2W3O Hydrolase,Transferase Peptide date Nov 13, 2008
title Crystal Structure Of The Human Pnkp Fha Domain In Complex With An Xrcc1-Derived Phosphopeptide
authors A.W.Oliver, A.A.E.Ali, L.H.Pearl
compound source
Molecule: Bifunctional Polynucleotide Phosphatasekinase
Chain: A, B
Fragment: Fha Domain, Residues 1-110
Synonym: Fha Domain Of Polynucleotide Kinase 3' Phosphatase, Dna 5'-Kinase3'-Phosphatase, Polynucleotide 5'-Hydroxyl-Kinase, Polynucleotide 3'-Phosphatase;
Ec: 3.1.3.32, 2.7.1.78
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta2(De3)Plyss
Expression_system_plasmid: Ptwo-E
Other_details: Synthetic Gene

Molecule: Dna Repair Protein Xrcc1
Chain: C, D
Fragment: Residues 515-522
Synonym: X-Ray Repair Cross-Complementing Protein 1, Xrcc1-Derived Phosphopeptide

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 3
R_factor 0.178 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.900 56.900 62.770 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.85 Å
ligand CA, SEP, TPO enzyme Hydrolase E.C.3.1.3.32 BRENDA
Primary referenceSpecific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK., Ali AA, Jukes RM, Pearl LH, Oliver AW, Nucleic Acids Res. 2009 Jan 20. PMID:19155274
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (2w3o.pdb1.gz) 21 Kb
  • Biological Unit Coordinates (2w3o.pdb2.gz) 21 Kb
  • LPC: Ligand-Protein Contacts for 2W3O
  • CSU: Contacts of Structural Units for 2W3O
  • Likely Quarternary Molecular Structure file(s) for 2W3O
  • Structure Factors (127 Kb)
  • Retrieve 2W3O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2W3O from S2C, [Save to disk]
  • Re-refined 2w3o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2W3O 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 2W3O
  • 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 2W3O, from MSDmotif at EBI
  • Fold representative 2w3o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2w3o] [2w3o_C] [2w3o_D] [2w3o_A] [2w3o_B]
  • SWISS-PROT database: [Q96T60] [P18887]
  • Domain organization of [PNKP_HUMAN] [XRCC1_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2W3O with the sequences similar proteins can be viewed for 2W3O's classification [PNKP_HUMAN] [XRCC1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [PNKP_HUMAN] [XRCC1_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2W3O
  • Community annotation for 2W3O 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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