BioLiP

Structure of PDB 6isf Chain B

Receptor sequence

>6isfB (length=756) Species: 103799 (Thermococcus sp. 9oN-7) [Search protein sequence]

MILDTDYITENGKPVIRVFKKENGEFKIEYDRTFEPYFYALLKDDSAIED
VKKVTAKRHGTVVKVKRAEKVQKKFLGRPIEVWKLYFNHPQDVPAIRDRI
RAHPAVVDIYEYDIPFAKRYLIDKGLIPMEGDEELTMLAFAIATLYHEGE
EFGTGPILMISYADGSEARVITWKKIDLPYVDVVSTEKEMIKRFLRVVRE
KDPDVLITYNGDNFDFAYLKKRCEELGIKFTLGRDGSEPKIQRMGDRFAV
EVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGKPKEKVYAEEIAQAWE
SGEGLERVARYSMEDAKVTYELGREFFPMEAQLSRLIGQSLWDVSRSSTG
NLVEWFLLRKAYKRNELAPNKPDERELARRRGGYAGGYVKEPERGLWDNI
VYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPEVGHKFCKDFPGFIP
SLLGDLLEERQKIKRKMKATVDPLEKKLLDYRQRLIKILANSFYGYYGYA
KARWYCKECAESVTAWGREYIEMVIRELEEKFGFKVLYADTDGLHATIPG
ADAETVKKKAKEFLKYINPKLPGLLELEYEGFYVRGFFVTKKKYAVIDEE
GKITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKL
SKYEVPPEKLVIHEQITRDLRDYKATGPHVAVAKRLAARGVKIRPGTVIS
YIVLKGSGRIGDRAIPADEFDPTKHRYDAEYYIENQVLPAVERILKAFGY
RKEDLR

3D structure

PDB

6isf Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.

Chain

Resolution

2.8 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)
BS01	dna	B	N269 D540 D542 K592 Y594 R606 G607 V611 R612 R613 Q665 T667 R668 Y673 A675 H679	N269 D540 D542 K592 Y594 R606 G607 V611 R612 R613 Q665 T667 R668 Y673 A675 H679
BS02	dna	B	S348 T349 G350 Y384 A385 G386 G387 V389 S492 G495 G498 Y499 T590 K591 K592 K593 W615 R709 I710 G711 Y731 R743	S348 T349 G350 Y384 A385 G386 G387 V389 S492 G495 G498 Y499 T590 K591 K592 K593 W615 R709 I710 G711 Y731 R743
BS03	CA	B	D4 D343	D4 D343
BS04	CA	B	R101 A102 H103 V106	R101 A102 H103 V106
BS05	CA	B	N568 L571 L575	N568 L571 L575

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

View graph for
Molecular Function

View graph for
Biological Process

PDB	RCSB:6isf, PDBe:6isf, PDBj:6isf
PDBsum	6isf
PubMed	31240262
UniProt	Q56366\|DPOL_THES9 DNA polymerase (Gene Name=pol)