Structure of PDB 3avy Chain A Binding Site BS03

Receptor Information

>3avy Chain A (length=1203) Species: 39803,83334

AEITASLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAAK
KAGNVAADGVIKTKIDGNYGIILEVNCQTDFVAKDAGFQAFADKVLDAAV
AGKITDVEVLKAQFEEERVALVAKIGENINIRRVAALEGDVLGSYQHGAR
IGVLVAAKGADEELVKHIAMHVAASKPEFIKPEDVSAEVVEKEYQVQLDI
AMQSGKPKEIAEKMVEGRMKKFTGEVSLTGQPFVMEPSKTVGQLLKEHNA
EVTGFIRFEVGEGIEKVETDFAAEVAAMSKQSHMSFERTKPHVNVGTIGH
VDHGKTTLTAAITTVLAKTYGGNTSHVEYDTPTRHYAHVDCPGHADYVKN
MITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMV
DDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILE
LAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGE
EVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQ
VLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGT
IELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAK
VLSGASSRNSLSAQLRRAANTRIEVEGNLALSIANDLLLAYGQSPFNSEA
ECISFSPRFDGTPDDFRINYLKAEIMSKYDDFSLGIDTEAVAWEKFLAAE
AECALTNARLYRPDYSEDFNFSLGESCIHMARRKIAKLIGDVPSVEGMLR
HCRFSGGATTTNNRSYGHPSFKFALPQACTPRALKYVLALRASTHFDIRI
SDISPFNKAVTVPKNSKTDRCIAIEPGWNMFFQLGIGGILRDRLRCWGID
LNDQTINQRRAHEGSVTNNLATVDLSAASDSISLALCELLLPPGWFEVLM
DLRSPKGRLPDGSVVTYEKISSMGNGYTFELESLIFASLARSVCEILDLD
SSEVTVYGDDIILPSCAVPALREVFKYVGFTTNTKKTFSEGPFRESCGKH
YYSGVDVTPFYIRHRIVSPADLILVLNNLYRWATIDGVWDPRAHSVYLKY
RKLLPKQLQRNTIPDGYGDGALVGSVLINPFAKNRGWIRYVPVITDHTRD
RERAELGSYLYDLFSRCLSESNAIDQLICRSNPTKISRSTGKFDIQYIAC
SSR

Ligand information

• Ligand ID: CH1
• InChI: InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-6(13)3-5(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
• InChIKey: CHKFLBOLYREYDO-SHYZEUOFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1[C@H](O[C@H]([C@@H]1O)N2C=CC(=NC2=O)N)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)C[C@H]2O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C[CH]2O
  OpenEye OEToolkits 1.5.0: C1C(OC(C1O)N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2
• Formula: C9 H16 N3 O13 P3
• Name: 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL480328
• ZINC: ZINC000031440313
• PDB chain: 3avy Chain A Residue 2501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3avy Molecular basis for RNA polymerization by Q beta replicase
• Resolution: 2.616 Å
• Binding residue (original residue number in PDB): K908 R914 S970 A972 S973 M1017 E1026 D1053
• Binding residue (residue number reindexed from 1): K864 R870 S926 A928 S929 M973 E982 D1009
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D306 K309 T310 H369
• Catalytic site (residue number reindexed from 1): D302 K305 T306 H344
• Enzyme Commision number:
  2.7.7.48: RNA-directed RNA polymerase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding
• GO:0097216 guanosine tetraphosphate binding

Biological Process

• GO:0001172 RNA-templated transcription
• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0019079 viral genome replication
• GO:0039694 viral RNA genome replication
• GO:0046677 response to antibiotic

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005886 plasma membrane

External links

• PDB: RCSB:3avy, PDBe:3avy, PDBj:3avy
• PDBsum: 3avy
• PubMed: 22245970
• UniProt: P0A6N3;
  P0A6P3;
  P14647|RDRP_BPQBE RNA-directed RNA polymerase subunit beta