BioLiP

Receptor Information

>4oio Chain D (length=1479) 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
HEIVVREADCGTTNYISVPLFQPTRSLRLRKRADIEAGLYGRVLAREVEV
LGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCY
GYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRQGLPRVIELFEARRPK
AKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYV
EAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIE
IVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKP
LLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILG
RLIPAGTGSDFVRFTQVVDQKTLKAIEEA

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

4oio Chain D Residue 2006 [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	4oio GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.
Resolution	3.1 Å
Binding residue (original residue number in PDB)	R704 P706 N737 R1029
Binding residue (residue number reindexed from 1)	R702 P704 N735 R1027
Annotation score	1

Enzyme Commision number

2.7.7.6: DNA-directed RNA polymerase.

	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:4oio, PDBe:4oio, PDBj:4oio
PDBsum	4oio
PubMed	24755292
UniProt	Q8RQE8\|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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Structure of PDB 4oio Chain D Binding Site BS06