BioLiP

Receptor Information

>8w8p Chain D (length=1497) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQL
LTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV
ALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFR
AEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQ
PLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMN
VVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYP
FEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDI
DARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAF
LDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNN
RLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRS
LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALEL
FKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLL
NRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLS
SFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGA
GLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLA
VAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQL
DVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGID
DAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEK
VTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGET
FEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVT
HEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLARE
VEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQ
KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVADITQG
LPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKL
PKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKV
YRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNE
RLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGK
KDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEA

Ligand ID

2TM

InChI

InChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1

InChIKey

STGUOVSTMBLHFT-ZOQUXTDFSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6	C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
CACTVS 3.385	NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
CACTVS 3.385	NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O

Formula

C10 H18 N3 O13 P3

Name

5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine;
CMPcPP

PDB chain

8w8p Chain D Residue 1606 [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	8w8p Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.
Resolution	3.165 Å
Binding residue (original residue number in PDB)	R704 P706 N737 M1238 T1240
Binding residue (residue number reindexed from 1)	R702 P704 N735 M1236 T1238
Annotation score	1

	Molecular Function
GO:0000287	magnesium ion binding
GO:0003677	DNA binding
GO:0003899	DNA-directed 5'-3' RNA polymerase activity
GO:0005515	protein binding
GO:0008270	zinc ion binding
GO:0016779	nucleotidyltransferase activity
GO:0034062	5'-3' RNA polymerase activity
GO:0046872	metal ion binding

	Biological Process
GO:0006351	DNA-templated transcription

	Cellular Component
GO:0000428	DNA-directed RNA polymerase complex

PDB	RCSB:8w8p, PDBe:8w8p, PDBj:8w8p
PDBsum	8w8p
PubMed	38990947
UniProt	Q8RQE8\|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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Structure of PDB 8w8p Chain D Binding Site BS08