Structure of PDB 2ppb Chain D Binding Site BS08

Receptor Information
>2ppb Chain D (length=1314) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQ
LLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG
VALYRFASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGR
VEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHP
SRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGR
FATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDN
GRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVG
PQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIK
DEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCE
AFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD
IILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRET
SVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFAR
IVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDAL
KYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLT
DRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQ
IRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADT
ALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRL
RKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQ
EVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGT
QLTMRTFHTDITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLS
VFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGP
EAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLE
GQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQ
NTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKT
LKAIEEARKEAVEA
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain2ppb Chain D Residue 5999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ppb Structural basis for substrate loading in bacterial RNA polymerase.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		R704 P706 N737 R1029
Binding residue
(residue number reindexed from 1)		R520 P522 N553 R845
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2ppb, PDBe:2ppb, PDBj:2ppb
PDBsum2ppb
PubMed17581591
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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