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.
2NZ8
Asym. Unit
Info
Asym.Unit (171 KB)
Biol.Unit 1 (166 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
N-TERMINAL DHPH CASSETTE OF TRIO IN COMPLEX WITH NUCLEOTIDE-FREE RAC1
Authors
:
M. K. Chhatriwala, L. Betts, D. K. Worthylake, J. Sondek
Date
:
22 Nov 06 (Deposition) - 10 Apr 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Trio; Rac1; Dbl-Family Gef; Rho-Family Gtpase; Dh/Ph Cassette, Signaling Protein, Cell Cycle
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. K. Chhatriwala, L. Betts, D. K. Worthylake, J. Sondek
The Dh And Ph Domains Of Trio Coordinately Engage Rho Gtpases For Their Efficient Activation
J. Mol. Biol. V. 368 1307 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(11, 11)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_014540 (N26D, chain A, )
02: VAR_014541 (F28L, chain A, )
03: VAR_014542 (A59T, chain A, )
04: VAR_014543 (D63G, chain A, )
05: VAR_014545 (V93G, chain A, )
06: VAR_014544 (V93I, chain A, )
07: VAR_014546 (T108I, chain A, )
08: VAR_014547 (K130R, chain A, )
09: VAR_014548 (K133E, chain A, )
10: VAR_033303 (T135I, chain A, )
11: VAR_069371 (D1309V, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_014540
N
26
D
RAC1_HUMAN
Polymorphism
5830
A
N
26
D
02
UniProt
VAR_014541
F
28
L
RAC1_HUMAN
Polymorphism
5832
A
F
28
L
03
UniProt
VAR_014542
A
59
T
RAC1_HUMAN
Polymorphism
5837
A
A
59
T
04
UniProt
VAR_014543
D
63
G
RAC1_HUMAN
Polymorphism
5831
A
D
63
G
05
UniProt
VAR_014545
V
93
G
RAC1_HUMAN
Polymorphism
5826
A
V
93
G
06
UniProt
VAR_014544
V
93
I
RAC1_HUMAN
Polymorphism
5825
A
V
93
I
07
UniProt
VAR_014546
T
108
I
RAC1_HUMAN
Polymorphism
5838
A
T
108
I
08
UniProt
VAR_014547
K
130
R
RAC1_HUMAN
Polymorphism
5828
A
K
130
R
09
UniProt
VAR_014548
K
133
E
RAC1_HUMAN
Polymorphism
5835
A
K
133
E
10
UniProt
VAR_033303
T
135
I
RAC1_HUMAN
Polymorphism
11540455
A
T
135
I
11
UniProt
VAR_069371
D
1368
V
TRIO_HUMAN
Polymorphism
---
B
D
1309
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: RHO (A:1-176)
2: DH_2 (B:1233-1408|-)
3: PH_DOMAIN (B:1423-1532|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RHO
PS51420
small GTPase Rho family profile.
RAC1_HUMAN
1-176
1
A:1-176
2
DH_2
PS50010
Dbl homology (DH) domain profile.
TRIO_HUMAN
1292-1467
1969-2145
1
B:1233-1408
-
3
PH_DOMAIN
PS50003
PH domain profile.
