Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4OGB

Crystal structure of the catalytic domain of PDE4D2 with compound 2

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	8
Details	BINDING SITE FOR RESIDUE 2SR A 501

Chain	Residue
A	HIS160
A	MET273
A	LEU319
A	MET357
A	SER368
A	GLN369
A	PHE372
A	ILE376

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 502

Chain	Residue
C	LYS239
A	GLU218

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 503

Chain	Residue
A	LEU132
A	LYS136
A	HOH628
D	ASP394

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEG A 504

Chain	Residue
A	GLU150
A	ASP151
A	TYR153
A	HOH640
C	ARG346

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 505

Chain	Residue
A	LYS255
A	GLN256
D	GLU182
D	DMS504

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 506

Chain	Residue
A	PHE238
A	PHE249
A	ARG257
A	HOH609
A	HOH631

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO A 507

Chain	Residue
A	ASN278

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 508

Chain	Residue
A	LYS239
A	GLN242
A	GLU243
A	HOH608
C	ASN216
D	GLN242

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN A 509

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH668
A	HOH707

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN A 510

Chain	Residue
A	ASP201
A	HOH606
A	HOH614
A	HOH616
A	HOH668
A	HOH708

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DMS A 511

Chain	Residue
A	PRO138
A	ASP140
A	THR141
A	HOH686

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 512

Chain	Residue
A	LYS262
A	ILE265
A	ASP266
A	HOH633
B	HOH616

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DMS A 513

Chain	Residue
A	HIS105
A	VAL106
A	PHE107
A	ARG108
A	GLN327
A	GLN331

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 514

Chain	Residue
A	HIS152
A	GLU243
C	SER217
C	ARG350

site_id	BC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 2SR B 501

Chain	Residue
B	HIS160
B	MET273
B	LEU319
B	MET357
B	SER368
B	GLN369
B	PHE372
B	DMS510
B	HOH613

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 502

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH617
B	HOH690

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 503

Chain	Residue
B	ASP201
B	HOH603
B	HOH606
B	HOH609
B	HOH617
B	HOH689

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 504

Chain	Residue
B	SER208
B	PHE340
B	PRO356
B	CYS358
B	HOH692

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 505

Chain	Residue
B	PHE107
B	GLN331
B	ASP334
B	ARG335

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 506

Chain	Residue
B	HOH625
D	SER294
D	SER295
A	GLN258
B	ASN214
B	EDO507

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO B 507

Chain	Residue
B	PHE211
B	ASN214
B	GLU347
B	MET352
B	GLU353
B	SER355
B	EDO506
B	HOH625

site_id	CC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO B 508

Chain	Residue
B	ALA183

site_id	CC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO B 509

Chain	Residue
B	LYS101
B	TRP102
B	GLY103
B	LEU104
B	VAL106
B	ASP167
B	GLN170
B	LYS324

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DMS B 510

Chain	Residue
B	TYR159
B	ASN321
B	PRO322
B	THR333
B	PHE372
B	2SR501

site_id	CC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO B 511

Chain	Residue
B	ASP140

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DMS B 512

Chain	Residue
B	GLU349
B	ARG350
D	ASP140
D	ILE143
D	THR144

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 501

Chain	Residue
C	THR148
C	HIS152
C	GLU243

site_id	DC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 2SR C 502

Chain	Residue
C	HIS160
C	MET273
C	LEU319
C	MET357
C	GLN369
C	PHE372

site_id	DC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 503

Chain	Residue
C	ASN115
C	ALA155
C	ASN161
C	ASN162
C	ILE163
C	ARG335

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 504

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

site_id	DC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 505

Chain	Residue
B	PRO179
C	LEU188
C	LYS255

site_id	DC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EPE C 506

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

site_id	DC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 507

Chain	Residue
C	LYS262
C	ASP266
D	ASN224
D	ASP225

site_id	DC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 508

Chain	Residue
C	ASP266
C	LEU269
C	LYS275
C	GLN311

site_id	DC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 509

Chain	Residue
C	ASN115
C	GLU150
C	ASP151
C	TYR153
C	ASN162

site_id	DC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 510

Chain	Residue
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	HOH601
C	HOH666

site_id	EC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 511

Chain	Residue
C	ASP201
C	HOH602
C	HOH613
C	HOH664
C	HOH665
C	HOH666

site_id	EC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 512

Chain	Residue
C	LEU219
C	MET222
C	TYR223

site_id	EC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 513

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

site_id	EC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 501

Chain	Residue
B	PHE211
B	THR215
B	ARG350
D	THR148
D	HIS152
D	GLU243
D	HOH691

site_id	EC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 2SR D 502

Chain	Residue
D	HIS160
D	MET273
D	LEU319
D	PHE340
D	MET357
D	SER368
D	GLN369
D	PHE372
D	ILE376

site_id	EC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 503

Chain	Residue
D	THR178
D	TRP384
D	VAL388
D	ASP391
D	PEG515
D	PEG516
D	HOH671

site_id	EC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE DMS D 504

Chain	Residue
A	EDO505
D	SER177
D	GLU182

site_id	EC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO D 505

Chain	Residue
D	VAL120
D	HIS123

site_id	EC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 506

Chain	Residue
D	ASP266
D	GLN311
D	PEG507

site_id	FC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG D 507

Chain	Residue
C	ASP225
C	HOH628
D	LYS262
D	ASP266
D	EDO506
D	HOH670

site_id	FC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DMS D 508

Chain	Residue
D	GLU150
D	ASP151
D	TYR153
D	ASN162
D	EDO510

site_id	FC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 509

Chain	Residue
D	ASP266
D	LYS275
D	GLN311

site_id	FC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 510

Chain	Residue
D	ASN115
D	ALA155
D	ASN161
D	ASN162
D	ILE163
D	DMS508

site_id	FC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 511

Chain	Residue
D	GLU128
D	HIS173
D	SER177

site_id	FC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 512

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	HOH711
D	HOH712

site_id	FC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 513

Chain	Residue
D	ASP201
D	HOH606
D	HOH623
D	HOH662
D	HOH711
D	HOH713

site_id	FC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 514

Chain	Residue
A	THR134
A	ASN251
A	GLN256
D	PRO179
D	ASP391
D	HOH717

site_id	FC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG D 515

Chain	Residue
A	THR134
A	HOH661
D	ASP391
D	EDO503
D	PEG516
D	HOH717

site_id	GC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PEG D 516

Chain	Residue
D	LYS101
D	TRP102
D	VAL174
D	ASP394
D	ILE395
D	EDO503
D	PEG515
D	HOH615

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)