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.
3UGX
Asym. Unit
Info
Asym.Unit (477 KB)
Biol.Unit 1 (125 KB)
Biol.Unit 2 (118 KB)
Biol.Unit 3 (122 KB)
Biol.Unit 4 (116 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 VISUAL ARRESTIN
Authors
:
R. Batra-Safferling, J. Granzin
Date
:
03 Nov 11 (Deposition) - 08 Feb 12 (Release) - 21 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Arrestin Fold, Signal Termination, Gpcr, Outer Segment, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Granzin, A. Cousin, M. Weirauch, R. Schlesinger, G. Buldt, R. Batra-Safferling
Crystal Structure Of P44, A Constitutively Active Splice Variant Of Visual Arrestin.
J. Mol. Biol. V. 416 611 2012
[
close entry info
]
Hetero Components
(5, 27)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
2a: IMIDAZOLE (IMDa)
2b: IMIDAZOLE (IMDb)
2c: IMIDAZOLE (IMDc)
3a: POTASSIUM ION (Ka)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: PENTANEDIAL (PTDa)
5b: PENTANEDIAL (PTDb)
5c: PENTANEDIAL (PTDc)
5d: PENTANEDIAL (PTDd)
5e: PENTANEDIAL (PTDe)
5f: PENTANEDIAL (PTDf)
5g: PENTANEDIAL (PTDg)
5h: PENTANEDIAL (PTDh)
5i: PENTANEDIAL (PTDi)
5j: PENTANEDIAL (PTDj)
5k: PENTANEDIAL (PTDk)
5l: PENTANEDIAL (PTDl)
5m: PENTANEDIAL (PTDm)
5n: PENTANEDIAL (PTDn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
2
IMD
3
Ligand/Ion
IMIDAZOLE
3
K
1
Ligand/Ion
POTASSIUM ION
4
NA
2
Ligand/Ion
SODIUM ION
5
PTD
14
Ligand/Ion
PENTANEDIAL
[
close Hetero Component info
]
Sites
(27, 27)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:19 , LYS A:55 , HIS A:155 , MET A:198
BINDING SITE FOR RESIDUE PTD A 405
02
AC2
SOFTWARE
TYR A:58 , GLN A:87 , GLN C:87 , PHE C:152
BINDING SITE FOR RESIDUE PTD A 406
03
AC3
SOFTWARE
VAL A:248 , TYR A:250 , SER A:252 , PTD A:412
BINDING SITE FOR RESIDUE PTD A 407
04
AC4
SOFTWARE
THR A:258 , ALA A:261 , ASN A:286 , ASN A:287 , HOH A:430
BINDING SITE FOR RESIDUE PTD A 408
05
AC5
SOFTWARE
LYS A:14 , TYR A:25 , PHE A:377
BINDING SITE FOR RESIDUE PTD A 409
06
AC6
SOFTWARE
PRO A:127 , CYS A:128 , VAL A:130 , GLN A:178 , SER A:308 , SER A:309 , THR A:310 , ILE A:311 , ILE A:323 , HOH A:436
BINDING SITE FOR RESIDUE PTD A 410
07
AC7
SOFTWARE
TYR A:125 , VAL C:94 , GLY C:95 , ALA C:96
BINDING SITE FOR RESIDUE PTD A 411
08
AC8
SOFTWARE
LYS A:318 , LEU A:324 , PTD A:407
BINDING SITE FOR RESIDUE PTD A 412
09
AC9
SOFTWARE
SER A:199 , GLU A:231
BINDING SITE FOR RESIDUE NA A 413
10
BC1
SOFTWARE
TYR A:84 , PHE A:85 , VAL C:88 , GLN C:89 , VAL C:94
BINDING SITE FOR RESIDUE EDO A 414
11
BC2
SOFTWARE
LYS A:267 , PHE B:197 , ASP B:200
BINDING SITE FOR RESIDUE EDO A 415
