Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1MKD

crystal structure of PDE4D catalytic domain and zardaverine complex

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
E	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
E	0007165	biological_process	signal transduction
E	0008081	molecular_function	phosphoric diester hydrolase activity
F	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
F	0007165	biological_process	signal transduction
F	0008081	molecular_function	phosphoric diester hydrolase activity
G	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
G	0007165	biological_process	signal transduction
G	0008081	molecular_function	phosphoric diester hydrolase activity
H	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
H	0007165	biological_process	signal transduction
H	0008081	molecular_function	phosphoric diester hydrolase activity
I	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
I	0007165	biological_process	signal transduction
I	0008081	molecular_function	phosphoric diester hydrolase activity
J	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
J	0007165	biological_process	signal transduction
J	0008081	molecular_function	phosphoric diester hydrolase activity
K	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
K	0007165	biological_process	signal transduction
K	0008081	molecular_function	phosphoric diester hydrolase activity
L	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
L	0007165	biological_process	signal transduction
L	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 2001

Chain	Residue
A	HIS261
A	HIS297
A	ASP298
A	ASP415
A	HOH1001

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 2002

Chain	Residue
A	ASP298
A	GLU327
A	THR368

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 2003

Chain	Residue
B	HIS297
B	ASP298
B	ASP415
B	MG2004
B	HIS261

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG B 2004

Chain	Residue
B	ASP298
B	ZN2003

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 2005

Chain	Residue
C	HIS261
C	HIS297
C	ASP298
C	ASP415

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG C 2006

Chain	Residue
C	ASP298
C	GLU327

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 2007

Chain	Residue
D	HIS261
D	HIS297
D	ASP298
D	ASP415

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MG D 2008

Chain	Residue
D	ASP298

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 2009

Chain	Residue
E	HIS261
E	HIS297
E	ASP298
E	ASP415

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG E 2010

Chain	Residue
E	HIS297
E	ASP298
E	GLU327
E	THR368

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 2011

Chain	Residue
F	HIS261
F	HIS297
F	ASP298
F	ASP415

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG F 2012

Chain	Residue
F	ASP298
F	GLU327

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN G 2013

Chain	Residue
G	HIS261
G	HIS297
G	ASP298
G	ASP415

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG G 2014

Chain	Residue
G	ASP298
G	GLU327

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 2015

Chain	Residue
H	HIS261
H	HIS297
H	ASP298
H	ASP415

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG H 2016

Chain	Residue
H	ASP298
H	GLU327

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN I 2017

Chain	Residue
I	HIS261
I	HIS297
I	ASP298
I	ASP415

site_id	BC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG I 2018

Chain	Residue
I	ASP298
I	GLU327

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN J 2019

Chain	Residue
J	HIS261
J	HIS297
J	ASP298
J	ASP415
J	MG2020

site_id	CC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG J 2020

Chain	Residue
J	ASP298
J	ZN2019

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN K 2021

Chain	Residue
K	HIS261
K	HIS297
K	ASP298
K	ASP415

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG K 2022

Chain	Residue
K	HIS297
K	ASP298
K	THR368

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN L 2023

Chain	Residue
L	HIS261
L	HIS297
L	ASP298
L	ASP415

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG L 2024

Chain	Residue
L	ASP298
L	GLU327

site_id	CC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZAR A 3001

Chain	Residue
A	MET370
A	ASN418
A	PRO419
A	TYR426
A	TRP429
A	THR430
A	ILE433
A	MET454
A	GLN466
A	PHE469

site_id	CC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZAR B 3002

Chain	Residue
B	MET370
B	ASN418
B	PRO419
B	TYR426
B	TRP429
B	THR430
B	ILE433
B	MET454
B	GLN466
B	PHE469

site_id	CC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZAR C 3003

Chain	Residue
C	ASN418
C	PRO419
C	TYR426
C	TRP429
C	THR430
C	ILE433
C	MET454
C	GLN466
C	PHE469
C	MET370

site_id	DC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZAR D 3004

Chain	Residue
D	MET370
D	ASN418
D	PRO419
D	TYR426
D	TRP429
D	THR430
D	ILE433
D	MET454
D	GLN466
D	PHE469

site_id	DC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZAR E 3005

Chain	Residue
E	MET370
E	ASN418
E	PRO419
E	TYR426
E	TRP429
E	THR430
E	ILE433
E	MET454
E	GLN466
E	PHE469

site_id	DC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZAR F 3006

Chain	Residue
F	MET370
F	ASN418
F	PRO419
F	TYR426
F	TRP429
F	THR430
F	ILE433
F	MET454
F	GLN466
F	PHE469

site_id	DC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE ZAR G 3007

Chain	Residue
G	MET370
G	ASN418
G	PRO419
G	TYR426
G	TRP429
G	THR430
G	ILE433
G	MET454
G	GLN466
G	PHE469
G	HOH1007

site_id	DC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZAR H 3008

Chain	Residue
H	MET370
H	ASN418
H	PRO419
H	TYR426
H	TRP429
H	THR430
H	ILE433
H	MET454
H	GLN466
H	PHE469

site_id	DC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ZAR I 3009

Chain	Residue
I	MET370
I	ASN418
I	TYR426
I	TRP429
I	THR430
I	ILE433
I	MET454
I	GLN466
I	PHE469

site_id	DC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZAR J 3010

Chain	Residue
J	MET370
J	ASN418
J	PRO419
J	TYR426
J	TRP429
J	THR430
J	ILE433
J	MET454
J	GLN466
J	PHE469

site_id	DC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ZAR K 3011

Chain	Residue
K	MET370
K	ASN418
K	TYR426
K	TRP429
K	THR430
K	ILE433
K	MET454
K	GLN466
K	PHE469

site_id	DC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ZAR L 3012

Chain	Residue
L	MET370
L	ASN418
L	PRO419
L	TYR426
L	TRP429
L	THR430
L	ILE433
L	MET454
L	GLN466
L	PHE469

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	HIS297-PHE308

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
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	36
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	12
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	24
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	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)