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.
3D6T
Asym. Unit
Info
Asym.Unit (29 KB)
Biol.Unit 1 (22 KB)
Biol.Unit 2 (43 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 THE ROC DOMAIN FROM THE PARKINSON'S DISEASE-ASSOCIATED LEUCINE-RICH REPEAT KINASE 2 REVEALS A DIMERIC GTPASE
Authors
:
J. Deng
Date
:
20 May 08 (Deposition) - 10 Jun 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.43
Chains
:
Asym. Unit : B
Biol. Unit 1: B (1x)
Biol. Unit 2: B (2x)
Keywords
:
Parkinson'S Disease, Lrrk2, Roc, Gtpase, Roco, Kinase, Atp-Binding, Disease Mutation, Gtp-Binding, Gtpase Activation, Leucine-Rich Repeat, Membrane, Nucleotide-Binding, Parkinson Disease, Serine/Threonine-Protein Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Deng, P. A. Lewis, E. Greggio, E. Sluch, A. Beilina, M. R. Cookson
Structure Of The Roc Domain From The Parkinson'S Disease-Associated Leucine-Rich Repeat Kinase 2 Reveals A Dimeric Gtpase
Proc. Natl. Acad. Sci. Usa V. 105 1499 2008
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2a: MAGNESIUM ION (MGa)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
MSE
5
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR B:1348
BINDING SITE FOR RESIDUE MG B 2
2
AC2
SOFTWARE
GLY B:1344 , SER B:1345 , GLY B:1346 , LYS B:1347 , THR B:1348 , THR B:1349 , TYR B:1402 , PRO B:1433 , PHE B:1436 , ASN B:1437 , HIS B:1453 , ASP B:1455 , ASN B:1489 , ALA B:1490
BINDING SITE FOR RESIDUE GDP B 1
[
close Site info
]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_024943 (I1371V, chain B, )
2: VAR_047022 (D1375E, chain B, )
3: VAR_024944 (R1398H, chain B, )
4: VAR_024945 (R1441C, chain B, )
5: VAR_024946 (R1441G, chain B, )
6: VAR_024947 (R1441H, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024943
I
1371
V
LRRK2_HUMAN
Unclassified
17466213
B
I
1371
V
2
UniProt
VAR_047022
D
1375
E
LRRK2_HUMAN
Polymorphism
28365226
B
D
1375
E
3
UniProt
VAR_024944
R
1398
H
LRRK2_HUMAN
Polymorphism
7133914
B
R
1398
H
4
UniProt
VAR_024945
R
1441
C
LRRK2_HUMAN
Unclassified
---
B
R
1441
C
5
UniProt
VAR_024946
R
1441
G
LRRK2_HUMAN
Disease (PARK8)
33939927
B
R
1441
G
6
UniProt
VAR_024947
R
1441
H
LRRK2_HUMAN
Disease (PARK8)
34995376
B
R
1441
H
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
(3, 3)
Info
All Exons
Exon 1.31 (B:1335-1397 (gaps))
Exon 1.32 (B:1397-1439)
Exon 1.33 (B:1440-1505 (gaps))
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.30/1.31
2: Boundary 1.31/1.32
3: Boundary 1.32/1.33
4: Boundary 1.33/1.35
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
1.2b
ENST00000298910
2b
ENSE00001860962
chr12:
40618876-40619084
209
LRRK2_HUMAN
1-51
51
0
-
-
1.3a
ENST00000298910
3a
ENSE00001778760
chr12:
40619357-40619442
86
LRRK2_HUMAN
51-79
29
0
-
-
1.4a
ENST00000298910
4a
ENSE00001649052
chr12:
40626076-40626185
110
