Structure of PDB 6qv3 Chain A Binding Site BS03

Receptor Information

>6qv3 Chain A (length=1657) Species: 209285 (Thermochaetoides thermophila)

GTTKRVFKGYEEIHVPPPKKRSDPTDQNIPVTELPEWARIPFNTTKTLNK
IQSKCFPTAFLDDGNMLVCAPTGSGKTNVAMLTMLREIGKNRNEKGEIDL
DAFKIVYIAPLKALVQEQVGNFGKRLEPYGIKVSELTGDRQLTKQQISET
QVIVTTPEKWDVITRKATDISYTNLVRLIIIDEIHLLHDDRGPVLESIVS
RTIRRTEQTGEPVRIIGLSATLPNYRDVASFLRVDFEKGLFYFDGSYRPC
PLRQEFIGVQLKTMNDITYQKVLEHVGQNRNQMLIFVHSRKETAKTAKYI
RDKALEMDTINQILKHDAGTREVLQEAASSVNNTDLKDLLPYGFGIHHAG
MSRADRTDVEDLFASGHIQVLVCTATLAWGVNLPAHTVIIKGTQVYSPEK
GSWVELSPQDVLQMLGRAGRPQYDTYGEGIIITTQGEIPYYLSLLNQQLP
IESQLVSKLVDSLNAEIVLGNVRNRDEGVEWLGYTYLFVRMLRSPGLYSV
GAEYEDDVALEQKRVDLIHSAAMVLKKSNLIKYDEKTGKMQATELGRIAS
HYYISHESMDTYNKLIHPAMNDVELFRVFAQSGEFKYIPVRQEEKLELAK
LLARVPIPVKESIEEPTAKINVLLQAYISRLKLEGLALMADMVYVTQSAG
RILRAIFEICLKKGWASVAKLALNMCKMAEKRMWPTMSPLRQYPTCPAEI
IKKAERMDVPWSSYFDLDPPRMGELLGMPKAGKTVCALVSKFPRVEIQGN
VQPMTRSMLRIELTITPNFQWDVELHGVTESFWILVEDCDGEEILFHDVF
ILRKDLAEAEENEHTVEFTVPISEPMPPNYFISVISDRWMHSETRMPVSF
QKLILPERFPPHTELLDLQPLPVSALKAKDYAALYPNWQQFNKIQTQTFN
SLYNTDNNVLVAAPTGSGKTVCAEFALLRHWAKKDAGRAVYIAPFQELVD
LRFQDWQKRLSHLRGGKEIVKLTGETTTDLKLLEQGDLILATPLQWDVLS
RQWKRRKNVQTVELFIADDLHMLGGQMGYIYEIVVSRMHFIRTQTELPMR
IVGLSVSLANARDIGEWIDAKKHDIYNFSPHVRPVPLELHIQSYTIPHFP
SLMLAMAKPTYLAITQLSPDQPAIVFVPSRKQTRATARDLLTACLADDDE
DRFLHVEVDQIRKLLDHVQEEALAEALSHGVGYYHEALSQSDKRIVKHLY
NNGAIQVLIASRDVCWELDFTAHLVVVMGTQFFEGKEHRYIDYPLSEVLQ
MFGKALQPSKDGRSRGVLMLPAVKREYYKKFLNEALPVESHLHNFLPDAF
VTEISTKMIESGEDAINWATFTYFYRRLLANPSYYGLQDPTHDGLSQYLS
DLVETTLKQLSDARIIEMDEDEGTVAPLNAAMIAAYYNISYMTMEMFLLS
LSHKSKLRTILEIVTAATEFESIQTRRHEEGILKRIYDHVPVKMNNPVWD
SAHFKAFVLVQAHFSRMNLPIDLAKDQEVILQKILSLLSAIVDILSSEGH
LNALNAMEMSQMVVQAMWDRDSPLKQIPNFTPEVVKVANKYGINDIFDFM
EQMNPEENPNYASLVKDLGLTQAQLAQAANFTNNKYPDITLPAYLKIHIE
REDPTVHAPFYPGKKSENWWLVVTLLAIKRVTVGKELNVKLEFVFLMSDS
YVGVDQD

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 6qv3 Chain A Residue 2203

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qv3 Molecular Mechanism Underlying Inhibition of Intrinsic ATPase Activity in a Ski2-like RNA Helicase.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): F1288 I1289 R1291 H1586 H1726 Y1728
• Binding residue (residue number reindexed from 1): F800 I801 R803 H1098 H1238 Y1240
• Annotation score: 5

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity

External links

• PDB: RCSB:6qv3, PDBe:6qv3, PDBj:6qv3
• PDBsum: 6qv3
• PubMed: 31859026
• UniProt: G0S0B9