Structure of PDB 8vfa Chain A

Receptor sequence

>8vfaA (length=320) Species: 9606 (Homo sapiens) [Search protein sequence]

TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEA
KKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPS
AARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQ
DIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRL
IPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPAGEPLPVDS
EKDIFDYIQWKYREPKDRSE

3D structure

PDB

8vfa Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta.

Chain

Resolution

2.05 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.7.7.7: DNA-directed DNA polymerase.
4.2.99.-
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

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	A	H34 S229 K230 G231 T233 K234 R283 L287 E295 Y296	H25 S220 K221 G222 T224 K225 R274 L278 E286 Y287
BS02	dna	A	G107 P108 S109 A110	G98 P99 S100 A101
BS03	dna	A	H34 K35 A38 Y39 G64 V65 G66 K68 I69	H25 K26 A29 Y30 G55 V56 G57 K59 I60
BS04	G2P	A	R149 S180 S188 G189 D190 D192 Y271 F272 T273 G274 D276 N279 R283	R140 S171 S179 G180 D181 D183 Y262 F263 T264 G265 D267 N270 R274
BS05	MN	A	D190 D192	D181 D183
BS06	MN	A	D190 D192 D256	D181 D183 D247

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003684	damaged DNA binding
GO:0003887	DNA-directed DNA polymerase activity
GO:0003906	DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0005515	protein binding
GO:0008017	microtubule binding
GO:0016779	nucleotidyltransferase activity
GO:0016829	lyase activity
GO:0019899	enzyme binding
GO:0034061	DNA polymerase activity
GO:0046872	metal ion binding
GO:0051575	5'-deoxyribose-5-phosphate lyase activity
GO:0140078	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

	Biological Process
GO:0001701	in utero embryonic development
GO:0006259	DNA metabolic process
GO:0006260	DNA replication
GO:0006261	DNA-templated DNA replication
GO:0006281	DNA repair
GO:0006284	base-excision repair
GO:0006287	base-excision repair, gap-filling
GO:0006290	pyrimidine dimer repair
GO:0006297	nucleotide-excision repair, DNA gap filling
GO:0006303	double-strand break repair via nonhomologous end joining
GO:0006915	apoptotic process
GO:0006954	inflammatory response
GO:0006974	DNA damage response
GO:0007435	salivary gland morphogenesis
GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010332	response to gamma radiation
GO:0016445	somatic diversification of immunoglobulins
GO:0016446	somatic hypermutation of immunoglobulin genes
GO:0045471	response to ethanol
GO:0048535	lymph node development
GO:0048536	spleen development
GO:0048872	homeostasis of number of cells
GO:0051402	neuron apoptotic process
GO:0055093	response to hyperoxia
GO:0071707	immunoglobulin heavy chain V-D-J recombination
GO:0071897	DNA biosynthetic process

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005874	microtubule
GO:0005876	spindle microtubule
GO:0032991	protein-containing complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:8vfa, PDBe:8vfa, PDBj:8vfa
PDBsum	8vfa
PubMed	38634780
UniProt	P06746\|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

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