Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3Q9C

Crystal Structure of H159A APAH complexed with N8-acetylspermidine

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004407	molecular_function	histone deacetylase activity
A	0016787	molecular_function	hydrolase activity
A	0040029	biological_process	epigenetic regulation of gene expression
A	0046872	molecular_function	metal ion binding
A	0047609	molecular_function	acetylputrescine deacetylase activity
A	0047611	molecular_function	acetylspermidine deacetylase activity
B	0004407	molecular_function	histone deacetylase activity
B	0016787	molecular_function	hydrolase activity
B	0040029	biological_process	epigenetic regulation of gene expression
B	0046872	molecular_function	metal ion binding
B	0047609	molecular_function	acetylputrescine deacetylase activity
B	0047611	molecular_function	acetylspermidine deacetylase activity
C	0004407	molecular_function	histone deacetylase activity
C	0016787	molecular_function	hydrolase activity
C	0040029	biological_process	epigenetic regulation of gene expression
C	0046872	molecular_function	metal ion binding
C	0047609	molecular_function	acetylputrescine deacetylase activity
C	0047611	molecular_function	acetylspermidine deacetylase activity
D	0004407	molecular_function	histone deacetylase activity
D	0016787	molecular_function	hydrolase activity
D	0040029	biological_process	epigenetic regulation of gene expression
D	0046872	molecular_function	metal ion binding
D	0047609	molecular_function	acetylputrescine deacetylase activity
D	0047611	molecular_function	acetylspermidine deacetylase activity
E	0004407	molecular_function	histone deacetylase activity
E	0016787	molecular_function	hydrolase activity
E	0040029	biological_process	epigenetic regulation of gene expression
E	0046872	molecular_function	metal ion binding
E	0047609	molecular_function	acetylputrescine deacetylase activity
E	0047611	molecular_function	acetylspermidine deacetylase activity
F	0004407	molecular_function	histone deacetylase activity
F	0016787	molecular_function	hydrolase activity
F	0040029	biological_process	epigenetic regulation of gene expression
F	0046872	molecular_function	metal ion binding
F	0047609	molecular_function	acetylputrescine deacetylase activity
F	0047611	molecular_function	acetylspermidine deacetylase activity
G	0004407	molecular_function	histone deacetylase activity
G	0016787	molecular_function	hydrolase activity
G	0040029	biological_process	epigenetic regulation of gene expression
G	0046872	molecular_function	metal ion binding
G	0047609	molecular_function	acetylputrescine deacetylase activity
G	0047611	molecular_function	acetylspermidine deacetylase activity
H	0004407	molecular_function	histone deacetylase activity
H	0016787	molecular_function	hydrolase activity
H	0040029	biological_process	epigenetic regulation of gene expression
H	0046872	molecular_function	metal ion binding
H	0047609	molecular_function	acetylputrescine deacetylase activity
H	0047611	molecular_function	acetylspermidine deacetylase activity
I	0004407	molecular_function	histone deacetylase activity
I	0016787	molecular_function	hydrolase activity
I	0040029	biological_process	epigenetic regulation of gene expression
I	0046872	molecular_function	metal ion binding
I	0047609	molecular_function	acetylputrescine deacetylase activity
I	0047611	molecular_function	acetylspermidine deacetylase activity
J	0004407	molecular_function	histone deacetylase activity
J	0016787	molecular_function	hydrolase activity
J	0040029	biological_process	epigenetic regulation of gene expression
J	0046872	molecular_function	metal ion binding
J	0047609	molecular_function	acetylputrescine deacetylase activity
J	0047611	molecular_function	acetylspermidine deacetylase activity
K	0004407	molecular_function	histone deacetylase activity
K	0016787	molecular_function	hydrolase activity
K	0040029	biological_process	epigenetic regulation of gene expression
K	0046872	molecular_function	metal ion binding
K	0047609	molecular_function	acetylputrescine deacetylase activity
K	0047611	molecular_function	acetylspermidine deacetylase activity
L	0004407	molecular_function	histone deacetylase activity
L	0016787	molecular_function	hydrolase activity
L	0040029	biological_process	epigenetic regulation of gene expression
L	0046872	molecular_function	metal ion binding
L	0047609	molecular_function	acetylputrescine deacetylase activity
L	0047611	molecular_function	acetylspermidine deacetylase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE Q9C A 401

