Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3IAD

Crystal structure of human phosphodiesterase 4D with bound allosteric modulator

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	10
Details	BINDING SITE FOR RESIDUE 15X A 901

Chain	Residue
A	HOH34
A	THR603
A	HIS326
A	SER374
A	LEU485
A	ILE502
A	SER534
A	GLN535
A	PHE538
A	PHE599

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 620

Chain	Residue
A	HOH178
A	HIS330
A	HIS366
A	ASP367
A	ASP484

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 621

Chain	Residue
A	HOH178
A	HOH190
A	ASP367

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EPE A 806

Chain	Residue
A	HIS271
A	VAL272
A	PHE273
A	ARG274
A	GLU277
A	LEU494
A	GLN497

site_id	AC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE 15X B 901

Chain	Residue
B	HOH31
B	HOH73
B	HOH163
B	HIS326
B	HIS370
B	VAL373
B	SER374
B	LEU485
B	ILE502
B	PHE506
B	SER534
B	GLN535
B	PHE538
B	PHE599
B	THR603
B	PHE604

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 620

Chain	Residue
B	HOH180
B	HOH195
B	HIS330
B	HIS366
B	ASP367
B	ASP484

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 621

Chain	Residue
B	HOH31
B	HOH170
B	HOH180
B	HOH181
B	ASP367
B	GLU396

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EPE B 801

Chain	Residue
B	HOH112
B	ASP306
B	THR307
B	ASN411
B	GLN416
B	LYS456
B	LYS457
C	THR419
C	LYS420

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EPE B 802

Chain	Residue
B	HIS271
B	VAL272
B	PHE273
B	ARG274
B	GLU277
B	GLN493
B	GLN497

site_id	BC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE 15X C 901

Chain	Residue
C	HIS326
C	HIS370
C	VAL373
C	SER374
C	LEU485
C	ILE502
C	SER534
C	GLN535
C	PHE538
C	PHE599
C	PHE604

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 620

Chain	Residue
C	HOH182
C	HOH186
C	HIS330
C	HIS366
C	ASP367
C	ASP484

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 621

Chain	Residue
C	HOH182
C	HOH183
C	HOH184
C	HOH185
C	ASP367

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EPE C 803

Chain	Residue
C	HIS271
C	VAL272
C	PHE273
C	ARG274
C	GLU277
C	GLN493
C	LEU494
C	GLN497

site_id	BC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE 15X D 901

Chain	Residue
D	HOH203
D	HIS326
D	HIS370
D	VAL373
D	SER374
D	LEU485
D	THR499
D	ILE502
D	MET523
D	SER534
D	GLN535
D	PHE538
D	PHE599

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 620

Chain	Residue
D	HOH179
D	HOH196
D	HIS330
D	HIS366
D	ASP367
D	ASP484

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 621

Chain	Residue
D	HOH179
D	HOH189
D	HOH192
D	HOH197
D	HOH203
D	ASP367

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EPE D 804

Chain	Residue
D	GLU261
D	ASP264
D	TRP268
D	HIS271

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EPE D 805

Chain	Residue
D	HIS271
D	PHE273
D	ARG274
D	GLU277
D	GLN493
D	LEU494
D	GLN497

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	HIS366-PHE377

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)