3SL3

Crystal structure of the apo form of the catalytic domain of PDE4D2

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
A	0007165	biological_process	signal transduction
A	0008081	molecular_function	phosphoric diester hydrolase activity
B	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
B	0007165	biological_process	signal transduction
B	0008081	molecular_function	phosphoric diester hydrolase activity
C	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
C	0007165	biological_process	signal transduction
C	0008081	molecular_function	phosphoric diester hydrolase activity
D	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
D	0007165	biological_process	signal transduction
D	0008081	molecular_function	phosphoric diester hydrolase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 1

Chain	Residue
A	LYS262
A	ASP266
A	HOH550
A	HOH588
B	HOH531

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 2

Chain	Residue
D	DMS6
D	GLU182
A	EDO20
A	LEU188
A	LYS255
A	GLN256

---

site_id	AC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 3

Chain	Residue
A	EDO9
A	ASN115
A	ARG116
A	GLU150
A	ASP151
A	TYR153
A	ASN162
A	HOH545

---

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 4

Chain	Residue
A	PHE238
A	ARG257
A	HOH590
A	HOH602

---

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 5

Chain	Residue
A	EDO12
A	ASP156
A	ALA158
A	PRO205
A	ARG342
A	ARG346
A	HOH599

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 6

Chain	Residue
A	EDO7
A	PHE135
A	GLN256
A	HOH511
D	DMS6

---

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 7

Chain	Residue
A	EDO6
A	THR134
A	LYS136
D	EDO9
D	PRO179
D	ASP391

---

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 8

Chain	Residue
A	GLN250
A	ASN251
A	HOH548
A	HOH577
D	HOH556

---

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 9

Chain	Residue
A	EDO3
A	ASP151
A	TYR153
A	HIS154
A	ALA155
A	HOH545
C	ASP156
C	HOH483

---

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 10

Chain	Residue
A	THR178
A	ASP391

---

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 11

Chain	Residue
A	PO416
A	GLU230
A	THR271
A	ASP272
A	MET273
A	HOH567
A	HOH574

---

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 12

Chain	Residue
A	EDO5
A	HIS154
A	ASP156
A	VAL157
A	PRO205
C	HOH474

---

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PEG A 13

Chain	Residue
A	LEU132
A	LYS136
A	ILE137

---

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN A 14

Chain	Residue
A	PO416
A	ASP201
A	HOH528
A	HOH529
A	HOH573
A	HOH574

---

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN A 15

Chain	Residue
A	PO416
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH573

---

site_id	BC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 A 16

Chain	Residue
A	EDO11
A	ZN14
A	ZN15
A	HIS160
A	HIS164
A	ASP201
A	ASP318
A	HOH509
A	HOH530
A	HOH573

---

site_id	BC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO A 17

Chain	Residue
A	LYS275

---

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 18

Chain	Residue
A	PHE340
A	GLN343
A	HIS204
A	GLY206
A	VAL207
A	GLU339

---

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 19

Chain	Residue
A	THR148
A	HIS152
A	GLU243
A	HOH555
C	SER217
C	ARG350

---

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 20

Chain	Residue
A	EDO2
A	THR186
A	LEU188
A	SER259
A	MET263
A	HOH580

---

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 21

Chain	Residue
A	LYS239
A	GLN242
A	GLU243
C	EDO18
C	ASN216
C	SER217
C	GLU218
D	GLN242

---

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 1

Chain	Residue
B	DMS15
B	GLN210
B	HOH511
B	HOH531

---

site_id	CC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO B 2

Chain	Residue
B	ALA183
B	VAL184

---

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 3

Chain	Residue
B	THR289
B	LYS291
B	LEU298
B	LEU299

---

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 4

Chain	Residue
B	ASN115
B	ALA155
B	ASN161
B	ASN162
B	ARG335

---

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 5

Chain	Residue
B	LEU175
B	THR178
B	TRP384
B	ASP391

---

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 6

Chain	Residue
B	ASP374
B	HIS378
B	HOH541

---

site_id	DC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO B 7

Chain	Residue
B	DMS14
B	HIS204
B	GLY206
B	VAL207
B	GLU339
B	PHE340
B	GLN343
B	HOH517

