Structure of PDB 2ppb Chain N Binding Site BS05

Receptor Information

>2ppb Chain N (length=1314) Species: 300852 (Thermus thermophilus HB8)

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 ID: STD
• InChI: InChI=1S/C32H44N2O9/c1-16(14-17(2)28-18(3)23-12-13-32(15-40-32)31(6,42-23)43-28)8-9-22(36)25-27(37)26(19(4)29(38)33-7)34(30(25)39)24-11-10-21(35)20(5)41-24/h8-9,12-14,17-21,23-24,26,28,35-36H,10-11,15H2,1-7H3,(H,33,38)/b9-8+,16-14+,25-22+/t17-,18+,19+,20+,21+,23-,24+,26+,28-,31-,32-/m1/s1
• InChIKey: KVTPRMVXYZKLIG-NCAOFHFGSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1C2C=CC3(CO3)C(O2)(OC1C(C)C=C(C)C=CC(=C4C(=O)C(N(C4=O)C5CCC(C(O5)C)O)C(C)C(=O)NC)O)C
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]2C=C[C@@]3(CO3)[C@](O2)(O[C@@H]1[C@H](C)\C=C(/C)\C=C\C(=C/4\C(=O)[C@@H](N(C4=O)[C@@H]5CC[C@@H]([C@@H](O5)C)O)[C@H](C)C(=O)NC)\O)C
  CACTVS 3.341: CNC(=O)[C@@H](C)[C@@H]1N([C@@H]2CC[C@H](O)[C@H](C)O2)C(=O)\C(=C(O)/C=C/C(C)=C/[C@@H](C)[C@H]3O[C@@]4(C)O[C@H](C=C[C@@]45CO5)[C@@H]3C)C1=O
  ACDLabs 10.04: O=C(NC)C(C)C2C(=O)/C(C(=O)N2C1OC(C)C(O)CC1)=C(\O)/C=C/C(=C/C(C5OC4(OC(C=CC34OC3)C5C)C)C)C
  CACTVS 3.341: CNC(=O)[CH](C)[CH]1N([CH]2CC[CH](O)[CH](C)O2)C(=O)C(=C(O)C=CC(C)=C[CH](C)[CH]3O[C]4(C)O[CH](C=C[C]45CO5)[CH]3C)C1=O
• Formula: C32 H44 N2 O9
• Name: STREPTOLYDIGIN;
  2-PYRROLIDINEACETAMIDE;
  PORTAMYCIN
• ChEMBL: CHEMBL1236068
• DrugBank: DB04785
• ZINC: ZINC000169363256
• PDB chain: 2ppb Chain N Residue 8001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ppb Structural basis for substrate loading in bacterial RNA polymerase.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): A1082 A1085 L1086 R1087 D1090 P1257
• Binding residue (residue number reindexed from 1): A898 A901 L902 R903 D906 P1066
• Annotation score: 1

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

External links

• PDB: RCSB:2ppb, PDBe:2ppb, PDBj:2ppb
• PDBsum: 2ppb
• PubMed: 17581591
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)