3MBY	Transferase, Lyase Dna	date	Mar 26, 2010
title	Ternary Complex Of Dna Polymerase Beta With Template Base A 8oxodgtp In The Active Site With A Dideoxy Terminated Prime
authors	V.K.Batra, W.A.Beard, E.W.Hou, L.C.Pedersen, R.Prasad, S.H.Wilson
compound		source
Molecule: Dna Polymerase Beta Chain: A Ec: 2.7.7.7, 4.2.99.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Polb Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: P56 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pwl11
Molecule: Dna (5'-D(Cpcpgpapcpapgpcpgpcpaptpcp 3'); Chain: T Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgp(Doc))-3') Chain: P Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Pgptpcpgpg)-3') Chain: D Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.190 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 50.830 80.030 55.420 90.00 107.70 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	8DG, CL, DOC, MG, NA	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site., Batra VK, Beard WA, Hou EW, Pedersen LC, Prasad R, Wilson SH, Nat Struct Mol Biol. 2010 Jul;17(7):889-90. Epub 2010 Jun 6. PMID:20526335

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk] Biological Unit Coordinates (3mby.pdb1.gz) 74 Kb LPC: Ligand-Protein Contacts for 3MBY CSU: Contacts of Structural Units for 3MBY Structure Factors (233 Kb) Retrieve 3MBY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3MBY from S2C, [Save to disk] Re-refined 3mby structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3MBY 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 3MBY

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 3MBY, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3mby_P] [3mby_A] [3mby] [3mby_T] [3mby_D] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3MBY: [HhH1] [POLXc ] by SMART

Other resources with information on 3MBY

Community annotation for 3MBY at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---