---

site_id	DC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 8

Chain	Residue
B	PO410
B	ASP201
B	HOH524
B	HOH525
B	HOH526
B	HOH569

---

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 9

Chain	Residue
B	PO410
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH569

---

site_id	DC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PO4 B 10

Chain	Residue
B	ZN8
B	ZN9
B	HIS160
B	HIS164
B	ASP201
B	ASP318
B	HOH567
B	HOH569
B	HOH574

---

site_id	DC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 11

Chain	Residue
B	GLU218
D	HIS152
D	LYS239
D	HOH594

---

site_id	DC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 12

Chain	Residue
B	ILE354
B	SER355
B	MET357
B	CYS358
B	ASP359
B	ASN362

---

site_id	DC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 13

Chain	Residue
B	ASP334
B	MET337
B	GLU338
B	PHE341

---

site_id	DC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DMS B 14

Chain	Residue
B	EDO7
B	SER208
B	GLN343
B	PRO356
B	CYS358
B	HOH565

---

site_id	DC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DMS B 15

Chain	Residue
B	EDO1
B	GLN210
B	SER274
B	HOH577
B	HOH584

---

site_id	EC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 16

Chain	Residue
B	THR186
B	ASP187
B	HOH582

---

site_id	EC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PEG B 17

Chain	Residue
B	HIS152
B	GLU243
B	HOH519
D	THR215
D	SER217
D	GLU218
D	LEU219
D	ARG350

---

site_id	EC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 1

Chain	Residue
A	ARG350
C	HIS152
C	GLU243

---

site_id	EC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 7

Chain	Residue
A	GLU244
C	ASN214
C	ARG350
C	MET352
C	HOH506
D	LYS254

---

site_id	EC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 2

Chain	Residue
A	GLU218
C	TYR223
C	HIS232
C	ALA235
C	HOH463

---

site_id	EC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 3

Chain	Residue
A	ASP156
C	EDO13
C	GLU150
C	ASP151
C	TYR153
C	ASN162

---

site_id	EC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EPE C 4

Chain	Residue
C	HIS105
C	VAL106
C	PHE107
C	ARG108
C	GLU111
C	GLN327
C	LEU328
C	GLN331

---

site_id	EC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE DMS C 5

Chain	Residue
C	ARG257
C	ARG261

---

site_id	EC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 6

Chain	Residue
C	LYS262
C	ASP266
D	ASN224

---

site_id	FC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 12

Chain	Residue
C	LYS275
C	HOH465

---

site_id	FC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 8

Chain	Residue
B	HIS389
B	PRO390
C	THR134
C	PHE135
C	LYS136
C	ASN251
C	GLN256

---

site_id	FC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 9

Chain	Residue
C	ASP203
C	LEU219

---

site_id	FC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 10

Chain	Residue
C	ASP156
C	VAL157
C	PRO205
C	ARG342
C	ARG346
C	HOH468
C	HOH502

---

site_id	FC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 11

Chain	Residue
C	HIS160
C	HIS204
C	GLY206
C	VAL207
C	GLU339
C	PHE340
C	GLN343

---

site_id	FC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 13

Chain	Residue
C	EDO3
C	ASN115
C	ALA155
C	ASN161
C	ASN162
C	ILE163

---

site_id	FC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 14

Chain	Residue
C	PO416
C	ASP201
C	HOH456
C	HOH457
C	HOH458
C	HOH459

---

site_id	FC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 15

Chain	Residue
C	PO416
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	HOH458

