1XON - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

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 4D IN COMPLEX WITH PICLAMILAST

Authors :   G. L. Card, B. P. England, Y. Suzuki, D. Fong, B. Powell, B. Lee, C. Luu, M. Tabrizizad, S. Gillette, P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. S. -H. Kim, J. Schlessinger, K. Y. J. Zhang

Date :   06 Oct 04 (Deposition) - 14 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

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

Keywords :   Phosphodiesterase, Pde, Pde4D, Piclamilast, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. L. Card, B. P. England, Y. Suzuki, D. Fong, B. Powell, B. Lee, C. Luu, M. Tabrizizad, S. Gillette, P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. Milburn, S. -H. Kim, J. Schlessinger, K. Y. J. Zhang
Structural Basis For The Activity Of Drugs That Inhibit Phosphodiesterases.
Structure V. 12 2233 2004
PubMed-ID: 15576036 | Reference-DOI: 10.1016/J.STR.2004.10.004

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4D
	Chains	:	A, B
	EC Number	:	3.1.4.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)CODON PLUS(RIL)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D
	Gene	:	PDE4D
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DPDE3, PDE43

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 42)

No.	Name	Count	Type	Full Name
1	B3P	1	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	EDO	35	Ligand/Ion	1,2-ETHANEDIOL
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	PIL	2	Ligand/Ion	3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 22)

No.	Name	Count	Type	Full Name
1	B3P	1	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	EDO	20	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PIL	1	Ligand/Ion	3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 16)

