Structure of PDB 3rh5 Chain A

Receptor sequence

>3rh5A (length=326) Species: 9606 (Homo sapiens) [Search protein sequence]

TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEA
KKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPS
AARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQ
DIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRL
IPKDQYYCGVLAFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGE
PLPVDSEKDIFDYIQWKYREPKDRSE

3D structure

PDB

3rh5 Molecular insights into DNA polymerase deterrents for ribonucleotide insertion.

Chain

Resolution

2.096 Å

3D
structure

Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

Enzymatic activity

Catalytic site (original residue number in PDB)	D190 D192 D256
Catalytic site (residue number reindexed from 1)	D181 D183 D247
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 R258 K280 R283 L287 T292 I293 N294 E295 Y296	H25 S220 K221 G222 T224 K225 R249 K271 R274 L278 T283 I284 N285 E286 Y287
BS02	dna	A	S104 G105 G107 P108 S109 A110 R254 D256	S95 G96 G98 P99 S100 A101 R245 D247
BS03	dna	A	K35 A38 Y39 P63 G64 G66 K68 I69	K26 A29 Y30 P54 G55 G57 K59 I60
BS04	DCP	A	G179 S180 R183 G189 D190 D192 F272 T273 G274 D276 N279	G170 S171 R174 G180 D181 D183 F263 T264 G265 D267 N270
BS05	DCP	A	I174 T176 T196 K262 Y265 Y266	I165 T167 T187 K253 Y256 Y257
BS06	MN	A	D190 D192	D181 D183
BS07	MN	A	D190 D192 D256	D181 D183 D247
BS08	MN	A	D145 H252	D136 H243

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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:3rh5, PDBe:3rh5, PDBj:3rh5
PDBsum	3rh5
PubMed	21733843
UniProt	P06746\|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

[Back to BioLiP]