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Receptor Information

>5c53 Chain A (length=983) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

MLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPAVPLPDVELRL
PPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEGWTR
YGPEGEAVPVAIPEERALVFDVEVCLAEGTCPTLAVAISPSAWYSWCSQR
LVEERYSWTSQLSPADLIPLEVQEQLVVGHNVSFDRAHIREQYLIQGSRM
RFLDTMSMHMAISGLSSFQRSLWIAAKAISSWDWLDISSVNSLAEVHRLY
VGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPL
FLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGTYEELQREMKKSL
MDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKKAKKVKKEPATALGP
CSEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCPRLDD
PAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLNLAKLPTGT
TLESAGVVCPYRAIESLYRKHCLEPYNDVDIPGCWFFKLPHKDGNSCNVG
SPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMV
VWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTAS
NARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGC
TAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQPFAE
RLLMQFNHRLTQQEAAEKAQQMYAATKGLLRKVQRETARKSQWKKWEVVA
ERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRALEPSAVQEEFMTS
RVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED
RYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDRCLRKEVTM
DCKTPSNPTGMERRYGIPQGEALDIYQIIELTK

Ligand ID

4Y3

InChI

InChI=1S/C8H15FN3O12P3S/c9-4-1-12(8(13)11-7(4)10)5-3-28-6(22-5)2-21-26(17,18)24-27(19,20)23-25(14,15)16/h1,5-6H,2-3,28H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t5-,6+/m1/s1

InChIKey

XWOCIBWGJKRZIQ-RITPCOANSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.7	C1[C@@H](O[C@@H]([SH2]1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F
CACTVS 3.385	NC1=NC(=O)N(C=C1F)[CH]2C[SH2][CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 2.0.7	C1C(OC([SH2]1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F
CACTVS 3.385	NC1=NC(=O)N(C=C1F)[C@H]2C[SH2][C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2

Formula

C8 H15 F N3 O12 P3 S

Name

[[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3$l^{4}-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

PDB chain

5c53 Chain A Residue 4003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5c53 Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma.
Resolution	3.567 Å
Binding residue (original residue number in PDB)	S893 Q894 E895 K947 Y951 D1135
Binding residue (residue number reindexed from 1)	S680 Q681 E682 K734 Y738 D890
Annotation score	1

Enzyme Commision number

2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
4.2.99.-

	Molecular Function
GO:0002020	protease binding
GO:0003677	DNA binding
GO:0003682	chromatin binding
GO:0003887	DNA-directed DNA polymerase activity
GO:0005515	protein binding
GO:0008310	single-stranded DNA 3'-5' DNA exonuclease activity
GO:0008408	3'-5' exonuclease activity
GO:0016787	hydrolase activity
GO:0016829	lyase activity
GO:0051575	5'-deoxyribose-5-phosphate lyase activity

	Biological Process
GO:0006259	DNA metabolic process
GO:0006260	DNA replication
GO:0006261	DNA-templated DNA replication
GO:0006264	mitochondrial DNA replication
GO:0006281	DNA repair
GO:0006284	base-excision repair
GO:0006287	base-excision repair, gap-filling
GO:0045004	DNA replication proofreading
GO:0071897	DNA biosynthetic process

	Cellular Component
GO:0000262	mitochondrial chromosome
GO:0005739	mitochondrion
GO:0005759	mitochondrial matrix
GO:0005760	gamma DNA polymerase complex
GO:0032991	protein-containing complex
GO:0042645	mitochondrial nucleoid
GO:0043231	intracellular membrane-bounded organelle

PDB	RCSB:5c53, PDBe:5c53, PDBj:5c53
PDBsum	5c53
PubMed	26124101
UniProt	P54098\|DPOG1_HUMAN DNA polymerase subunit gamma-1 (Gene Name=POLG)

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Structure of PDB 5c53 Chain A Binding Site BS04