No.	Name	Count	Type	Full Name
1	B3P	-1	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	EDO	15	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PIL	1	Ligand/Ion	3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (42, 42)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , HOH A:1007 , HOH A:1008	BINDING SITE FOR RESIDUE ZN A 1001
02	AC2	SOFTWARE	ASP A:201 , HOH A:1003 , HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1007	BINDING SITE FOR RESIDUE MG A 1002
03	AC3	SOFTWARE	HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , HOH B:2007 , HOH B:2008	BINDING SITE FOR RESIDUE ZN B 1001
04	AC4	SOFTWARE	ASP B:201 , HOH B:2003 , HOH B:2004 , HOH B:2005 , HOH B:2006 , HOH B:2007	BINDING SITE FOR RESIDUE MG B 1002
05	AC5	SOFTWARE	THR A:271 , MET A:273 , ASP A:318 , LEU A:319 , ASN A:321 , THR A:333 , ILE A:336 , PHE A:340 , MET A:357 , GLN A:369 , PHE A:372 , EDO A:744 , HOH A:1005 , HOH A:1010	BINDING SITE FOR RESIDUE PIL A 501
06	AC6	SOFTWARE	TYR B:159 , THR B:271 , MET B:273 , ASP B:318 , LEU B:319 , ASN B:321 , THR B:333 , ILE B:336 , PHE B:340 , MET B:357 , GLN B:369 , PHE B:372 , HOH B:2005 , HOH B:2010 , HOH B:2104	BINDING SITE FOR RESIDUE PIL B 502
07	AC7	SOFTWARE	LYS A:94 , GLU A:95 , GLU A:97 , ASP A:98 , HIS A:105 , ARG A:108 , HOH A:1165 , HOH A:1215 , ASP B:394 , ASP B:397 , ASP B:401 , HOH B:2079	BINDING SITE FOR RESIDUE B3P A 601
08	AC8	SOFTWARE	GLU B:366 , HOH B:2057	BINDING SITE FOR RESIDUE EDO B 701
09	AC9	SOFTWARE	LYS A:262 , ILE A:265 , ASP A:266 , HOH A:1037 , ASN B:224	BINDING SITE FOR RESIDUE EDO A 702
10	BC1	SOFTWARE	GLN A:210 , HOH A:1025 , HOH A:1038 , HOH A:1041	BINDING SITE FOR RESIDUE EDO A 704
11	BC2	SOFTWARE	ASP B:98 , GLY B:103 , HIS B:105	BINDING SITE FOR RESIDUE EDO B 706
12	BC3	SOFTWARE	ASN A:115 , ARG A:116 , HOH A:1123 , HOH A:1124 , ALA B:183 , VAL B:184 , HOH B:2165	BINDING SITE FOR RESIDUE EDO A 707
13	BC4	SOFTWARE	ASP A:151 , THR B:186 , ARG B:306 , EDO B:743 , HOH B:2043 , HOH B:2107	BINDING SITE FOR RESIDUE EDO A 742
14	BC5	SOFTWARE	SER B:208 , PHE B:340 , PRO B:356 , HOH B:2203	BINDING SITE FOR RESIDUE EDO B 708
15	BC6	SOFTWARE	ASN B:302 , TYR B:303 , EDO B:743	BINDING SITE FOR RESIDUE EDO B 709
16	BC7	SOFTWARE	EDO A:742 , EDO B:709	BINDING SITE FOR RESIDUE EDO B 743
17	BC8	SOFTWARE	PRO A:179 , ALA A:180 , HIS A:389 , ASP A:391 , ARG B:350	BINDING SITE FOR RESIDUE EDO A 712
18	BC9	SOFTWARE	ASN A:115 , ALA A:155 , ASN A:162 , ILE A:163 , HOH A:1086	BINDING SITE FOR RESIDUE EDO A 715
19	CC1	SOFTWARE	THR A:178 , TRP A:384 , ASP A:391 , ALA A:392 , ILE A:395 , HOH A:1114	BINDING SITE FOR RESIDUE EDO A 716
20	CC2	SOFTWARE	PHE B:238 , ARG B:257 , EDO B:718 , HOH B:2040 , HOH B:2148	BINDING SITE FOR RESIDUE EDO B 717
21	CC3	SOFTWARE	HOH A:1202 , ARG B:257 , GLN B:258 , ARG B:261 , EDO B:717	BINDING SITE FOR RESIDUE EDO B 718
22	CC4	SOFTWARE	VAL A:184 , LEU A:298 , LEU A:299 , LEU A:300 , ARG A:306	BINDING SITE FOR RESIDUE EDO A 719
23	CC5	SOFTWARE	PHE A:238 , ARG A:257 , ARG A:261 , HOH A:1138	BINDING SITE FOR RESIDUE EDO A 720
24	CC6	SOFTWARE	SER A:208 , PHE A:340 , PRO A:356 , HOH A:1106 , HOH A:1216	BINDING SITE FOR RESIDUE EDO A 722
25	CC7	SOFTWARE	ASP A:156 , VAL A:157 , ALA A:158 , GLU A:339 , ARG A:342 , HOH A:1040 , HOH A:1161	BINDING SITE FOR RESIDUE EDO A 745
26	CC8	SOFTWARE	MET A:273 , PHE A:372 , ILE A:376 , PIL A:501 , EDO A:723 , HOH A:1095	BINDING SITE FOR RESIDUE EDO A 744
27	CC9	SOFTWARE	ILE A:376 , EDO A:744 , HOH A:1145	BINDING SITE FOR RESIDUE EDO A 723
28	DC1	SOFTWARE	MET A:222 , HOH A:1020	BINDING SITE FOR RESIDUE EDO A 724
29	DC2	SOFTWARE	LYS B:262 , ILE B:265 , ASP B:266 , HOH B:2022	BINDING SITE FOR RESIDUE EDO B 725
30	DC3	SOFTWARE	GLN A:407 , GLU B:150 , ASP B:151 , TYR B:153 , ALA B:155 , ASN B:162 , HOH B:2115	BINDING SITE FOR RESIDUE EDO B 726
31	DC4	SOFTWARE	GLN A:327 , HOH A:1081 , TRP B:405 , EDO B:728 , HOH B:2093	BINDING SITE FOR RESIDUE EDO B 727
32	DC5	SOFTWARE	PRO B:325 , LEU B:326 , ASP B:401 , ASN B:402 , EDO B:727	BINDING SITE FOR RESIDUE EDO B 728
33	DC6	SOFTWARE	ASP A:151 , HIS A:152 , TYR A:153 , HOH A:1015 , ASP B:301 , HOH B:2024 , HOH B:2107	BINDING SITE FOR RESIDUE EDO A 729
34	DC7	SOFTWARE	ASP B:156 , VAL B:157 , ALA B:158 , GLU B:339 , ARG B:342 , HOH B:2030 , HOH B:2039	BINDING SITE FOR RESIDUE EDO B 730
35	DC8	SOFTWARE	GLY A:371 , ASP A:374 , TYR A:375 , HOH A:1116 , ASP B:151 , HIS B:152	BINDING SITE FOR RESIDUE EDO A 731
36	DC9	SOFTWARE	ILE A:213 , ASN A:216 , SER A:217 , ALA A:220 , LEU A:221 , ASP A:225 , HOH A:1202 , ARG B:261	BINDING SITE FOR RESIDUE EDO A 732
37	EC1	SOFTWARE	HIS A:154 , ASP A:203 , LEU A:219	BINDING SITE FOR RESIDUE EDO A 733
38	EC2	SOFTWARE	ASN B:115 , ALA B:155 , ASN B:162 , ILE B:163	BINDING SITE FOR RESIDUE EDO B 734
39	EC3	SOFTWARE	GLU A:338 , PHE A:341 , ASP A:345	BINDING SITE FOR RESIDUE EDO A 736
40	EC4	SOFTWARE	GLN A:327 , ARG A:330 , GLN A:331 , HOH A:1155 , HOH B:2054	BINDING SITE FOR RESIDUE EDO A 739
41	EC5	SOFTWARE	LYS B:367 , VAL B:370 , GLN B:407 , ILE B:410 , HOH B:2074	BINDING SITE FOR RESIDUE EDO B 740
42	EC6	SOFTWARE	GLN B:210 , HOH B:2015 , HOH B:2033 , HOH B:2034 , HOH B:2070	BINDING SITE FOR RESIDUE EDO B 741

