removed By 3c Protease Cl

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cks2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Gst-3c
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
69.200 70.150 156.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand MPD enzyme Transferase E.C. BRENDA
  • virus receptor activity
  • histone kinase activity

  • B


    Primary referenceCDK1 structures reveal conserved and unique features of the essential cell cycle CDK., Brown NR, Korolchuk S, Martin MP, Stanley WA, Moukhametzianov R, Noble ME, Endicott JA, Nat Commun. 2015 Apr 13;6:6769. doi: 10.1038/ncomms7769. PMID:25864384
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (230 Kb) [Save to disk]
  • Biological Unit Coordinates (4yc3.pdb1.gz) 223 Kb
  • LPC: Ligand-Protein Contacts for 4YC3
  • CSU: Contacts of Structural Units for 4YC3
  • Structure Factors (176 Kb)
  • Retrieve 4YC3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YC3 from S2C, [Save to disk]
  • Re-refined 4yc3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YC3 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 4YC3
  • 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
  • Fold representative 4yc3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yc3_A] [4yc3_B] [4yc3_C] [4yc3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YC3: [CKS] [CYCLIN] [Cyclin_C] [S_TKc ] by SMART
  • Other resources with information on 4YC3
  • Community annotation for 4YC3 at PDBWiki (http://pdbwiki.org)

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