Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6IBF

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-417

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	7
Details	binding site for residue ZN A 501

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	MG502
A	HOH611
A	HOH639

site_id	AC2
Number of Residues	7
Details	binding site for residue MG A 502

Chain	Residue
A	HOH606
A	HOH608
A	HOH611
A	HOH646
A	HOH665
A	ASP201
A	ZN501

site_id	AC3
Number of Residues	3
Details	binding site for residue EDO A 503

Chain	Residue
A	ASN115
A	ALA155
A	ASN162

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

Chain	Residue
A	THR186
A	LEU188
A	GLU189
A	SER259
A	MET263
A	HOH620

site_id	AC5
Number of Residues	3
Details	binding site for residue EDO A 505

Chain	Residue
A	LYS262
A	ASP266
B	HOH611

site_id	AC6
Number of Residues	4
Details	binding site for residue EDO A 506

Chain	Residue
A	LEU175
A	THR178
A	TRP384
A	ASP391

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

Chain	Residue
A	GLU218
C	VAL236
C	LYS239

site_id	AC8
Number of Residues	4
Details	binding site for residue EDO A 508

Chain	Residue
A	ASP266
A	LEU269
A	LYS275
A	GLN311

site_id	AC9
Number of Residues	6
Details	binding site for residue EDO A 509

Chain	Residue
A	THR148
A	HIS152
A	GLU243
C	SER217
C	ARG350
C	EDO507

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

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

site_id	AD2
Number of Residues	2
Details	binding site for residue EDO A 511

Chain	Residue
A	ASP140
A	ASN245

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

Chain	Residue
A	ARG116
A	GLU150
A	ASP151
A	TYR153
A	ALA155
C	ARG346

site_id	AD4
Number of Residues	14
Details	binding site for residue 4I7 A 513

Chain	Residue
A	MET273
A	LEU319
A	THR333
A	ILE336
A	MET337
A	PHE340
A	PRO356
A	MET357
A	SER368
A	GLN369
A	PHE372
A	ILE376
A	HOH638
A	HOH639

site_id	AD5
Number of Residues	6
Details	binding site for residue ZN B 501

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH603
B	HOH673

site_id	AD6
Number of Residues	6
Details	binding site for residue MG B 502

Chain	Residue
B	ASP201
B	HOH603
B	HOH617
B	HOH650
B	HOH653
B	HOH659

site_id	AD7
Number of Residues	4
Details	binding site for residue EDO B 503

Chain	Residue
B	SER208
B	PHE340
B	PRO356
B	HOH607

site_id	AD8
Number of Residues	4
Details	binding site for residue EDO B 504

Chain	Residue
B	ASN115
B	ALA155
B	ASN161
B	ASN162

site_id	AD9
Number of Residues	4
Details	binding site for residue EDO B 505

Chain	Residue
A	ASN224
A	ASP225
B	LYS262
B	ASP266

site_id	AE1
Number of Residues	1
Details	binding site for residue EDO B 506

Chain	Residue
B	VAL292

site_id	AE2
Number of Residues	4
Details	binding site for residue EDO B 507

Chain	Residue
B	HOH630
D	THR144
B	GLU349
B	ARG350

site_id	AE3
Number of Residues	3
Details	binding site for residue EDO B 508

Chain	Residue
B	ALA183
B	VAL184
B	PHE185

site_id	AE4
Number of Residues	1
Details	binding site for residue EDO B 509

Chain	Residue
B	GLN256

site_id	AE5
Number of Residues	7
Details	binding site for residue EPE B 510

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

site_id	AE6
Number of Residues	6
Details	binding site for residue EDO B 511

Chain	Residue
B	PHE211
B	THR215
B	SER217
B	ARG350
D	HIS152
D	GLU243

site_id	AE7
Number of Residues	5
Details	binding site for residue EDO B 512

Chain	Residue
B	HIS152
B	GLU243
D	THR215
D	SER217
D	ARG350

site_id	AE8
Number of Residues	14
Details	binding site for residue 4I7 B 513

Chain	Residue
B	MET273
B	ASP318
B	LEU319
B	ASN321
B	ILE336
B	MET337
B	PHE340
B	MET357
B	SER368
B	GLN369
B	PHE372
B	HOH671
B	HOH673
B	HOH685

