BioLiP

Receptor Information

>5c51 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
TAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKRFNYGRIYGAGQPFAE
RLLMQFNHRLTQQEAAEKAQQMYAATKGLLRKVQRETARKSQWKKWEVVA
ERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRALEPSAVQEEFMTS
RVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED
RYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDRCLRKEVTM
DCKTPSNPTGMERRYGIPQGEALDIYQIIELTK

Ligand ID

1RY

InChI

InChI=1S/C8H13FN3O12P3S/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,2-3H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t5-,6+/m0/s1

InChIKey

WIEOLFZNMKSGEX-NTSWFWBYSA-N

SMILES

Software	SMILES
CACTVS 3.370	NC1=NC(=O)N(C=C1F)[CH]2CS[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.7.6	C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F
CACTVS 3.370	NC1=NC(=O)N(C=C1F)[C@@H]2CS[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.7.6	C1C(OC(S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F

Formula

C8 H13 F N3 O12 P3 S

Name

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

PDB chain

5c51 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	5c51 Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma.
Resolution	3.426 Å
Binding residue (original residue number in PDB)	R853 D890 V891 D892 Q894 K947 R948 Y951 D1135
Binding residue (residue number reindexed from 1)	R640 D677 V678 D679 Q681 K734 R735 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:5c51, PDBe:5c51, PDBj:5c51
PDBsum	5c51
PubMed	26124101
UniProt	P54098\|DPOG1_HUMAN DNA polymerase subunit gamma-1 (Gene Name=POLG)

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Structure of PDB 5c51 Chain A Binding Site BS04