TRIO_HUMAN
1479-1591
2157-2271
1
B:1423-1532
-
[
close PROSITE info
]
Exons
(16, 16)
Info
All Exons
Exon 1.24a (B:1231-1235)
Exon 1.25 (B:1235-1257)
Exon 1.26 (B:1258-1294)
Exon 1.27 (B:1294-1317)
Exon 1.29 (B:1318-1347)
Exon 1.30 (B:1348-1378)
Exon 1.31a (B:1379-1416)
Exon 1.32a (B:1416-1479 (gaps))
Exon 1.33 (B:1480-1513 (gaps))
Exon 1.34 (B:1514-1535)
Exon 2.1a (A:1-12)
Exon 2.3 (A:12-36)
Exon 2.5 (A:36-75)
Exon 2.7b (A:76-96)
Exon 2.8b (A:97-150)
Exon 2.9f (A:150-177)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.23b/1.24a
02: Boundary 1.24a/1.25
03: Boundary 1.25/1.26
04: Boundary 1.26/1.27
05: Boundary 1.27/1.29
06: Boundary 1.29/1.30
07: Boundary 1.30/1.31a
08: Boundary 1.31a/1.32a
09: Boundary 1.32a/1.33
10: Boundary 1.33/1.34
11: Boundary 1.34/1.35b
12: Boundary -/2.1a
13: Boundary 2.1a/2.3
14: Boundary 2.3/2.5
15: Boundary 2.5/2.7b
16: Boundary 2.7b/2.8b
17: Boundary 2.8b/2.9f
18: Boundary 2.9f/-
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
1.1
ENST00000344204
1
ENSE00002146523
chr5:
14143811-14143991
181
TRIO_HUMAN
1-53
53
0
-
-
1.3b
ENST00000344204
3b
ENSE00001365846
chr5:
14270934-14271008
75
TRIO_HUMAN
53-78
26
0
-
-
1.4
ENST00000344204
4
ENSE00001737349
chr5:
14280431-14280545
115
TRIO_HUMAN
78-116
39
0
-
-
1.5a
ENST00000344204
5a
ENSE00001133893
chr5:
14286980-14287172
193
TRIO_HUMAN
116-180
65
0
-
-
1.6b
ENST00000344204
6b
ENSE00001133883
chr5:
14290825-14291337
513
TRIO_HUMAN
181-351
171
0
-
-
1.7a
ENST00000344204
7a
ENSE00001133874
chr5:
14293121-14293243
123
TRIO_HUMAN
352-392
41
0
-
-
1.8a
ENST00000344204
8a
ENSE00001292823
chr5:
14297181-14297372
192
TRIO_HUMAN
393-456
64
0
-
-
1.9
ENST00000344204
9
ENSE00001264084
chr5:
14304570-14304701
132
TRIO_HUMAN
457-500
44
0
-
-
1.10
ENST00000344204
10
ENSE00001082639
chr5:
14316622-14316852
231
TRIO_HUMAN
501-577
77
0
-
-
1.11
ENST00000344204
11
ENSE00000971019
chr5:
14330887-14331009
123
TRIO_HUMAN
578-618
41
0
-
-
1.12
ENST00000344204
12
ENSE00001697533
chr5:
14336645-14336836
192
TRIO_HUMAN
619-682
64
0
-
-
1.13
ENST00000344204
13
ENSE00001133823
chr5:
14358287-14358456
170
TRIO_HUMAN
683-739
57
0
-
-
1.14
ENST00000344204
14
ENSE00000846188
chr5:
14359466-14359640
175
TRIO_HUMAN
739-797
59
0
-
-
1.15
ENST00000344204
15
ENSE00000846186
chr5:
14363841-14364036
196
TRIO_HUMAN
798-863
66
0
-
-
1.16
ENST00000344204
16
ENSE00000728495
chr5:
14364759-14364925
167
TRIO_HUMAN
863-918
56
0
-
-
1.17
ENST00000344204
17
ENSE00000728487
chr5:
14366969-14367088
120
TRIO_HUMAN
919-958
40
0
-
-
1.18
ENST00000344204
18
ENSE00000846181
chr5:
14368817-14369008
192
TRIO_HUMAN
959-1022
64
0
-
-
1.19
ENST00000344204
19
ENSE00000728472
chr5:
14369483-14369632
150
TRIO_HUMAN
1023-1072
50
0
-
-
1.20
ENST00000344204
20
ENSE00000846177
chr5:
14374338-14374452
115
TRIO_HUMAN
1073-1111
39
0
-
-
1.21
ENST00000344204
21
ENSE00000728457
chr5:
14378121-14378236
116
TRIO_HUMAN
1111-1149
39
0
-
-
1.22
ENST00000344204
22
ENSE00000846173
chr5:
14381239-14381361
123
TRIO_HUMAN
1150-1190
41
0
-
-
1.23b
ENST00000344204
23b
ENSE00000728443
chr5:
14387547-14387741
195
TRIO_HUMAN
1191-1255
65
0
-
-
1.24a
ENST00000344204
24a
ENSE00001325217
chr5:
