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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   INHIBITION OF PROLYL OLIGOPEPTIDASE WITH A SYNTHETIC UNNATURAL DIPEPTIDE

Authors :   D. T. Racys, D. Rea, V. Fulop, M. Wills

Date :   09 May 10 (Deposition) - 23 Jun 10 (Release) - 28 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym./Biol. Unit : A,P

Keywords :   Alpha/Beta-Hydrolase, Amnesia, Beta-Propeller, Hydrolase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. T. Racys, D. Rea, V. Fulop, M. Wills
Inhibition Of Prolyl Oligopeptidase With A Synthetic Unnatural Dipeptide
Bioorg. Med. Chem. V. 18 4775 2010
PubMed-ID: 20627594 | Reference-DOI: 10.1016/J.BMC.2010.05.012

Molecule 1 - PROLYL ENDOPEPTIDASE
	Chains	:	A
	EC Number	:	3.4.21.26
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	JM105
	Expression System Taxid	:	562
	Organ	:	BRAIN
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Synonym	:	POST-PROLINE CLEAVING ENZYME, PE, PROLYL OLIGOPEPTIDASE

Molecule 2 - SYNTHETIC PEPTIDE PHQ-PRO-YCP
	Chains	:	P
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 12)

No.	Name	Count	Type	Full Name
1	GOL	9	Ligand/Ion	GLYCEROL
2	PHQ	1	Mod. Amino Acid	BENZYL CHLOROCARBONATE
3	TAM	1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE
4	YCP	1	Mod. Amino Acid	(2S)-PIPERIDINE-2-CARBOXYLIC ACID

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:118 , LEU A:119 , SER A:120 , ASP A:121 , LYS A:445 , ASP A:446 , ASN A:522 , ASN A:525 , HOH A:2123 , HOH A:2308 , HOH A:2868 , HOH A:3041 , HOH A:3042 , HOH A:3043	BINDING SITE FOR RESIDUE TAM A1711
02	AC2	SOFTWARE	LYS A:48 , ARG A:312 , GLU A:323 , TRP A:326 , VAL A:328 , HOH A:2668 , HOH A:3044	BINDING SITE FOR RESIDUE GOL A1712
03	AC3	SOFTWARE	ALA A:226 , GLU A:227 , PHE A:228 , ILE A:276 , LYS A:281 , HOH A:3045 , HOH A:3046 , HOH A:3047	BINDING SITE FOR RESIDUE GOL A1713
04	AC4	SOFTWARE	GLY A:553 , SER A:554 , VAL A:578 , HIS A:680 , HOH A:3048	BINDING SITE FOR RESIDUE GOL A1714
05	AC5	SOFTWARE	PRO A:568 , ASP A:569 , PHE A:571 , GLY A:572 , ILE A:628 , GLN A:629 , PRO A:631 , ASN A:668 , HOH A:3050 , HOH A:3051	BINDING SITE FOR RESIDUE GOL A1715
06	AC6	SOFTWARE	GLU A:239 , ASP A:291 , TYR A:292 , HOH A:2555 , HOH A:3053 , HOH A:3054 , HOH A:3055 , HOH A:3056 , HOH A:3057	BINDING SITE FOR RESIDUE GOL A1716
07	AC7	SOFTWARE	VAL A:341 , HOH A:2633 , HOH A:3054 , HOH A:3055 , HOH A:3058 , HOH A:3059	BINDING SITE FOR RESIDUE GOL A1717
08	AC8	SOFTWARE	PRO A:7 , ASP A:8 , VAL A:9 , TRP A:30 , GLN A:38 , ALA A:41 , PHE A:42 , HOH A:2435 , HOH A:3060 , HOH A:3061 , HOH A:3062 , HOH A:3063	BINDING SITE FOR RESIDUE GOL A1718
09	AC9	SOFTWARE	GLU A:287 , ASN A:305 , GLU A:512 , LYS A:516 , HOH A:2646 , HOH A:2855 , HOH A:3064 , HOH A:3065	BINDING SITE FOR RESIDUE GOL A1719
10	BC1	SOFTWARE	TYR A:190 , PRO A:191 , GLN A:193 , THR A:204 , ASN A:205 , LEU A:206 , HOH A:2459 , HOH A:3068	BINDING SITE FOR RESIDUE GOL A1720

(no "SS Bond" information available for 2XDW)

(no "Cis Peptide Bond" information available for 2XDW)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PPCE_PIG_001 *	A	29	H	PPCE_PIG	---	---	A	A	29	H
	* ID not provided by source

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRO_ENDOPEP_SER	PS00708	Prolyl endopeptidase family serine active site.	PPCE_PIG	529-559	1	A:529-559

