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.
1L9H
Biol. Unit 2
Info
Asym.Unit (124 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (55 KB)
Biol.Unit 3 (115 KB)
Biol.Unit 4 (115 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 BOVINE RHODOPSIN AT 2.6 ANGSTROMS RESOLUTION
Authors
:
T. Okada, Y. Fujiyoshi, M. Silow, J. Navarro, E. M. Landau, Y. Shichida
Date
:
23 Mar 02 (Deposition) - 15 May 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Biol. Unit 4: A,B (1x)
Keywords
:
G Protein-Coupled Receptor, Membrane Protein, Retinal Protein, Photoreceptor, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Okada, Y. Fujiyoshi, M. Silow, J. Navarro, E. M. Landau, Y. Shichida
Functional Role Of Internal Water Molecules In Rhodopsin Revealed By X-Ray Crystallography.
Proc. Natl. Acad. Sci. Usa V. 99 5982 2002
[
close entry info
]
Hetero Components
(6, 12)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: B-NONYLGLUCOSIDE (BNGa)
2b: B-NONYLGLUCOSIDE (BNGb)
2c: B-NONYLGLUCOSIDE (BNGc)
2d: B-NONYLGLUCOSIDE (BNGd)
2e: B-NONYLGLUCOSIDE (BNGe)
2f: B-NONYLGLUCOSIDE (BNGf)
2g: B-NONYLGLUCOSIDE (BNGg)
3a: MERCURY (II) ION (HGa)
3b: MERCURY (II) ION (HGb)
3c: MERCURY (II) ION (HGc)
3d: MERCURY (II) ION (HGd)
3e: MERCURY (II) ION (HGe)
3f: MERCURY (II) ION (HGf)
4a: HEPTANE-1,2,3-TRIOL (HTOa)
4b: HEPTANE-1,2,3-TRIOL (HTOb)
4c: HEPTANE-1,2,3-TRIOL (HTOc)
4d: HEPTANE-1,2,3-TRIOL (HTOd)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
5c: ALPHA-D-MANNOSE (MANc)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7a: PALMITIC ACID (PLMa)
7b: PALMITIC ACID (PLMb)
7c: PALMITIC ACID (PLMc)
7d: PALMITIC ACID (PLMd)
7e: PALMITIC ACID (PLMe)
8a: RETINAL (RETa)
8b: RETINAL (RETb)
9a: ZINC ION (ZNa)
9b: ZINC ION (ZNb)
9c: ZINC ION (ZNc)
9d: ZINC ION (ZNd)
9e: ZINC ION (ZNe)
9f: ZINC ION (ZNf)
9g: ZINC ION (ZNg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
1
Mod. Amino Acid
ACETYL GROUP
2
BNG
2
Ligand/Ion
B-NONYLGLUCOSIDE
3
HG
-1
Ligand/Ion
MERCURY (II) ION
4
HTO
-1
Ligand/Ion
HEPTANE-1,2,3-TRIOL
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
PLM
2
Ligand/Ion
PALMITIC ACID
8
RET
1
Ligand/Ion
RETINAL
9
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
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: BC9 (SOFTWARE)
16: CC2 (SOFTWARE)
17: CC4 (SOFTWARE)
18: CC6 (SOFTWARE)
19: CC7 (SOFTWARE)
20: CC8 (SOFTWARE)
21: CC9 (SOFTWARE)
22: DC1 (SOFTWARE)
23: DC3 (SOFTWARE)
24: DC4 (SOFTWARE)
25: DC6 (SOFTWARE)
26: DC8 (SOFTWARE)
27: DC9 (SOFTWARE)
28: EC3 (SOFTWARE)
29: EC4 (SOFTWARE)
30: EC5 (SOFTWARE)
31: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAG A:504 , LYS B:16
BINDING SITE FOR RESIDUE MAN A 503
02
AC2
SOFTWARE
MAN A:503 , NAG A:505 , LYS B:16
BINDING SITE FOR RESIDUE NAG A 504
03
AC3
SOFTWARE
THR A:4 , ASN A:15 , GLY A:18 , VAL A:20 , NAG A:504 , NAG B:605
BINDING SITE FOR RESIDUE NAG A 505
04
AC4
SOFTWARE
MAN B:603
BINDING SITE FOR RESIDUE MAN B 602
05
AC5
SOFTWARE
LYS A:16 , MAN B:602 , NAG B:604
BINDING SITE FOR RESIDUE MAN B 603
06
AC6
SOFTWARE
LYS A:16 , THR A:17 , MAN B:603 , NAG B:605
BINDING SITE FOR RESIDUE NAG B 604
07
AC7
SOFTWARE
NAG A:505 , THR B:4 , ASN B:15 , GLY B:18 , VAL B:20 , NAG B:604
BINDING SITE FOR RESIDUE NAG B 605
08
AC8
SOFTWARE
NAG A:705 , GLU B:197
BINDING SITE FOR RESIDUE NAG A 704
09
AC9
SOFTWARE
ASN A:2 , GLY A:280 , SER A:281 , ASP A:282 , NAG A:704 , HOH A:2002 , GLU B:197
BINDING SITE FOR RESIDUE NAG A 705
10
BC1
SOFTWARE
NAG B:805
BINDING SITE FOR RESIDUE NAG B 804
11
BC2
SOFTWARE
PRO A:7 , ZN A:2011 , ASN B:2 , GLY B:280 , SER B:281 , ASP B:282 , NAG B:804
BINDING SITE FOR RESIDUE NAG B 805
12
BC3
SOFTWARE
ALA A:234 , ALA A:235 , ARG A:252 , ILE A:305 , MET A:308 , TRP B:35 , SER B:38 , MET B:39 , LEU B:99