14387841-14387956
116
TRIO_HUMAN
1256-1294
39
1
B:1231-1235
5
1.25
ENST00000344204
25
ENSE00000846165
chr5:
14388722-14388788
67
TRIO_HUMAN
1294-1316
23
1
B:1235-1257
23
1.26
ENST00000344204
26
ENSE00001670384
chr5:
14389398-14389507
110
TRIO_HUMAN
1317-1353
37
1
B:1258-1294
37
1.27
ENST00000344204
27
ENSE00000846161
chr5:
14390340-14390409
70
TRIO_HUMAN
1353-1376
24
1
B:1294-1317
24
1.29
ENST00000344204
29
ENSE00000846158
chr5:
14391010-14391099
90
TRIO_HUMAN
1377-1406
30
1
B:1318-1347
30
1.30
ENST00000344204
30
ENSE00000846157
chr5:
14394147-14394239
93
TRIO_HUMAN
1407-1437
31
1
B:1348-1378
31
1.31a
ENST00000344204
31a
ENSE00001698500
chr5:
14397152-14397263
112
TRIO_HUMAN
1438-1475
38
1
B:1379-1416
38
1.32a
ENST00000344204
32a
ENSE00000846153
chr5:
14398989-14399179
191
TRIO_HUMAN
1475-1538
64
1
B:1416-1479 (gaps)
64
1.33
ENST00000344204
33
ENSE00000419579
chr5:
14401072-14401173
102
TRIO_HUMAN
1539-1572
34
1
B:1480-1513 (gaps)
34
1.34
ENST00000344204
34
ENSE00001082642
chr5:
14405957-14406099
143
TRIO_HUMAN
1573-1620
48
1
B:1514-1535
22
1.35b
ENST00000344204
35b
ENSE00001082641
chr5:
14406682-14406781
100
TRIO_HUMAN
1620-1653
34
0
-
-
1.37b
ENST00000344204
37b
ENSE00001325352
chr5:
14419887-14420130
244
TRIO_HUMAN
1654-1735
82
0
-
-
1.40
ENST00000344204
40
ENSE00001169289
chr5:
14461128-14461420
293
TRIO_HUMAN
1735-1832
98
0
-
-
1.41
ENST00000344204
41
ENSE00001123722
chr5:
14462864-14463034
171
TRIO_HUMAN
1833-1889
57
0
-
-
1.42a
ENST00000344204
42a
ENSE00001123717
chr5:
14465654-14465749
96
TRIO_HUMAN
1890-1921
32
0
-
-
1.43
ENST00000344204
43
ENSE00001188306
chr5:
14471427-14471575
149
TRIO_HUMAN
1922-1971
50
0
-
-
1.44
ENST00000344204
44
ENSE00001169316
chr5:
14472701-14472767
67
TRIO_HUMAN
1971-1993
23
0
-
-
1.45a
ENST00000344204
45a
ENSE00001014185
chr5:
14474103-14474206
104
TRIO_HUMAN
1994-2028
35
0
-
-
1.46a
ENST00000344204
46a
ENSE00001014225
chr5:
14477003-14477072
70
TRIO_HUMAN
2028-2051
24
0
-
-
1.47a
ENST00000344204
47a
ENSE00001014221
chr5:
14479370-14479459
90
TRIO_HUMAN
2052-2081
30
0
-
-
1.48
ENST00000344204
48
ENSE00001014201
chr5:
14480028-14480120
93
TRIO_HUMAN
2082-2112
31
0
-
-
1.49
ENST00000344204
49
ENSE00001014199
chr5:
14481343-14481393
51
TRIO_HUMAN
2113-2129
17
0
-
-
1.50a
ENST00000344204
50a
ENSE00001014186
chr5:
14481650-14481727
78
TRIO_HUMAN
2130-2155
26
0
-
-
1.51b
ENST00000344204
51b
ENSE00001014193
chr5:
14482691-14482882
192
TRIO_HUMAN
2156-2219
64
0
-
-
1.52
ENST00000344204
52
ENSE00001014202
chr5:
14485178-14485355
178
TRIO_HUMAN
2220-2279
60
0
-
-
1.53c
ENST00000344204
53c
ENSE00001188272
chr5:
14487573-14488369
797
TRIO_HUMAN
2279-2544
266
0
-
-
1.54b
ENST00000344204
54b
ENSE00001123707
chr5:
14492676-14492923
248
TRIO_HUMAN
2545-2627
83
0
-
-
1.55b
ENST00000344204
55b
ENSE00001264248
chr5:
14496988-14497126
139
TRIO_HUMAN
2627-2673
47
0
-
-
1.56
ENST00000344204
56
ENSE00001123693
chr5:
14497956-14497983
28
TRIO_HUMAN
2674-2683
10
0
-
-
1.57a
ENST00000344204
57a
ENSE00001014212
chr5:
14498198-14498360
163
TRIO_HUMAN
2683-2737
55
0
-
-
1.58b
ENST00000344204
58b
ENSE00001263926
chr5:
14498628-14498749
122
TRIO_HUMAN
2737-2778
42
0
-
-
1.59
ENST00000344204
