Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5LBO

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-001

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 1001

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH1108
A	HOH1124

site_id	AC2
Number of Residues	6
Details	binding site for residue MG A 1002

Chain	Residue
A	HOH1134
A	HOH1169
A	HOH1191
A	ASP201
A	HOH1108
A	HOH1110

site_id	AC3
Number of Residues	3
Details	binding site for residue EDO A 1003

Chain	Residue
A	SER208
A	PRO356
A	HOH1125

site_id	AC4
Number of Residues	3
Details	binding site for residue EDO A 1004

Chain	Residue
A	ASN115
A	ALA155
A	ASN162

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO A 1005

Chain	Residue
A	THR186
A	GLU189
A	SER259
A	HOH1123

site_id	AC6
Number of Residues	4
Details	binding site for residue EDO A 1006

Chain	Residue
A	LYS262
A	ASP266
A	HOH1107
A	HOH1109

site_id	AC7
Number of Residues	4
Details	binding site for residue EDO A 1007

Chain	Residue
A	VAL174
A	THR178
A	ASP391
A	ILE395

site_id	AC8
Number of Residues	2
Details	binding site for residue EDO A 1008

Chain	Residue
A	GLU218
C	LYS239

site_id	AC9
Number of Residues	2
Details	binding site for residue EDO A 1009

Chain	Residue
A	ASP266
A	LEU269

site_id	AD1
Number of Residues	2
Details	binding site for residue DTT A 1010

Chain	Residue
A	THR134
A	ASP187

site_id	AD2
Number of Residues	12
Details	binding site for residue 6M5 A 1011

Chain	Residue
A	MET273
A	LEU319
A	ASN321
A	ILE336
A	MET357
A	SER368
A	GLN369
A	GLY371
A	PHE372
A	TYR375
A	HOH1153
A	HOH1192

site_id	AD3
Number of Residues	5
Details	binding site for residue EDO A 1012

Chain	Residue
A	HIS152
A	GLU243
C	THR215
C	SER217
C	ARG350

site_id	AD4
Number of Residues	9
Details	binding site for residue DTT A 1013

Chain	Residue
A	GLU150
A	ASP151
A	TYR153
A	HIS154
A	ALA155
A	HOH1156
C	ASP156
C	HOH1158
C	HOH1173

site_id	AD5
Number of Residues	6
Details	binding site for residue ZN B 1001

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	HOH1108
B	HOH1149

site_id	AD6
Number of Residues	6
Details	binding site for residue MG B 1002

Chain	Residue
B	ASP201
B	HOH1108
B	HOH1116
B	HOH1154
B	HOH1162
B	HOH1182

site_id	AD7
Number of Residues	5
Details	binding site for residue EDO B 1003

Chain	Residue
B	SER208
B	PHE340
B	PRO356
B	CYS358
B	HOH1120

site_id	AD8
Number of Residues	4
Details	binding site for residue EDO B 1004

Chain	Residue
B	ASN115
B	ALA155
B	ASN162
B	ILE163

site_id	AD9
Number of Residues	4
Details	binding site for residue EDO B 1005

Chain	Residue
A	ASN224
A	ASP225
B	LYS262
B	ASP266

site_id	AE1
Number of Residues	2
Details	binding site for residue EDO B 1006

Chain	Residue
B	VAL292
B	HOH1143

site_id	AE2
Number of Residues	6
Details	binding site for residue EDO B 1007

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

site_id	AE3
Number of Residues	6
Details	binding site for residue EDO B 1008

Chain	Residue
D	HIS152
D	GLU243
B	PHE211
B	THR215
B	ARG346
B	ARG350

site_id	AE4
Number of Residues	3
Details	binding site for residue EDO B 1009

Chain	Residue
B	GLU349
B	ARG350
D	ILE143

site_id	AE5
Number of Residues	5
Details	binding site for residue EPE B 1010

Chain	Residue
B	ASP140
B	GLN250
B	HOH1102
C	THR253
C	LYS254

site_id	AE6
Number of Residues	10
Details	binding site for residue 6M5 B 1011

Chain	Residue
B	MET273
B	LEU319
B	ASN321
B	ILE336
B	MET357
B	SER368
B	GLN369
B	PHE372
B	TYR375
B	HOH1156

site_id	AE7
Number of Residues	6
Details	binding site for residue ZN C 1001

Chain	Residue
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	HOH1105
C	HOH1126

