Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3Q9F

Crystal Structure of APAH complexed with CAPS

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	13
Details	BINDING SITE FOR RESIDUE CXS A 401

Chain	Residue
A	GLU117
A	GLY321
A	ZN345
A	HOH1304
A	HOH1305
A	HIS158
A	HIS159
A	GLY167
A	TYR168
A	ASP195
A	HIS197
A	PHE225
A	ASP284

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 A 353

Chain	Residue
A	HIS54
A	GLY55
A	ARG180
A	HOH370

site_id	AC3
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	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA A 343

Chain	Residue
A	PHE206
A	ARG209
A	VAL212
A	THR243
A	HOH376

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE K A 344

Chain	Residue
A	PHE286
A	GLU287
A	ASP289
A	SER292
A	PHE294
A	HOH745

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 345

Chain	Residue
A	ASP195
A	HIS197
A	ASP284
A	CXS401

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CXS B 402

Chain	Residue
B	HIS158
B	HIS159
B	GLY167
B	TYR168
B	ASP195
B	HIS197
B	PHE225
B	ASP284
B	ILE291
B	GLY321
B	TYR323
B	ZN344

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 B 352

Chain	Residue
B	HIS54
B	GLY55
B	ARG180
B	HOH364

site_id	AC9
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	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA B 343

Chain	Residue
B	PHE206
B	ARG209
B	VAL212
B	THR243
B	HOH347
B	HOH794

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 344

Chain	Residue
B	ASP195
B	HIS197
B	ASP284
B	CXS402

site_id	BC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE CXS C 403

Chain	Residue
C	HIS158
C	HIS159
C	GLY167
C	TYR168
C	ASP195
C	HIS197
C	PHE225
C	ASP284
C	GLY321
C	ZN345
C	HOH1301

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 C 353

Chain	Residue
C	HIS54
C	GLY55
C	ARG180
C	HOH475
C	HOH476

site_id	BC5
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	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA C 343

Chain	Residue
C	PHE206
C	ARG209
C	VAL212
C	THR243
C	HOH366

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE K C 344

Chain	Residue
C	HOH1274
C	PHE286
C	GLU287
C	ASP289
C	SER292
C	PHE294

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 345

Chain	Residue
C	ASP195
C	HIS197
C	ASP284
C	CXS403

site_id	BC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE CXS D 404

Chain	Residue
D	GLU117
D	HIS158
D	HIS159
D	GLY167
D	TYR168
D	ASP195
D	HIS197
D	PHE225
D	ASP284
D	GLY321
D	ZN345

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PO4 D 352

Chain	Residue
D	HIS54
D	ARG180
D	HOH364

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K D 342

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

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA D 343

Chain	Residue
D	PHE206
D	ARG209
D	VAL212
D	THR243
D	HOH366

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE K D 344

Chain	Residue
D	PHE286
D	GLU287
D	ASP289
D	SER292
D	PHE294
D	HOH1275

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 345

Chain	Residue
D	ASP195
D	HIS197
D	ASP284
D	CXS404

site_id	CC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE CXS E 405

Chain	Residue
E	HIS158
E	HIS159
E	GLY167
E	TYR168
E	ASP195
E	HIS197
E	PHE225
E	ASP284
E	ILE291
E	GLY321
E	TYR323
E	ZN345
E	HOH1003

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 E 353

Chain	Residue
E	HIS54
E	GLY55
E	ARG180
E	HOH477

site_id	CC8
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	CC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA E 343

Chain	Residue
E	PHE206
E	ARG209
E	VAL212
E	THR243
E	HOH359
E	HOH558

site_id	DC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE K E 344

Chain	Residue
E	PHE286
E	GLU287
E	ASP289
E	SER292
E	PHE294
E	HOH1288
E	HOH1289

site_id	DC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 345

Chain	Residue
E	ASP195
E	HIS197
E	ASP284
E	CXS405

site_id	DC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CXS F 406

Chain	Residue
F	HIS158
F	HIS159
F	GLY167
F	TYR168
F	ASP195
F	HIS197
F	PHE225
F	ASP284
F	GLY321
F	ZN345

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 F 352

Chain	Residue
F	HIS54
F	GLY55
F	ARG180
F	HOH364
F	HOH366

site_id	DC5
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	DC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA F 343