Chain	Residue
A	TYR19
A	PHE225
A	GLY321
A	TYR323
A	ZN343
A	HOH1000
I	GLU106
A	GLU117
A	PRO156
A	HIS158
A	GLY167
A	TYR168
A	CYS169
A	ASP195
A	HIS197

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K A 342

Chain	Residue
A	ASP193
A	ASP195
A	HIS197
A	SER216
A	LEU217

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 343

Chain	Residue
A	ASP195
A	HIS197
A	ASP284
A	TYR323
A	Q9C401

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA A 344

Chain	Residue
A	PHE206
A	ARG209
A	VAL212
A	THR243
A	HOH353

site_id	AC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE Q9C B 402

Chain	Residue
B	TYR19
B	GLU117
B	PRO156
B	HIS158
B	GLY167
B	TYR168
B	CYS169
B	ASP195
B	HIS197
B	PHE225
B	TYR323
B	ZN343
B	HOH565
B	HOH1449
F	GLU106

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K B 342

Chain	Residue
B	ASP193
B	ASP195
B	HIS197
B	SER216
B	LEU217

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 343

Chain	Residue
B	ASP195
B	HIS197
B	ASP284
B	Q9C402

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA B 344

Chain	Residue
B	PHE206
B	ARG209
B	VAL212
B	THR243
B	HOH352

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE Q9C C 403

Chain	Residue
C	TYR19
C	GLU117
C	HIS158
C	GLY167
C	TYR168
C	ASP195
C	HIS197
C	PHE225
C	TYR323
C	ZN343
C	HOH578
C	HOH1084
K	GLU106

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K C 342

Chain	Residue
C	ASP193
C	ASP195
C	HIS197
C	SER216
C	LEU217

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 343

Chain	Residue
C	ASP195
C	HIS197
C	ASP284
C	Q9C403

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA C 344

Chain	Residue
C	PHE206
C	ARG209
C	VAL212
C	THR243
C	HOH351

site_id	BC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE Q9C D 404

Chain	Residue
D	GLU117
D	PRO156
D	HIS158
D	GLY167
D	TYR168
D	ASP195
D	HIS197
D	PHE225
D	GLY321
D	TYR323
D	ZN343
D	HOH1003

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K D 342

Chain	Residue
D	ASP195
D	HIS197
D	SER216
D	LEU217
D	ASP193

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 343

Chain	Residue
D	ASP195
D	HIS197
D	ASP284
D	Q9C404

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA D 344

Chain	Residue
D	PHE206
D	ARG209
D	VAL212
D	THR243
D	HOH351

site_id	BC8
Number of Residues	16
Details	BINDING SITE FOR RESIDUE Q9C E 405

Chain	Residue
E	TYR19
E	GLU117
E	PRO156
E	HIS158
E	GLY167
E	TYR168
E	CYS169
E	ASP195
E	HIS197
E	PHE225
E	GLY321
E	TYR323
E	ZN343
E	HOH569
H	TYR83
H	GLU106

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K E 342

Chain	Residue
E	ASP193
E	ASP195
E	HIS197
E	SER216
E	LEU217

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 343

Chain	Residue
E	ASP195
E	HIS197
E	ASP284
E	Q9C405

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA E 344

Chain	Residue
E	PHE206
E	ARG209
E	VAL212
E	THR243
E	HOH348

site_id	CC3
Number of Residues	14
Details	BINDING SITE FOR RESIDUE Q9C F 406

Chain	Residue
B	TYR83
F	GLU117
F	PRO156
F	HIS158
F	GLY167
F	TYR168
F	CYS169
F	ASP195
F	HIS197
F	PHE225
F	GLY321
F	TYR323
F	ZN343
F	HOH573

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K F 342

Chain	Residue
F	ASP193
F	ASP195
F	HIS197
F	SER216
F	LEU217

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 343

Chain	Residue
F	ASP195
F	HIS197
F	ASP284
F	Q9C406

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA F 344

Chain	Residue
F	PHE206
F	ARG209
F	VAL212
F	THR243
F	HOH1031

site_id	CC7
Number of Residues	16
Details	BINDING SITE FOR RESIDUE Q9C G 407

Chain	Residue
G	TYR19
G	GLU117
G	PRO156
G	HIS158
G	GLY167
G	TYR168
G	CYS169
G	ASP195
G	HIS197
G	PHE225
G	GLY321
G	TYR323
G	ZN343
G	HOH1083
G	HOH1759
L	GLU106

