PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4BCC
Asym. Unit
Info
Asym.Unit (254 KB)
Biol.Unit 1 (247 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND P2-SUBSTITUTED N-ACYL-PROLYLPYRROLIDINE INHIBITOR
Authors
:
P. Vanderveken, V. Fulop, D. Rea, M. Gerard, R. Vanelzen, J. Joossens, J V. Baekelandt, I. Demeester, A. M. Lambeir, K. Augustyns
Date
:
01 Oct 12 (Deposition) - 13 Mar 13 (Release) - 01 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Alpha-Beta-Hydrolase, Amnesia, Hydrolase, Parkinsons Disease, Alzheimers Disease, Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Van Der Veken, V. Fulop, D. Rea, M. Gerard, R. Van Elzen, J. Joossens, J. D. Cheng, V. Baekelandt, I. De Meester, A. M. Lambeir, K. Augustyns
P2-Substituted N-Acylprolylpyrrolidine Inhibitors Of Prolyl Oligopeptidase: Biochemical Evaluation, Binding Mode Determination, And Assessment In A Cellular Model Of Synucleinopathy.
J. Med. Chem. V. 55 9856 2012
[
close entry info
]
Hetero Components
(3, 11)
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: TERT-BUTYL N-[[1-[(3S,5S)-5-[(2S)-... (JKTa)
3a: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
9
Ligand/Ion
GLYCEROL
2
JKT
1
Ligand/Ion
TERT-BUTYL N-[[1-[(3S,5S)-5-[(2S)-2-[AZANYL(OXIDANYL)METHYL]PYRROLIDIN-1-YL]CARBONYL-1-(4-PHENYLBUTANOYL)PYRROLIDIN-3-YL]-1,2,3-TRIAZOL-4-YL]METHYL]CARBAMATE
3
TAM
1
Ligand/Ion
TRIS(HYDROXYETHYL)AMINOMETHANE
[
close Hetero Component info
]
Sites
(11, 11)
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)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:173 , GLY A:254 , TYR A:473 , PHE A:476 , SER A:554 , ASN A:555 , VAL A:580 , TRP A:595 , TYR A:599 , ARG A:643 , VAL A:644 , HIS A:680 , GOL A:1714 , HOH A:2810
BINDING SITE FOR RESIDUE JKT A 791
02
AC2
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:2234 , HOH A:2640 , HOH A:2687
BINDING SITE FOR RESIDUE TAM A1711
03
AC3
SOFTWARE
LYS A:48 , GLU A:323 , TRP A:326 , VAL A:328 , HOH A:2522
BINDING SITE FOR RESIDUE GOL A1712
04
AC4
SOFTWARE
ALA A:226 , GLU A:227 , PHE A:228 , TRP A:262 , ILE A:276 , LYS A:281 , HOH A:2811 , HOH A:2812
BINDING SITE FOR RESIDUE GOL A1713
05
AC5
SOFTWARE
GLY A:553 , SER A:554 , HIS A:680 , JKT A:791
BINDING SITE FOR RESIDUE GOL A1714
06
AC6
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:2703 , HOH A:2779
BINDING SITE FOR RESIDUE GOL A1715
07
AC7
SOFTWARE
GLU A:239 , ASP A:291 , TYR A:292 , HOH A:2426 , HOH A:2492 , HOH A:2493 , HOH A:2495
BINDING SITE FOR RESIDUE GOL A1716
08
AC8
SOFTWARE
VAL A:341 , HOH A:2493 , HOH A:2495 , HOH A:2814 , HOH A:2815
BINDING SITE FOR RESIDUE GOL A1717
09
AC9
SOFTWARE
ASP A:8 , GLN A:38 , ALA A:41 , PHE A:42 , HOH A:2024 , HOH A:2816
BINDING SITE FOR RESIDUE GOL A1718
10
BC1
SOFTWARE
VAL A:258 , GLU A:287 , ASN A:305 , GLU A:512 , LYS A:516 , HOH A:2506 , HOH A:2507
BINDING SITE FOR RESIDUE GOL A1719
11
BC2
SOFTWARE
TYR A:190 , PRO A:191 , GLN A:193 , THR A:204 , ASN A:205 , LEU A:206 , HOH A:2817
BINDING SITE FOR RESIDUE GOL A1720
[
close Site info
]
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)
[
close SNP/Variant info
]
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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_d4bcca1 (A:1-430)
2a: SCOP_d4bcca2 (A:431-710)
View:
Select:
Label:
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
d4bcca1
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
d4bcca2
A:431-710
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (254 KB)
Header - Asym.Unit
Biol.Unit 1 (247 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4BCC
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