BINDING SITE FOR RESIDUE BNG A 1500
13
BC4
SOFTWARE
ALA A:233 , ARG A:252 , ILE A:256 , BNG B:1502
BINDING SITE FOR RESIDUE BNG A 1501
14
BC5
SOFTWARE
BNG A:1501 , GLU B:33 , TRP B:35
BINDING SITE FOR RESIDUE BNG B 1502
15
BC9
SOFTWARE
ASP B:282 , PHE B:283 , GLY B:284 , PRO B:285 , ILE B:286 , PHE B:287
BINDING SITE FOR RESIDUE BNG B 1506
16
CC2
SOFTWARE
CYS B:264 , THR B:297
BINDING SITE FOR RESIDUE HG B 902
17
CC4
SOFTWARE
ALA B:132 , CYS B:222 , TYR B:223
BINDING SITE FOR RESIDUE HG B 904
18
CC6
SOFTWARE
HIS B:65 , LYS B:66 , LYS B:67 , CYS B:316
BINDING SITE FOR RESIDUE HG B 906
19
CC7
SOFTWARE
PRO B:7 , HIS B:195 , GLU B:197
BINDING SITE FOR RESIDUE ZN B 956
20
CC8
SOFTWARE
GLU A:201 , GLN A:279 , GLU B:196
BINDING SITE FOR RESIDUE ZN A 957
21
CC9
SOFTWARE
GLU A:196 , GLU B:201 , GLN B:279
BINDING SITE FOR RESIDUE ZN B 958
22
DC1
SOFTWARE
LYS A:311 , ARG A:314 , GLY A:329 , ASP A:330 , TYR B:96 , HIS B:100
BINDING SITE FOR RESIDUE ZN A 959
23
DC3
SOFTWARE
GLU B:122 , TRP B:126 , MET B:163 , ALA B:164 , CYS B:167 , HIS B:211
BINDING SITE FOR RESIDUE ZN B 963
24
DC4
SOFTWARE
PRO A:7 , HIS A:195 , GLU A:197 , NAG B:805
BINDING SITE FOR RESIDUE ZN A 2011
25
DC6
SOFTWARE
SER A:38 , LEU A:99 , MET B:308 , ARG B:314
BINDING SITE FOR RESIDUE HTO A 1401
26
DC8
SOFTWARE
MET A:317 , LEU A:321 , LEU A:328 , PHE B:45 , ILE B:48 , THR B:92 , TYR B:96
BINDING SITE FOR RESIDUE HTO A 1405
27
DC9
SOFTWARE
TYR B:301
BINDING SITE FOR RESIDUE PLM B 1407
28
EC3
SOFTWARE
PHE A:56 , CYS A:322 , PLM A:1323 , MET B:49
BINDING SITE FOR RESIDUE PLM A 1322
29
EC4
SOFTWARE
LEU A:321 , CYS A:322 , CYS A:323 , PLM A:1322 , PHE B:88
BINDING SITE FOR RESIDUE PLM A 1323
30
EC5
SOFTWARE
ALA B:117 , THR B:118 , GLY B:121 , CYS B:187 , ILE B:189 , MET B:207 , PHE B:212 , PHE B:261 , TRP B:265 , TYR B:268 , ALA B:269 , ALA B:292 , LYS B:296
BINDING SITE FOR RESIDUE RET B 1296
31
EC6
SOFTWARE
PHE A:52 , CYS B:322
BINDING SITE FOR RESIDUE PLM B 1322
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: G_PROTEIN_RECEP_F1_1 (B:123-139)
2: OPSIN (B: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
1
-
B:123-139
2
OPSIN
PS00238
Visual pigments (opsins) retinal binding site.
OPSD_BOVIN
290-306
1
-
B:290-306
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1l9ha_ (A:)
1b: SCOP_d1l9hb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Family A G protein-coupled receptor-like
(138)
Superfamily
:
Family A G protein-coupled receptor-like
(138)
Family
:
Rhodopsin-like
(16)
Protein domain
:
Rhodopsin
(8)
Cow (Bos taurus) [TaxId: 9913]
(8)
1a
d1l9ha_
A:
1b
d1l9hb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1l9hB00 (B:1-326)
1b: CATH_1l9hA00 (A:1-348)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Homologous Superfamily
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Cattle (Bos taurus)
(9)
1a
1l9hB00
B:1-326
1b
1l9hA00
A:1-348
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_7tm_1_1l9hB01 (B:54-306)
1b: PFAM_7tm_1_1l9hB02 (B:54-306)
2a: PFAM_Rhodopsin_N_1l9hB03 (B:2-37)
2b: PFAM_Rhodopsin_N_1l9hB04 (B:2-37)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GPCR_A
(90)
Family
:
7tm_1
(47)
Bos taurus (Bovine)
(9)
1a
7tm_1-1l9hB01
B:54-306
1b
7tm_1-1l9hB02
B:54-306
Clan
:
no clan defined [family: Rhodopsin_N]
(7)
Family
:
Rhodopsin_N
(7)
Bos taurus (Bovine)
(7)
2a
Rhodopsin_N-1l9hB03
B:2-37
2b
Rhodopsin_N-1l9hB04
B:2-37
[
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 (124 KB)
Header - Asym.Unit
Biol.Unit 1 (63 KB)
Header - Biol.Unit 1
Biol.Unit 2 (55 KB)
Header - Biol.Unit 2
Biol.Unit 3 (115 KB)
Header - Biol.Unit 3
Biol.Unit 4 (115 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
1L9H
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help