Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3SL8

Crystal structure of the catalytic domain of PDE4D2 with compound 10o

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	6
Details	BINDING SITE FOR RESIDUE EDO A 1

Chain	Residue
A	EDO16
A	THR186
A	LEU188
A	GLU189
A	SER259
A	HOH485

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 3

Chain	Residue
A	ASP318
A	HOH453
A	HIS164
A	HIS200
A	ASP201

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 4

Chain	Residue
A	ASP201
A	HOH480
A	HOH481
A	HOH482

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 5

Chain	Residue
A	VAL174
A	THR178
A	ASP391

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

Chain	Residue
A	HOH70
A	THR134
A	PHE135
A	ASN251
A	GLN256
D	ASP391

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 7

Chain	Residue
A	ASP156
A	GLY206
A	GLU339
A	ARG342
A	GLN343
A	ARG346

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 8

Chain	Residue
A	LYS262
A	ILE265
A	ASP266
B	SER226
B	HOH440

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 9

Chain	Residue
A	GLN256
D	GLU182

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 11

Chain	Residue
A	PHE238
A	PHE249
A	ARG257
A	ARG261
A	HOH465
A	HOH477

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEG A 12

Chain	Residue
A	LEU132
A	LYS136
A	ILE137
A	PRO138
A	VAL139

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 13

Chain	Residue
A	THR144
A	THR148
A	GLU243
A	GLU244
A	CYS246
A	HOH472
C	THR215
C	ARG350

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 14

Chain	Residue
A	LYS284
A	ASP386

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 15

Chain	Residue
A	ALA183
A	VAL184
A	PHE185
A	HOH467

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 16

Chain	Residue
A	EDO1
A	SER259
A	LYS262
A	TYR303
A	HOH478

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 17

Chain	Residue
A	GLU87
A	GLN88

site_id	BC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE JN7 A 18

Chain	Residue
A	HOH30
A	TYR159
A	MET273
A	LEU319
A	ASN321
A	TYR329
A	THR333
A	ILE336
A	PHE340
A	SER368
A	GLN369
A	PHE372
A	ILE376

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 440

Chain	Residue
A	HIS152
A	GLU243
C	THR215
C	SER217
C	ARG350

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 2

Chain	Residue
B	PO44
B	HOH11
B	ASP201
B	HOH466
B	HOH469

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 3

Chain	Residue
B	PO44
B	HIS164
B	HIS200
B	ASP201
B	ASP318

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PO4 B 4

Chain	Residue
B	HIS160
B	ASP201
B	ASP318
B	HOH449
B	ZN2
B	ZN3

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 6

Chain	Residue
B	ASN214
B	MET352
D	EDO7
D	GLU244

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 8

Chain	Residue
B	ASP156
B	VAL157
B	ALA158
B	GLU338
B	GLU339
B	ARG342

site_id	CC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE JN7 B 1

Chain	Residue
B	TYR159
B	MET273
B	LEU319
B	ASN321
B	TYR329
B	THR333
B	MET337
B	PHE340
B	SER368
B	GLN369
B	PHE372
B	ILE376
B	HOH468

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 2

Chain	Residue
C	TYR223
C	HIS232
C	ALA235

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 440

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

site_id	CC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 3

Chain	Residue
C	LYS262
C	ASP266
D	ASP225

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN C 4

Chain	Residue
C	ASP201
C	HOH467
C	HOH468

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 5

Chain	Residue
C	HIS164
C	HIS200
C	ASP201
C	ASP318

site_id	DC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 C 6

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

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DMS C 7

Chain	Residue
C	ASN115
C	ARG116
C	GLU150
C	TYR153
C	ALA155
C	ASN162

site_id	DC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE JN7 C 1

Chain	Residue
C	TYR159
C	MET273
C	ASP318
C	LEU319
C	ASN321
C	PRO322
C	TYR329
C	THR333
C	ILE336
C	PHE340
C	SER368
C	GLN369
C	PHE372
C	ILE376
C	HOH458

site_id	DC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 10

Chain	Residue
D	ASP266
D	TYR303
D	GLN311

site_id	DC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 7

Chain	Residue
B	EDO6
B	THR215
B	ARG350
D	THR148
D	GLU243
D	GLU244
D	CYS246

site_id	DC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO D 2

Chain	Residue
D	HIS123
D	ILE143

site_id	DC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 3

Chain	Residue
D	THR186
D	LEU188
D	SER259

site_id	DC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 4

Chain	Residue
D	LEU175
D	THR178
D	EDO441

site_id	EC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PEG D 5

Chain	Residue
C	ASP225
D	LYS262
D	ASP266

site_id	EC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 6

Chain	Residue
D	ASP201
D	HOH448
D	HOH469
D	HOH473

site_id	EC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 440

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	HOH489

site_id	EC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 8

Chain	Residue
D	LEU181
D	ALA183
D	VAL184
D	PHE185
D	HOH490

site_id	EC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 9

Chain	Residue
B	ASP156
D	ASP151
D	TYR153
D	HIS154
D	ALA155
D	HOH460

site_id	EC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 441

Chain	Residue
D	EDO4
D	ASN100
D	LYS101
D	TRP102
D	HOH453

site_id	EC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 11

Chain	Residue
A	ALA183
D	ASN100
D	GLU128

site_id	EC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 12

Chain	Residue
D	LYS284
D	THR383
D	ASP386

site_id	EC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 13

Chain	Residue
D	THR141
D	ASN245
D	CYS246
D	ASP247
D	GLN250
D	HOH476

site_id	FC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS D 14

Chain	Residue
D	ASN115
D	ALA155
D	ASN161
D	ASN162

site_id	FC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 15

Chain	Residue
D	HOH67
D	MET277
D	LEU280
D	TYR375

site_id	FC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE JN7 D 1

Chain	Residue
D	HOH22
D	TYR159
D	MET273
D	LEU319
D	ASN321
D	THR333
D	ILE336
D	PHE340
D	SER368
D	GLN369
D	PHE372
D	ILE376

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

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