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.
2I37
Asym. Unit
Info
Asym.Unit (144 KB)
Biol.Unit 1 (47 KB)
Biol.Unit 2 (48 KB)
Biol.Unit 3 (48 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 A PHOTOACTIVATED RHODOPSIN
Authors
:
D. T. Lodowski, R. E. Stenkamp, D. Salom, I. Le Trong, K. Palczewski
Date
:
17 Aug 06 (Deposition) - 17 Oct 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
4.15
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Trans-Membrane Protein, Gpcr, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Salom, D. T. Lodowski, R. E. Stenkamp, I. L. Trong, M. Golczak, B. Jastrzebska, T. Harris, J. A. Ballesteros, K. Palczewski
Crystal Structure Of A Photoactivated Deprotonated Intermediate Of Rhodopsin.
Proc. Natl. Acad. Sci. Usa V. 103 16123 2006
[
close entry info
]
Hetero Components
(5, 21)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
1c: ACETYL GROUP (ACEc)
2a: BETA-D-MANNOSE (BMAa)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
3
Mod. Amino Acid
ACETYL GROUP
2
BMA
1
Ligand/Ion
BETA-D-MANNOSE
3
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:15 , GLY A:18 , VAL A:19 , VAL A:20 , ARG A:21 , SER A:22 , NAG A:504
BINDING SITE FOR RESIDUE NAG A 505
02
AC2
SOFTWARE
MAN A:503 , NAG A:505
BINDING SITE FOR RESIDUE NAG A 504
03
AC3
SOFTWARE
NAG A:504
BINDING SITE FOR RESIDUE MAN A 503
04
AC4
SOFTWARE
ASN A:2 , GLY A:280 , ASP A:282 , NAG A:704
BINDING SITE FOR RESIDUE NAG A 705
05
AC5
SOFTWARE
NAG A:705
BINDING SITE FOR RESIDUE NAG A 704
06
AC6
SOFTWARE
ASN B:15 , GLY B:18 , VAL B:20 , NAG B:504 , NAG C:504 , NAG C:505
BINDING SITE FOR RESIDUE NAG B 505
07
AC7
SOFTWARE
MAN B:503 , NAG B:505 , NAG C:504
BINDING SITE FOR RESIDUE NAG B 504
08
AC8
SOFTWARE
BMA B:502 , NAG B:504
BINDING SITE FOR RESIDUE MAN B 503
09
AC9
SOFTWARE
NAG B:501 , MAN B:503
BINDING SITE FOR RESIDUE BMA B 502
10
BC1
SOFTWARE
BMA B:502
BINDING SITE FOR RESIDUE NAG B 501
11
BC2
SOFTWARE
ASN B:2 , GLY B:280 , SER B:281 , NAG B:704
BINDING SITE FOR RESIDUE NDG B 705
12
BC3
SOFTWARE
NDG B:705
BINDING SITE FOR RESIDUE NAG B 704
13
BC4
SOFTWARE
NAG B:505 , THR C:4 , ASN C:15 , VAL C:20 , ARG C:21 , NAG C:504
BINDING SITE FOR RESIDUE NAG C 505
14
BC5
SOFTWARE
SER B:22 , NAG B:504 , NAG B:505 , MAN C:503 , NAG C:505
BINDING SITE FOR RESIDUE NAG C 504
15
BC6
SOFTWARE
MAN C:502 , NAG C:504
BINDING SITE FOR RESIDUE MAN C 503
16
BC7
SOFTWARE
ARG B:21 , MAN C:503
BINDING SITE FOR RESIDUE MAN C 502
17
BC8
SOFTWARE
GLN B:279 , ASN C:2 , GLY C:280 , ASP C:282 , NAG C:704
BINDING SITE FOR RESIDUE NDG C 705
18
BC9
SOFTWARE
NDG C:705
BINDING SITE FOR RESIDUE NAG C 704
[
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
(2, 6)
Info
All PROSITE Patterns/Profiles
1: G_PROTEIN_RECEP_F1_1 (A:123-139,B:123-139,C:127-139)
2: OPSIN (A:290-306,B:290-306,C:290-306)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
G_PROTEIN_RECEP_F1_1
PS00237
G-protein coupled receptors family 1 signature.
OPSD_BOVIN
123-139
3
A:123-139
B:123-139
C:127-139
2
OPSIN
PS00238
Visual pigments (opsins) retinal binding site.
OPSD_BOVIN
290-306
3
A:290-306
B:290-306
C:290-306
[
close PROSITE info
]
Exons
(5, 15)
Info
All Exons
Exon 1.1 (A:1-124 | B:1-124 | C:1-121)
Exon 1.2 (A:124-180 | B:124-180 (gaps) | C:1...)
Exon 1.3 (A:180-229 | B:180-234 | C:180-235 ...)
Exon 1.4 (A:239-315 (gaps) | B:238-315 | C:2...)
Exon 1.5 (A:316-329 | B:316-327 | C:316-333)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/-
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
ENSBTAT00000001730
1
ENSBTAE00000013842
chr22:
57733705-57733336
370
OPSD_BOVIN
1-124
124
3
A:1-124
B:1-124
C:1-121
124
124
121
1.2
ENSBTAT00000001730
2
ENSBTAE00000013843
chr22:
57731646-57731478
169
OPSD_BOVIN
124-180
57
3
A:124-180
B:124-180 (gaps)
C:127-180
57
57
54
1.3
ENSBTAT00000001730
3
ENSBTAE00000013844
chr22:
57730259-57730094
166
OPSD_BOVIN
180-235
56
3
A:180-229
B:180-234
C:180-235 (gaps)
50
55
56
1.4
ENSBTAT00000001730
4
ENSBTAE00000013845
chr22:
57729975-57729736
240
OPSD_BOVIN
236-315
80
3
A:239-315 (gaps)
B:238-315
C:242-315
77
78
74
1.5
ENSBTAT00000001730
5
ENSBTAE00000326840
chr22:
57728876-57728766
111
OPSD_BOVIN
316-351
36
3
A:316-329
B:316-327
C:316-333
14
12
18
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (144 KB)
Header - Asym.Unit
Biol.Unit 1 (47 KB)
Header - Biol.Unit 1
Biol.Unit 2 (48 KB)
Header - Biol.Unit 2
Biol.Unit 3 (48 KB)
Header - Biol.Unit 3
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
2I37
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help