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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3UIP
Asym. Unit
Info
Asym.Unit (87 KB)
Biol.Unit 1 (81 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
COMPLEX BETWEEN HUMAN RANGAP1-SUMO1, UBC9 AND THE IR1 DOMAIN FROM RANBP2 CONTAINING IR2 MOTIF II
Authors
:
J. R. Gareau, D. Reverter, C. D. Lima
Date
:
05 Nov 11 (Deposition) - 28 Dec 11 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.29
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
E3, Ligase, Sumo, Ubc9, Ranbp2, Nuclear Pore Complex, Ligase- Isomerase-Protein Binding Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Gareau, D. Reverter, C. D. Lima
Determinants Of Small Ubiquitin-Like Modifier 1 (Sumo1) Protein Specificity, E3 Ligase, And Sumo-Rangap1 Binding Activities Of Nucleoporin Ranbp2.
J. Biol. Chem. V. 287 4740 2012
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEa)
1b: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEb)
2a: 3-SULFINOALANINE (CSDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CME
2
Mod. Amino Acid
S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2
CSD
1
Mod. Amino Acid
3-SULFINOALANINE
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_CONJUGAT_2 (A:7-146)
2: UBIQUITIN_2 (B:20-97)
3: UBIQUITIN_CONJUGAT_1 (A:82-97)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_CONJUGAT_2
PS50127
Ubiquitin-conjugating enzymes family profile.
UBC9_HUMAN
7-146
1
A:7-146
2
UBIQUITIN_2
PS50053
Ubiquitin domain profile.
SUMO1_HUMAN
20-97
1
B:20-97
3
UBIQUITIN_CONJUGAT_1
PS00183
Ubiquitin-conjugating enzymes active site.
UBC9_HUMAN
82-97
1
A:82-97
[
close PROSITE info
]
Exons
(17, 17)
Info
All Exons
Exon 1.22 (D:2630-2674)
Exon 1.23 (D:2674-2690)
Exon 2.16b (C:432-460)
Exon 2.17b (C:461-495)
Exon 2.18 (C:495-524)
Exon 2.19 (C:525-565)
Exon 2.20c (C:565-587)
Exon 3.5 (B:20-29)
Exon 3.6b (B:30-55)
Exon 3.7b (B:56-79)
Exon 3.9j (B:80-97)
Exon 4.4b (A:2-22)
Exon 4.5 (A:23-50)
Exon 4.6a (A:51-75)
Exon 4.7 (A:75-111)
Exon 4.8a (A:112-138)
Exon 4.9c (A:138-158)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.21a/1.22
02: Boundary 1.22/1.23
03: Boundary 1.23/1.24
04: Boundary 2.15/2.16b
05: Boundary 2.16b/2.17b
06: Boundary 2.17b/2.18
07: Boundary 2.18/2.19
08: Boundary 2.19/2.20c
09: Boundary 2.20c/-
10: Boundary 3.1a/3.5
11: Boundary 3.5/3.6b
12: Boundary 3.6b/3.7b
13: Boundary 3.7b/3.9j
14: Boundary 3.9j/-
15: Boundary 4.3c/4.4b
16: Boundary 4.4b/4.5
17: Boundary 4.5/4.6a
18: Boundary 4.6a/4.7
19: Boundary 4.7/4.8a
20: Boundary 4.8a/4.9c
21: Boundary 4.9c/-
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
1.1b
ENST00000283195
1b
ENSE00001427934
chr2:
109335937-109336134
198
RBP2_HUMAN
1-24
24
0
-
-
1.3a
ENST00000283195
3a
ENSE00001628671
chr2:
109345588-109345655
68
RBP2_HUMAN
25-47
23
0
-
-
1.5b
ENST00000283195
5b
ENSE00001658463
chr2:
109347230-109347341
112
RBP2_HUMAN
47-84
38
0
-
-
1.6a
ENST00000283195
6a
ENSE00001642732
chr2:
109347778-109347930
153
RBP2_HUMAN
85-135
51
0
-
-
1.7b
ENST00000283195
7b
ENSE00001779112
chr2:
109351988-109352218
231
RBP2_HUMAN
136-212
77
0
-
-
1.8
ENST00000283195
8
ENSE00001730926
