2PY5	Replication, Transferase Dna	date	May 15, 2007
title	Phi29 Dna Polymerase Complexed With Single-Stranded Dna
authors	A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lazaro, M.De Vega, L.Bla M.Salas, T.A.Steitz
compound		source
Molecule: 5'-D(Ggacttt)-3' Chain: J, Y, D, E, L Engineered: Yes		Synthetic: Yes
Molecule: Dna Polymerase Chain: A, B Synonym: Early Protein Gp2 Ec: 2.7.7.7 Engineered: Yes Mutation: Yes		Organism_scientific: Bacillus Phage Phi29 Organism_taxid: 10756 Gene: 2, Gp2 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 1 21 1	R_factor 0.164 R_Free 0.194
crystal cell	length a length b length c angle alpha angle beta angle gamma 54.195 200.178 66.989 90.00 109.40 90.00
method	X-Ray Diffraction	resolution	1.60 Å
ligand	EDO	enzyme	Transferase E.C.2.7.7.7 BRENDA
note	2PY5 is a representative structure
Gene Ontology	Chain Function Process Component A, B DNA-directed DNA polymerase ... nuclease activity exonuclease activity
Primary reference	Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases., Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA, EMBO J. 2007 Jul 5;. PMID:17611604

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (229 Kb) [Save to disk] Biological Unit Coordinates (2py5.pdb1.gz) 117 Kb Biological Unit Coordinates (2py5.pdb2.gz) 109 Kb LPC: Ligand-Protein Contacts for 2PY5 CSU: Contacts of Structural Units for 2PY5 Likely Quarternary Molecular Structure file(s) for 2PY5 Structure Factors (2507 Kb) Retrieve 2PY5 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2PY5 from S2C, [Save to disk] Re-refined 2py5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2PY5 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 2PY5

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 2PY5, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2py5_J] [2py5] [2py5_E] [2py5_A] [2py5_Y] [2py5_B] [2py5_D] [2py5_L] SWISS-PROT database: [P03680] Domain organization of [DPOL_BPPH2] by SWISSPFAM Domain found in 2PY5: [POLBc ] by SMART

Other resources with information on 2PY5

Community annotation for 2PY5 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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