59
ENSE00001123660
chr5:
14502688-14502766
79
TRIO_HUMAN
2778-2804
27
0
-
-
1.60a
ENST00000344204
60a
ENSE00001123652
chr5:
14504502-14504702
201
TRIO_HUMAN
2804-2871
68
0
-
-
1.61
ENST00000344204
61
ENSE00001014227
chr5:
14507231-14507369
139
TRIO_HUMAN
2871-2917
47
0
-
-
1.62d
ENST00000344204
62d
ENSE00001856401
chr5:
14507989-14510313
2325
TRIO_HUMAN
2918-3097
180
0
-
-
2.1a
ENST00000348035
1a
ENSE00001876788
chr7:
6414154-6414401
248
RAC1_HUMAN
1-12
12
1
A:1-12
12
2.3
ENST00000348035
3
ENSE00001676753
chr7:
6426843-6426914
72
RAC1_HUMAN
12-36
25
1
A:12-36
25
2.5
ENST00000348035
5
ENSE00001643043
chr7:
6431555-6431672
118
RAC1_HUMAN
36-75
40
1
A:36-75
40
2.7b
ENST00000348035
7b
ENSE00000831659
chr7:
6439757-6439819
63
RAC1_HUMAN
76-96
21
1
A:76-96
21
2.8b
ENST00000348035
8b
ENSE00001637705
chr7:
6441499-6441658
160
RAC1_HUMAN
97-150
54
1
A:97-150
54
2.9f
ENST00000348035
9f
ENSE00001551063
chr7:
6441947-6443608
1662
RAC1_HUMAN
150-192
43
1
A:150-177
28
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2nz8b1 (B:1231-1414)
2a: SCOP_d2nz8b2 (B:1415-1535)
3a: SCOP_d2nz8a_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DBL homology domain (DH-domain)
(22)
Superfamily
:
DBL homology domain (DH-domain)
(22)
Family
:
DBL homology domain (DH-domain)
(19)
Protein domain
:
Triple functional domain protein TRIO
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2nz8b1
B:1231-1414
Class
:
All beta proteins
(24004)
Fold
:
PH domain-like barrel
(258)
Superfamily
:
PH domain-like
(257)
Family
:
Pleckstrin-homology domain (PH domain)
(102)
Protein domain
:
Triple functional domain protein TRIO
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d2nz8b2
B:1415-1535
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
:
G proteins
(693)
Protein domain
:
Rac
(17)
Human (Homo sapiens) [TaxId: 9606]
(17)
3a
d2nz8a_
A:
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2nz8A00 (A:1-177)
2a: CATH_2nz8B01 (B:1231-1411)
3a: CATH_2nz8B02 (B:1412-1535)
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
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Human (Homo sapiens)
(413)
1a
2nz8A00
A:1-177
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Dbl Homology Domain; Chain A
(13)
Homologous Superfamily
:
Dbl Homology Domain; Chain A
(13)
Human (Homo sapiens)
(6)
2a
2nz8B01
B:1231-1411
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
PH-domain like
(150)
Homologous Superfamily
:
Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
(147)
Human (Homo sapiens)
(85)
3a
2nz8B02
B:1412-1535
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Ras_2nz8A01 (A:5-177)
2a: PFAM_RhoGEF_2nz8B01 (B:1237-1407)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Ras
(176)
Homo sapiens (Human)
(141)
1a
Ras-2nz8A01
A:5-177
Clan
:
no clan defined [family: RhoGEF]
(22)
Family
:
RhoGEF
(22)
Homo sapiens (Human)
(16)
2a
RhoGEF-2nz8B01
B:1237-1407
[
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
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 (171 KB)
Header - Asym.Unit
Biol.Unit 1 (166 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
2NZ8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help