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3DQB
Asym. Unit
Info
Asym.Unit (66 KB)
Biol.Unit 1 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE ACTIVE G-PROTEIN-COUPLED RECEPTOR OPSIN IN COMPLEX WITH A C-TERMINAL PEPTIDE DERIVED FROM THE GALPHA SUBUNIT OF TRANSDUCIN
Authors
:
P. Scheerer, J. H. Park, P. W. Hildebrand, Y. J. Kim, N. Krauss, H. -W. Cho K. P. Hofmann, O. P. Ernst
Date
:
09 Jul 08 (Deposition) - 23 Sep 08 (Release) - 05 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Protein, Retinal Protein, Photoreceptor, Ligand-Free State, Chromophore, G-Protein Coupled Receptor, Glycoprotein, Lipoprotein, Palmitate, Phosphoprotein, Photoreceptor Protein, Sensory Transduction, Transducer, Transmembrane, Vision, Signaling Protein, G-Protein, Transducin, Galpha Subunit, Membrane, Receptor, Gtp- Binding, Myristate, Nucleotide-Binding, G-Protein-Coupled Receptor, Rhodopsin, Opsin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Scheerer, J. H. Park, P. W. Hildebrand, Y. J. Kim, N. Krauss, H. -W. Choe, K. P. Hofmann, O. P. Ernst
Crystal Structure Of Opsin In Its G-Protein-Interacting Conformation
Nature V. 455 497 2008
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Hetero Components
(5, 11)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: B-OCTYLGLUCOSIDE (BOGa)
2b: B-OCTYLGLUCOSIDE (BOGb)
2c: B-OCTYLGLUCOSIDE (BOGc)
3a: ALPHA-D-MANNOSE (MANa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5a: PALMITIC ACID (PLMa)
5b: PALMITIC ACID (PLMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
BOG
3
Ligand/Ion
B-OCTYLGLUCOSIDE
3
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
PLM
2
Ligand/Ion
PALMITIC ACID
[
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:4 , PHE A:9 , ASN A:15 , GLY A:18 , VAL A:20 , NAG A:402
BINDING SITE FOR RESIDUE NAG A 401
02
AC2
SOFTWARE
ARG A:21 , NAG A:401 , BMA A:403
BINDING SITE FOR RESIDUE NAG A 402
03
AC3
SOFTWARE
NAG A:402 , MAN A:404
BINDING SITE FOR RESIDUE BMA A 403
04
AC4
SOFTWARE
BMA A:403
BINDING SITE FOR RESIDUE MAN A 404
05
AC5
SOFTWARE
MET A:1 , ASN A:2 , GLY A:280 , ASP A:282 , NAG A:502
BINDING SITE FOR RESIDUE NAG A 501
06
AC6
SOFTWARE
NAG A:501
BINDING SITE FOR RESIDUE NAG A 502
07
AC7
SOFTWARE
GLN A:36
BINDING SITE FOR RESIDUE BOG A 601
08
AC8
SOFTWARE
PHE A:220 , LYS A:231 , THR A:251 , VAL A:254
BINDING SITE FOR RESIDUE BOG A 602
09
AC9
SOFTWARE
TRP A:35 , TYR A:96 , HIS A:100
BINDING SITE FOR RESIDUE BOG A 603
10
BC1
SOFTWARE
ARG A:252 , ILE A:256 , THR A:297 , VAL A:304 , LEU A:321 , CYS A:322 , CYS A:323 , PLM A:702
BINDING SITE FOR RESIDUE PLM A 701
11
BC2
SOFTWARE
ILE A:54 , ARG A:252 , MET A:309 , CYS A:322 , PLM A:701
BINDING SITE FOR RESIDUE PLM A 702
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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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
(6, 6)
Info
All Exons
Exon 1.1 (A:1-124)
Exon 1.2 (A:124-180)
Exon 1.3 (A:180-235)
Exon 1.4 (A:236-315)
Exon 1.5 (A:316-326)
Exon 2.8 (B:340-350)
View:
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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/-
7: Boundary 2.7/2.8
8: Boundary 2.8/2.9
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
1
A:1-124
124
1.2
ENSBTAT00000001730
2
ENSBTAE00000013843
chr22:
57731646-57731478
169
OPSD_BOVIN
124-180
57
1
A:124-180
57
1.3
ENSBTAT00000001730
3
ENSBTAE00000013844
chr22:
57730259-57730094
166
OPSD_BOVIN
180-235
56
1
A:180-235
56
1.4
ENSBTAT00000001730
4
ENSBTAE00000013845
chr22:
57729975-57729736
240
OPSD_BOVIN
236-315
80
1
A:236-315
80
1.5
ENSBTAT00000001730
5
ENSBTAE00000326840
chr22:
57728876-57728766
111
OPSD_BOVIN
316-351
36
1
A:316-326
11
2.1
ENSBTAT00000023990
1
ENSBTAE00000247883
chr22:
51063839-51063597
243
GNAT1_BOVIN
1-36
36
0
-
-
2.2
ENSBTAT00000023990
2
ENSBTAE00000388493
chr22:
51062405-51062363
43
GNAT1_BOVIN
36-50
15
0
-
-
2.3
ENSBTAT00000023990
3
ENSBTAE00000247881
chr22:
51062224-51062083
142
GNAT1_BOVIN
50-97
48
0
-
-
2.4
ENSBTAT00000023990
4
ENSBTAE00000247880
chr22:
51061992-51061835
158
GNAT1_BOVIN
98-150
53
0
-
-
2.5
ENSBTAT00000023990
5
ENSBTAE00000195357
chr22:
51061741-51061613
129
GNAT1_BOVIN
150-193
44
0
-
-
2.6
ENSBTAT00000023990
6
ENSBTAE00000419260
chr22:
51061351-51061222
130
GNAT1_BOVIN
193-236
44
0
-
-
2.7
ENSBTAT00000023990
7
ENSBTAE00000195359
chr22:
51060899-51060746
154
GNAT1_BOVIN
237-288
52
0
-
-
2.8
ENSBTAT00000023990
8
ENSBTAE00000195360
chr22:
51060623-51060432
192
GNAT1_BOVIN
288-350
63
1
B:340-350
11
2.9
ENSBTAT00000023990
9
ENSBTAE00000195361
chr22:
51060077-51058825
1253
GNAT1_BOVIN
-
0
0
-
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3dqbA00 (A:1-326)
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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)
Bovine (Bos taurus)
(4)
1a
3dqbA00
A:1-326
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Nucleic
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Protein & NOT Site
Protein & NOT PROSITE
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Asymmetric Unit 1
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