Chain	Residue
F	PHE206
F	ARG209
F	VAL212
F	THR243
F	HOH367

site_id	DC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K F 344

Chain	Residue
F	PHE286
F	GLU287
F	ASP289
F	SER292
F	PHE294

site_id	DC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 345

Chain	Residue
F	ASP195
F	HIS197
F	ASP284
F	CXS406

site_id	DC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE CXS G 407

Chain	Residue
G	HIS158
G	HIS159
G	GLY167
G	TYR168
G	ASP195
G	HIS197
G	PHE225
G	ASP284
G	GLY321
G	TYR323
G	ZN345
G	HOH603
G	HOH1004

site_id	EC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 G 353

Chain	Residue
G	HIS54
G	GLY55
G	ARG180
G	HOH360
G	HOH472

site_id	EC2
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	EC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA G 343

Chain	Residue
G	PHE206
G	ARG209
G	VAL212
G	THR243
G	HOH361

site_id	EC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE K G 344

Chain	Residue
G	PHE286
G	GLU287
G	ASP289
G	SER292
G	PHE294
G	HOH1286
G	HOH1287

site_id	EC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN G 345

Chain	Residue
G	ASP195
G	HIS197
G	ASP284
G	CXS407

site_id	EC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CXS H 408

Chain	Residue
H	GLU117
H	HIS158
H	HIS159
H	GLY167
H	TYR168
H	ASP195
H	HIS197
H	ASP284
H	GLY321
H	ZN345

site_id	EC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PO4 H 352

Chain	Residue
H	HIS54
H	GLY55
H	ARG180

site_id	EC8
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	EC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA H 343

Chain	Residue
H	PHE206
H	ARG209
H	VAL212
H	THR243
H	HOH362

site_id	FC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K H 344

Chain	Residue
H	PHE286
H	GLU287
H	ASP289
H	SER292
H	PHE294

site_id	FC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 345

Chain	Residue
H	ASP195
H	HIS197
H	ASP284
H	CXS408

site_id	FC3
Number of Residues	14
Details	BINDING SITE FOR RESIDUE CXS I 409

Chain	Residue
I	GLU117
I	HIS158
I	HIS159
I	GLY167
I	TYR168
I	ASP195
I	HIS197
I	PHE225
I	ASP284
I	ILE291
I	GLY321
I	TYR323
I	ZN344
I	HOH536

site_id	FC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 I 353

Chain	Residue
I	HIS54
I	GLY55
I	ARG180
I	HOH479
I	HOH480

site_id	FC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE K I 342

Chain	Residue
I	ASP193
I	ASP195
I	HIS197
I	SER216
I	LEU217
I	HIS218

site_id	FC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA I 343

Chain	Residue
I	PHE206
I	ARG209
I	VAL212
I	THR243
I	HOH369

site_id	FC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN I 344

Chain	Residue
I	ASP195
I	HIS197
I	ASP284
I	CXS409

site_id	FC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE CXS J 410

Chain	Residue
J	GLU117
J	HIS158
J	HIS159
J	GLY167
J	TYR168
J	ASP195
J	HIS197
J	PHE225
J	ASP284
J	GLY321
J	TYR323
J	ZN344

site_id	FC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 J 352

Chain	Residue
J	HIS54
J	GLY55
J	ARG180
J	HOH377

site_id	GC1
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	GC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA J 343

Chain	Residue
J	PHE206
J	ARG209
J	VAL212
J	THR243
J	HOH379

site_id	GC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN J 344

Chain	Residue
J	ASP195
J	HIS197
J	ASP284
J	CXS410

site_id	GC4
Number of Residues	14
Details	BINDING SITE FOR RESIDUE CXS K 411

Chain	Residue
K	TYR19
K	GLU117
K	HIS158
K	HIS159
K	GLY167
K	TYR168
K	ASP195
K	HIS197
K	PHE225
K	ASP284
K	ILE291
K	GLY321
K	TYR323
K	ZN344

site_id	GC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 K 353

Chain	Residue
K	HIS54
K	GLY55
K	ARG180
K	HOH365
K	HOH473

site_id	GC6
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	GC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA K 343

