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.
3BWE
Biol. Unit 4
Info
Asym.Unit (205 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (60 KB)
Biol.Unit 4 (58 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF AGGREGATED FORM OF DJ1
Authors
:
S. S. Cha
Date
:
09 Jan 08 (Deposition) - 14 Oct 08 (Release) - 14 Apr 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G (2x)
Keywords
:
Crystal Structure, Dj-1, Filamentous Aggregates, Chaperone, Cytoplasm, Disease Mutation, Nucleus, Oncogene, Oxidation, Parkinson Disease, Phosphoprotein, Polymorphism, Ubl Conjugation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. S. Cha, H. I. Jung, H. Jeon, Y. J. An, I. K. Kim, S. Yun, H. J. Ahn, K. C. Chung, S. H. Lee, P. G. Suh, S. O. Kang
Crystal Structure Of Filamentous Aggregates Of Human Dj-1 Formed In An Inorganic Phosphate-Dependent Manner.
J. Biol. Chem. V. 283 34069 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 8)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1ac: SELENOMETHIONINE (MSEac)
1ad: SELENOMETHIONINE (MSEad)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
2
PO4
-1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
ARG E:848 , ASN E:876 , HOH G:174 , GLN G:1380
BINDING SITE FOR RESIDUE PO4 E 6
2
AC7
SOFTWARE
GLN F:1180 , GLU G:1215 , ARG G:1248 , GLY G:1275 , ASN G:1276 , LEU G:1277
BINDING SITE FOR RESIDUE PO4 F 5
[
close Site info
]
SAPs(SNPs)/Variants
(10, 20)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_020492 (M1226I, chain A/B/C/D/E/F/G, )
02: VAR_072589 (A1239S, chain A/B/C/D/E/F/G, )
03: VAR_020493 (E1264D, chain A/B/C/D/E/F/G, )
04: VAR_020494 (R1298Q, chain A/B/C/D/E/F/G, )
05: VAR_020495 (A1304T, chain A/B/C/D/E/F/G, )
06: VAR_020496 (D1349A, chain A/B/C/D/E/F/G, )
07: VAR_020497 (G1350S, chain A/B/C/D/E/F/G, )
08: VAR_034801 (E1363K, chain A/B/C/D/E/F/G, )
09: VAR_020498 (L1366P, chain A/B/C/D/E/F/G, )
10: VAR_020499 (A1371S, chain A/B/C/D/E/F/G, )
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
B
C
D
E
F
G
M
26
226
426
626
826
1026
1226
I
02
UniProt
VAR_072589
A
39
S
PARK7_HUMAN
Disease
---
A
B
C
D
E
F
G
A
39
239
439
639
839
1039
1239
S
03
UniProt
VAR_020493
E
64
D
PARK7_HUMAN
Disease (PARK7)
---
A
B
C
D
E
F
G
E
64
264
464
664
864
1064
1264
D
04
UniProt
VAR_020494
R
98
Q
PARK7_HUMAN
Polymorphism
71653619
A
B
C
D
E
F
G
R
98
298
498
698
898
1098
1298
Q
05
UniProt
VAR_020495
A
104
T
PARK7_HUMAN
Disease (PARK7)
---
A
B
C
D
E
F
G
A
104
304
504
704
904
1104
1304
T
06
UniProt
VAR_020496
D
149
A
PARK7_HUMAN
Disease (PARK7)
74315352
A
B
C
D
E
F
G
D
149
349
549
749
949
1149
1349
A
07
UniProt
VAR_020497
G
150
S
PARK7_HUMAN
Polymorphism
---
A
B
C
D
E
F
G
G
150
350
550
750
950
1150
1350
S
08
UniProt
VAR_034801
E
163
K
PARK7_HUMAN
Polymorphism
---
A
B
C
D
E
F
G
E
163
363
563
763
963
1163
1363
K
09
UniProt
VAR_020498
L
166
P
PARK7_HUMAN
Disease (PARK7)
28938172
A
B
C
D
E
F
G
L
166
366
566
766
966
1166
1366
P
10
UniProt
VAR_020499
A
171
S
PARK7_HUMAN
Polymorphism
---
A
B
C
D
E
F
G
A
171
371
571
771
971
1171
1371
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 7)
Info
All SCOP Domains
1a: SCOP_d3bwea_ (A:)
1b: SCOP_d3bweb_ (B:)
1c: SCOP_d3bwec_ (C:)
1d: SCOP_d3bwed_ (D:)
1e: SCOP_d3bwee_ (E:)
1f: SCOP_d3bwef_ (F:)
1g: SCOP_d3bweg_ (G:)
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
d3bwea_
A:
1b
d3bweb_
B:
1c
d3bwec_
C:
1d
d3bwed_
D:
1e
d3bwee_
E:
1f
d3bwef_
F:
1g
d3bweg_
G:
[
close SCOP info
]
CATH Domains
(1, 7)
Info
all CATH domains
1a: CATH_3bweE00 (E:802-989)
1b: CATH_3bweA00 (A:2-188)
1c: CATH_3bweB00 (B:202-388)
1d: CATH_3bweC00 (C:402-588)
1e: CATH_3bweD00 (D:603-788)
1f: CATH_3bweF00 (F:1003-1188)
1g: CATH_3bweG00 (G:1203-1388)
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
3bweE00
E:802-989
1b
3bweA00
A:2-188
1c
3bweB00
B:202-388
1d
3bweC00
C:402-588
1e
3bweD00
D:603-788
1f
3bweF00
F:1003-1188
1g
3bweG00
G:1203-1388
[
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 G
Asymmetric Unit 1
Asymmetric Unit 2
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 (205 KB)
Header - Asym.Unit
Biol.Unit 1 (61 KB)
Header - Biol.Unit 1
Biol.Unit 2 (61 KB)
Header - Biol.Unit 2
Biol.Unit 3 (60 KB)
Header - Biol.Unit 3
Biol.Unit 4 (58 KB)
Header - Biol.Unit 4
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
3BWE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
