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1U19
Biol. Unit 1
Info
Asym.Unit (131 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (64 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BOVINE RHODOPSIN AT 2.2 ANGSTROMS RESOLUTION
Authors
:
T. Okada, M. Sugihara, A. N. Bondar, M. Elstner, P. Entel, V. Buss
Date
:
15 Jul 04 (Deposition) - 12 Oct 04 (Release) - 25 Mar 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
G Protein-Coupled Receptor, Membrane Protein, Retinal Protein, Photoreceptor, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Okada, M. Sugihara, A. N. Bondar, M. Elstner, P. Entel, V. Buss
The Retinal Conformation And Its Environment In Rhodopsin I Light Of A New 2. 2 A Crystal Structure
J. Mol. Biol. V. 342 571 2004
[
close entry info
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Hetero Components
(6, 11)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
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: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGa)
4b: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGb)
4c: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGc)
4d: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGd)
5a: HEPTANE-1,2,3-TRIOL (HTOa)
6a: ALPHA-D-MANNOSE (MANa)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
8a: PALMITIC ACID (PLMa)
8b: PALMITIC ACID (PLMb)
8c: PALMITIC ACID (PLMc)
8d: PALMITIC ACID (PLMd)
8e: PALMITIC ACID (PLMe)
8f: PALMITIC ACID (PLMf)
9a: RETINAL (RETa)
9b: RETINAL (RETb)
10a: ZINC ION (ZNa)
10b: ZINC ION (ZNb)
10c: ZINC ION (ZNc)
10d: ZINC ION (ZNd)
10e: ZINC ION (ZNe)
10f: ZINC ION (ZNf)
10g: ZINC ION (ZNg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
1
Mod. Amino Acid
ACETYL GROUP
2
BMA
-1
Ligand/Ion
BETA-D-MANNOSE
3
HG
-1
Ligand/Ion
MERCURY (II) ION
4
HTG
1
Ligand/Ion
HEPTYL 1-THIOHEXOPYRANOSIDE
5
HTO
-1
Ligand/Ion
HEPTANE-1,2,3-TRIOL
6
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
PLM
3
Ligand/Ion
PALMITIC ACID
9
RET
1
Ligand/Ion
RETINAL
10
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(29, 29)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC5 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC8 (SOFTWARE)
08: AC9 (SOFTWARE)
09: BC1 (SOFTWARE)
10: BC2 (SOFTWARE)
11: BC3 (SOFTWARE)
12: BC5 (SOFTWARE)
13: BC7 (SOFTWARE)
14: BC9 (SOFTWARE)
15: CC1 (SOFTWARE)
16: CC2 (SOFTWARE)
17: CC3 (SOFTWARE)
18: CC4 (SOFTWARE)
19: CC6 (SOFTWARE)
20: CC7 (SOFTWARE)
21: CC8 (SOFTWARE)
22: CC9 (SOFTWARE)
23: DC2 (SOFTWARE)
24: DC3 (SOFTWARE)
25: DC4 (SOFTWARE)
26: DC6 (SOFTWARE)
27: DC8 (SOFTWARE)
28: DC9 (SOFTWARE)
29: EC1 (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 , ASN B:15 , NAG B:605
BINDING SITE FOR RESIDUE NAG A 505
04
AC5
SOFTWARE
LYS A:16 , ARG B:147 , BMA B:602 , NAG B:604
BINDING SITE FOR RESIDUE BMA B 603
05
AC6
SOFTWARE
LYS A:16 , ALA B:348 , BMA B:603 , NAG B:605
BINDING SITE FOR RESIDUE NAG B 604
06
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
07
AC8
SOFTWARE
NAG A:705 , GLU B:197
BINDING SITE FOR RESIDUE NAG A 704
08
AC9
SOFTWARE
ASN A:2 , GLY A:280 , SER A:281 , ASP A:282 , NAG A:704 , GLU B:197 , ZN B:956
BINDING SITE FOR RESIDUE NAG A 705
09
BC1
SOFTWARE
GLU A:197 , NAG B:805
BINDING SITE FOR RESIDUE NAG B 804
10
BC2
SOFTWARE
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
11
BC3
SOFTWARE
CYS A:264 , THR A:297 , TYR A:301
BINDING SITE FOR RESIDUE HG A 901
12
BC5
SOFTWARE
ALA A:132 , CYS A:222
