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3OAX
Asym. Unit
Info
Asym.Unit (133 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (65 KB)
Biol.Unit 3 (125 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BOVINE RHODOPSIN WITH BETA-IONONE
Authors
:
C. L. Makino, C. K. Riley, J. Looney, R. K. Crouch, T. Okada
Date
:
05 Aug 10 (Deposition) - 19 Jan 11 (Release) - 19 Jan 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)
Keywords
:
7Tm, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. L. Makino, C. K. Riley, J. Looney, R. K. Crouch, T. Okada
Binding Of More Than One Retinoid To Visual Opsins
Biophys. J. V. 99 2366 2010
[
close entry info
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Hetero Components
(12, 41)
Info
All Hetero Components
01a: (4E,6E)-HEXADECA-1,4,6-TRIENE (4E6a)
01b: (4E,6E)-HEXADECA-1,4,6-TRIENE (4E6b)
02a: ACETYL GROUP (ACEa)
02b: ACETYL GROUP (ACEb)
03a: BETA-D-MANNOSE (BMAa)
03b: BETA-D-MANNOSE (BMAb)
04a: MERCURY (II) ION (HGa)
04b: MERCURY (II) ION (HGb)
04c: MERCURY (II) ION (HGc)
04d: MERCURY (II) ION (HGd)
04e: MERCURY (II) ION (HGe)
04f: MERCURY (II) ION (HGf)
05a: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGa)
05b: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGb)
05c: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGc)
05d: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGd)
06a: HEPTANE-1,2,3-TRIOL (HTOa)
07a: (3E)-4-(2,6,6-TRIMETHYLCYCLOHEX-1-... (ID3a)
07b: (3E)-4-(2,6,6-TRIMETHYLCYCLOHEX-1-... (ID3b)
08a: ALPHA-D-MANNOSE (MANa)
09a: N-ACETYL-D-GLUCOSAMINE (NAGa)
09b: N-ACETYL-D-GLUCOSAMINE (NAGb)
09c: N-ACETYL-D-GLUCOSAMINE (NAGc)
09d: N-ACETYL-D-GLUCOSAMINE (NAGd)
09e: N-ACETYL-D-GLUCOSAMINE (NAGe)
09f: N-ACETYL-D-GLUCOSAMINE (NAGf)
09g: N-ACETYL-D-GLUCOSAMINE (NAGg)
09h: N-ACETYL-D-GLUCOSAMINE (NAGh)
10a: PALMITIC ACID (PLMa)
10b: PALMITIC ACID (PLMb)
10c: PALMITIC ACID (PLMc)
10d: PALMITIC ACID (PLMd)
11a: RETINAL (RETa)
11b: RETINAL (RETb)
12a: ZINC ION (ZNa)
12b: ZINC ION (ZNb)
12c: ZINC ION (ZNc)
12d: ZINC ION (ZNd)
12e: ZINC ION (ZNe)
12f: ZINC ION (ZNf)
12g: ZINC ION (ZNg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4E6
2
Ligand/Ion
(4E,6E)-HEXADECA-1,4,6-TRIENE
2
ACE
2
Mod. Amino Acid
ACETYL GROUP
3
BMA
2
Ligand/Ion
BETA-D-MANNOSE
4
HG
6
Ligand/Ion
MERCURY (II) ION
5
HTG
4
Ligand/Ion
HEPTYL 1-THIOHEXOPYRANOSIDE
6
HTO
1
Ligand/Ion
HEPTANE-1,2,3-TRIOL
7
ID3
2
Ligand/Ion
(3E)-4-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)BUT-3-EN-2-ONE
8
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
9
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
10
PLM
4
Ligand/Ion
PALMITIC ACID
11
RET
2
Ligand/Ion
RETINAL
12
ZN
7
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(39, 39)
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)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:151 , NAG A:504 , LYS B:16
BINDING SITE FOR RESIDUE BMA A 503
02
