Structure of PDB 3avt Chain A Binding Site BS02

Receptor Information

>3avt 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: GH3
• InChI: InChI=1S/C10H16N5O13P3/c11-10-13-7-6(8(17)14-10)12-3-15(7)9-5(16)1-4(26-9)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-5,9,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,9+/m0/s1
• InChIKey: QGYIFQKZZSSUCR-OBXARNEKSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H](C[C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C[CH]3O
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)C[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(CC(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
• Formula: C10 H16 N5 O13 P3
• Name: 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL480707
• ZINC: ZINC000031430873
• PDB chain: 3avt Chain A Residue 2502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3avt Molecular basis for RNA polymerization by Q beta replicase
• Resolution: 2.607 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:3avt, PDBe:3avt, PDBj:3avt
• PDBsum: 3avt
• PubMed: 22245970
• UniProt: P0A6N3;
  P0A6P3;
  P14647|RDRP_BPQBE RNA-directed RNA polymerase subunit beta