(no "Exon" information available for 2XDW)

Asymmetric/Biological 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:710
 aligned with PPCE_PIG | P23687 from UniProtKB/Swiss-Prot  Length:710

    Alignment length:710
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710
             PPCE_PIG     1 MLSFQYPDVYRDETAIQDYHGHKVCDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNAYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESNGITGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRHSPNYRLINIDFTDPEESKWKVLVPEHEKDVLEWVACVRSNFLVLCYLHDVKNTLQLHDLATGALLKIFPLEVGSVVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGVLAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVATCANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLIKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQNNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNIDWIP 710
               SCOP domains d2xdwa1 A:1-430 Prolyl oligopeptidase, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                      d2xdwa2 A:431-710 Prolyl oligopeptidase, C-terminal domain                                                                                                                                                                                                                               SCOP domains
               CATH domains 2xdwA01 A:1-73,A:427-710  [code=3.40.50.1820, no name defined]           2xdwA02 A:74-426 Prolyl oligopeptidase, N-terminal domain                                                                                                                                                                                                                                                                                                        2xdwA01 A:1-73,A:427-710  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                               CATH domains
               Pfam domains ------Peptidase_S9_N-2xdwA02 A:7-423                                                                                                                                                                                                                                                                                                                                                                                                   ----------------------------------------------------------Peptidase_S9-2xdwA01 A:482-707                                                                                                                                                                                                    --- Pfam domains
         Sec.struct. author ...............eeee..eeee..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee...eee..eeeeeee.......eeeee.......eeeehhhhhh....eeeeeeee.....eeeeeeee.....eeeeeee....eeeeeeeeee....eee.....eeeeee...................eeeeee...hhhhheeee........eeeeee.....eeeeeee.......eeeeee.hhh..........eeee......eeeeeee..eeeeee.......eeeeee....hhhhheeee......eeeeeeee...eeeeeeee..eeeeeeee.....eeeee.....eeeeee......eeeeeee......eeeeee........eeeee......hhh.eeeeeeeee.....eeeeeeeee..........eeee.............hhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeehhhhhhhhhhhhhhhhhh.eeeee.......hhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhh............eeeeeee.......hhhhhhhhhhhhhhh.........eeeeee.........hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------H--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PRO_ENDOPEP_SER  PDB: A:529-559------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xdw A   1 MLSFQYPDVYRDETAIQDYHGHKVCDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNAYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESNGITGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRHSPNYRLINIDFTDPEESKWKVLVPEHEKDVLEWVACVRSNFLVLCYLHDVKNTLQLHDLATGALLKIFPLEVGSVVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGVLAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVATCANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLIKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQNNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNIDWIP 710
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710

Chain P from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 2xdw P 791 xPx 793
                            | |
                          791-PHQ
                            793-YCP

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1820, no name defined] (692)

Pig (Sus scrofa) (22)

2xdwA01

A:1-73,A:427-710

Class: Mainly Beta (13760)

Architecture: 7 Propellor (136)

Topology: Methylamine Dehydrogenase; Chain H (136)

Homologous Superfamily: Prolyl oligopeptidase, N-terminal domain (21)

Pig (Sus scrofa) (11)

2xdwA02

A:74-426

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AB_hydrolase (347)

Family: Peptidase_S9 (57)

Sus scrofa (Pig) (11)

Peptidase_S9-2xdwA01

A:482-707

Clan: Beta_propeller (192)

Family: Peptidase_S9_N (11)

Sus scrofa (Pig) (9)

Peptidase_S9_N-2xdwA02

A:7-423

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PPCE_PIG | P23687)

molecular function
	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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0070008	serine-type exopeptidase activity	Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xdw)

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	2xdw
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	3.4.21.26
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1e5t	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT
1e8m	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT, COMPLEXED WITH INHIBITOR
1e8n	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT, COMPLEXED WITH PEPTIDE
1h2w	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN
1h2x	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y473F MUTANT
1h2y	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y473F MUTANT WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL
1h2z	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND SUC- GLY-PRO
1o6f	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, D641A MUTANT WITH BOUND PEPTIDE LIGAND SUC- GLY-PRO
1o6g	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, D641N MUTANT WITH BOUND PEPTIDE LIGAND SUC- GLY-PRO
1qfm	PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE
1qfs	PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL
1uoo	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND GLY- PHE-ARG-PRO
1uop	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND GLY- PHE-GLU-PRO
1uoq	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND GLU- PHE-SER-PRO
1vz2	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y73C /V427C/C255T MUTANT
1vz3	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, T597C MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (7, 7)

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Related Entries Specified in the PDB File