Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3G4K

Crystal structure of human phosphodiesterase 4d with rolipram

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 801

Chain	Residue
A	HIS330
A	HIS366
A	ASP367
A	ASP484
A	HOH646

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 802

Chain	Residue
A	HOH723
A	HOH90
A	ASP367
A	HOH626
A	HOH646

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	HOH830

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ROL A 901

Chain	Residue
A	TYR325
A	HIS326
A	LEU485
A	ASN487
A	THR499
A	ILE502
A	MET503
A	PHE506
A	GLN535
A	PHE538

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 624

Chain	Residue
A	LYS405
A	GLN408
A	GLU409
A	HOH638
A	HOH790
C	SER383
C	GLU384

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 4

Chain	Residue
A	LYS428
A	ASP432
A	HOH791
B	HOH148
B	HOH780

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 6

Chain	Residue
A	HIS318
A	GLU409
C	HOH102
C	LEU378
C	THR381
C	ARG516

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 7

Chain	Residue
A	HOH237
A	PHE404
A	PHE415
A	ARG423
A	ARG427
A	HOH686
A	HOH960

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 9

Chain	Residue
A	SER374
A	PHE506
A	GLN509
A	PRO522

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 12

Chain	Residue
A	PHE377
A	THR381
A	SER383
A	ARG516
C	THR314
C	HIS318
C	GLU409

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 13

Chain	Residue
A	THR300
A	ASN417
A	GLN422
A	HOH659
D	ASP557

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 14

Chain	Residue
A	LEU341
A	THR344
A	TRP550
A	VAL554
A	ASP557
A	HOH983

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN B 803

Chain	Residue
B	HIS330
B	HIS366
B	ASP367
B	ASP484
B	HOH674
B	HOH733

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 804

Chain	Residue
B	HOH109
B	HOH128
B	ASP367
B	HOH640
B	HOH674
B	HOH981

site_id	BC6
Number of Residues	14
Details	BINDING SITE FOR RESIDUE ROL B 902

Chain	Residue
B	HOH981
B	TYR325
B	HIS326
B	LEU485
B	ASN487
B	THR499
B	ILE502
B	MET503
B	MET523
B	SER534
B	GLN535
B	PHE538
B	HOH733
B	HOH913

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 3

Chain	Residue
B	THR314
B	HIS318
B	GLU409
B	HOH650
B	HOH660
D	PHE377
D	THR381

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 8

Chain	Residue
A	HOH685
B	HOH103
B	LYS428
B	ASP432

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 11

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

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN C 805

Chain	Residue
C	HIS330
C	HIS366
C	ASP367
C	ASP484
C	HOH642
C	HOH796

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 806

Chain	Residue
C	HOH130
C	ASP367
C	HOH642
C	HOH684
C	HOH729
C	HOH880

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 C 3

Chain	Residue
C	HIS271
C	VAL272
C	PHE273
C	ARG274
C	LEU494
C	GLN497
C	HOH647

site_id	CC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ROL C 903

Chain	Residue
C	TYR325
C	HIS326
C	LEU485
C	ASN487
C	THR499
C	ILE502
C	MET503
C	MET523
C	SER534
C	GLN535
C	PHE538
C	HOH796
C	HOH880

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 5

Chain	Residue
C	LYS428
C	ASP432
C	HOH638
D	HOH239

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ZN D 807

Chain	Residue
D	HOH45
D	HIS330
D	HIS366
D	ASP367
D	ASP484
D	HOH798

site_id	CC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 808

Chain	Residue
D	HOH76
D	ASP367
D	HOH626
D	HOH656
D	HOH798
D	HOH1063

site_id	CC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 D 2

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

site_id	CC9
Number of Residues	16
Details	BINDING SITE FOR RESIDUE ROL D 904

Chain	Residue
D	HOH45
D	TYR325
D	HIS326
D	LEU485
D	ASN487
D	TYR495
D	TRP498
D	THR499
D	ILE502
D	PHE506
D	MET523
D	SER534
D	GLN535
D	PHE538
D	HOH1063
D	HOH1067

site_id	DC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 624

Chain	Residue
C	HOH36
C	HOH672
D	LYS428
D	ASP432

site_id	DC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO D 10

Chain	Residue
B	PHE377
B	LEU378
B	THR381
B	ARG516
D	HOH221
D	THR314
D	HIS318
D	GLU409

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)