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.
3B3A
Asym. Unit
Info
Asym.Unit (38 KB)
Biol.Unit 1 (66 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF E163K/R145E DJ-1
Authors
:
M. Lakshminarasimhan, M. T. Maldonado, W. Zhou, A. L. Fink, M. A. Wilson
Date
:
19 Oct 07 (Deposition) - 15 Jan 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Parkinson'S Disease, Thij, Pfpi, Chaperone, Cytoplasm, Disease Mutation, Nucleus, Oncogene, Oxidation, Parkinson Disease, Phosphorylation, Polymorphism, Ubl Conjugation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Lakshminarasimhan, M. T. Maldonado, W. Zhou, A. L. Fink, M. A. Wilson
Structural Impact Of Three Parkinsonism-Associated Missense Mutations On Human Dj-1.
Biochemistry V. 47 1381 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:48 , GLY A:75 , ASN A:76 , GLY A:120 , EDO A:193
BINDING SITE FOR RESIDUE CL A 190
2
AC2
SOFTWARE
ASN A:76 , CYS A:106 , ALA A:107 , HIS A:126 , EDO A:193 , HOH A:249 , HOH A:274
BINDING SITE FOR RESIDUE EDO A 191
3
AC3
SOFTWARE
GLY A:65 , PRO A:66 , TYR A:67 , GLU A:94 , GLN A:95 , HOH A:335
BINDING SITE FOR RESIDUE EDO A 192
4
AC4
SOFTWARE
GLU A:15 , ARG A:28 , HIS A:126 , PRO A:158 , PRO A:184 , CL A:190 , EDO A:191 , HOH A:249
BINDING SITE FOR RESIDUE EDO A 193
[
close Site info
]
SAPs(SNPs)/Variants
(10, 10)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_020492 (M26I, chain A, )
02: VAR_072589 (A39S, chain A, )
03: VAR_020493 (E64D, chain A, )
04: VAR_020494 (R98Q, chain A, )
05: VAR_020495 (A104T, chain A, )
06: VAR_020496 (D149A, chain A, )
07: VAR_020497 (G150S, chain A, )
08: VAR_034801 (K163K, chain A, )
09: VAR_020498 (L166P, chain A, )
10: VAR_020499 (A171S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_020492
M
26
I
PARK7_HUMAN
Disease (PARK7)
---
A
M
26
I
02
UniProt
VAR_072589
A
39
S
PARK7_HUMAN
Disease
---
A
A
39
S
03
UniProt
VAR_020493
E
64
D
PARK7_HUMAN
Disease (PARK7)
---
A
E
64
D
04
UniProt
VAR_020494
R
98
Q
PARK7_HUMAN
Polymorphism
71653619
A
R
98
Q
05
UniProt
VAR_020495
A
104
T
PARK7_HUMAN
Disease (PARK7)
---
A
A
104
T
06
UniProt
VAR_020496
D
149
A
PARK7_HUMAN
Disease (PARK7)
74315352
A
D
149
A
07
UniProt
VAR_020497
G
150
S
PARK7_HUMAN
Polymorphism
---
A
G
150
S
08
UniProt
VAR_034801
E
163
K
PARK7_HUMAN
Polymorphism
---
A
K
163
K
09
UniProt
VAR_020498
L
166
P
PARK7_HUMAN
Disease (PARK7)
28938172
A
L
166
P
10
UniProt
VAR_020499
A
171
S
PARK7_HUMAN
Polymorphism
---
A
A
171
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(6, 6)
Info
All Exons
Exon 1.4a (A:2-30)
Exon 1.5a (A:31-64)
Exon 1.7 (A:65-84)
Exon 1.8a (A:85-108)
Exon 1.10 (A:108-137)
Exon 1.11d (A:137-188)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3a/1.4a
2: Boundary 1.4a/1.5a
3: Boundary 1.5a/1.7
4: Boundary 1.7/1.8a
5: Boundary 1.8a/1.10
6: Boundary 1.10/1.11d
7: Boundary 1.11d/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.3a
ENST00000377491
3a
ENSE00001474095
chr1:
8021954-8022141
188
PARK7_HUMAN
-
0
0
-
-
1.4a
ENST00000377491
4a
ENSE00002182513
chr1:
8022823-8022935
113
PARK7_HUMAN
1-30
30
1
A:2-30
29
1.5a
ENST00000377491
5a
ENSE00000737026
chr1:
8025384-8025485
102
PARK7_HUMAN
31-64
34
1
A:31-64
34
1.7
ENST00000377491
7
ENSE00000737024
chr1:
8029405-8029464
60
PARK7_HUMAN
65-84
20
1
A:65-84
20
1.8a
ENST00000377491
8a
ENSE00000737022
chr1:
8030954-8031023
70
PARK7_HUMAN
85-108
24
1
A:85-108
24
1.10
ENST00000377491
10
ENSE00000737020
chr1:
8037712-8037798
87
PARK7_HUMAN
108-137
30
1
A:108-137
30
1.11d
ENST00000377491
11d
ENSE00001474089
chr1:
8044954-8045310
357
PARK7_HUMAN
137-189
53
1
A:137-188
52
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3b3aa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Class I glutamine amidotransferase-like
(173)
Family
:
DJ-1/PfpI
(54)
Protein domain
:
DJ-1
(34)
Human (Homo sapiens) [TaxId: 9606]
(34)
1a
d3b3aa_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3b3aA00 (A:2-188)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.880, no name defined]
(97)
Human (Homo sapiens)
(27)
1a
3b3aA00
A:2-188
[
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 (38 KB)
Header - Asym.Unit
Biol.Unit 1 (66 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
3B3A
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
