Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6FTW

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-048

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	HOH626
A	HOH649

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

Chain	Residue
A	HOH628
A	HOH688
A	HOH717
A	ASP201
A	HOH613
A	HOH626

site_id	AC3
Number of Residues	5
Details	binding site for residue EDO A 503

Chain	Residue
A	SER208
A	PRO356
A	CYS358
A	E6Z517
A	HOH618

site_id	AC4
Number of Residues	5
Details	binding site for residue EDO A 504

Chain	Residue
A	ASN115
A	ALA155
A	ASN161
A	ASN162
A	ARG335

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	EDO512

site_id	AC6
Number of Residues	6
Details	binding site for residue EDO A 506

Chain	Residue
A	GLU218
A	HOH722
C	HIS152
C	LYS239
C	LEU240
C	HOH614

site_id	AC7
Number of Residues	4
Details	binding site for residue EDO A 507

Chain	Residue
A	LEU175
A	THR178
A	TRP384
A	ASP391

site_id	AC8
Number of Residues	3
Details	binding site for residue EDO A 508

Chain	Residue
A	THR134
A	LYS136
A	EDO509

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

Chain	Residue
A	THR134
A	PHE135
A	ASN251
A	GLN256
A	EDO508

site_id	AD1
Number of Residues	4
Details	binding site for residue EDO A 510

Chain	Residue
A	HIS152
A	GLU243
C	SER217
C	ARG350

site_id	AD2
Number of Residues	6
Details	binding site for residue EDO A 511

Chain	Residue
A	PHE238
A	PHE249
A	ARG257
A	ARG261
A	HOH633
A	HOH642

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

Chain	Residue
A	SER259
A	LYS262
A	TYR303
A	EDO505
A	EDO514
A	HOH660

site_id	AD4
Number of Residues	7
Details	binding site for residue EDO A 513

Chain	Residue
A	ARG116
A	GLU150
A	ASP151
A	TYR153
A	HOH604
A	HOH719
C	EDO510

site_id	AD5
Number of Residues	3
Details	binding site for residue EDO A 514

Chain	Residue
A	EDO512
A	HOH602
A	HOH721

site_id	AD6
Number of Residues	9
Details	binding site for residue EPE A 515

Chain	Residue
A	HIS105
A	VAL106
A	PHE107
A	ARG108
A	GLU111
A	GLN327
A	LEU328
A	GLN331
A	HOH691

site_id	AD7
Number of Residues	5
Details	binding site for residue EDO A 516

Chain	Residue
A	LYS262
A	ASP266
A	HOH700
B	HOH619
B	HOH655

site_id	AD8
Number of Residues	15
Details	binding site for residue E6Z A 517

Chain	Residue
A	HOH717
A	MET273
A	ASP318
A	LEU319
A	THR333
A	ILE336
A	MET337
A	MET357
A	SER368
A	GLN369
A	PHE372
A	ILE376
A	EDO503
A	HOH618
A	HOH693

site_id	AD9
Number of Residues	6
Details	binding site for residue ZN B 501

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH626
B	HOH673

site_id	AE1
Number of Residues	6
Details	binding site for residue MG B 502

Chain	Residue
B	ASP201
B	HOH614
B	HOH626
B	HOH646
B	HOH654
B	HOH658

site_id	AE2
Number of Residues	3
Details	binding site for residue EDO B 503

Chain	Residue
B	SER208
B	PRO356
B	HOH630

site_id	AE3
Number of Residues	5
Details	binding site for residue EDO B 504

Chain	Residue
B	GLU218
B	EDO507
B	HOH632
C	MET222
D	LYS239

site_id	AE4
Number of Residues	4
Details	binding site for residue EDO B 505

Chain	Residue
B	ASN115
B	ALA155
B	ASN162
B	ARG335

site_id	AE5
Number of Residues	6
Details	binding site for residue EDO B 506

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

site_id	AE6
Number of Residues	3
Details	binding site for residue EDO B 507

Chain	Residue
B	GLU218
B	EDO504
D	LYS239

site_id	AE7
Number of Residues	8
Details	binding site for residue EPE B 508

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

site_id	AE8
Number of Residues	11
Details	binding site for residue E6Z B 509

Chain	Residue
B	MET273
B	ASP318
B	ILE336
B	MET337
B	MET357
B	VAL365
B	SER368
B	GLN369
B	PHE372
B	HOH671
B	HOH673

site_id	AE9
Number of Residues	6
Details	binding site for residue ZN C 501

Chain	Residue
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	HOH625
C	HOH658