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K G 342

Chain	Residue
G	ASP193
G	ASP195
G	HIS197
G	SER216
G	LEU217

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN G 343

Chain	Residue
G	ASP195
G	HIS197
G	ASP284
G	Q9C407

site_id	DC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA G 344

Chain	Residue
G	PHE206
G	ARG209
G	VAL212
G	THR243
G	HOH347

site_id	DC2
Number of Residues	16
Details	BINDING SITE FOR RESIDUE Q9C H 408

Chain	Residue
E	GLU106
H	TYR19
H	GLU117
H	PRO156
H	HIS158
H	GLY167
H	TYR168
H	CYS169
H	ASP195
H	HIS197
H	PHE225
H	GLY321
H	TYR323
H	ZN343
H	HOH556
H	HOH990

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K H 342

Chain	Residue
H	ASP193
H	ASP195
H	HIS197
H	SER216
H	LEU217

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN H 343

Chain	Residue
H	ASP195
H	HIS197
H	ASP284
H	TYR323
H	Q9C408

site_id	DC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA H 344

Chain	Residue
H	PHE206
H	ARG209
H	VAL212
H	THR243
H	HOH381

site_id	DC6
Number of Residues	17
Details	BINDING SITE FOR RESIDUE Q9C I 409

Chain	Residue
A	GLU106
I	TYR19
I	GLU117
I	PRO156
I	HIS158
I	GLY167
I	TYR168
I	CYS169
I	ASP195
I	HIS197
I	PHE225
I	ASP284
I	GLY321
I	TYR323
I	ZN343
I	HOH558
I	HOH559

site_id	DC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K I 342

Chain	Residue
I	ASP193
I	ASP195
I	HIS197
I	SER216
I	LEU217

site_id	DC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN I 343

Chain	Residue
I	ASP195
I	HIS197
I	ASP284
I	Q9C409

site_id	DC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA I 344

Chain	Residue
I	PHE206
I	ARG209
I	VAL212
I	THR243
I	HOH402

site_id	EC1
Number of Residues	16
Details	BINDING SITE FOR RESIDUE Q9C J 410

Chain	Residue
D	GLU106
J	TYR19
J	GLU117
J	PRO156
J	HIS158
J	GLY167
J	TYR168
J	CYS169
J	ASP195
J	HIS197
J	PHE225
J	GLY321
J	TYR323
J	ZN343
J	HOH555
J	HOH575

site_id	EC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K J 342

Chain	Residue
J	ASP193
J	ASP195
J	HIS197
J	SER216
J	LEU217

site_id	EC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN J 343

Chain	Residue
J	ASP195
J	HIS197
J	ASP284
J	Q9C410

site_id	EC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA J 344

Chain	Residue
J	PHE206
J	ARG209
J	VAL212
J	THR243
J	HOH363

site_id	EC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE Q9C K 411

Chain	Residue
C	GLU106
K	TYR19
K	GLU117
K	PRO156
K	HIS158
K	GLY167
K	TYR168
K	ASP195
K	HIS197
K	PHE225
K	ASP284
K	GLY321
K	TYR323
K	ZN343
K	HOH561
K	HOH579

site_id	EC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K K 342

Chain	Residue
K	ASP193
K	ASP195
K	HIS197
K	SER216
K	LEU217

site_id	EC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN K 343

Chain	Residue
K	ASP195
K	HIS197
K	ASP284
K	Q9C411

site_id	EC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA K 344

Chain	Residue
K	PHE206
K	ARG209
K	VAL212
K	THR243
K	HOH355

site_id	EC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE Q9C L 412

Chain	Residue
G	TYR83
L	TYR19
L	GLU117
L	PRO156
L	HIS158
L	GLY167
L	TYR168
L	CYS169
L	HIS197
L	PHE225
L	TYR323
L	ZN343
L	HOH1002

site_id	FC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K L 342

Chain	Residue
L	ASP193
L	ASP195
L	HIS197
L	SER216
L	LEU217

site_id	FC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN L 343

Chain	Residue
L	ASP195
L	HIS197
L	ASP284
L	Q9C412

site_id	FC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA L 344

Chain	Residue
L	PHE206
L	ARG209
L	VAL212
L	THR243
L	HOH1032

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"PubMed","id":"21268586","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26200446","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"21268586","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3Q9E","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"21268586","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3Q9C","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"21268586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26200446","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3Q9B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3Q9E","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	12
Details	Site: {"description":"Polarizes the scissile carbonyl of the substrate","evidences":[{"source":"PubMed","id":"21268586","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)