4D2G Transcription date May 09, 2014
title Crystal Structure Of Human Pcna In Complex With P15 Peptide
authors A.Debiasio, A.Ibanez, G.Mortuza, R.Molina, T.N.Cordeiro, F.Castil M.Villate, N.Merino, M.Lelli, T.Diercks, I.Luque, P.Bernardo, G.M F.J.Blanco
compound source
Molecule: Proliferating Cell Nuclear Antigen
Chain: A, B, C
Synonym: Pcna, Cyclin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet24d
Expression_system_plasmid: Cdfduet1

Molecule: P15
Chain: D, E

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.1703 R_Free 0.2499
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.053 41.228 141.121 90.00 105.39 90.00
method X-Ray Diffractionresolution 2.65 Å
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


D, E


Primary referenceStructure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair., De Biasio A, de Opakua AI, Mortuza GB, Molina R, Cordeiro TN, Castillo F, Villate M, Merino N, Delgado S, Gil-Carton D, Luque I, Diercks T, Bernado P, Montoya G, Blanco FJ, Nat Commun. 2015 Mar 12;6:6439. doi: 10.1038/ncomms7439. PMID:25762514
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (270 Kb) [Save to disk]
  • Biological Unit Coordinates (4d2g.pdb1.gz) 264 Kb
  • CSU: Contacts of Structural Units for 4D2G
  • Structure Factors (404 Kb)
  • Retrieve 4D2G in mmCIF format [Save to disk]
  • Re-refined 4d2g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D2G 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 4D2G
  • 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 4D2G, from MSDmotif at EBI
  • Fold representative 4d2g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d2g_A] [4d2g_C] [4d2g_D] [4d2g_E] [4d2g] [4d2g_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4D2G
  • Community annotation for 4D2G at PDBWiki (http://pdbwiki.org)

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