3ODA	Dna Binding Protein Dna	date	Aug 11, 2010
title	Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
authors	J.M.Pascal, M.F.Langelier
compound		source
Molecule: Poly [Adp-Ribose] Polymerase 1 Chain: A, B, C, D, E, F, G, H Fragment: Parp-1 Zinc Finger 1, Zn1, Unp Residues 2-96 Synonym: Parp-1, Nad(+) Adp-Ribosyltransferase 1, Adprt 1, Ribose] Synthase 1; Ec: 2.4.2.30 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Adprt, Parp1, Ppol Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Rosetta2 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28
Molecule: 5'-D(Gpcpcptpgpcpapgpgpc)-3' Chain: I, J, K, L, M, N, O, P Engineered: Yes		Synthetic: Yes Other_details: Chemically Synthesized Dna
symmetry	Space Group: P 1 21 1	R_factor 0.196 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 62.812 107.334 86.998 90.00 100.61 90.00
method	X-Ray Diffraction	resolution	2.64 Å
ligand	ZN	enzyme	Transferase E.C.2.4.2.30 BRENDA
Gene Ontology	Chain Function Process Component F, A, E, B, H, C, D, G
Primary reference	Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY., Langelier MF, Planck JL, Roy S, Pascal JM, J Biol Chem. 2011 Mar 25;286(12):10690-701. Epub 2011 Jan 13. PMID:21233213

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk] Biological Unit Coordinates (3oda.pdb1.gz) 40 Kb Biological Unit Coordinates (3oda.pdb2.gz) 41 Kb Biological Unit Coordinates (3oda.pdb3.gz) 40 Kb Biological Unit Coordinates (3oda.pdb4.gz) 41 Kb LPC: Ligand-Protein Contacts for 3ODA CSU: Contacts of Structural Units for 3ODA Structure Factors (1402 Kb) Retrieve 3ODA in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3ODA from S2C, [Save to disk] Re-refined 3oda structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3ODA 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 3ODA

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 3D motif for 3ODA, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3oda_H] [3oda_M] [3oda_E] [3oda_L] [3oda_J] [3oda_C] [3oda_A] [3oda_D] [3oda_O] [3oda_B] [3oda_N] [3oda] [3oda_P] [3oda_I] [3oda_G] [3oda_F] [3oda_K] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3ODA: [zf-PARP ] by SMART

Other resources with information on 3ODA

Community annotation for 3ODA 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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