5TZW - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH 1-[(3, 4-DIFLUOROPHENYL)CARBONYL]-3,3-DIFLUORO-5-{5-METHYL-[1,2, 4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL}PIPERIDINE

Authors :   R. Xu, K. Aertgeerts

Date :   22 Nov 16 (Deposition) - 22 Feb 17 (Release) - 22 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.59

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

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

Reference :   L. Gomez, M. E. Massari, T. Vickers, G. Freestone, W. Vernier, K. Ly, R. Xu, M. Mccarrick, T. Marrone, M. Metz, Y. G. Yan, Z. W. Yoder, R. Lemus N. J. Broadbent, R. Barido, N. Warren, K. Schmelzer, D. Neul, D. Lee, C. B. Andersen, K. Sebring, K. Aertgeerts, X. Zhou, A. Tabatabaei, M. Peters, J. G. Breitenbucher
Design And Synthesis Of Novel And Selective Phosphodiesterase 2 (Pde2A) Inhibitors For The Treatment Of Memory Disorders.
J. Med. Chem. V. 60 2037 2017
PubMed-ID: 28165743 | Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01793

Molecule 1 - CGMP-DEPENDENT 3',5'-CYCLIC PHOSPHODIESTERASE
	Chains	:	A, B, C, D
	EC Number	:	3.1.4.17
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Strain	:	BACULOVIRUS INSECT CELL HI5
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACMID
	Fragment	:	CATALYTIC DOMAIN, UNP RESIDUES 323-663
	Gene	:	PDE2A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYCLIC GMP-STIMULATED PHOSPHODIESTERASE,CGSPDE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	7P4	4	Ligand/Ion	[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL](3,4-DIFLUOROPHENYL)METHANONE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	7P4	1	Ligand/Ion	[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL](3,4-DIFLUOROPHENYL)METHANONE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	7P4	1	Ligand/Ion	[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL](3,4-DIFLUOROPHENYL)METHANONE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	7P4	1	Ligand/Ion	[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL](3,4-DIFLUOROPHENYL)METHANONE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	7P4	1	Ligand/Ion	[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL](3,4-DIFLUOROPHENYL)METHANONE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:655 , HIS A:656 , LEU A:770 , GLN A:812 , ILE A:826 , TYR A:827 , PHE A:830 , MET A:847 , LEU A:858 , GLN A:859 , PHE A:862 , ILE A:866 , HOH A:1219 , HOH A:1285 , HOH A:1358	binding site for residue 7P4 A 1001
02	AC2	SOFTWARE	HIS A:660 , HIS A:696 , ASP A:697 , ASP A:808 , HOH A:1210 , HOH A:1219	binding site for residue ZN A 1002
03	AC3	SOFTWARE	ASP A:697 , HOH A:1152 , HOH A:1181 , HOH A:1196 , HOH A:1200 , HOH A:1210	binding site for residue MG A 1003
04	AC4	SOFTWARE	TYR B:655 , HIS B:656 , GLN B:812 , ILE B:826 , PHE B:830 , MET B:847 , LEU B:858 , GLN B:859 , PHE B:862 , HOH B:1263	binding site for residue 7P4 B 1001
05	AC5	SOFTWARE	HIS B:660 , HIS B:696 , ASP B:697 , ASP B:808 , HOH B:1126 , HOH B:1263	binding site for residue ZN B 1002
06	AC6	SOFTWARE	ASP B:697 , HOH B:1126 , HOH B:1153 , HOH B:1171 , HOH B:1188 , HOH B:1207	binding site for residue MG B 1003
07	AC7	SOFTWARE	TYR C:655 , HIS C:656 , LEU C:770 , GLN C:812 , ILE C:826 , TYR C:827 , PHE C:830 , MET C:847 , GLN C:859 , PHE C:862 , HOH C:1257	binding site for residue 7P4 C 1001
08	AC8	SOFTWARE	HIS C:660 , HIS C:696 , ASP C:697 , ASP C:808 , HOH C:1151 , HOH C:1152	binding site for residue ZN C 1002
09	AC9	SOFTWARE	ASP C:697 , HOH C:1143 , HOH C:1152 , HOH C:1189 , HOH C:1211 , HOH C:1228	binding site for residue MG C 1003
10	AD1	SOFTWARE	TYR D:655 , HIS D:656 , LEU D:770 , LEU D:809 , GLN D:812 , ILE D:826 , TYR D:827 , PHE D:830 , MET D:847 , GLN D:859 , PHE D:862 , HOH D:1237 , HOH D:1303	binding site for residue 7P4 D 1001
11	AD2	SOFTWARE	HIS D:660 , HIS D:696 , ASP D:697 , ASP D:808 , MG D:1003 , HOH D:1168 , HOH D:1237	binding site for residue ZN D 1002
12	AD3	SOFTWARE	ASP D:697 , ZN D:1002 , HOH D:1148 , HOH D:1168 , HOH D:1183 , HOH D:1244 , HOH D:1249	binding site for residue MG D 1003

(no "SS Bond" information available for 5TZW)

(no "Cis Peptide Bond" information available for 5TZW)

(no "SAP(SNP)/Variant" information available for 5TZW)

(no "PROSITE Motif" information available for 5TZW)

(no "Exon" information available for 5TZW)

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
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Chain A from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5tzw A 576 SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD 917
                                   585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915

Chain B from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tzw B 578 MDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                   587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907

Chain C from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tzw C 589 GIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                   598       608       618       628       638       648       658       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

Chain D from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tzw D 590 IQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                   599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5TZW)

(no "CATH Domain" information available for 5TZW)

(no "Pfam Domain" information available for 5TZW)

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