12
BC3
SOFTWARE
ARG B:66 , GLU B:70 , MET B:131 , CYS B:143 , ASP B:146 , HOH B:435
BINDING SITE FOR RESIDUE IMD B 405
13
BC4
SOFTWARE
TYR B:67 , TYR B:250 , SER B:251
BINDING SITE FOR RESIDUE PTD B 406
14
BC5
SOFTWARE
LYS B:318 , LEU B:324
BINDING SITE FOR RESIDUE PTD B 407
15
BC6
SOFTWARE
VAL A:159 , GLN B:195 , HOH B:411 , HOH B:426 , HOH B:431
BINDING SITE FOR RESIDUE NA B 408
16
BC7
SOFTWARE
ASN A:271 , SER A:272 , SER A:273 , GLU B:350
BINDING SITE FOR RESIDUE EDO B 409
17
BC8
SOFTWARE
TYR C:250 , SER C:251 , SER C:252
BINDING SITE FOR RESIDUE PTD C 405
18
BC9
SOFTWARE
ASP B:73 , VAL B:74 , GLY B:76 , GLN C:187 , PRO C:188 , ARG C:189 , GLU C:350 , PRO C:352 , HOH C:455
BINDING SITE FOR RESIDUE PTD C 406
19
CC1
SOFTWARE
GLU C:212 , THR C:310 , VAL C:325 , SER C:326 , PRO C:352 , PHE C:353 , ARG C:354 , HOH C:412
BINDING SITE FOR RESIDUE PTD C 407
20
CC2
SOFTWARE
GLU D:350
BINDING SITE FOR RESIDUE K C 408
21
CC3
SOFTWARE
GLU A:160 , ASP A:162 , LYS C:150 , ILE C:164 , LYS C:166
BINDING SITE FOR RESIDUE EDO C 409
22
CC4
SOFTWARE
VAL A:88 , GLN A:89 , VAL A:94 , TYR C:84 , PHE C:85
BINDING SITE FOR RESIDUE EDO C 410
23
CC5
SOFTWARE
LEU C:274 , THR C:275 , GLU D:346 , ALA D:348
BINDING SITE FOR RESIDUE EDO C 411
24
CC6
SOFTWARE
ARG D:66 , CYS D:143 , ASP D:146 , HOH D:430
BINDING SITE FOR RESIDUE IMD D 405
25
CC7
SOFTWARE
PRO D:127 , CYS D:128 , VAL D:130 , THR D:310 , ILE D:323 , HOH D:432 , HOH D:443
BINDING SITE FOR RESIDUE IMD D 406
26
CC8
SOFTWARE
LYS D:318 , LEU D:324
BINDING SITE FOR RESIDUE PTD D 407
27
CC9
SOFTWARE
GLN D:187 , LYS D:211 , ILE D:213 , TYR D:215 , GLU D:218
BINDING SITE FOR RESIDUE EDO D 408
[
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ARRESTINS (A:65-83,B:65-83,C:65-83,D:65-83)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ARRESTINS
PS00295
Arrestins signature.
ARRS_BOVIN
65-83
4
A:65-83
B:65-83
C:65-83
D:65-83
[
close PROSITE info
]
Exons
(15, 58)
Info
All Exons
Exon 1.2 (A:9-25 | B:11-25 | C:9-25 | D:9-25)
Exon 1.3 (A:26-46 | B:26-46 | C:26-46 | D:26...)
Exon 1.4 (A:46-61 | B:46-61 | C:46-61 | D:46...)
Exon 1.5 (A:61-125 | B:61-125 (gaps) | C:61-...)
Exon 1.6 (A:126-145 | B:126-145 | C:126-145 ...)
Exon 1.7 (A:146-171 | B:146-171 (gaps) | C:1...)
Exon 1.8 (A:171-216 | B:171-216 | C:171-216 ...)
Exon 1.9 (A:217-245 | B:217-245 | C:217-245 ...)
Exon 1.10 (A:245-269 | B:245-269 | C:245-269 ...)
Exon 1.11 (A:269-315 | B:269-315 | C:269-315 ...)
Exon 1.12 (A:315-341 | B:315-338 | C:315-339 ...)
Exon 1.13 (A:341-349 | B:343-349 | C:344-349 ...)
Exon 1.14 (A:349-362 | B:349-362 | C:349-362 ...)
