1SO2 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH A DIHYDROPYRIDAZINE INHIBITOR

Authors :   G. Scapin, S. B. Patel, C. Chung, J. P. Varnerin, S. D. Edmondson, A. Mastracchio, E. R. Parmee, J. W. Becker, S. B. Singh, L. H. Van Der Ploeg, M. R. Tota

Date :   12 Mar 04 (Deposition) - 11 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Pde3B Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Scapin, S. B. Patel, C. Chung, J. P. Varnerin, S. D. Edmondson, A. Mastracchio, E. R. Parmee, S. B. Singh, J. W. Becker, L. H. Van Der Ploeg, M. R. Tota
Crystal Structure Of Human Phosphodiesterase 3B: Atomic Basis For Substrate And Inhibitor Specificity
Biochemistry V. 43 6091 2004
PubMed-ID: 15147193 | Reference-DOI: 10.1021/BI049868I
(for further references see the PDB file header)

Molecule 1 - CGMP-INHIBITED 3',5'-CYCLIC PHOSPHODIESTERASE B
	Chains	:	A, B, C, D
	EC Number	:	3.1.4.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30A
	Expression System Strain	:	CODONPLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 654-1073
	Gene	:	PDE3B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYCLIC GMP INHIBITED PHOSPHODIESTERASE B, CGI-PDE B, CGIPDE1, CGIP1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 17)

No.	Name	Count	Type	Full Name
1	666	4	Ligand/Ion	6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE
2	HG9	4	Ligand/Ion	1-DEOXY-1-[(2-HYDROXYETHYL)(NONANOYL)AMINO]HEXITOL
3	MG	9	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	666	2	Ligand/Ion	6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE
2	HG9	4	Ligand/Ion	1-DEOXY-1-[(2-HYDROXYETHYL)(NONANOYL)AMINO]HEXITOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	666	2	Ligand/Ion	6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE
2	HG9	-1	Ligand/Ion	1-DEOXY-1-[(2-HYDROXYETHYL)(NONANOYL)AMINO]HEXITOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:11 , HIS A:741 , HIS A:821 , ASP A:822 , ASP A:937	BINDING SITE FOR RESIDUE MG A 471
02	AC2	SOFTWARE	HOH A:11 , HOH A:12 , HOH A:13 , HOH A:14 , HOH A:15 , ASP A:822	BINDING SITE FOR RESIDUE MG A 472
03	AC3	SOFTWARE	HOH B:21 , MG B:474 , HIS B:741 , HIS B:821 , ASP B:822 , ASP B:937	BINDING SITE FOR RESIDUE MG B 473
