Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3G4I

Crystal structure of human phosphodiesterase 4d with d155871

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 801

Chain	Residue
A	HIS330
A	HIS366
A	ASP367
A	ASP484
A	HOH721
A	HOH737

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 802

Chain	Residue
A	HOH738
A	HOH749
A	HOH946
A	ASP367
A	HOH687
A	HOH721

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 3

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

site_id	AC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE D71 A 901

Chain	Residue
A	HOH30
A	HOH51
A	TYR325
A	HIS326
A	LEU485
A	ASN487
A	THR499
A	ILE502
A	MET503
A	PHE506
A	MET523
A	SER534
A	GLN535
A	PHE538
A	HOH690

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EOH A 5

Chain	Residue
A	LYS428
A	ASP432
A	HOH655
B	HOH89
B	HOH704

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EOH A 9

Chain	Residue
A	THR314
A	HIS318
A	GLU409
A	HOH709
C	PHE377
C	THR381

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EOH A 12

Chain	Residue
A	HOH42
A	PHE404
A	ARG423
A	HOH723

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 803

Chain	Residue
B	HIS330
B	HIS366
B	ASP367
B	ASP484
B	HOH655
B	HOH683

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 804

Chain	Residue
B	ASP367
B	HOH655
B	HOH699
B	HOH705
B	HOH723
B	HOH725

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 4

Chain	Residue
B	HIS271
B	VAL272
B	PHE273
B	ARG274
B	GLN493
B	LEU494
B	GLN497

site_id	BC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE D71 B 902

Chain	Residue
B	HOH56
B	HOH143
B	TYR325
B	HIS326
B	LEU485
B	ASN487
B	THR499
B	ILE502
B	MET523
B	SER534
B	GLN535
B	PHE538
B	HOH657
B	HOH914

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EOH B 8

Chain	Residue
B	SER374
B	PRO522

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EOH B 10

Chain	Residue
B	HOH111
B	HIS318
B	GLU409
D	THR381

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EOH B 11

Chain	Residue
A	HOH40
A	HOH633
B	LYS428
B	ASP432

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 805

Chain	Residue
C	HIS330
C	HIS366
C	ASP367
C	ASP484
C	HOH851
C	HOH915

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 806

Chain	Residue
C	HOH697
C	HOH721
C	HOH733
C	HOH851
C	ASP367
C	HOH629

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 2

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

site_id	BC9
Number of Residues	15
Details	BINDING SITE FOR RESIDUE D71 C 903

Chain	Residue
C	HOH49
C	TYR325
C	HIS326
C	LEU485
C	ASN487
C	THR499
C	ILE502
C	MET503
C	PHE506
C	MET523
C	SER534
C	GLN535
C	PHE538
C	HOH686
C	HOH722

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EOH C 6

Chain	Residue
C	LYS428
C	ASP432
D	HOH96
D	HOH668

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 807

Chain	Residue
D	HIS330
D	HIS366
D	ASP367
D	ASP484
D	HOH723
D	HOH755

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 808

Chain	Residue
D	ASP367
D	HOH714
D	HOH747
D	HOH751
D	HOH755
D	HOH756

site_id	CC4
Number of Residues	14
Details	BINDING SITE FOR RESIDUE D71 D 904

Chain	Residue
D	HOH129
D	HOH171
D	TYR325
D	HIS326
D	LEU485
D	ASN487
D	THR499
D	ILE502
D	PHE506
D	MET523
D	SER534
D	GLN535
D	PHE538
D	HOH706

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EOH D 7

Chain	Residue
C	HOH127
C	HOH137
D	LYS428
D	ASP432

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	4
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)