Exon 1.15 (A:372-373 | - | C:372-373 | -)
Exon 1.17 (A:373-386 | B:376-385 | C:373-386 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.17
16: Boundary 1.17/-
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
ENSBTAT00000028633
1
ENSBTAE00000264532
chr3:
120323559-120323664
106
ARRS_BOVIN
-
0
0
-
-
1.2
ENSBTAT00000028633
2
ENSBTAE00000264531
chr3:
120324357-120324487
131
ARRS_BOVIN
1-25
25
4
A:9-25
B:11-25
C:9-25
D:9-25
17
15
17
17
1.3
ENSBTAT00000028633
3
ENSBTAE00000233945
chr3:
120328854-120328914
61
ARRS_BOVIN
26-46
21
4
A:26-46
B:26-46
C:26-46
D:26-46
21
21
21
21
1.4
ENSBTAT00000028633
4
ENSBTAE00000233946
chr3:
120331269-120331313
45
ARRS_BOVIN
46-61
16
4
A:46-61
B:46-61
C:46-61
D:46-61
16
16
16
16
1.5
ENSBTAT00000028633
5
ENSBTAE00000233947
chr3:
120333403-120333596
194
ARRS_BOVIN
61-125
65
4
A:61-125
B:61-125 (gaps)
C:61-125 (gaps)
D:61-125 (gaps)
65
65
65
65
1.6
ENSBTAT00000028633
6
ENSBTAE00000233948
chr3:
120334857-120334916
60
ARRS_BOVIN
126-145
20
4
A:126-145
B:126-145
C:126-145
D:126-145
20
20
20
20
1.7
ENSBTAT00000028633
7
ENSBTAE00000264537
chr3:
120336535-120336611
77
ARRS_BOVIN
146-171
26
4
A:146-171
B:146-171 (gaps)
C:146-171
D:146-171 (gaps)
26
26
26
26
1.8
ENSBTAT00000028633
8
ENSBTAE00000233950
chr3:
120337650-120337785
136
ARRS_BOVIN
171-216
46
4
A:171-216
B:171-216
C:171-216
D:171-216
46
46
46
46
1.9
ENSBTAT00000028633
9
ENSBTAE00000233951
chr3:
120338752-120338836
85
ARRS_BOVIN
217-245
29
4
A:217-245
B:217-245
C:217-245
D:217-245
29
29
29
29
1.10
ENSBTAT00000028633
10
ENSBTAE00000233952
chr3:
120340732-120340804
73
ARRS_BOVIN
245-269
25
4
A:245-269
B:245-269
C:245-269
D:245-269
25
25
25
25
1.11
ENSBTAT00000028633
11
ENSBTAE00000233953
chr3:
120343177-120343314
138
ARRS_BOVIN
269-315
47
4
A:269-315
B:269-315
C:269-315
D:269-315
47
47
47
47
1.12
ENSBTAT00000028633
12
ENSBTAE00000233954
chr3:
120345389-120345466
78
ARRS_BOVIN
315-341
27
4
A:315-341
B:315-338
C:315-339
D:315-337
27
24
25
23
1.13
ENSBTAT00000028633
13
ENSBTAE00000423082
chr3:
120348241-120348264
24
ARRS_BOVIN
341-349
9
4
A:341-349
B:343-349
C:344-349
D:343-349
9
7
6
7
1.14
ENSBTAT00000028633
14
ENSBTAE00000264530
chr3:
120350100-120350155
56
ARRS_BOVIN
349-368
20
4
A:349-362
B:349-362
C:349-362
D:349-361
14
14
14
13
1.15
ENSBTAT00000028633
15
ENSBTAE00000392917
chr3:
120352804-120352819
16
ARRS_BOVIN
368-373
6
2
A:372-373
-
C:372-373
-
2
-
2
-
1.17
ENSBTAT00000028633
17
ENSBTAE00000233957
chr3:
120353845-120353953
109
ARRS_BOVIN
373-408
36
4
A:373-386
B:376-385
C:373-386
D:374-385
14
10
14
12
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3ugxa1 (A:9-182)
1b: SCOP_d3ugxa2 (A:183-386)
1c: SCOP_d3ugxb1 (B:11-182)
1d: SCOP_d3ugxb2 (B:183-385)
1e: SCOP_d3ugxc1 (C:9-182)
1f: SCOP_d3ugxc2 (C:183-386)
1g: SCOP_d3ugxd1 (D:9-182)
1h: SCOP_d3ugxd2 (D:183-385)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
Arrestin/Vps26-like
(13)
Protein domain
:
automated matches
(4)
Cow (Bos taurus) [TaxId: 9913]
(4)
1a
d3ugxa1
A:9-182
1b
d3ugxa2
A:183-386
1c
d3ugxb1
B:11-182
1d
d3ugxb2
B:183-385
1e
d3ugxc1
C:9-182
1f
d3ugxc2
C:183-386
1g
d3ugxd1
D:9-182
1h
d3ugxd2
D:183-385
[
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 (477 KB)
Header - Asym.Unit
Biol.Unit 1 (125 KB)
Header - Biol.Unit 1
Biol.Unit 2 (118 KB)
Header - Biol.Unit 2
Biol.Unit 3 (122 KB)
Header - Biol.Unit 3
Biol.Unit 4 (116 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
3UGX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help