04	AC4	SOFTWARE	HOH B:21 , HOH B:22 , HOH B:23 , HOH B:24 , HOH B:26 , MG B:473 , ASP B:822	BINDING SITE FOR RESIDUE MG B 474
05	AC5	SOFTWARE	HOH C:31 , HIS C:741 , HIS C:821 , ASP C:822 , ASP C:937	BINDING SITE FOR RESIDUE MG C 475
06	AC6	SOFTWARE	HOH C:31 , HOH C:32 , HOH C:33 , HOH C:34 , HOH C:36 , ASP C:822	BINDING SITE FOR RESIDUE MG C 476
07	AC7	SOFTWARE	HOH D:41 , MG D:478 , HIS D:741 , HIS D:821 , ASP D:822 , ASP D:937	BINDING SITE FOR RESIDUE MG D 477
08	AC8	SOFTWARE	HOH D:41 , HOH D:42 , HOH D:43 , HOH D:44 , HOH D:46 , MG D:477 , HIS D:821 , ASP D:822	BINDING SITE FOR RESIDUE MG D 478
09	AC9	SOFTWARE	HOH A:51 , HOH A:52 , HOH A:53 , HOH A:54 , ASN A:968 , ASP B:875	BINDING SITE FOR RESIDUE MG A 479
10	BC1	SOFTWARE	HOH B:223 , HOH B:256 , HOH B:385 , HOH B:391 , ASN B:957 , ARG B:979 , LEU B:984 , ALA D:985 , ILE D:1071 , LYS D:1073	BINDING SITE FOR RESIDUE HG9 B 451
11	BC2	SOFTWARE	ALA B:985 , LYS B:1070 , ILE B:1071 , LYS B:1073 , LEU D:949 , ASN D:957 , TYR D:960 , ARG D:979 , LEU D:984	BINDING SITE FOR RESIDUE HG9 B 452
12	BC3	SOFTWARE	HOH A:126 , HOH A:301 , GLU A:953 , ASN A:957 , ARG A:979 , LEU A:984 , ARG B:783 , ALA C:985 , ILE C:1071 , LYS C:1073	BINDING SITE FOR RESIDUE HG9 A 453
13	BC4	SOFTWARE	ALA A:985 , ILE A:1071 , LYS A:1073 , HOH C:288 , ASN C:957 , ARG C:979	BINDING SITE FOR RESIDUE HG9 A 454
14	BC5	SOFTWARE	HOH A:148 , HOH A:200 , TYR A:736 , THR A:829 , ILE A:938 , GLY A:940 , PRO A:941 , HIS A:948 , TRP A:951 , THR A:952 , LEU A:987 , GLN A:988 , SER A:990 , PHE A:991	BINDING SITE FOR RESIDUE 666 A 461
15	BC6	SOFTWARE	TYR B:736 , ILE B:938 , GLY B:940 , PRO B:941 , HIS B:948 , TRP B:951 , THR B:952 , PHE B:976 , LEU B:987 , GLN B:988 , SER B:990 , PHE B:991	BINDING SITE FOR RESIDUE 666 B 462
16	BC7	SOFTWARE	HOH C:182 , TYR C:736 , THR C:829 , LEU C:895 , ILE C:938 , GLY C:940 , PRO C:941 , HIS C:948 , THR C:952 , LEU C:987 , GLN C:988 , SER C:990 , PHE C:991	BINDING SITE FOR RESIDUE 666 C 463
17	BC8	SOFTWARE	HOH D:320 , TYR D:736 , THR D:829 , ILE D:938 , GLY D:940 , PRO D:941 , HIS D:948 , TRP D:951 , THR D:952 , LEU D:987 , GLN D:988 , PHE D:991	BINDING SITE FOR RESIDUE 666 D 464