chr2:
109352560-109352705
146
RBP2_HUMAN
213-261
49
0
-
-
1.9
ENST00000283195
9
ENSE00001785652
chr2:
109356945-109357137
193
RBP2_HUMAN
261-325
65
0
-
-
1.10
ENST00000283195
10
ENSE00001713500
chr2:
109363167-109363254
88
RBP2_HUMAN
326-355
30
0
-
-
1.11a
ENST00000283195
11a
ENSE00001718980
chr2:
109365376-109365585
210
RBP2_HUMAN
355-425
71
0
-
-
1.12
ENST00000283195
12
ENSE00001776974
chr2:
109367720-109367901
182
RBP2_HUMAN
425-485
61
0
-
-
1.13a
ENST00000283195
13a
ENSE00001779700
chr2:
109367984-109368159
176
RBP2_HUMAN
486-544
59
0
-
-
1.13e
ENST00000283195
13e
ENSE00001761857
chr2:
109368327-109368450
124
RBP2_HUMAN
544-585
42
0
-
-
1.14b
ENST00000283195
14b
ENSE00001718984
chr2:
109369454-109369615
162
RBP2_HUMAN
586-639
54
0
-
-
1.15
ENST00000283195
15
ENSE00001757154
chr2:
109369882-109370019
138
RBP2_HUMAN
640-685
46
0
-
-
1.16
ENST00000283195
16
ENSE00001624597
chr2:
109370281-109370427
147
RBP2_HUMAN
686-734
49
0
-
-
1.17
ENST00000283195
17
ENSE00001686256
chr2:
109371361-109371540
180
RBP2_HUMAN
735-794
60
0
-
-
1.18
ENST00000283195
18
ENSE00001591933
chr2:
109371632-109371715
84
RBP2_HUMAN
795-822
28
0
-
-
1.19
ENST00000283195
19
ENSE00001791450
chr2:
109374869-109375004
136
RBP2_HUMAN
823-868
46
0
-
-
1.20
ENST00000283195
20
ENSE00001684879
chr2:
109378557-109378651
95
RBP2_HUMAN
868-899
32
0
-
-
1.21a
ENST00000283195
21a
ENSE00001147357
chr2:
109379693-109384844
5152
RBP2_HUMAN
900-2617
1718
0
-
-
1.22
ENST00000283195
22
ENSE00001009418
chr2:
109388157-109388327
171
RBP2_HUMAN
2617-2674
58
1
D:2630-2674
45
1.23
ENST00000283195
23
ENSE00001009429
chr2:
109388945-109389037
93
RBP2_HUMAN
2674-2705
32
1
D:2674-2690
17
1.24
ENST00000283195
24
ENSE00001291545
chr2:
109389324-109389502
179
RBP2_HUMAN
2705-2764
60
0
-
-
1.25
ENST00000283195
25
ENSE00001009419
chr2:
109392188-109392392
205
RBP2_HUMAN
2765-2833
69
0
-
-
1.26
ENST00000283195
26
ENSE00001009428
chr2:
109393586-109393687
102
RBP2_HUMAN
2833-2867
35
0
-
-
1.27
ENST00000283195
27
ENSE00001377207
chr2:
109397725-109397885
161
RBP2_HUMAN
2867-2920
54
0
-
-
1.28
ENST00000283195
28
ENSE00001383394
chr2:
109398584-109398857
274
RBP2_HUMAN
2921-3012
92
0
-
-
1.29
ENST00000283195
29
ENSE00001147257
chr2:
109398984-109399318
335
RBP2_HUMAN
3012-3123
112
0
-
-
1.30b
ENST00000283195
30b
ENSE00001316371
chr2:
109400052-109402267
2216
RBP2_HUMAN
3124-3224
101
0
-
-
2.3
ENST00000356244
3
ENSE00001525423
chr22:
41682255-41681990
266
RAGP1_HUMAN
-
0
0
-
-
2.6e
ENST00000356244
6e
ENSE00002184389
chr22:
41677086-41676937
150
RAGP1_HUMAN
1-38
38
0
-
-
2.7a
ENST00000356244
7a
ENSE00000655593
chr22:
41670731-41670604
128
RAGP1_HUMAN
38-80
43
0
-
-
2.8
ENST00000356244
8
ENSE00002178724
chr22:
41664160-41664101
60
RAGP1_HUMAN
81-100
20
0
-
-
2.9b
ENST00000356244
9b
ENSE00000655579
chr22:
41660847-41660668
180
RAGP1_HUMAN
101-160
60
0
-
-
2.10
ENST00000356244
10
ENSE00000655571
chr22:
41657584-41657450
135
RAGP1_HUMAN
161-205
45
0
-
-
2.11
ENST00000356244
11
ENSE00000655562
chr22:
41654110-41653952
159
RAGP1_HUMAN
206-258
53
0
-
-
2.12
ENST00000356244
12
ENSE00000655554
chr22:
41652828-41652715
114
RAGP1_HUMAN
259-296
38
0
-
-
2.13