Chain	Residue
K	PHE206
K	ARG209
K	VAL212
K	THR243
K	HOH369

site_id	GC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN K 344

Chain	Residue
K	ASP195
K	HIS197
K	ASP284
K	CXS411

site_id	GC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE CXS L 412

Chain	Residue
L	GLU117
L	HIS158
L	HIS159
L	GLY167
L	TYR168
L	ASP195
L	HIS197
L	PHE225
L	ASP284
L	GLY321
L	ZN345
L	HOH1017
L	HOH1299

site_id	HC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 L 352

Chain	Residue
L	HIS54
L	GLY55
L	ARG180
L	HOH372

site_id	HC2
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	HC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA L 343

Chain	Residue
L	PHE206
L	ARG209
L	VAL212
L	THR243
L	THR244
L	HOH373

site_id	HC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE K L 344

Chain	Residue
L	PHE286
L	GLU287
L	ASP289
L	SER292
L	PHE294
L	HOH1265

site_id	HC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN L 345

Chain	Residue
L	ASP195
L	HIS197
L	ASP284
L	CXS412

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	ACT_SITE: Proton donor/acceptor => ECO:0000305\|PubMed:21268586, ECO:0000305\|PubMed:26200446

Chain	Residue	Details
A	HIS159
J	HIS159
K	HIS159
L	HIS159
B	HIS159
C	HIS159
D	HIS159
E	HIS159
F	HIS159
G	HIS159
H	HIS159
I	HIS159

site_id	SWS_FT_FI2
Number of Residues	36
Details	BINDING: BINDING => ECO:0000269\|PubMed:21268586, ECO:0007744\|PDB:3Q9E

Chain	Residue	Details
A	TYR19
D	TYR19
D	GLU117
D	TYR323
E	TYR19
E	GLU117
E	TYR323
F	TYR19
F	GLU117
F	TYR323
G	TYR19
A	GLU117
G	GLU117
G	TYR323
H	TYR19
H	GLU117
H	TYR323
I	TYR19
I	GLU117
I	TYR323
J	TYR19
J	GLU117
A	TYR323
J	TYR323
K	TYR19
K	GLU117
K	TYR323
L	TYR19
L	GLU117
L	TYR323
B	TYR19
B	GLU117
B	TYR323
C	TYR19
C	GLU117
C	TYR323

site_id	SWS_FT_FI3
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:21268586, ECO:0007744\|PDB:3Q9C

Chain	Residue	Details
A	GLU106
J	GLU106
K	GLU106
L	GLU106
B	GLU106
C	GLU106
D	GLU106
E	GLU106
F	GLU106
G	GLU106
H	GLU106
I	GLU106

site_id	SWS_FT_FI4
Number of Residues	36
Details	BINDING: BINDING => ECO:0000269\|PubMed:21268586, ECO:0000269\|PubMed:26200446, ECO:0007744\|PDB:3Q9B, ECO:0007744\|PDB:3Q9E

Chain	Residue	Details
A	ASP195
D	ASP195
D	HIS197
D	ASP284
E	ASP195
E	HIS197
E	ASP284
F	ASP195
F	HIS197
F	ASP284
G	ASP195
A	HIS197
G	HIS197
G	ASP284
H	ASP195
H	HIS197
H	ASP284
I	ASP195
I	HIS197
I	ASP284
J	ASP195
J	HIS197
A	ASP284
J	ASP284
K	ASP195
K	HIS197
K	ASP284
L	ASP195
L	HIS197
L	ASP284
B	ASP195
B	HIS197
B	ASP284
C	ASP195
C	HIS197
C	ASP284

site_id	SWS_FT_FI5
Number of Residues	12
Details	SITE: Polarizes the scissile carbonyl of the substrate => ECO:0000305\|PubMed:21268586

Chain	Residue	Details
A	TYR323
J	TYR323
K	TYR323
L	TYR323
B	TYR323
C	TYR323
D	TYR323
E	TYR323
F	TYR323
G	TYR323
H	TYR323
I	TYR323

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