Structure of PDB 5yv5 Chain A Binding Site BS03

Receptor Information
>5yv5 Chain A (length=517) Species: 1185654 (Pyrococcus furiosus COM1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHLEEDCVHRYGVNAFVLYRLPVVKEGMVVGIVGPNGTGKSTAVKILAGQ
LIPNLCGDNDSWDGVIRAFRGNELQNYFEKLKNGEIRPVVKPQYVDLIPK
AVKGKVIELLKKADETGKLEEVVKALELENVLDREIQHLSGGELQRVAIA
AALLRNATFYFFDEPSSYLDIRQRLNAARAIRRLSEEGKSVLVVEHDLAV
LDYLSDIIHVVYGEPGVYGIFSQPKGTRNGINEFLRGYLKDENVRFRPYE
IKFTKTGERVEIERETLVTYPRLVKDYGSFRLEVEPGEIKKGEVIGIVGP
NGIGKTTFVKMLAGVEEPTEGKIEWDLTVAYKPQYIKADYEGTVYELLSK
IDASKLNSNFYKTELLKPLGIIDLYDREVNELSGGELQRVAIAATLLRDA
DIYLLDEPSAYLDVEQRLAVSRAIRHLMEKNEKTALVVEHDVLMIDYVSD
RLMVFEGEPGKYGRALPPMGMREGMNRFLASIGITFRRDPDTGRPRANKE
GSVKDREQKEKGEYYYI
Ligand information
Ligand IDADP
InChIInChI=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
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-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)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5yv5 Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5yv5 The ribosomal stalk protein is crucial for the action of the conserved ATPase ABCE1
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y349 F352 N373 G374 I375 G376 K377 T378 T379
Binding residue
(residue number reindexed from 1)		Y277 F280 N301 G302 I303 G304 K305 T306 T307
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity

View graph for
Molecular Function
External links
PDB RCSB:5yv5, PDBe:5yv5, PDBj:5yv5
PDBsum5yv5
PubMed30010948
UniProtI6V0C7

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