Structure of PDB 6wdv Chain A

Receptor sequence
>6wdvA (length=638) Species: 7955 (Danio rerio) [Search protein sequence]
AASGSALIFDEEMSRYKLLWTDPECEIEVPERLTVSYEALRTHGLAQRCK
AVPVRQATEQEILLAHSEEYLEAVKQTPGMNVEELMAFSKKYNAVYFHQN
IYHCAKLAAGATLQLVDSVMKREVRNGMALVRPPGHHSQRSAANGFCVFN
NVAFAALYAKKNYNLNRILIVDWDVHHGQGIQYCFEEDPSVLYFSWHRYE
HQSFWPNLPESDYSSVGKGKGSGFNINLPWNKVGMTNSDYLAAFFHVLLP
VAYEFDPELVIVSAGFDSAIGDPEGEMCALPEIFAHLTHLLMPLAAGKMC
VVLEGGYNLTSLGQSVCQTVHSLLGDPTPRISGLGTACDSALESIQNVRN
VQSSYWSSFKHLAQSETDIVWPEPLKRMPASVRTVVVPPPGVELTLPKNC
QHSISESTAKEVQRIRDKHFLTDQNILRSLGNIISVLDRMMRSDEVCNGC
VVVSDLSVSVQCALQHALTEPAERVLVVYVGDGELPVKTNDGKVFLVQIC
TKETEDKCVNRLTLCLREGESLTAGFMQALLGLILPVAYEFNPALVLGIV
EETARLMRVWGHMTCLIQGLARGRMLTLLQGYDKDLLELTVSALSGASIS
PLGPLRAPKPEDVEMMEKQRQRLQERWGLLRCTVSESW
3D structure
PDB6wdv Structural Basis for the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase.
ChainA
Resolution2.4 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.5.1.48: acetylspermidine deacetylase.
3.5.1.62: acetylputrescine deacetylase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 TWM A E24 H136 H137 F146 D174 H176 W205 D267 E274 Y307 E24 H136 H137 F146 D174 H176 W205 D267 E274 Y307 MOAD: ic50=5nM
BS02 ZN A D174 H176 D267 D174 H176 D267
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0019213 deacetylase activity
GO:0033558 protein lysine deacetylase activity
GO:0046872 metal ion binding
GO:0047609 acetylputrescine deacetylase activity
GO:0047611 acetylspermidine deacetylase activity
Biological Process
GO:0016236 macroautophagy
GO:0035825 homologous recombination
GO:0036269 swimming behavior
GO:0040029 epigenetic regulation of gene expression
GO:0090043 regulation of tubulin deacetylation
GO:0106047 polyamine deacetylation
GO:0106048 spermidine deacetylation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6wdv, PDBe:6wdv, PDBj:6wdv
PDBsum6wdv
PubMed32659072
UniProtF1QCV2|HDA10_DANRE Polyamine deacetylase HDAC10 (Gene Name=hdac10)

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