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

Asymmetric Unit

No.	Residues
1	His A:389	-	Pro A:390
2	His B:389	-	Pro B:390

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068245	T	587	P	PDE4D_HUMAN	Disease (ACRDYS2)	397514467	A/B	T	285	P
2	UniProt	VAR_069453	E	590	A	PDE4D_HUMAN	Disease (ACRDYS2)	---	A/B	E	288	A
3	UniProt	VAR_069454	G	673	D	PDE4D_HUMAN	Disease (ACRDYS2)	397514469	A/B	G	371	D
4	UniProt	VAR_069455	I	678	T	PDE4D_HUMAN	Disease (ACRDYS2)	587777188	A/B	I	376	T

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068245	T	587	P	PDE4D_HUMAN	Disease (ACRDYS2)	397514467	A	T	285	P
2	UniProt	VAR_069453	E	590	A	PDE4D_HUMAN	Disease (ACRDYS2)	---	A	E	288	A
3	UniProt	VAR_069454	G	673	D	PDE4D_HUMAN	Disease (ACRDYS2)	397514469	A	G	371	D
4	UniProt	VAR_069455	I	678	T	PDE4D_HUMAN	Disease (ACRDYS2)	587777188	A	I	376	T

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068245	T	587	P	PDE4D_HUMAN	Disease (ACRDYS2)	397514467	B	T	285	P
2	UniProt	VAR_069453	E	590	A	PDE4D_HUMAN	Disease (ACRDYS2)	---	B	E	288	A
3	UniProt	VAR_069454	G	673	D	PDE4D_HUMAN	Disease (ACRDYS2)	397514469	B	G	371	D
4	UniProt	VAR_069455	I	678	T	PDE4D_HUMAN	Disease (ACRDYS2)	587777188	B	I	376	T

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDEASE_I	PS00126	3'5'-cyclic nucleotide phosphodiesterases signature.	PDE4D_HUMAN	502-513	2	A:200-211 B:200-211

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDEASE_I	PS00126	3'5'-cyclic nucleotide phosphodiesterases signature.	PDE4D_HUMAN	502-513	1	A:200-211 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDEASE_I	PS00126	3'5'-cyclic nucleotide phosphodiesterases signature.	PDE4D_HUMAN	502-513	1	- B:200-211

