Structure of PDB 2py5 Chain A

Receptor sequence

>2py5A (length=564) Species: 10756 (Salasvirus phi29)

PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKV
QADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMID
ICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPV
GYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITT
KKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLY
PAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQI
GNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFK
DFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGA
LGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIH
LTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDG
KLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQV
PGGVVLVDDTFTIK

3D structure

• PDB: 2py5 Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases
• Chain: A
• Resolution: 1.6 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	E14 T15 N62 F65 L123 P129 V130 Y148 L567	E10 T11 N58 F61 L119 P125 V126 Y144 L556
BS02	dna	A	K64 M97 G98 N313 K402 F414 A531 Q560	K60 M93 G94 N302 K391 F403 A520 Q549
BS03	dna	A	I93 M97 Q99 M102 M188 T189 S192 R223 G391 K392 S395 N396 K422	I89 M93 Q95 M98 M184 T185 S188 R219 G380 K381 S384 N385 K411

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0001882 nucleoside binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0004527 exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0039693 viral DNA genome replication

External links

• PDB: RCSB:2py5, PDBe:2py5, PDBj:2py5
• PDBsum: 2py5
• PubMed: 17611604
• UniProt: P03680|DPOL_BPPH2 DNA polymerase (Gene Name=2)