Structure of PDB 6pek Chain D Binding Site BS03

Receptor Information
>6pek Chain D (length=293) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RNVDSNLANLIMNEIVDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPEL
FTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVG
EGEKLVRALFAVARELQPSIIFIDEVDSLLCERREGEHDASRRLKTEFLI
EFDGVQSAGDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLL
LKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKDAALGPIRELKPE
QVKNMSASEMRNIRLSDFTESLKKIKRSVSPQTLEAYIRWNKD
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 chain6pek Chain D Residue 701 [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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PDB6pek Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation.
Resolution4.2 Å
Binding residue
(original residue number in PDB)		D343 A345 G385 N386 G387 K388 T389 M390 G546
Binding residue
(residue number reindexed from 1)		D26 A28 G68 N69 G70 K71 T72 M73 G229
Annotation score5
Enzymatic activity
Enzyme Commision number 5.6.1.1: microtubule-severing ATPase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008568 microtubule severing ATPase activity
GO:0016887 ATP hydrolysis activity

View graph for
Molecular Function
External links
PDB RCSB:6pek, PDBe:6pek, PDBj:6pek
PDBsum6pek
PubMed31767681
UniProtQ9UBP0|SPAST_HUMAN Spastin (Gene Name=SPAST)

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