BINDING SITE FOR RESIDUE HG A 903
13
BC7
SOFTWARE
GLN A:312 , CYS A:316 , THR A:336 , VAL A:337 , HOH A:2061
BINDING SITE FOR RESIDUE HG A 905
14
BC9
SOFTWARE
NAG A:705 , HIS B:195 , GLU B:197
BINDING SITE FOR RESIDUE ZN B 956
15
CC1
SOFTWARE
GLU A:201 , GLN A:279 , GLU B:196
BINDING SITE FOR RESIDUE ZN A 957
16
CC2
SOFTWARE
GLU A:196 , GLU B:201 , GLN B:279
BINDING SITE FOR RESIDUE ZN B 958
17
CC3
SOFTWARE
LYS A:311 , GLY A:329 , ASP A:330 , HIS B:100
BINDING SITE FOR RESIDUE ZN A 959
18
CC4
SOFTWARE
GLU A:122 , TRP A:126 , MET A:163 , ALA A:164 , CYS A:167 , HIS A:211
BINDING SITE FOR RESIDUE ZN A 962
19
CC6
SOFTWARE
HIS A:195 , GLU A:197 , NAG B:805
BINDING SITE FOR RESIDUE ZN A 2011
20
CC7
SOFTWARE
ALA A:117 , THR A:118 , CYS A:187 , ILE A:189 , TYR A:191 , PHE A:212 , PHE A:261 , TRP A:265 , TYR A:268 , ALA A:269 , ALA A:292 , LYS A:296
BINDING SITE FOR RESIDUE RET A 1296
21
CC8
SOFTWARE
PRO A:53 , LEU A:321 , CYS A:322 , PLM A:1323 , MET B:49 , PHE B:52
BINDING SITE FOR RESIDUE PLM A 1322
22
CC9
SOFTWARE
LEU A:321 , CYS A:322 , CYS A:323 , PLM A:1322 , PHE B:88
BINDING SITE FOR RESIDUE PLM A 1323
23
DC2
SOFTWARE
ILE A:48 , MET A:49 , LEU B:321 , CYS B:322 , PLM B:1323
BINDING SITE FOR RESIDUE PLM B 1322
24
DC3
SOFTWARE
PHE A:85 , PHE A:88 , LEU B:321 , CYS B:322 , CYS B:323 , PLM B:1322
BINDING SITE FOR RESIDUE PLM B 1323
25
DC4
SOFTWARE
ALA A:41 , LEU A:99 , MET B:308 , ARG B:314 , HTG B:1509
BINDING SITE FOR RESIDUE HTO B 1401
26
DC6
SOFTWARE
VAL A:300 , ILE A:305 , LEU B:46
BINDING SITE FOR RESIDUE PLM A 1410
27
DC8
SOFTWARE
LEU A:266 , PRO A:267 , GLY A:270 , VAL A:271 , TYR A:274 , PHE A:283 , PHE A:287
BINDING SITE FOR RESIDUE HTG A 1507
28
DC9
SOFTWARE
ARG A:252 , ILE A:256 , VAL A:304 , ILE A:305 , MET A:309 , TRP B:35 , SER B:38 , ALA B:42
BINDING SITE FOR RESIDUE HTG B 1508
29
EC1
SOFTWARE
LEU A:99 , HIS A:100 , GLN A:344 , LYS B:311 , ARG B:314 , ASN B:315 , ASP B:330 , HTO B:1401
BINDING SITE FOR RESIDUE HTG B 1509
[
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
[
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]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: G_PROTEIN_RECEP_F1_1 (A:123-139)
2: OPSIN (A: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
A:123-139
-
2
OPSIN
PS00238
Visual pigments (opsins) retinal binding site.
OPSD_BOVIN
290-306
1
A:290-306
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d1u19a_ (A:)
1b: SCOP_d1u19b_ (B:)
View:
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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
d1u19a_
A:
1b
d1u19b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1u19A00 (A:1-348)
1b: CATH_1u19B00 (B:1-348)
View:
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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
1u19A00
A:1-348
1b
1u19B00
B:1-348
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_7tm_1_1u19B01 (B:54-306)
1b: PFAM_7tm_1_1u19B02 (B:54-306)
2a: PFAM_Rhodopsin_N_1u19B03 (B:2-37)
2b: PFAM_Rhodopsin_N_1u19B04 (B:2-37)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GPCR_A
(90)
Family
:
7tm_1
(47)
Bos taurus (Bovine)
(9)
1a
7tm_1-1u19B01
B:54-306
1b
7tm_1-1u19B02
B:54-306
Clan
:
no clan defined [family: Rhodopsin_N]
(7)
Family
:
Rhodopsin_N
(7)
Bos taurus (Bovine)
(7)
2a
Rhodopsin_N-1u19B03
B:2-37
2b
Rhodopsin_N-1u19B04
B:2-37
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]
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