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Asym. Unit
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Asym.Unit (255 KB)
Biol.Unit 1 (248 KB)
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(1)
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. Unit : A,P
Biol. Unit 1: A,P (1x)
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
[
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Hetero Components
(4, 12)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
2a: BENZYL CHLOROCARBONATE (PHQa)
3a: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMa)
4a: (2S)-PIPERIDINE-2-CARBOXYLIC ACID (YCPa)
View:
Select:
Label:
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
[
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
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
[
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]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_PPCE_PIG_001 (A29H, chain A, )
View:
Select:
Label:
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)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PRO_ENDOPEP_SER (A:529-559)
;
View:
Select:
Label:
End label:
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
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2xdwa1 (A:1-430)
2a: SCOP_d2xdwa2 (A:431-710)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
7-bladed beta-propeller
(245)
Superfamily
:
Peptidase/esterase 'gauge' domain
(47)
Family
:
Prolyl oligopeptidase, N-terminal domain
(29)
Protein domain
:
Prolyl oligopeptidase, N-terminal domain
(27)
Pig (Sus scrofa) [TaxId: 9823]
(27)
1a
d2xdwa1
A:1-430
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
Prolyl oligopeptidase, C-terminal domain
(28)
Protein domain
:
Prolyl oligopeptidase, C-terminal domain
(27)
Pig (Sus scrofa) [TaxId: 9823]
(27)
2a
d2xdwa2
A:431-710
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2xdwA01 (A:1-73,A:427-710)
2a: CATH_2xdwA02 (A:74-426)
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)
(
)
Architectures
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)
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)
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)
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)
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)
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)
1a
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)
2a
2xdwA02
A:74-426
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_S9_2xdwA01 (A:482-707)
2a: PFAM_Peptidase_S9_N_2xdwA02 (A:7-423)
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Clans
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
AB_hydrolase
(347)
Family
:
Peptidase_S9
(57)
Sus scrofa (Pig)
(11)
1a
Peptidase_S9-2xdwA01
A:482-707
Clan
:
Beta_propeller
(192)
Family
:
Peptidase_S9_N
(11)
Sus scrofa (Pig)
(9)
2a
Peptidase_S9_N-2xdwA02
A:7-423
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]
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Protein & NOT PROSITE
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Chain P
Asymmetric Unit 1
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