Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3G58

Crystal structure of human phosphodiesterase 4d with d155988/pmnpq

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 624

Chain	Residue
A	HIS330
A	HIS366
A	ASP367
A	ASP484
A	HOH792

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 625

Chain	Residue
A	HOH792
A	HOH1105
A	ASP367
A	HOH672
A	HOH756
A	HOH776

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 1

Chain	Residue
A	HIS271
A	VAL272
A	PHE273
A	ARG274
A	LEU494
A	GLN497
A	HOH939

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 988 A 901

Chain	Residue
A	ASN487
A	THR499
A	ILE502
A	PHE506
A	SER534
A	GLN535
A	PHE538
A	HOH679

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 6

Chain	Residue
A	HOH193
A	HIS318
A	GLU409
C	THR381
C	SER383
C	ARG516
C	HOH941

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 7

Chain	Residue
A	HOH37
A	PHE404
A	ARG423
A	ARG427
A	HOH651

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 9

Chain	Residue
A	SER374
A	PRO522
A	CYS524
A	HOH679
A	HOH697

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 12

Chain	Residue
A	HOH99
A	LYS428
A	ASP432
B	HOH216
B	SER392
B	HOH751

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 624

Chain	Residue
B	HIS330
B	HIS366
B	ASP367
B	ASP484
B	HOH876

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 625

Chain	Residue
B	ASP367
B	HOH639
B	HOH728
B	HOH758
B	HOH760
B	HOH876

site_id	BC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 988 B 902

Chain	Residue
B	MET439
B	ASN487
B	THR499
B	ILE502
B	MET523
B	SER534
B	GLN535
B	PHE538
B	HOH697

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 3

Chain	Residue
B	HOH88
B	THR314
B	HIS318
B	GLU409
B	HOH1033
D	THR381

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 8

Chain	Residue
B	HOH70
B	LYS428
B	ASP432
B	HOH689

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 10

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

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 17

Chain	Residue
B	SER374
B	PRO522
B	HOH697
B	HOH774

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 624

Chain	Residue
C	HOH230
C	HIS330
C	HIS366
C	ASP367
C	ASP484
C	HOH1089

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 625

Chain	Residue
C	HOH733
C	HOH1089
C	ASP367
C	HOH635
C	HOH682
C	HOH725

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE 988 C 903

Chain	Residue
C	ASN487
C	THR499
C	ILE502
C	MET523
C	GLN535
C	PHE538
C	HOH1002

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 5

Chain	Residue
C	LYS428
C	ASP432
C	HOH640
D	HOH717

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 13

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

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 16

Chain	Residue
A	THR381
A	ARG516
C	THR314
C	HIS318
C	GLU409
C	HOH666

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 18

Chain	Residue
C	HOH121
C	PHE404
C	ARG423
C	ARG427

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN D 624

Chain	Residue
D	HIS330
D	HIS366
D	ASP367
D	ASP484
D	HOH852

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 625

Chain	Residue
D	ASP367
D	HOH630
D	HOH722
D	HOH724
D	HOH852
D	HOH1023

site_id	CC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE 988 D 904

Chain	Residue
D	MET439
D	ASN487
D	THR499
D	ILE502
D	PHE506
D	MET523
D	GLN535
D	PHE538
D	THR595
D	PHE598
D	GLN599
D	HOH873

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 2

Chain	Residue
C	HOH66
C	HOH809
D	LYS428
D	ASP432

site_id	CC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 4

Chain	Residue
D	SER374
D	PRO522
D	CYS524
D	PHE598
D	GLU601
D	HOH654
D	HOH873

site_id	DC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 11

Chain	Residue
D	HIS271
D	PHE273
D	ARG274
D	GLN493
D	LEU494
D	GLN497
D	HOH1109

site_id	DC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 14

Chain	Residue
D	ARG295
D	ASP353
D	ILE356

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 15

Chain	Residue
D	HOH229
D	PHE404
D	ARG423
D	ARG427
D	HOH637

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)