site_id	AF1
Number of Residues	6
Details	binding site for residue MG C 502

Chain	Residue
C	ASP201
C	HOH607
C	HOH625
C	HOH645
C	HOH657
C	HOH675

site_id	AF2
Number of Residues	4
Details	binding site for residue EDO C 503

Chain	Residue
C	PHE249
C	ARG257
C	HOH605
C	HOH653

site_id	AF3
Number of Residues	4
Details	binding site for residue EDO C 504

Chain	Residue
C	LEU175
C	THR178
C	TRP384
C	ALA392

site_id	AF4
Number of Residues	3
Details	binding site for residue EDO C 505

Chain	Residue
A	LYS239
B	MET222
C	GLU218

site_id	AF5
Number of Residues	3
Details	binding site for residue EDO C 506

Chain	Residue
C	THR148
C	HIS152
C	GLU243

site_id	AF6
Number of Residues	5
Details	binding site for residue EDO C 507

Chain	Residue
C	ASN115
C	ARG116
C	GLU150
C	ASP151
C	TYR153

site_id	AF7
Number of Residues	3
Details	binding site for residue EDO C 508

Chain	Residue
C	PRO356
C	E6Z512
C	HOH638

site_id	AF8
Number of Residues	3
Details	binding site for residue EDO C 509

Chain	Residue
C	LYS262
C	ASP266
D	ASP225

site_id	AF9
Number of Residues	5
Details	binding site for residue EDO C 510

Chain	Residue
A	GLY114
A	ASN115
A	EDO513
C	ARG342
C	HOH619

site_id	AG1
Number of Residues	8
Details	binding site for residue EPE C 511

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

site_id	AG2
Number of Residues	12
Details	binding site for residue E6Z C 512

Chain	Residue
C	HIS160
C	MET273
C	LEU319
C	ILE336
C	MET337
C	MET357
C	SER368
C	GLN369
C	PHE372
C	EDO508
C	HOH638
C	HOH656

site_id	AG3
Number of Residues	3
Details	binding site for residue EDO C 513

Chain	Residue
C	ASN214
C	GLU353
D	GLN258

site_id	AG4
Number of Residues	6
Details	binding site for residue ZN D 501

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	HOH617
D	HOH654

site_id	AG5
Number of Residues	6
Details	binding site for residue MG D 502

Chain	Residue
D	ASP201
D	HOH617
D	HOH652
D	HOH671
D	HOH689
D	HOH709

site_id	AG6
Number of Residues	4
Details	binding site for residue EDO D 503

Chain	Residue
D	SER294
D	SER295
D	HOH609
D	HOH660

site_id	AG7
Number of Residues	4
Details	binding site for residue EDO D 504

Chain	Residue
D	PHE340
D	PRO356
D	CYS358
D	E6Z516

site_id	AG8
Number of Residues	5
Details	binding site for residue EDO D 505

Chain	Residue
D	PHE238
D	ARG257
D	ARG261
D	HOH647
D	HOH672

site_id	AG9
Number of Residues	4
Details	binding site for residue EDO D 506

Chain	Residue
C	HOH621
D	LYS262
D	ASP266
D	HOH657

site_id	AH1
Number of Residues	4
Details	binding site for residue EDO D 507

Chain	Residue
D	ASN115
D	ALA155
D	ASN161
D	ASN162

site_id	AH2
Number of Residues	6
Details	binding site for residue EDO D 508

Chain	Residue
D	LEU175
D	THR178
D	TRP384
D	VAL388
D	ASP391
D	HOH662

site_id	AH3
Number of Residues	6
Details	binding site for residue EDO D 509

Chain	Residue
D	GLN250
D	LEU252
D	THR253
D	ARG257
D	HOH632
D	HOH728

site_id	AH4
Number of Residues	4
Details	binding site for residue EDO D 510

Chain	Residue
D	ARG129
D	LEU131
D	ASP187
D	ILE190

site_id	AH5
Number of Residues	1
Details	binding site for residue EDO D 511

Chain	Residue
D	GLU182

site_id	AH6
Number of Residues	1
Details	binding site for residue EDO D 512

Chain	Residue
D	GLN393

site_id	AH7
Number of Residues	1
Details	binding site for residue EDO D 513

Chain	Residue
D	ASP98

site_id	AH8
Number of Residues	7
Details	binding site for residue EPE D 514

Chain	Residue
C	ASP394
D	HIS105
D	VAL106
D	PHE107
D	ARG108
D	LEU328
D	GLN331

site_id	AH9
Number of Residues	2
Details	binding site for residue EDO D 515

Chain	Residue
D	HIS152
D	GLU243

site_id	AI1
Number of Residues	10
Details	binding site for residue E6Z D 516

Chain	Residue
D	MET273
D	ASP318
D	LEU319
D	ILE336
D	MET337
D	MET357
D	SER368
D	GLN369
D	PHE372
D	EDO504

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)