(no "SS Bond" information available for 1SO2)

(no "Cis Peptide Bond" information available for 1SO2)

(no "SAP(SNP)/Variant" information available for 1SO2)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDEASE_I	PS00126	3'5'-cyclic nucleotide phosphodiesterases signature.	PDE3B_HUMAN	821-832	4	A:821-832 B:821-832 C:821-832 D:821-832

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDEASE_I	PS00126	3'5'-cyclic nucleotide phosphodiesterases signature.	PDE3B_HUMAN	821-832	2	A:821-832 B:821-832 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDEASE_I	PS00126	3'5'-cyclic nucleotide phosphodiesterases signature.	PDE3B_HUMAN	821-832	2	- - C:821-832 D:821-832

Asymmetric Unit (8, 32)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000282096	1a	ENSE00001262747	chr11:14665269-14666599	1331	PDE3B_HUMAN	1-326	326	0	-	-
1.4a	ENST00000282096	4a	ENSE00001004419	chr11:14793483-14793533	51	PDE3B_HUMAN	327-343	17	0	-	-
1.5b	ENST00000282096	5b	ENSE00001004407	chr11:14807983-14808231	249	PDE3B_HUMAN	344-426	83	0	-	-
1.6b	ENST00000282096	6b	ENSE00001004406	chr11:14810652-14810788	137	PDE3B_HUMAN	427-472	46	0	-	-
1.7	ENST00000282096	7	ENSE00001004411	chr11:14825490-14825596	107	PDE3B_HUMAN	472-508	37	0	-	-
1.8	ENST00000282096	8	ENSE00001004410	chr11:14839729-14839939	211	PDE3B_HUMAN	508-578	71	0	-	-
1.9b	ENST00000282096	9b	ENSE00001004414	chr11:14840682-14840755	74	PDE3B_HUMAN	578-603	26	0	-	-
1.10	ENST00000282096	10	ENSE00001004408	chr11:14852244-14852392	149	PDE3B_HUMAN	603-652	50	0	-	-
1.11	ENST00000282096	11	ENSE00001004417	chr11:14853186-14853323	138	PDE3B_HUMAN	653-698	46	4	A:659-698 B:659-698 C:659-698 D:659-698	40 40 40 40
1.12	ENST00000282096	12	ENSE00001004418	chr11:14854268-14854379	112	PDE3B_HUMAN	699-736	38	4	A:699-736 B:699-736 C:699-736 D:699-736	38 38 38 38
1.13	ENST00000282096	13	ENSE00001004415	chr11:14856528-14856641	114	PDE3B_HUMAN	736-774	39	4	A:736-766 B:736-766 C:736-774 (gaps) D:736-766	31 31 39 31
1.14	ENST00000282096	14	ENSE00001004409	chr11:14865373-14865572	200	PDE3B_HUMAN	774-840	67	4	A:782-840 B:782-840 C:774-840 D:780-840	59 59 67 61
1.15	ENST00000282096	15	ENSE00001004413	chr11:14880589-14880792	204	PDE3B_HUMAN	841-908	68	4	A:841-908 B:841-908 C:841-908 D:841-908	68 68 68 68
1.16	ENST00000282096	16	ENSE00001004416	chr11:14882751-14882912	162	PDE3B_HUMAN	909-962	54	4	A:909-962 B:909-962 C:909-962 D:909-962	54 54 54 54
1.17	ENST00000282096	17	ENSE00001004412	chr11:14889052-14889304	253	PDE3B_HUMAN	963-1047	85	4	A:963-1015 B:963-1015 C:963-1015 D:963-1017	53 53 53 55
1.18b	ENST00000282096	18b	ENSE00001329007	chr11:14891007-14892350	1344	PDE3B_HUMAN	1047-1112	66	4	A:1053-1073 B:1053-1073 C:1053-1073 D:1055-1073	21 21 21 19

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:363
 aligned with PDE3B_HUMAN | Q13370 from UniProtKB/Swiss-Prot  Length:1112

    Alignment length:415
                                   668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068     
         PDE3B_HUMAN    659 LDLILVEEYDSLIEKMSNWNFPIFELVEKMGEKSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNGCGTGNETDSDGRINHGRIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFKRFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSSPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLEAEEDNDTESGDDEDGEELDTEDEEMENNLNPKPPRRKSRRRIFCQLMHHLTENHKIWK 1073
               SCOP domains d1so2a_ A: cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...ee........---------------.................eehhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhh.....ee..-------------------------------------....eehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: A:659-698 [INCOMPLETE]  Exon 1.12  PDB: A:699-736             -------------------------------------Exon 1.14  PDB: A:782-840 UniProt: 774-840 [INCOMPLETE]            Exon 1.15  PDB: A:841-908 UniProt: 841-908                          Exon 1.16  PDB: A:909-962 UniProt: 909-962            Exon 1.17  PDB: A:963-1015 UniProt: 963-1047 [INCOMPLETE]                            -------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------Exon 1.13  PDB: A:736-766 [INCOMPLETE] --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.18b  PDB: A:1053-107 Transcript 1 (2)
                1so2 A  659 LDLILVEEYDSLIEKMSNWNFPIFELVEKMGEKSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNG---------------GRIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFKRFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSSPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLE-------------------------------------SRRRIFCQLMHHLTENHKIWK 1073
                                   668       678       688       698       708       718       728       738       748       758       | -         -   |   788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      |  -         -         -         -    | 1058      1068     
                                                                                                                                     766             782                                                                                                                                                                                                                                     1015                                  1053