---

site_id	FC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 C 16

Chain	Residue
C	ZN14
C	ZN15
C	HOH58
C	HIS160
C	HIS164
C	ASP201
C	ASP318
C	HOH458

---

site_id	GC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 18

Chain	Residue
A	EDO21
A	GLU243
A	HOH555
C	GLU218

---

site_id	GC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO D 4

Chain	Residue
D	ASP266
D	GLN311

---

site_id	GC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DMS D 6

Chain	Residue
A	EDO2
A	EDO6
D	SER177
D	PRO179
D	GLU182
D	HOH553

---

site_id	GC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 1

Chain	Residue
B	SER217
B	HOH502
D	EDO23
D	THR148
D	HIS152
D	GLU243

---

site_id	GC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 9

Chain	Residue
A	EDO7
A	THR134
A	PHE135
A	ASN251
A	GLN256
D	PRO179
D	ASP391

---

site_id	GC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 2

Chain	Residue
D	EDO5
D	LEU175
D	THR178
D	VAL388
D	ASP391
D	HOH541

---

site_id	GC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 3

Chain	Residue
D	LEU181
D	ALA183
D	VAL184
D	PHE185
D	HOH553

---

site_id	GC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS D 25

Chain	Residue
D	GLU150
D	ASP151
D	TYR153
D	ASN162

---

site_id	GC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 5

Chain	Residue
D	EDO2
D	ASN100
D	LYS101
D	TRP102
D	HOH550

---

site_id	HC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 27

Chain	Residue
D	ASN100
D	GLU128
D	HIS173
D	SER177

---

site_id	HC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO D 7

Chain	Residue
D	HIS123

---

site_id	HC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEG D 8

Chain	Residue
C	ASP225
C	HOH461
D	GLN258
D	LYS262
D	ASP266

---

site_id	HC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 10

Chain	Residue
D	ASN302
D	TYR303
D	SER304

---

site_id	HC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG D 11

Chain	Residue
D	THR186
D	LEU188
D	GLU189
D	SER259
D	MET263
D	HOH523

---

site_id	HC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 12

Chain	Residue
D	ASP247
D	PHE249
D	ARG257

---

site_id	HC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 13

Chain	Residue
D	ASP156
D	VAL157
D	ALA158
D	GLU338
D	GLU339
D	HOH605

---

site_id	HC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 14

Chain	Residue
D	PRO325
D	LEU326
D	GLN327
D	HOH582

---

site_id	HC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 15

Chain	Residue
D	GLU244
D	ASN245
D	SER294
D	GLY296
D	HOH520

---

site_id	IC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 16

Chain	Residue
D	THR134
D	LYS136
D	ASN251
D	GLN256

---

site_id	IC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 17

Chain	Residue
D	PO419
D	ASP201
D	HOH535
D	HOH536
D	HOH537

---

site_id	IC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 18

Chain	Residue
D	PO419
D	HIS164
D	HIS200
D	ASP201
D	ASP318

---

site_id	IC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 D 19

Chain	Residue
D	ZN17
D	ZN18
D	HIS160
D	HIS164
D	ASP201
D	ASP318
D	HOH574

---

site_id	IC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 20

Chain	Residue
D	MET286
D	THR289
D	ASP305

---

site_id	IC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO D 21

Chain	Residue
D	GLN127
D	HOH507

---

site_id	IC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 22

Chain	Residue
D	ASP98
D	LYS101
D	TRP102

---

site_id	IC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO D 23

Chain	Residue
B	THR215
B	ARG350
D	EDO1
D	THR148
D	GLU243
D	GLU244
D	CYS246
D	HOH554

---

site_id	IC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 24

Chain	Residue
D	ASN321
D	THR333
D	ILE336
D	GLN369
D	HOH529

---

site_id	JC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO D 26

Chain	Residue
D	ASP266
D	GLN311

---

Functional Information from PROSITE/UniProt

site_id	PS00126
Number of Residues	12
Details	PDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDVdHpGvsNqF

Chain	Residue	Details
A	HIS200-PHE211

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton donor","evidences":[{"source":"UniProtKB","id":"Q07343","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)"}

Chain

Residue

Details

---