AC2
SOFTWARE
ARG A:21 , BMA 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 , HOH B:2040
BINDING SITE FOR RESIDUE NAG A 505
04
AC4
SOFTWARE
ALA A:117 , THR A:118 , GLY A:121 , GLU A:122 , CYS A:187 , ILE A:189 , TYR A:191 , MET A:207 , PHE A:212 , PHE A:261 , TYR A:268 , ALA A:292 , LYS A:296
BINDING SITE FOR RESIDUE RET A 1296
05
AC5
SOFTWARE
CYS A:322
BINDING SITE FOR RESIDUE PLM A 1322
06
AC6
SOFTWARE
LEU A:321 , CYS A:322 , CYS A:323
BINDING SITE FOR RESIDUE PLM A 1323
07
AC7
SOFTWARE
NAG A:705 , GLU B:197
BINDING SITE FOR RESIDUE NAG A 704
08
AC8
SOFTWARE
ASN A:2 , GLY A:280 , SER A:281 , ASP A:282 , NAG A:704 , HOH A:2072 , ZN B:956
BINDING SITE FOR RESIDUE NAG A 705
09
AC9
SOFTWARE
CYS A:264 , THR A:297 , TYR A:301
BINDING SITE FOR RESIDUE HG A 901
10
BC1
SOFTWARE
ALA A:132 , CYS A:222 , TYR A:223
BINDING SITE FOR RESIDUE HG A 903
11
BC2
SOFTWARE
GLN A:312 , CYS A:316 , THR A:336 , VAL A:337 , HOH A:2061
BINDING SITE FOR RESIDUE HG A 905
12
BC3
SOFTWARE
GLU A:201 , GLN A:279 , GLU B:196
BINDING SITE FOR RESIDUE ZN A 957
13
BC4
SOFTWARE
LYS A:311 , ASP A:330 , HIS B:100
BINDING SITE FOR RESIDUE ZN A 959
14
BC5
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
15
BC6
SOFTWARE
HIS A:195 , GLU A:197
BINDING SITE FOR RESIDUE ZN A 2011
16
BC7
SOFTWARE
VAL A:300 , TYR A:301 , LEU B:46
BINDING SITE FOR RESIDUE 4E6 A 1410
17
BC8
SOFTWARE
TYR A:274 , PHE A:287 , ID3 A:6025
BINDING SITE FOR RESIDUE HTG A 1507
18
BC9
SOFTWARE
MET A:309 , TRP B:35 , ALA B:42
BINDING SITE FOR RESIDUE HTG A 1508
19
CC1
SOFTWARE
GLY A:284 , PRO A:285 , ILE A:286 , PHE A:287 , HTG A:1507
BINDING SITE FOR RESIDUE ID3 A 6025
20
CC2
SOFTWARE
GLU B:113 , ALA B:117 , THR B:118 , GLY B:121 , GLU B:122 , CYS B:187 , TYR B:191 , 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
21
CC3
SOFTWARE
PHE A:45 , CYS B:322
BINDING SITE FOR RESIDUE PLM B 1322
22
CC4
SOFTWARE
PHE A:88 , LEU B:321 , CYS B:322 , CYS B:323
BINDING SITE FOR RESIDUE PLM B 1323
23
CC5
SOFTWARE
ARG B:147 , PRO B:347 , BMA B:603
BINDING SITE FOR RESIDUE MAN B 602
24
CC6
SOFTWARE
LYS A:16 , ARG B:147 , MAN B:602 , NAG B:604
BINDING SITE FOR RESIDUE BMA B 603
25
CC7
SOFTWARE
LYS A:16 , ARG B:21 , ALA B:348 , BMA B:603 , NAG B:605
BINDING SITE FOR RESIDUE NAG B 604
26
CC8
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
27
CC9
SOFTWARE
GLU A:197 , NAG B:805
BINDING SITE FOR RESIDUE NAG B 804
28
DC1
SOFTWARE
PRO A:7 , ASN B:2 , GLY B:280 , ASP B:282 , NAG B:804 , HOH B:2108
BINDING SITE FOR RESIDUE NAG B 805
29
DC2
SOFTWARE
ALA B:260 , CYS B:264 , THR B:297 , TYR B:301 , HOH B:2112
BINDING SITE FOR RESIDUE HG B 902
30
DC3
SOFTWARE
CYS B:222
BINDING SITE FOR RESIDUE HG B 904
31
DC4
SOFTWARE
GLN B:312 , CYS B:316 , GLU B:332 , THR B:336 , VAL B:337
BINDING SITE FOR RESIDUE HG B 906
32
DC5
SOFTWARE
NAG A:705 , HIS B:195 , GLU B:197
BINDING SITE FOR RESIDUE ZN B 956
33
DC6
SOFTWARE
GLU A:196 , GLU B:201 , GLN B:279