Chain B from PDB  Type:PROTEIN  Length:363
 aligned with PDE3B_HUMAN | Q13370 from UniProtKB/Swiss-Prot  Length:1112

    Alignment length:415
                                   668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068     
         PDE3B_HUMAN    659 LDLILVEEYDSLIEKMSNWNFPIFELVEKMGEKSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNGCGTGNETDSDGRINHGRIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFKRFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSSPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLEAEEDNDTESGDDEDGEELDTEDEEMENNLNPKPPRRKSRRRIFCQLMHHLTENHKIWK 1073
               SCOP domains d1so2b_ B: cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.ee........---------------.................eehhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhh.....ee..-------------------------------------....eehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: B:659-698 [INCOMPLETE]  Exon 1.12  PDB: B:699-736             -------------------------------------Exon 1.14  PDB: B:782-840 UniProt: 774-840 [INCOMPLETE]            Exon 1.15  PDB: B:841-908 UniProt: 841-908                          Exon 1.16  PDB: B:909-962 UniProt: 909-962            Exon 1.17  PDB: B:963-1015 UniProt: 963-1047 [INCOMPLETE]                            -------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------Exon 1.13  PDB: B:736-766 [INCOMPLETE] --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.18b  PDB: B:1053-107 Transcript 1 (2)
                1so2 B  659 LDLILVEEYDSLIEKMSNWNFPIFELVEKMGEKSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNG---------------GRIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFKRFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSSPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLE-------------------------------------SRRRIFCQLMHHLTENHKIWK 1073
                                   668       678       688       698       708       718       728       738       748       758       | -         -   |   788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      |  -         -         -         -    | 1058      1068     
                                                                                                                                     766             782                                                                                                                                                                                                                                     1015                                  1053

Chain C from PDB  Type:PROTEIN  Length:372
 aligned with PDE3B_HUMAN | Q13370 from UniProtKB/Swiss-Prot  Length:1112

    Alignment length:415
                                   668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068     
         PDE3B_HUMAN    659 LDLILVEEYDSLIEKMSNWNFPIFELVEKMGEKSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNGCGTGNETDSDGRINHGRIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFKRFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSSPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLEAEEDNDTESGDDEDGEELDTEDEEMENNLNPKPPRRKSRRRIFCQLMHHLTENHKIWK 1073
               SCOP domains d1so2c_ C: cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.ee.........------.........................eehhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhh.....ee..-------------------------------------....eehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: C:659-698 [INCOMPLETE]  Exon 1.12  PDB: C:699-736             -------------------------------------Exon 1.14  PDB: C:774-840 UniProt: 774-840                         Exon 1.15  PDB: C:841-908 UniProt: 841-908                          Exon 1.16  PDB: C:909-962 UniProt: 909-962            Exon 1.17  PDB: C:963-1015 UniProt: 963-1047 [INCOMPLETE]                            -------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------Exon 1.13  PDB: C:736-774 (gaps)       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.18b  PDB: C:1053-107 Transcript 1 (2)
                1so2 C  659 LDLILVEEYDSLIEKMSNWNFPIFELVEKMGEKSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNGC------DSDGRINHGRIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFKRFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSSPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLE-------------------------------------SRRRIFCQLMHHLTENHKIWK 1073
                                   668       678       688       698       708       718       728       738       748       758        |-     | 778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      |  -         -         -         -    | 1058      1068     
                                                                                                                                      767    774                                                                                                                                                                                                                                             1015                                  1053

Chain D from PDB  Type:PROTEIN  Length:365
 aligned with PDE3B_HUMAN | Q13370 from UniProtKB/Swiss-Prot  Length:1112