site_id	AE8
Number of Residues	6
Details	binding site for residue MG C 1002

Chain	Residue
C	ASP201
C	HOH1105
C	HOH1114
C	HOH1123
C	HOH1144
C	HOH1167

site_id	AE9
Number of Residues	4
Details	binding site for residue EDO C 1003

Chain	Residue
C	SER208
C	PRO356
C	HOH1107
C	HOH1174

site_id	AF1
Number of Residues	2
Details	binding site for residue EDO C 1004

Chain	Residue
C	ARG257
C	ARG261

site_id	AF2
Number of Residues	2
Details	binding site for residue EDO C 1005

Chain	Residue
C	LYS255
C	SER259

site_id	AF3
Number of Residues	4
Details	binding site for residue EDO C 1006

Chain	Residue
C	THR178
C	TRP384
C	ASP391
C	ILE395

site_id	AF4
Number of Residues	8
Details	binding site for residue EPE C 1007

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

site_id	AF5
Number of Residues	11
Details	binding site for residue 6M5 C 1008

Chain	Residue
C	MET273
C	LEU319
C	ASN321
C	ILE336
C	MET357
C	SER368
C	GLN369
C	PHE372
C	TYR375
C	HOH1135
C	HOH1174

site_id	AF6
Number of Residues	6
Details	binding site for residue ZN D 1001

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	HOH1122
D	HOH1174

site_id	AF7
Number of Residues	6
Details	binding site for residue MG D 1002

Chain	Residue
D	ASP201
D	HOH1122
D	HOH1124
D	HOH1165
D	HOH1173
D	HOH1206

site_id	AF8
Number of Residues	1
Details	binding site for residue EDO D 1003

Chain	Residue
D	SER294

site_id	AF9
Number of Residues	5
Details	binding site for residue EDO D 1004

Chain	Residue
D	SER208
D	SER355
D	PRO356
D	CYS358
D	HOH1134

site_id	AG1
Number of Residues	3
Details	binding site for residue EDO D 1005

Chain	Residue
D	LYS262
D	ASP266
D	HOH1114

site_id	AG2
Number of Residues	8
Details	binding site for residue EDO D 1006

Chain	Residue
D	ASN115
D	ALA155
D	ASN161
D	ASN162
D	ILE163
D	ARG335
D	DTT1014
D	HOH1179

site_id	AG3
Number of Residues	1
Details	binding site for residue EDO D 1007

Chain	Residue
D	HOH1166

site_id	AG4
Number of Residues	5
Details	binding site for residue EDO D 1008

Chain	Residue
D	THR186
D	LEU188
D	SER259
D	EDO1010
D	HOH1161

site_id	AG5
Number of Residues	4
Details	binding site for residue EDO D 1009

Chain	Residue
D	THR134
D	LYS136
D	ASN251
D	GLN256

site_id	AG6
Number of Residues	3
Details	binding site for residue EDO D 1010

Chain	Residue
D	SER259
D	TYR303
D	EDO1008

site_id	AG7
Number of Residues	1
Details	binding site for residue EDO D 1011

Chain	Residue
D	GLU182

site_id	AG8
Number of Residues	7
Details	binding site for residue PEG D 1012

Chain	Residue
D	VAL174
D	LEU175
D	THR178
D	TRP384
D	VAL388
D	PEG1013
D	HOH1125

site_id	AG9
Number of Residues	3
Details	binding site for residue PEG D 1013

Chain	Residue
D	PRO179
D	ASP391
D	PEG1012

site_id	AH1
Number of Residues	12
Details	binding site for residue DTT D 1014

Chain	Residue
B	ASP156
B	HOH1165
D	ASN115
D	ARG116
D	GLU150
D	ASP151
D	TYR153
D	HIS154
D	ALA155
D	EDO1006
D	HOH1103
D	HOH1205

site_id	AH2
Number of Residues	10
Details	binding site for residue 6M5 D 1015

Chain	Residue
D	MET273
D	LEU319
D	ASN321
D	ILE336
D	MET357
D	SER368
D	GLN369
D	PHE372
D	TYR375
D	HOH1137

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)