ENST00000356244
13
ENSE00001388340
chr22:
41652294-41652195
100
RAGP1_HUMAN
297-330
34
0
-
-
2.14
ENST00000356244
14
ENSE00002167356
chr22:
41652109-41652025
85
RAGP1_HUMAN
330-358
29
0
-
-
2.15
ENST00000356244
15
ENSE00001615125
chr22:
41650498-41650312
187
RAGP1_HUMAN
358-420
63
0
-
-
2.16b
ENST00000356244
16b
ENSE00001786527
chr22:
41648995-41648876
120
RAGP1_HUMAN
421-460
40
1
C:432-460
29
2.17b
ENST00000356244
17b
ENSE00001635042
chr22:
41647113-41647011
103
RAGP1_HUMAN
461-495
35
1
C:461-495
35
2.18
ENST00000356244
18
ENSE00001708342
chr22:
41645821-41645733
89
RAGP1_HUMAN
495-524
30
1
C:495-524
30
2.19
ENST00000356244
19
ENSE00001792763
chr22:
41645455-41645334
122
RAGP1_HUMAN
525-565
41
1
C:525-565
41
2.20c
ENST00000356244
20c
ENSE00001563055
chr22:
41642676-41641615
1062
RAGP1_HUMAN
565-587
23
1
C:565-587
23
3.1a
ENST00000392246
1a
ENSE00001771214
chr2:
203103331-203103163
169
SUMO1_HUMAN
1-4
4
0
-
-
3.5
ENST00000392246
5
ENSE00001634753
chr2:
203084829-203084755
75
SUMO1_HUMAN
5-29
25
1
B:20-29
10
3.6b
ENST00000392246
6b
ENSE00001733147
chr2:
203079157-203079080
78
SUMO1_HUMAN
30-55
26
1
B:30-55
26
3.7b
ENST00000392246
7b
ENSE00001777388
chr2:
203075529-203075458
72
SUMO1_HUMAN
56-79
24
1
B:56-79
24
3.9j
ENST00000392246
9j
ENSE00001390654
chr2:
203072044-203070903
1142
SUMO1_HUMAN
80-101
22
1
B:80-97
18
4.2b
ENST00000397515
2b
ENSE00001529011
chr16:
1359636-1359774
139
UBC9_HUMAN
-
0
0
-
-
4.3c
ENST00000397515
3c
ENSE00001529008
chr16:
1362348-1362604
257
UBC9_HUMAN
-
0
0
-
-
4.4b
ENST00000397515
4b
ENSE00002200477
chr16:
1364021-1364097
77
UBC9_HUMAN
1-22
22
1
A:2-22
21
4.5
ENST00000397515
5
ENSE00000665751
chr16:
1364294-1364377
84
UBC9_HUMAN
23-50
28
1
A:23-50
28
4.6a
ENST00000397515
6a
ENSE00000873575
chr16:
1365655-1365727
73
UBC9_HUMAN
51-75
25
1
A:51-75
25
4.7
ENST00000397515
7
ENSE00000873577
chr16:
1370175-1370284
110
UBC9_HUMAN
75-111
37
1
A:75-111
37
4.8a
ENST00000397515
8a
ENSE00001287298
chr16:
1370439-1370518
80
UBC9_HUMAN
112-138
27
1
A:112-138
27
4.9c
ENST00000397515
9c
ENSE00001287274
chr16:
1374731-1377019
2289
UBC9_HUMAN
138-158
21
1
A:138-158
21
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3uipc_ (C:)
2a: SCOP_d3uipb_ (B:)
3a: SCOP_d3uipa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain
(13)
Family
:
Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain
(13)
Protein domain
:
automated matches
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d3uipc_
C:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Ubiquitin-like
(546)
Family
:
Ubiquitin-related
(337)
Protein domain
:
SUMO-1 (smt3 homologue)
(12)
Human (Homo sapiens) [TaxId: 9606]
(8)
2a
d3uipb_
B:
Fold
:
UBC-like
(176)
Superfamily
:
UBC-like
(176)
Family
:
UBC-related
(135)
Protein domain
:
Ubiquitin conjugating enzyme, UBC
(84)
Human (Homo sapiens), ubc9 [TaxId: 9606]
(20)
3a
d3uipa_
A:
[
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
Chain B
Chain C
Chain D
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 (87 KB)
Header - Asym.Unit
Biol.Unit 1 (81 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
3UIP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help