BINDING SITE FOR RESIDUE ZN B 958
34
DC7
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
35
DC8
SOFTWARE
SER A:38 , ALA A:42 , MET B:308
BINDING SITE FOR RESIDUE HTO B 1401
36
DC9
SOFTWARE
MET B:39 , LEU B:46
BINDING SITE FOR RESIDUE 4E6 B 1407
37
EC1
SOFTWARE
VAL B:271 , TYR B:274 , PHE B:283 , ID3 B:6026
BINDING SITE FOR RESIDUE HTG B 1506
38
EC2
SOFTWARE
LEU A:99 , HIS A:100 , GLN A:344 , LYS B:311 , ARG B:314 , ASN B:315 , ASP B:330
BINDING SITE FOR RESIDUE HTG B 1509
39
EC3
SOFTWARE
PHE B:283 , GLY B:284 , ILE B:286 , PHE B:287 , HTG B:1506
BINDING SITE FOR RESIDUE ID3 B 6026
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: G_PROTEIN_RECEP_F1_1 (A:123-139,B:123-139)
2: OPSIN (A:290-306,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
2
A:123-139
B:123-139
2
OPSIN
PS00238
Visual pigments (opsins) retinal binding site.
OPSD_BOVIN
290-306
2
A:290-306
B:290-306
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.1 (A:1-124 | B:1-124)
Exon 1.2 (A:124-180 | B:124-180)
Exon 1.3 (A:180-235 | B:180-235)
Exon 1.4 (A:236-315 | B:236-315)
Exon 1.5 (A:316-348 | B:316-348)
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
2
A:1-124
B:1-124
124
124
1.2
ENSBTAT00000001730
2
ENSBTAE00000013843
chr22:
57731646-57731478
169
OPSD_BOVIN
124-180
57
2
A:124-180
B:124-180
57
57
1.3
ENSBTAT00000001730
3
ENSBTAE00000013844
chr22:
57730259-57730094
166
OPSD_BOVIN
180-235
56
2
A:180-235
B:180-235
56
56
1.4
ENSBTAT00000001730
4
ENSBTAE00000013845
chr22:
57729975-57729736
240
OPSD_BOVIN
236-315
80
2
A:236-315
B:236-315
80
80
1.5
ENSBTAT00000001730
5
ENSBTAE00000326840
chr22:
57728876-57728766
111
OPSD_BOVIN
316-351
36
2
A:316-348
B:316-348
33
33
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3oaxa_ (A:)
1b: SCOP_d3oaxb_ (B:)
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Protein Domains
(
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(
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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
:
automated matches
(8)
Cow (Bos taurus) [TaxId: 9913]
(8)
1a
d3oaxa_
A:
1b
d3oaxb_
B:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_7tm_1_3oaxB01 (B:54-306)
1b: PFAM_7tm_1_3oaxB02 (B:54-306)
2a: PFAM_Rhodopsin_N_3oaxB03 (B:2-37)
2b: PFAM_Rhodopsin_N_3oaxB04 (B:2-37)
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Clans
(
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Families
(
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(
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Organisms
(
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(
)
Clan
:
GPCR_A
(90)
Family
:
7tm_1
(47)
Bos taurus (Bovine)
(9)
1a
7tm_1-3oaxB01
B:54-306
1b
7tm_1-3oaxB02
B:54-306
Clan
:
no clan defined [family: Rhodopsin_N]
(7)
Family
:
Rhodopsin_N
(7)
Bos taurus (Bovine)
(7)
2a
Rhodopsin_N-3oaxB03
B:2-37
2b
Rhodopsin_N-3oaxB04
B:2-37
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