Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3SL5

Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d

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	5
Details	BINDING SITE FOR RESIDUE ZN A 438

Chain	Residue
A	HIS164
A	HIS200
A	ASP201
A	ASP318
A	HOH585

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 439

Chain	Residue
A	ASP201
A	HOH528
A	HOH529
A	HOH597

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE J25 A 1

Chain	Residue
A	TYR159
A	MET273
A	ASN321
A	PRO322
A	TYR329
A	PHE340
A	MET357
A	SER368
A	GLN369
A	PHE372
A	ILE376

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 2

Chain	Residue
A	LYS262
A	ASP266
B	HOH567

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE DMS A 3

Chain	Residue
A	ASP140
A	THR141

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 4

Chain	Residue
A	THR186
A	LEU188
A	GLU189
D	EDO4

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 438

Chain	Residue
B	HIS164
B	HIS200
B	ASP201
B	ASP318
B	ZN439
B	HOH564

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 439

Chain	Residue
B	ASP201
B	ZN438
B	HOH527
B	HOH566
B	HOH580
B	HOH587

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE J25 B 1

Chain	Residue
B	TYR159
B	MET273
B	LEU319
B	ASN321
B	PRO322
B	TYR329
B	THR333
B	MET337
B	PHE340
B	MET357
B	GLN369
B	PHE372
B	HOH591

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO B 2

Chain	Residue
B	GLU218
C	LEU221

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 3

Chain	Residue
B	HIS160
B	HIS204
B	GLY206
B	VAL207
B	GLU339
B	PHE340
B	GLN343

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EPE C 5

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

site_id	BC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ZN C 438

Chain	Residue
C	HIS164
C	HIS200
C	ASP201
C	ASP318
C	ZN439
C	HOH523
C	HOH556

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 439

Chain	Residue
C	ASP201
C	ZN438
C	HOH520
C	HOH523
C	HOH564
C	HOH581

site_id	BC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE J25 C 1

Chain	Residue
C	TYR159
C	MET273
C	ASN321
C	TYR329
C	TRP332
C	THR333
C	ILE336
C	PHE340
C	SER368
C	GLN369
C	PHE372
C	ILE376
C	HOH522

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 2

Chain	Residue
C	THR134
C	PHE135
C	LYS136
C	ASN251
C	GLN256
B	HIS389
B	PRO390

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 3

Chain	Residue
B	GLU182
C	LEU188
C	LYS255
C	SER259

site_id	BC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 4

Chain	Residue
C	GLU97
C	GLU128

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 6

Chain	Residue
C	ASP98
C	LYS101
C	TRP102
C	GLY103
C	HIS105

site_id	CC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 7

Chain	Residue
C	ASP266
C	LYS275
C	GLN311

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 2

Chain	Residue
B	THR215
B	SER217
D	HIS152
D	GLU243
D	HOH527

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 5

Chain	Residue
C	GLN242
D	ASN216
D	LEU221

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 438

Chain	Residue
D	HIS164
D	HIS200
D	ASP201
D	ASP318
D	ZN439
D	HOH606

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 439

Chain	Residue
D	ASP201
D	ZN438
D	HOH532
D	HOH542
D	HOH625

site_id	CC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE J25 D 1

Chain	Residue
D	TYR159
D	MET273
D	LEU319
D	ASN321
D	PRO322
D	TYR329
D	MET357
D	SER368
D	GLN369
D	PHE372
D	ILE376
D	HOH607

site_id	CC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 3

Chain	Residue
D	LEU181
D	ALA183
D	VAL184
D	PHE185
D	ILE190
D	HOH596
D	HOH619

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 4

Chain	Residue
A	EDO4
A	LEU188
A	LYS255
A	GLN256
D	GLU182

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 6

Chain	Residue
D	THR178
D	ILE395
D	HOH605

site_id	DC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 8

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

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 7

Chain	Residue
D	ASN115
D	ARG116
D	GLU150
D	ASP151
D	TYR153

site_id	DC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO D 9

Chain	Residue
D	ASN115
D	HOH583

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)