Structure of PDB 4fm0 Chain A

Receptor sequence

>4fm0A (length=754) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence]

AGMIIDADYITEDGKPIIRIFKKEKGEFKVEYDRTFRPYIYALLKDDSAI
DEVKKITAERHGKIVRITEVEKVQKKFLGRPIEVWKLYLEHPQDVPAIRE
KIREHPAVVDIFEYDIPFAKRYLIDKGLTPMEGNEELTFLAVDIETLYHE
GEEFGKGPIIMISYADEEGAKVITWKSIDLPYVEVVSSEREMIKRLVKVI
REKDPDVIITYNGDNFAFPYLLKRAEKLGIKLPLGRDNSEPKMQRMGDSL
AVEIKGRIHFDLFPVIRRTINLPTYTLEAVYEAIFGKSKEKVYAHEIAEA
WETGKGLERVAKYSMEDAKVTFELGKEFFPMEAQLARLVGQPVWDVSRSS
TGNLVEWFLLRKAYERNELAPNKPDEREYERRLRESYKEPEKGLWEGIVS
LDFRSLYPSIIITHNVSPDTLNRENCKEYDVAPQVGHRFCKDFPGFIPSL
LGNLLEERQKIKKRMKESKDPVEKKLLDYRQRAIKILANSYYGYYGYAKA
RWYCKECAESVTAWGRQYIDLVRRELESRGFKVLYIDTDGLYATIPGAKH
EEIKEKALKFVEYINSKLPGLLELEYEGFYARGFFVTKKKYALIDEEGKI
VTRGLEIVRRDWSEIAKETQAKVLEAILKHGNVDEAVKIVKEVTEKLSKY
EIPPEKLVIYEQITRPLSEYKAIGPHVAVAKRLAAKGVKVKPGMVIGYIV
LRGDGPISKRAIAIEEFDPKKHKYDAEYYIENQVLPAVERILRAFGYRKE
DLKY

3D structure

PDB

4fm0 Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase.

Chain

Resolution

3.12 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.7.7.7: DNA-directed DNA polymerase.

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	Y7 I8 T9 P36 H89 P90 Q91 V93 P94 R97 Y112 D113 I114 P115 F116 K118 Q242 K253 N351 K593 A675 I676 P709 I710 S711 Y731	Y9 I10 T11 P38 H91 P92 Q93 V95 P96 R99 Y114 D115 I116 P117 F118 K120 Q244 K255 N353 K590 A672 I673 P706 I707 S708 Y728
BS02	dna	A	R265 R612 R613 D614 E664 Q665 T667 R668 Y673 K674 H679	R267 R609 R610 D611 E661 Q662 T664 R665 Y670 K671 H676
BS03	MG	A	D141 E143 D315	D143 E145 D317

Gene Ontology

	Molecular Function
GO:0000166	nucleotide binding
GO:0003676	nucleic acid binding
GO:0003677	DNA binding
GO:0003887	DNA-directed DNA polymerase activity

	Biological Process
GO:0006260	DNA replication
GO:0006261	DNA-templated DNA replication
GO:0071897	DNA biosynthetic process

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Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:4fm0, PDBe:4fm0, PDBj:4fm0
PDBsum	4fm0
PubMed	22902479
UniProt	P0CL77\|DPOL_PYRAB DNA polymerase 1 (Gene Name=polI)

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