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.13a	ENST00000340635	13a	ENSE00001559328	chr5:59189625-59188995	631	PDE4D_HUMAN	1-152	152	0	-	-
1.21b	ENST00000340635	21b	ENSE00001136096	chr5:58511794-58511603	192	PDE4D_HUMAN	152-216	65	0	-	-
1.22	ENST00000340635	22	ENSE00001682119	chr5:58489362-58489326	37	PDE4D_HUMAN	216-228	13	0	-	-
1.23	ENST00000340635	23	ENSE00001754547	chr5:58481088-58481015	74	PDE4D_HUMAN	229-253	25	0	-	-
1.24	ENST00000340635	24	ENSE00001719283	chr5:58476470-58476421	50	PDE4D_HUMAN	253-270	18	0	-	-
1.31d	ENST00000340635	31d	ENSE00001750566	chr5:58334798-58334686	113	PDE4D_HUMAN	270-307	38	0	-	-
1.33b	ENST00000340635	33b	ENSE00000914184	chr5:58289292-58289199	94	PDE4D_HUMAN	308-339	32	0	-	-
1.34	ENST00000340635	34	ENSE00001136103	chr5:58287831-58287659	173	PDE4D_HUMAN	339-396	58	2	A:86-94 B:86-94	9 9
1.35	ENST00000340635	35	ENSE00001001090	chr5:58286729-58286631	99	PDE4D_HUMAN	397-429	33	2	A:95-127 B:95-127	33 33
1.36	ENST00000340635	36	ENSE00001001087	chr5:58285746-58285582	165	PDE4D_HUMAN	430-484	55	2	A:128-182 B:128-182	55 55
1.37	ENST00000340635	37	ENSE00001001091	chr5:58284419-58284320	100	PDE4D_HUMAN	485-518	34	2	A:183-216 B:183-216	34 34
1.38	ENST00000340635	38	ENSE00001175221	chr5:58273172-58273018	155	PDE4D_HUMAN	518-569	52	2	A:216-267 B:216-267	52 52
1.39	ENST00000340635	39	ENSE00001001088	chr5:58272299-58272177	123	PDE4D_HUMAN	570-610	41	2	A:268-308 (gaps) B:268-308	41 41
1.40	ENST00000340635	40	ENSE00001698537	chr5:58271666-58271484	183	PDE4D_HUMAN	611-671	61	2	A:309-369 B:309-369	61 61
1.41j	ENST00000340635	41j	ENSE00001989721	chr5:58270907-58264865	6043	PDE4D_HUMAN	672-809	138	2	A:370-411 B:370-411	42 42

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:322
 aligned with PDE4D_HUMAN | Q08499 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:326
                                   397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707      
          PDE4D_HUMAN   388 TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 713
               SCOP domains d1xona_ A: Catalytic domain of cyclic nucleotide phosphodiesterase pde4d                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1xonA00 A:86-411 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...----.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PDEASE_I    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.34Exon 1.35  PDB: A:95-127         Exon 1.36  PDB: A:128-182 UniProt: 430-484             Exon 1.37  PDB: A:183-216         ---------------------------------------------------Exon 1.39  PDB: A:268-308 (gaps)         Exon 1.40  PDB: A:309-369 UniProt: 611-671                   Exon 1.41j  PDB: A:370-411 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: A:216-267 UniProt: 518-569          ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1xon A  86 TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKV----VLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 411
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285      |  - |     305       315       325       335       345       355       365       375       385       395       405      
                                                                                                                                                                                                                                        292  297

Chain B from PDB  Type:PROTEIN  Length:326
 aligned with PDE4D_HUMAN | Q08499 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:326
                                   397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707      
          PDE4D_HUMAN   388 TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 713
               SCOP domains d1xonb_ B: Catalytic domain of cyclic nucleotide phosphodiesterase pde4d                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1xonB00 B:86-411 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) -------------------------------------------------------------------------PDEase_I-1xonB01 B:159-403                                                                                                                                                                                                                           -------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------PDEase_I-1xonB02 B:159-403                                                                                                                                                                                                                           -------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--A----------------------------------------------------------------------------------D----T----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PDEASE_I    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.34Exon 1.35  PDB: B:95-127         Exon 1.36  PDB: B:128-182 UniProt: 430-484             Exon 1.37  PDB: B:183-216         ---------------------------------------------------Exon 1.39  PDB: B:268-308                Exon 1.40  PDB: B:309-369 UniProt: 611-671                   Exon 1.41j  PDB: B:370-411 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------Exon 1.38  PDB: B:216-267 UniProt: 518-569          ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1xon B  86 TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP 411
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

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(

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Folds(

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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: Catalytic domain of cyclic nucleotide phosphodiesterase pde4d (33)

Human (Homo sapiens) [TaxId: 9606] (33)

1a	d1xona_	A:
1b	d1xonb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b (66)

Homologous Superfamily: Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b (66)

Human (Homo sapiens) (64)

1a	1xonB00	B:86-411
1b	1xonA00	A:86-411

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HD_PDEase (93)

Family: PDEase_I (77)

Homo sapiens (Human) (71)

1a	PDEase_I-1xonB01	B:159-403
1b	PDEase_I-1xonB02	B:159-403

Asymmetric Unit(hide GO term definitions)

