1BPY	Transferase Dna	date	Apr 15, 1997
title	Human Dna Polymerase Beta Complexed With Gapped Dna And Ddct
authors	M.R.Sawaya, H.Pelletier, R.Prasad, S.H.Wilson, J.Kraut
compound		source
Molecule: Dna (5'-D(Cpcpgpapcpgpgpcpgpcpaptpcp 3'); Chain: T Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpdoc)-3') Chain: P Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Dna (5'-D(Gptpcpgpg)-3') Chain: D Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Protein (Dna Polymerase Beta) Chain: A Synonym: Pol Beta, Beta-Pol Ec: 2.7.7.7 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Cellular_location: Nucleus Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 1 21 1	R_factor 0.232 R_Free 0.330
crystal cell	length a length b length c angle alpha angle beta angle gamma 50.543 79.817 54.942 90.00 107.11 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	DCT, DOC, MG, NA	enzyme	Transferase E.C.2.7.7.7 BRENDA
related structures	by homologous chain: 1BPB, 1TV9
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism., Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H, Biochemistry 1997 Sep 16;36(37):11205-15. PMID:9287163

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk] Biological Unit Coordinates (1bpy.pdb1.gz) 75 Kb LPC: Ligand-Protein Contacts for 1BPY CSU: Contacts of Structural Units for 1BPY Likely Quarternary Molecular Structure file(s) for 1BPY Structure Factors (146 Kb) Retrieve 1BPY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1BPY from S2C, [Save to disk] Re-refined 1bpy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1BPY 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 1BPY

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 1BPY, from MSDmotif at EBI Genome occurence of 1BPY's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1bpya1, region A:10-91 [Jmol] [rasmolscript] [script source]     - Domain d1bpya4, region A:149-335 [Jmol] [rasmolscript] [script source]     - Domain d1bpya3, region A:92-148 [Jmol] [rasmolscript] [script source] 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: [1bpy_A] [1bpy] [1bpy_P] [1bpy_D] [1bpy_T] SWISS-PROT database: [P06746] Domain organization of [DPOLB_HUMAN] by SWISSPFAM Domains found in 1BPY: [HhH1] [POLXc ] by SMART

Other resources with information on 1BPY

Community annotation for 1BPY at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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