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	HOH615
C	HOH638

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

Chain	Residue
C	ASP201
C	HOH615
C	HOH627
C	HOH629
C	HOH630
C	HOH678

site_id	AF2
Number of Residues	3
Details	binding site for residue EDO C 503

Chain	Residue
C	LEU188
C	LYS255
C	SER259

site_id	AF3
Number of Residues	7
Details	binding site for residue EDO C 504

Chain	Residue
C	VAL174
C	LEU175
C	THR178
C	TRP384
C	ASP391
C	ALA392
C	ILE395

site_id	AF4
Number of Residues	9
Details	binding site for residue EPE C 505

Chain	Residue
C	HIS105
C	VAL106
C	PHE107
C	ARG108
C	GLU111
C	GLN327
C	LEU328
C	GLN331
C	HOH647

site_id	AF5
Number of Residues	5
Details	binding site for residue EDO C 506

Chain	Residue
A	SER217
A	ARG350
C	THR148
C	HIS152
C	GLU243

site_id	AF6
Number of Residues	3
Details	binding site for residue EDO C 507

Chain	Residue
A	ASP151
A	EDO509
C	ARG346

site_id	AF7
Number of Residues	11
Details	binding site for residue 4I7 C 508

Chain	Residue
C	MET273
C	LEU319
C	ASN321
C	ILE336
C	MET337
C	PHE340
C	MET357
C	SER368
C	GLN369
C	PHE372
C	ILE376

site_id	AF8
Number of Residues	2
Details	binding site for residue EDO C 509

Chain	Residue
C	ASP98
C	TRP102

site_id	AF9
Number of Residues	6
Details	binding site for residue ZN D 501

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	HOH608
D	HOH669

site_id	AG1
Number of Residues	6
Details	binding site for residue MG D 502

Chain	Residue
D	ASP201
D	HOH608
D	HOH640
D	HOH641
D	HOH656
D	HOH673

site_id	AG2
Number of Residues	5
Details	binding site for residue EDO D 503

Chain	Residue
D	PHE340
D	PRO356
D	CYS358
D	4I7520
D	HOH678

site_id	AG3
Number of Residues	3
Details	binding site for residue EDO D 504

Chain	Residue
D	LYS262
D	ASP266
D	HOH629

site_id	AG4
Number of Residues	6
Details	binding site for residue EDO D 505

Chain	Residue
D	ASN115
D	ALA155
D	ASN161
D	ASN162
D	ILE163
D	HOH638

site_id	AG5
Number of Residues	3
Details	binding site for residue EDO D 507

Chain	Residue
D	THR186
D	GLU189
D	SER259

site_id	AG6
Number of Residues	3
Details	binding site for residue EDO D 508

Chain	Residue
D	THR134
D	ASN251
D	GLN256

site_id	AG7
Number of Residues	3
Details	binding site for residue EDO D 509

Chain	Residue
D	SER259
D	LYS262
D	TYR303

site_id	AG8
Number of Residues	1
Details	binding site for residue EDO D 510

Chain	Residue
D	GLU182

site_id	AG9
Number of Residues	7
Details	binding site for residue PEG D 511

Chain	Residue
D	VAL174
D	LEU175
D	THR178
D	TRP384
D	ASP391
D	PEG512
D	HOH633

site_id	AH1
Number of Residues	3
Details	binding site for residue PEG D 512

Chain	Residue
D	PRO179
D	ASP391
D	PEG511

site_id	AH2
Number of Residues	2
Details	binding site for residue EDO D 513

Chain	Residue
D	GLU128
D	SER177

site_id	AH3
Number of Residues	5
Details	binding site for residue EDO D 514

Chain	Residue
D	ASP98
D	TRP102
D	GLY103
D	HOH631
D	HOH636

site_id	AH4
Number of Residues	6
Details	binding site for residue EDO D 515

Chain	Residue
C	ASN231
C	LEU234
D	LEU221
D	MET222
D	ASN224
D	HOH607

site_id	AH5
Number of Residues	7
Details	binding site for residue EPE D 516

Chain	Residue
D	HIS105
D	VAL106
D	PHE107
D	ARG108
D	GLU111
D	LEU328
D	GLN331

site_id	AH6
Number of Residues	2
Details	binding site for residue EDO D 517

Chain	Residue
D	GLU218
D	MET222

site_id	AH7
Number of Residues	1
Details	binding site for residue EDO D 518

Chain	Residue
D	HOH630

site_id	AH8
Number of Residues	3
Details	binding site for residue EDO D 519

Chain	Residue
D	PHE238
D	ARG257
D	HOH626

site_id	AH9
Number of Residues	12
Details	binding site for residue 4I7 D 520

Chain	Residue
D	MET273
D	LEU319
D	ASN321
D	ILE336
D	MET337
D	PHE340
D	MET357
D	SER368
D	GLN369
D	PHE372
D	EDO503
D	HOH691

site_id	AI1
Number of Residues	1
Details	binding site for residue EDO D 521

Chain	Residue
D	GLU218

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)