Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6RCW

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053

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 501

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH650
A	HOH711

site_id	AC2
Number of Residues	6
Details	binding site for residue MG A 502

Chain	Residue
A	HOH650
A	HOH694
A	HOH730
A	ASP201
A	HOH629
A	HOH645

site_id	AC3
Number of Residues	4
Details	binding site for residue EDO A 503

Chain	Residue
A	SER208
A	PRO356
A	CYS358
A	HOH664

site_id	AC4
Number of Residues	6
Details	binding site for residue EDO A 504

Chain	Residue
A	ASN115
A	ALA155
A	VAL157
A	ASN161
A	ASN162
A	HOH627

site_id	AC5
Number of Residues	5
Details	binding site for residue EDO A 505

Chain	Residue
A	THR186
A	GLU189
A	SER259
A	MET263
A	HOH601

site_id	AC6
Number of Residues	3
Details	binding site for residue EDO A 506

Chain	Residue
A	SER226
A	ASN231
B	HOH659

site_id	AC7
Number of Residues	3
Details	binding site for residue EDO A 507

Chain	Residue
A	GLU218
A	EDO509
A	HOH603

site_id	AC8
Number of Residues	2
Details	binding site for residue EDO A 508

Chain	Residue
A	LYS275
A	HOH624

site_id	AC9
Number of Residues	5
Details	binding site for residue EDO A 509

Chain	Residue
A	GLU218
A	EDO507
A	HOH603
C	HIS152
C	HOH603

site_id	AD1
Number of Residues	7
Details	binding site for residue EDO A 510

Chain	Residue
A	PHE238
A	PHE249
A	ARG257
A	ARG261
A	HOH636
A	HOH637
A	HOH707

site_id	AD2
Number of Residues	5
Details	binding site for residue EDO A 511

Chain	Residue
A	LYS262
A	ASP266
A	HOH611
B	HOH637
B	HOH657

site_id	AD3
Number of Residues	6
Details	binding site for residue EDO A 512

Chain	Residue
A	MET286
A	THR289
A	LYS290
A	LYS291
A	LEU298
A	LEU299

site_id	AD4
Number of Residues	8
Details	binding site for residue EDO A 513

Chain	Residue
A	GLU243
A	GLU244
A	ASN245
A	HOH623
A	HOH625
A	HOH641
A	HOH727
D	ARG257

site_id	AD5
Number of Residues	5
Details	binding site for residue EDO A 514

Chain	Residue
A	THR148
A	HIS152
A	GLU243
C	THR215
C	ARG350

site_id	AD6
Number of Residues	7
Details	binding site for residue PEG A 515

Chain	Residue
A	VAL174
A	LEU175
A	THR178
A	TRP384
A	VAL388
A	ASP391
A	ILE395

site_id	AD7
Number of Residues	10
Details	binding site for residue DTT A 516

Chain	Residue
A	GLU150
A	ASP151
A	TYR153
A	HIS154
A	ALA155
A	HOH609
A	HOH658
C	ASP156
C	HOH670
C	HOH693

site_id	AD8
Number of Residues	6
Details	binding site for residue ZN B 501

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH612
B	HOH703

site_id	AD9
Number of Residues	6
Details	binding site for residue MG B 502

Chain	Residue
B	HOH667
B	ASP201
B	HOH601
B	HOH612
B	HOH644
B	HOH645

site_id	AE1
Number of Residues	5
Details	binding site for residue EDO B 503

Chain	Residue
B	SER208
B	PHE340
B	PRO356
B	MET357
B	HOH629

site_id	AE2
Number of Residues	3
Details	binding site for residue EDO B 504

Chain	Residue
B	GLU218
B	HOH622
D	LYS239

site_id	AE3
Number of Residues	4
Details	binding site for residue EDO B 505

Chain	Residue
A	GLN258
B	GLN210
B	ASN214
B	EDO510

site_id	AE4
Number of Residues	5
Details	binding site for residue EDO B 506

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

site_id	AE5
Number of Residues	3
Details	binding site for residue EDO B 507

Chain	Residue
A	ASN224
B	LYS262
B	ASP266

site_id	AE6
Number of Residues	4
Details	binding site for residue EDO B 508

Chain	Residue
B	HIS154
B	ASP203
B	LEU219
B	HIS232

site_id	AE7
Number of Residues	1
Details	binding site for residue EDO B 509

Chain	Residue
B	VAL292

site_id	AE8
Number of Residues	7
Details	binding site for residue EDO B 510

Chain	Residue
B	PHE211
B	ASN214
B	GLU347
B	MET352
B	GLU353
B	SER355
B	EDO505

site_id	AE9
Number of Residues	4
Details	binding site for residue EDO B 511

Chain	Residue
B	GLN210
B	HOH614
B	HOH635
B	HOH713

site_id	AF1
Number of Residues	3
Details	binding site for residue EDO B 512

Chain	Residue
B	THR289
B	LYS291
B	LEU299

site_id	AF2
Number of Residues	6
Details	binding site for residue EPE B 513

Chain	Residue
B	ASP140
B	THR141
B	ASN245
B	HOH670
C	THR253
C	LYS254

site_id	AF3
Number of Residues	12
Details	binding site for residue JX2 B 514

Chain	Residue
B	HIS160
B	MET273
B	ASP318
B	LEU319
B	ASN321
B	MET357
B	SER368
B	GLN369
B	PHE372
B	HOH667
B	HOH703
B	HOH705