Chain A,B (PDE4D_HUMAN | Q08499)

molecular function
	GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
	GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
	GO:0051117	ATPase binding	Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
	GO:0031698	beta-2 adrenergic receptor binding	Interacting selectively and non-covalently with a beta-2 adrenergic receptor.
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	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:0097110	scaffold protein binding	Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0071875	adrenergic receptor signaling pathway	A series of molecular signals generated as a consequence of an adrenergic receptor binding to one of its physiological ligands.
	GO:0086024	adrenergic receptor signaling pathway involved in positive regulation of heart rate	An adrenergic receptor signaling pathway that contributes to an increase in frequency or rate of heart contraction. Binding of adrenalin or noradrenalin to a beta-adrenergic receptor on the surface of the signal-receiving cell results in the activation of an intracellular Gs protein. Gs activates adenylate cyclase to increase intracellular cyclic-AMP (cAMP) levels. cAMP binds directly to F-channels to allow an inward flow of sodium (known as funny current, or If current). The funny current is responsible for membrane depolarization and an increase in heart rate.
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	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:0019933	cAMP-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
	GO:0071320	cellular response to cAMP	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 a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0071872	cellular response to epinephrine 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 epinephrine stimulus. Epinephrine is a catecholamine that has the formula C9H13NO3; it is secreted by the adrenal medulla to act as a hormone, and released by certain neurons to act as a neurotransmitter active in the central nervous system.
	GO:0071222	cellular response to lipopolysaccharide	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 a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0061028	establishment of endothelial barrier	The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0035264	multicellular organism growth	The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
	GO:0045822	negative regulation of heart contraction	Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction.
	GO:0033137	negative regulation of peptidyl-serine phosphorylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:1901898	negative regulation of relaxation of cardiac muscle	Any process that stops, prevents or reduces the frequency, rate or extent of relaxation of cardiac muscle.
	GO:0030593	neutrophil chemotaxis	The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
	GO:0032729	positive regulation of interferon-gamma production	Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0032743	positive regulation of interleukin-2 production	Any process that activates or increases the frequency, rate, or extent of interleukin-2 production.
	GO:0032754	positive regulation of interleukin-5 production	Any process that activates or increases the frequency, rate, or extent of interleukin-5 production.
	GO:0030814	regulation of cAMP metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0086004	regulation of cardiac muscle cell contraction	Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction.
	GO:1901844	regulation of cell communication by electrical coupling involved in cardiac conduction	Any process that modulates the frequency, rate or extent of cell communication by electrical coupling involved in cardiac conduction.
	GO:0002027	regulation of heart rate	Any process that modulates the frequency or rate of heart contraction.
	GO:0010469	regulation of receptor activity	Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
	GO:0060314	regulation of ryanodine-sensitive calcium-release channel activity	Any process that modulates the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
	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.
	GO:0006939	smooth muscle contraction	A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length.
cellular component
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0034704	calcium channel complex	An ion channel complex through which calcium ions pass.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0005891	voltage-gated calcium channel complex	A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.

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	Cis Peptide Bonds
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	1xon
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	PDE4D_HUMAN \| Q08499
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	3.1.4.17
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	614613
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1xlx	PDE4B IN COMPLEX WITH CILOMILAST
1xlz	PDE4B IN COMPLEX WITH FILAMINAST
1xm4	PDE4B IN COMPLEX WITH PICLAMILAST
1xm6	PDE4B IN COMPLEX WITH (R)-MESOPRAM
1xmu	PDE4B IN COMPLEX WITH ROFLUMILAST
1xmy	PDE4B IN COMPLEX WITH (R)-ROLIPRAM
1xn0	PDE4B IN COMPLEX WITH (R,S)-ROLIPRAM
1xom	PDE4B IN COMPLEX WITH CILOMILAST
1xoq	PDE4D IN COMPLEX WITH ROFLUMILAST
1xor	PDE4D IN COMPLEX WITH ZARDAVERINE
1xos	PDE4B IN COMPLEX WITH SILDENAFIL
1xot	PDE4B IN COMPLEX WITH VARDENAFIL
1xoz	PDE5A IN COMPLEX WITH TADALAFIL
1xp0	PDE5A IN COMPLEX WITH VARDENAFIL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 42)

Sites (42, 42)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

PROSITE Motifs (1, 2)

Exons (8, 16)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (52, 52)

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Related Entries

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Related Entries Specified in the PDB File