Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3SL6

Crystal structure of the catalytic domain of PDE4D2 with compound 12c

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 ZN A 10

Chain	Residue
A	ZN11
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH452

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 11

Chain	Residue
A	HOH449
A	HOH450
A	ZN10
A	ASP201
A	HOH448

site_id	AC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 2

Chain	Residue
A	GLU218
C	LYS239

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 4

Chain	Residue
A	THR134
A	LYS136
D	EDO7
D	PRO179
D	ASP391

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 5

Chain	Residue
A	LEU175
A	THR178
A	TRP384
A	ASP391

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

Chain	Residue
A	ASN115
A	ARG116
A	GLU150
A	ASP151
A	TYR153
A	ASN162
A	HOH453

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 7

Chain	Residue
A	ASP156
A	VAL157
A	ALA158
A	ARG346
A	HOH462

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 8

Chain	Residue
A	ASN278
A	LEU279

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 9

Chain	Residue
A	HOH26
A	HOH64
A	PHE238
A	PHE249
A	ARG257
A	ARG261

site_id	BC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE JN8 A 440

Chain	Residue
A	TYR159
A	MET273
A	LEU319
A	ASN321
A	PRO322
A	TYR329
A	ILE336
A	MET337
A	PHE340
A	MET357
A	SER368
A	GLN369
A	PHE372
A	ILE376
A	HOH451

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 441

Chain	Residue
A	LYS262
A	ASP266
A	HOH446
B	HOH452

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 442

Chain	Residue
A	HIS152
A	GLU243
C	ARG350

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 7

Chain	Residue
B	ZN8
B	HIS164
B	HIS200
B	ASP201
B	ASP318

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 8

Chain	Residue
B	ZN7
B	ASP201
B	HOH470
B	HOH471
B	HOH472

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 4

Chain	Residue
B	ASN115
B	ARG116
B	GLU150
B	ASP151
B	TYR153

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 5

Chain	Residue
B	LEU176
B	SER177
B	THR178
B	GLU182

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 6

Chain	Residue
B	ASP374
B	HIS378
B	PRO379
B	GLU382

site_id	BC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE JN8 B 440

Chain	Residue
B	HOH443
B	TYR159
B	MET273
B	LEU319
B	ASN321
B	THR333
B	ILE336
B	PHE340
B	MET357
B	CYS358
B	SER368
B	GLN369
B	PHE372

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS B 14

Chain	Residue
B	GLU95
B	ASP98
B	GLY103
B	HIS105

site_id	CC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 3

Chain	Residue
A	ARG350
C	HIS152
C	GLU243

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 10

Chain	Residue
C	ZN11
C	ASP201
C	HOH462
C	HOH464

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 11

Chain	Residue
C	ZN10
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	HOH467

site_id	CC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EPE C 2

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

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 440

Chain	Residue
C	LEU175
C	THR178
C	TRP384
C	ASP391
C	ALA392

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 4

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

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

Chain	Residue
C	GLU150
C	ASP151
C	TYR153
C	ALA155

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 7

Chain	Residue
B	LYS290
B	GLY296
C	THR253
C	LYS254
C	LYS255

site_id	DC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 8

Chain	Residue
C	LEU234
C	PHE238
C	ARG261
D	LEU221
D	ASN224

site_id	DC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 9

Chain	Residue
C	LYS262
C	ASP266
D	ASN224
D	ASP225

site_id	DC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE JN8 C 441

Chain	Residue
C	TYR159
C	LEU319
C	ASN321
C	THR333
C	ILE336
C	PHE340
C	CYS358
C	GLN369
C	PHE372
C	HOH463

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 3

Chain	Residue
B	THR215
B	ARG350
D	THR148
D	HIS152
D	GLU243

site_id	DC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 12

Chain	Residue
D	ZN13
D	ASP201
D	HOH442
D	HOH448
D	HOH450

site_id	DC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 13

Chain	Residue
D	ZN12
D	HIS164
D	HIS200
D	ASP201
D	ASP318

site_id	DC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 2

Chain	Residue
A	LEU188
A	LYS255
A	GLN256
A	SER259
D	GLU182

site_id	DC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 440

Chain	Residue
D	EDO8
D	LEU175
D	THR178
D	TRP384
D	ASP391
D	ILE395
D	HOH456

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

Chain	Residue
D	THR186
D	ASP187
D	LEU188
D	GLN256

site_id	EC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO D 5

Chain	Residue
D	HIS123

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

Chain	Residue
C	ASN224
C	SER226
D	EDO9
D	LYS262
D	ILE265
D	ASP266

site_id	EC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 7

Chain	Residue
A	EDO4
A	THR134
A	PHE135
A	ASN251
A	GLN256
D	PRO179
D	ASP391

site_id	EC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 8

Chain	Residue
D	TRP102
D	EDO440
D	HOH481

site_id	EC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 9

Chain	Residue
C	HOH14
C	HOH42
C	ASP225
D	EDO6
D	GLN258
D	ARG261
D	LYS262

site_id	EC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 10

Chain	Residue
D	PRO325
D	LEU326
D	THR398
D	ASN402

site_id	EC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 11

Chain	Residue
D	ASP156
D	VAL157
D	ALA158
D	GLU339

site_id	EC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE JN8 D 15

Chain	Residue
D	TYR159
D	MET273
D	LEU319
D	ASN321
D	PRO322
D	THR333
D	ILE336
D	PHE340
D	MET357
D	SER368
D	GLN369
D	PHE372
D	HOH474

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)