Structure of PDB 6ymw Chain A Binding Site BS04

Receptor Information
>6ymw Chain A (length=913) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
INFFEIYNSLPTLEEKKAFESALNIFNQDRQKVLENRATEAARERWKHDF
EEAKARGDISIEKNLNVKLWKWYNEMLPLVKEEINHCRSLLSEKLSDKKG
LNKVDTNRLGYGPYLTLIDPGKMCVITILELLKLNSTGGVIEGMRTARAV
ISVGKAIEMEFRSEQVLKSESQAKILWPQSIRARIGSVLISMLIQVAKVS
VQGVDPVTKAKVHGEAPAFAHGYQYHNGSKLGVLKIHKTLIRQLNGERLI
ASVQPQLLPMLVEPKPWVNWRSGGYHYTQSTLLRTKDSPEQVAYLKAASD
NGDIDRVYDGLNVLGRTPWTVNRKVFDVVSQVWNKGEGFLDIPGAQDEMV
LPPAPPKNSDPSILRAWKLQVKTIANKFSSDRSNRCDTNYKLEIARAFLG
EKLYFPHNLDFRGRAYPLSPHFNHLGNDMSRGLLIFWHGKKLGPSGLKWL
KIHLSNLFGFDKLPLKDRVAFTESHLQDIKDSAENPLTGDRWWTTADKPW
QALATCFELNEVMKMDNPEEFISHQPVHQDGTCNGLQHYAALGGDVEGAT
QVNLVPSDKPQDVYAHVARLVQKRLEIAAEKGDENAKILKDKITRKVVKQ
TVMTNVYGVTYVGATFQIAKQLSPIFDDRKESLDFSKYLTKHVFSAIREL
FHSAHLIQDWLGESAKRISKSIRLDVDEKSFKNGNKPDFMSSVIWTTPLG
LPIVQPYREESKKQVETNLQTVFISDPFAVNPVNARRQKAGLPPNFIHSL
DASHMLLSAAECGKQGLDFASVHDSYWTHASDIDTMNVVLREQFIKLHEV
DLVLRLKEEFDQRYKNYVKIGKLKRSTDLAQKIIRIRKDLSRKLGRSTTL
ADEIYFEKKRQELLNEDITDLDALELENGNSGMSVLLPLRLPEIPPKGDF
DVTVLRNSQYFFS
Ligand information
Ligand IDP5E
InChIInChI=1S/C9H15N2O14P3S/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(23-8)3-22-28(21,29)25-27(19,20)24-26(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,29)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-,28+/m1/s1
InChIKeyBWPNYQWDXHLOGU-KWWYXVLOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(OP(=O)(O)OP(=O)(O)O)S)O)O
OpenEye OEToolkits 2.0.7C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(OP(=O)(O)OP(=O)(O)O)S)O)O
CACTVS 3.385O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@@](S)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CO[P](S)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H15 N2 O14 P3 S
Name[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain6ymw Chain A Residue 1401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6ymw Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase.
Resolution3.71 Å
Binding residue
(original residue number in PDB)		R829 G946 T947 C948 Y979 R1010 K1014 M1018 Y1022 H1163 D1189
Binding residue
(residue number reindexed from 1)		R414 G531 T532 C533 Y564 R595 K599 M603 Y607 H748 D774
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0001018 mitochondrial promoter sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003896 DNA primase activity
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0000002 mitochondrial genome maintenance
GO:0006269 DNA replication, synthesis of primer
GO:0006351 DNA-templated transcription
GO:0006390 mitochondrial transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0034245 mitochondrial DNA-directed RNA polymerase complex
GO:0042645 mitochondrial nucleoid
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ymw, PDBe:6ymw, PDBj:6ymw
PDBsum6ymw
PubMed33278362
UniProtP13433|RPOM_YEAST DNA-directed RNA polymerase, mitochondrial (Gene Name=RPO41)

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