Structure of PDB 8dh1 Chain B Binding Site BS03

Receptor Information
>8dh1 Chain B (length=855) Species: 10760 (Escherichia phage T7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARF
RKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPT
AFQFLQEIKPEAVAYITIKTTLACLTSNTTVQAVASAIGRAIEDEARFGR
IRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSS
WHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEA
IATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKK
ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIP
AIEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYN
MDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAG
VDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYA
GVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQD
IYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQ
WLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQ
PNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEIL
RKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRDSEIDAHKQESGI
APNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAV
RETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILES
DFAFA
Ligand information
Ligand IDS8L
InChIInChI=1S/C10H16NO14P3/c12-4-6-2-1-3-11(6)10-9(14)8(13)7(23-10)5-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-4,7-10,13-14H,5H2,(H,18,19)(H,20,21)(H2,15,16,17)/t7-,8-,9-,10?/m1/s1
InChIKeyCLXMUGOYLDUWBK-PBVVMKELSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(n2cccc2C=O)C(O)C1O
OpenEye OEToolkits 2.0.7c1cc(n(c1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)C=O
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cccc2C=O
CACTVS 3.385O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cccc2C=O
OpenEye OEToolkits 2.0.7c1cc(n(c1)C2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)C=O
FormulaC10 H16 N O14 P3
Name1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-1H-pyrrole-2-carbaldehyde
ChEMBL
DrugBank
ZINC
PDB chain8dh1 Chain B Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dh1 Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		K472 Y571 R627 K631
Binding residue
(residue number reindexed from 1)		K453 Y552 R608 K612
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0019083 viral transcription
GO:0039695 DNA-templated viral transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8dh1, PDBe:8dh1, PDBj:8dh1
PDBsum8dh1
PubMed36635281
UniProtP00573|RPOL_BPT7 T7 RNA polymerase (Gene Name=1)

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