    Alignment length:415
                                   668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068     
         PDE3B_HUMAN    659 LDLILVEEYDSLIEKMSNWNFPIFELVEKMGEKSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNGCGTGNETDSDGRINHGRIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFKRFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSSPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLEAEEDNDTESGDDEDGEELDTEDEEMENNLNPKPPRRKSRRRIFCQLMHHLTENHKIWK 1073
               SCOP domains d1so2d_ D: cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------PDEase_I-1so2D01 D:798-1007                                                                                                                                                                                       ------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------PDEase_I-1so2D02 D:798-1007                                                                                                                                                                                       ------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------PDEase_I-1so2D03 D:798-1007                                                                                                                                                                                       ------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------PDEase_I-1so2D04 D:798-1007                                                                                                                                                                                       ------------------------------------------------------------------ Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh............-------------.....................hhhhh.hhhhhhhhhhhhh.........hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh....ee....-------------------------------------..eehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: D:659-698 [INCOMPLETE]  Exon 1.12  PDB: D:699-736             -------------------------------------Exon 1.14  PDB: D:780-840 UniProt: 774-840 [INCOMPLETE]            Exon 1.15  PDB: D:841-908 UniProt: 841-908                          Exon 1.16  PDB: D:909-962 UniProt: 909-962            Exon 1.17  PDB: D:963-1017 UniProt: 963-1047 [INCOMPLETE]                            -------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------Exon 1.13  PDB: D:736-766 [INCOMPLETE] --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.18b  PDB: D:1055-107 Transcript 1 (2)
                1so2 D  659 LDLILVEEYDSLIEKMSNWNFPIFELVEKMGEKSGRILSQVMYTLFQDTGLLEIFKIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQIHNG-------------NHGRIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNAFLVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFKRFRFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVCIKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSSPQLAKLQESFITHIVGPLCNSYDAAGLLPGQWLEAE-------------------------------------RRIFCQLMHHLTENHKIWK 1073
                                   668       678       688       698       708       718       728       738       748       758       | -         - |     788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008        |-         -         -         -      1058      1068     
                                                                                                                                     766           780                                                                                                                                                                                                                                         1017                                  1055

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: HD-domain/PDEase-like (204)

Superfamily: HD-domain/PDEase-like (204)

Family: PDEase (118)

Protein domain: cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d1so2a_	A:
1b	d1so2b_	B:
1c	d1so2c_	C:
1d	d1so2d_	D:

(no "CATH Domain" information available for 1SO2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HD_PDEase (93)

Family: PDEase_I (77)

Homo sapiens (Human) (71)

1a	PDEase_I-1so2D01	D:798-1007
1b	PDEase_I-1so2D02	D:798-1007
1c	PDEase_I-1so2D03	D:798-1007
1d	PDEase_I-1so2D04	D:798-1007

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PDE3B_HUMAN | Q13370)

molecular function
	GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
	GO:0047555	3',5'-cyclic-GMP phosphodiesterase activity	Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
	GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
	GO:0004119	cGMP-inhibited cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is decreased in the presence of cGMP.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0043422	protein kinase B binding	Interacting selectively and non-covalently with protein kinase B, an intracellular kinase that is important in regulating glucose metabolism.
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0006198	cAMP catabolic process	The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0032869	cellular response to insulin stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0016525	negative regulation of angiogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
	GO:0043951	negative regulation of cAMP-mediated signaling	Any process which stops, prevents, or reduces the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
	GO:0007162	negative regulation of cell adhesion	Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
	GO:0033629	negative regulation of cell adhesion mediated by integrin	Any process that stops, prevents, or reduces the frequency, rate, or extent of cell adhesion mediated by integrin.
	GO:0050995	negative regulation of lipid catabolic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0032045	guanyl-nucleotide exchange factor complex	A protein complex that stimulates the exchange of guanyl nucleotides associated with a GTPase.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		666	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HG9	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1so2)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1so2
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PDE3B_HUMAN \| Q13370
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.4.17
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PDE3B_HUMAN \| Q13370
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PDE3B_HUMAN \| Q13370	:	1soj

1soj	CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 3B: ATOMIC BASIS FOR SUBSTRATE AND INHIBITOR SPECIFICITY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (8, 32)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (24, 24)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File