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1VGO
Asym. Unit
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Asym.Unit (87 KB)
Biol.Unit 1 (81 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ARCHAERHODOPSIN-2
Authors
:
K. Yoshimura, N. Enami, M. Murakami, H. Okumura, K. Ihara, T. Kouyama
Date
:
28 Apr 04 (Deposition) - 04 Oct 05 (Release) - 10 Jun 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Retinal-Binding Protein, Proton Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Enami, K. Yoshimura, M. Murakami, H. Okumura, K. Ihara, T. Kouyama
Crystal Structures Of Archaerhodopsin-1 And -2: Common Structural Motif In Archaeal Light-Driven Proton Pumps
J. Mol. Biol. V. 358 675 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 17)
Info
All Hetero Components
1a: B-NONYLGLUCOSIDE (BNGa)
1b: B-NONYLGLUCOSIDE (BNGb)
1c: B-NONYLGLUCOSIDE (BNGc)
1d: B-NONYLGLUCOSIDE (BNGd)
1e: B-NONYLGLUCOSIDE (BNGe)
1f: B-NONYLGLUCOSIDE (BNGf)
1g: B-NONYLGLUCOSIDE (BNGg)
1h: B-NONYLGLUCOSIDE (BNGh)
1i: B-NONYLGLUCOSIDE (BNGi)
1j: B-NONYLGLUCOSIDE (BNGj)
1k: B-NONYLGLUCOSIDE (BNGk)
1l: B-NONYLGLUCOSIDE (BNGl)
2a: RETINAL (RETa)
2b: RETINAL (RETb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BNG
12
Ligand/Ion
B-NONYLGLUCOSIDE
2
RET
2
Ligand/Ion
RETINAL
3
SO4
3
Ligand/Ion
SULFATE ION
[
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Sites
(17, 17)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:110 , GLY A:114 , LEU A:132 , TRP A:142
BINDING SITE FOR RESIDUE BNG A 301
02
AC2
SOFTWARE
PRO A:136 , TYR A:140 , BNG A:303
BINDING SITE FOR RESIDUE BNG A 302
03
AC3
SOFTWARE
TYR A:155 , BNG A:302
BINDING SITE FOR RESIDUE BNG A 303
04
AC4
SOFTWARE
TYR A:140 , ILE A:195 , GLY A:200 , BNG A:305
BINDING SITE FOR RESIDUE BNG A 304
05
AC5
SOFTWARE
LEU A:151 , BNG A:304 , PHE B:152 , TYR B:155
BINDING SITE FOR RESIDUE BNG A 305
06
AC6
SOFTWARE
VAL A:185 , ILE A:208 , BNG A:307 , BNG A:308
BINDING SITE FOR RESIDUE BNG A 306
07
AC7
SOFTWARE
BNG A:306 , LEU B:158 , ALA B:184
BINDING SITE FOR RESIDUE BNG A 307
08
AC8
SOFTWARE
TRP A:16 , BNG A:306
BINDING SITE FOR RESIDUE BNG A 308
09
AC9
SOFTWARE
ILE A:68 , TYR A:85
BINDING SITE FOR RESIDUE BNG A 309
10
BC1
SOFTWARE
ARG A:168 , SER A:169 , VAL A:172 , ARG B:232
BINDING SITE FOR RESIDUE SO4 A 400
11
BC2
SOFTWARE
TRP A:91 , THR A:94 , THR A:95 , MET A:123 , TRP A:143 , SER A:146 , THR A:147 , TRP A:187 , TYR A:190 , PRO A:191 , TRP A:194 , ASP A:217 , LYS A:221
BINDING SITE FOR RESIDUE RET A 260
12
BC3
SOFTWARE
THR B:115 , VAL B:119 , TYR B:156
BINDING SITE FOR RESIDUE BNG B 310
13
BC4
SOFTWARE
ALA A:48 , TRP B:36
BINDING SITE FOR RESIDUE BNG B 311
14
BC5
SOFTWARE
ARG A:162 , ASN A:177 , LEU B:75 , SER B:77 , THR B:79 , PRO B:136 , ARG B:139 , TYR B:140 , ILE B:195 , GLY B:200 , ALA B:201
BINDING SITE FOR RESIDUE BNG B 312
15
BC6
SOFTWARE
ARG A:232 , ARG B:168 , SER B:169 , VAL B:172 , HOH B:700 , HOH B:704 , HOH B:708
BINDING SITE FOR RESIDUE SO4 B 401
16
BC7
SOFTWARE
VAL A:38 , ARG A:44 , HOH A:701 , TRP B:36 , VAL B:38 , THR B:39 , ARG B:44
BINDING SITE FOR RESIDUE SO4 B 402
17
BC8
SOFTWARE
TRP B:91 , THR B:94 , THR B:95 , TRP B:143 , SER B:146 , TRP B:187 , TYR B:190 , PRO B:191 , ASP B:217 , LYS B:221
BINDING SITE FOR RESIDUE RET B 261
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: BACTERIAL_OPSIN_1 (A:87-99,B:87-99)
2: BACTERIAL_OPSIN_RET (A:213-224,B:213-224)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BACTERIAL_OPSIN_1
PS00950
Bacterial rhodopsins signature 1.
BACR2_HALS2
93-105
2
A:87-99
B:87-99
2
BACTERIAL_OPSIN_RET
PS00327
Bacterial rhodopsins retinal binding site.
BACR2_HALS2
219-230
2
A:213-224
B:213-224
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1vgoa_ (A:)
1b: SCOP_d1vgob_ (B:)
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(
)
(
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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
:
Bacteriorhodopsin-like
(107)
Protein domain
:
automated matches
(33)
Halobacterium sp. [TaxId: 29285]
(3)
1a
d1vgoa_
A:
1b
d1vgob_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1vgoB00 (B:5-239)
1b: CATH_1vgoA00 (A:5-237)
View:
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(
)
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)
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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)
Halobacterium sp.. Organism_taxid: 29285. Strain: aus-2
(1)
1a
1vgoB00
B:5-239
1b
1vgoA00
A:5-237
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Bac_rhodopsin_1vgoB01 (B:14-239)
1b: PFAM_Bac_rhodopsin_1vgoB02 (B:14-239)
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(
)
Organisms
(
)
(
)
Clan
:
GPCR_A
(90)
Family
:
Bac_rhodopsin
(43)
Halobacterium sp. (strain aus-2)
(1)
1a
Bac_rhodopsin-1vgoB01
B:14-239
1b
Bac_rhodopsin-1vgoB02
B:14-239
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]
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