LRRK2_HUMAN
80-116
37
0
-
-
1.5
ENST00000298910
5
ENSE00001649709
chr12:
40629428-40629516
89
LRRK2_HUMAN
116-146
31
0
-
-
1.6
ENST00000298910
6
ENSE00001736708
chr12:
40631771-40631905
135
LRRK2_HUMAN
146-191
46
0
-
-
1.7
ENST00000298910
7
ENSE00001727339
chr12:
40634285-40634419
135
LRRK2_HUMAN
191-236
46
0
-
-
1.8
ENST00000298910
8
ENSE00001781025
chr12:
40637352-40637483
132
LRRK2_HUMAN
236-280
45
0
-
-
1.9
ENST00000298910
9
ENSE00001619675
chr12:
40643628-40643747
120
LRRK2_HUMAN
280-320
41
0
-
-
1.10
ENST00000298910
10
ENSE00001635586
chr12:
40645034-40645176
143
LRRK2_HUMAN
320-367
48
0
-
-
1.11
ENST00000298910
11
ENSE00001597461
chr12:
40645267-40645346
80
LRRK2_HUMAN
368-394
27
0
-
-
1.12a
ENST00000298910
12a
ENSE00001599015
chr12:
40646712-40646818
107
LRRK2_HUMAN
394-430
37
0
-
-
1.13
ENST00000298910
13
ENSE00001374694
chr12:
40651050-40651179
130
LRRK2_HUMAN
430-473
44
0
-
-
1.14
ENST00000298910
14
ENSE00001367134
chr12:
40653282-40653406
125
LRRK2_HUMAN
473-515
43
0
-
-
1.15
ENST00000298910
15
ENSE00001378233
chr12:
40657591-40657703
113
LRRK2_HUMAN
515-552
38
0
-
-
1.16
ENST00000298910
16
ENSE00001365484
chr12:
40668385-40668529
145
LRRK2_HUMAN
553-601
49
0
-
-
1.17
ENST00000298910
17
ENSE00001387519
chr12:
40668656-40668795
140
LRRK2_HUMAN
601-647
47
0
-
-
1.18
ENST00000298910
18
ENSE00001378687
chr12:
40671690-40671818
129
LRRK2_HUMAN
648-690
43
0
-
-
1.19
ENST00000298910
19
ENSE00001382909
chr12:
40671893-40672063
171
LRRK2_HUMAN
691-747
57
0
-
-
1.20b
ENST00000298910
20b
ENSE00001365419
chr12:
40677677-40677935
259
LRRK2_HUMAN
748-834
87
0
-
-
1.21
ENST00000298910
21
ENSE00001373174
chr12:
40681153-40681341
189
LRRK2_HUMAN
834-897
64
0
-
-
1.22
ENST00000298910
22
ENSE00001379815
chr12:
40687347-40687465
119
LRRK2_HUMAN
897-936
40
0
-
-
1.23
ENST00000298910
23
ENSE00001364454
chr12:
40688647-40688716
70
LRRK2_HUMAN
937-960
24
0
-
-
1.24a
ENST00000298910
24a
ENSE00001364875
chr12:
40689229-40689446
218
LRRK2_HUMAN
960-1032
73
0
-
-
1.25a
ENST00000298910
25a
ENSE00001374565
chr12:
40692045-40692295
251
LRRK2_HUMAN
1033-1116
84
0
-
-
1.26
ENST00000298910
26
ENSE00001368109
chr12:
40692911-40693059
149
LRRK2_HUMAN
1116-1166
51
0
-
-
1.28
ENST00000298910
28
ENSE00001764036
chr12:
40696591-40696684
94
LRRK2_HUMAN
1166-1197
32
0
-
-
1.29a
ENST00000298910
29a
ENSE00001650823
chr12:
40697750-40697936
187
LRRK2_HUMAN
1197-1259
63
0
-
-
1.30
ENST00000298910
30
ENSE00001626235
chr12:
40699587-40699768
182
LRRK2_HUMAN
1260-1320
61
0
-
-
1.31
ENST00000298910
31
ENSE00001675690
chr12:
40702269-40702498
230
LRRK2_HUMAN
1320-1397
78
1
B:1335-1397 (gaps)
63
1.32
ENST00000298910
32
ENSE00001754873
chr12:
40702908-40703035
128
LRRK2_HUMAN
1397-1439
43
1
B:1397-1439
43
1.33
ENST00000298910
33
ENSE00001668077
chr12:
40704233-40704451
219
LRRK2_HUMAN