site_id	AF4
Number of Residues	6
Details	binding site for residue ZN C 501

Chain	Residue
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	HOH604
C	HOH710

site_id	AF5
Number of Residues	6
Details	binding site for residue MG C 502

Chain	Residue
C	ASP201
C	HOH604
C	HOH622
C	HOH649
C	HOH651
C	HOH706

site_id	AF6
Number of Residues	3
Details	binding site for residue EDO C 503

Chain	Residue
C	SER208
C	PRO356
C	CYS358

site_id	AF7
Number of Residues	3
Details	binding site for residue EDO C 504

Chain	Residue
C	ARG257
C	HOH612
C	HOH689

site_id	AF8
Number of Residues	4
Details	binding site for residue EDO C 505

Chain	Residue
C	LEU188
C	LYS255
C	SER259
C	HOH607

site_id	AF9
Number of Residues	5
Details	binding site for residue EDO C 506

Chain	Residue
C	LEU175
C	THR178
C	TRP384
C	VAL388
C	ASP391

site_id	AG1
Number of Residues	5
Details	binding site for residue EDO C 507

Chain	Residue
C	ARG330
C	GLU366
C	TYR406
C	THR409
D	PRO411

site_id	AG2
Number of Residues	2
Details	binding site for residue EDO C 508

Chain	Residue
C	ASP203
C	LEU219

site_id	AG3
Number of Residues	9
Details	binding site for residue EPE C 509

Chain	Residue
C	HIS105
C	VAL106
C	PHE107
C	ARG108
C	GLU111
C	GLN327
C	LEU328
C	GLN331
C	HOH683

site_id	AG4
Number of Residues	15
Details	binding site for residue JX2 C 510

Chain	Residue
C	HIS160
C	MET273
C	ASP318
C	LEU319
C	ASN321
C	ILE336
C	MET357
C	SER368
C	GLN369
C	GLY371
C	PHE372
C	ILE376
C	HOH672
C	HOH706
C	HOH710

site_id	AG5
Number of Residues	10
Details	binding site for residue DTT D 501

Chain	Residue
B	ASP156
D	GLU150
D	ASP151
D	HIS152
D	TYR153
D	HIS154
D	ALA155
D	EDO509
D	HOH610
D	HOH735

site_id	AG6
Number of Residues	6
Details	binding site for residue ZN D 502

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	HOH619
D	HOH736

site_id	AG7
Number of Residues	6
Details	binding site for residue MG D 503

Chain	Residue
D	ASP201
D	HOH619
D	HOH630
D	HOH672
D	HOH698
D	HOH744

site_id	AG8
Number of Residues	2
Details	binding site for residue EDO D 504

Chain	Residue
D	PRO179
D	ASP391

site_id	AG9
Number of Residues	3
Details	binding site for residue EDO D 505

Chain	Residue
D	SER294
D	HOH617
D	HOH624

site_id	AH1
Number of Residues	6
Details	binding site for residue EDO D 506

Chain	Residue
D	SER208
D	PRO356
D	MET357
D	CYS358
D	JX2515
D	HOH647

site_id	AH2
Number of Residues	6
Details	binding site for residue EDO D 507

Chain	Residue
D	PHE238
D	PHE249
D	ARG257
D	ARG261
D	HOH621
D	HOH632

site_id	AH3
Number of Residues	5
Details	binding site for residue EDO D 508

Chain	Residue
C	HOH684
C	HOH702
D	LYS262
D	ASP266
D	HOH663

site_id	AH4
Number of Residues	6
Details	binding site for residue EDO D 509

Chain	Residue
D	ASN115
D	ALA155
D	ASN162
D	ILE163
D	DTT501
D	HOH615

site_id	AH5
Number of Residues	6
Details	binding site for residue EDO D 510

Chain	Residue
D	LEU175
D	THR178
D	TRP384
D	VAL388
D	ASP391
D	HOH652

site_id	AH6
Number of Residues	4
Details	binding site for residue EDO D 511

Chain	Residue
C	ASN214
C	GLU353
C	HOH618
D	GLN258

site_id	AH7
Number of Residues	4
Details	binding site for residue EDO D 512

Chain	Residue
B	THR215
D	THR148
D	HIS152
D	GLU243

site_id	AH8
Number of Residues	1
Details	binding site for residue EDO D 513

Chain	Residue
D	GLU182

site_id	AH9
Number of Residues	1
Details	binding site for residue PEG D 514

Chain	Residue
D	HIS123

site_id	AI1
Number of Residues	13
Details	binding site for residue JX2 D 515

Chain	Residue
D	HIS160
D	MET273
D	ASP318
D	LEU319
D	ASN321
D	MET357
D	SER368
D	GLN369
D	PHE372
D	EDO506
D	HOH727
D	HOH736
D	HOH744

site_id	AI2
Number of Residues	4
Details	binding site for residue PEG D 516

Chain	Residue
D	PRO325
D	LEU326
D	ASP401
D	ASN402

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)