1440-1512
73
1
B:1440-1505 (gaps)
66
1.35
ENST00000298910
35
ENSE00001630233
chr12:
40707774-40707975
202
LRRK2_HUMAN
1513-1580
68
0
-
-
1.36
ENST00000298910
36
ENSE00001768941
chr12:
40709014-40709102
89
LRRK2_HUMAN
1580-1609
30
0
-
-
1.37b
ENST00000298910
37b
ENSE00001704266
chr12:
40713790-40713977
188
LRRK2_HUMAN
1610-1672
63
0
-
-
1.38
ENST00000298910
38
ENSE00001782098
chr12:
40714836-40714990
155
LRRK2_HUMAN
1672-1724
53
0
-
-
1.39
ENST00000298910
39
ENSE00001609307
chr12:
40715837-40715983
147
LRRK2_HUMAN
1724-1773
50
0
-
-
1.40
ENST00000298910
40
ENSE00001755887
chr12:
40716121-40716312
192
LRRK2_HUMAN
1773-1837
65
0
-
-
1.41
ENST00000298910
41
ENSE00001792653
chr12:
40716962-40717108
147
LRRK2_HUMAN
1837-1886
50
0
-
-
1.42
ENST00000298910
42
ENSE00001700717
chr12:
40722162-40722262
101
LRRK2_HUMAN
1886-1919
34
0
-
-
1.43
ENST00000298910
43
ENSE00001675872
chr12:
40728769-40728959
191
LRRK2_HUMAN
1920-1983
64
0
-
-
1.44
ENST00000298910
44
ENSE00001681968
chr12:
40734096-40734256
161
LRRK2_HUMAN
1983-2037
55
0
-
-
1.45
ENST00000298910
45
ENSE00001677812
chr12:
40740555-40740725
171
LRRK2_HUMAN
2037-2094
58
0
-
-
1.46
ENST00000298910
46
ENSE00001751192
chr12:
40742211-40742311
101
LRRK2_HUMAN
2094-2127
34
0
-
-
1.47
ENST00000298910
47
ENSE00001619361
chr12:
40745341-40745535
195
LRRK2_HUMAN
2128-2192
65
0
-
-
1.48
ENST00000298910
48
ENSE00001794200
chr12:
40748101-40748294
194
LRRK2_HUMAN
2193-2257
65
0
-
-
1.49
ENST00000298910
49
ENSE00001703217
chr12:
40749917-40749989
73
LRRK2_HUMAN
2257-2281
25
0
-
-
1.50
ENST00000298910
50
ENSE00001779960
chr12:
40753062-40753246
185
LRRK2_HUMAN
2282-2343
62
0
-
-
1.51
ENST00000298910
51
ENSE00001613626
chr12:
40757204-40757356
153
LRRK2_HUMAN
2343-2394
52
0
-
-
1.52a
ENST00000298910
52a
ENSE00001649805
chr12:
40758644-40758852
209
LRRK2_HUMAN
2394-2464
71
0
-
-
1.52d
ENST00000298910
52d
ENSE00001604158
chr12:
40760808-40760879
72
LRRK2_HUMAN
2464-2488
25
0
-
-
1.52e
ENST00000298910
52e
ENSE00001182762
chr12:
40761446-40763083
1638
LRRK2_HUMAN
2488-2527
40
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3d6tb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
automated matches
(303)
Protein domain
:
automated matches
(303)
Human (Homo sapiens) [TaxId: 9606]
(86)
1a
d3d6tb_
B:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3d6tB01 (B:1336-1411)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2
(2)
Human (Homo sapiens)
(2)
1a
3d6tB01
B:1336-1411
[
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 B
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 (29 KB)
Header - Asym.Unit
Biol.Unit 1 (22 KB)
Header - Biol.Unit 1
Biol.Unit 2 (43 KB)
Header - Biol.Unit 2
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
3D6T
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help