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Asym. Unit
Info
Asym.Unit (255 KB)
Biol.Unit 1 (126 KB)
Biol.Unit 2 (126 KB)
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(1)
Title
:
AN M-LIKE REACTION STATE OF THE AZIDE-BOUND PURPLE FORM OF PHARAONIS HALORHODOPSIN
Authors
:
T. Kouyama, T. Nakanishi
Date
:
26 Jul 12 (Deposition) - 19 Jun 13 (Release) - 19 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Seven-Transmembrane-Retinylidene Protein, Chloride-Bound Purple Form, Light-Driven Chloride Ion Pump, Azide-Bound Purple Form, Light- Driven Proton Pump, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Nakanishi, S. Kanada, M. Murakami, K. Ihara, T. Kouyama
Large Deformation Of Helix F During The Photoreaction Cycle Of Pharaonis Halorhodopsin In Complex With Azide
Biophys. J. V. 104 377 2013
[
close entry info
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Hetero Components
(5, 19)
Info
All Hetero Components
1a: BACTERIORUBERIN (22Ba)
1b: BACTERIORUBERIN (22Bb)
2a: AZIDE ION (AZIa)
2b: AZIDE ION (AZIb)
2c: AZIDE ION (AZIc)
3a: B-NONYLGLUCOSIDE (BNGa)
3b: B-NONYLGLUCOSIDE (BNGb)
3c: B-NONYLGLUCOSIDE (BNGc)
3d: B-NONYLGLUCOSIDE (BNGd)
4a: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pa)
4b: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pb)
4c: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pc)
4d: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pd)
5a: RETINAL (RETa)
5b: RETINAL (RETb)
5c: RETINAL (RETc)
5d: RETINAL (RETd)
5e: RETINAL (RETe)
5f: RETINAL (RETf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
22B
2
Ligand/Ion
BACTERIORUBERIN
2
AZI
3
Ligand/Ion
AZIDE ION
3
BNG
4
Ligand/Ion
B-NONYLGLUCOSIDE
4
L3P
4
Ligand/Ion
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
5
RET
6
Ligand/Ion
RETINAL
[
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Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:127 , SER A:130 , THR A:131 , MET A:159 , GLY A:163 , TYR A:180 , SER A:183 , PHE A:187 , TRP A:222 , TYR A:225 , TRP A:229 , LYS A:256 , THR D:131 , TYR D:180 , CYS D:184 , PHE D:187 , TRP D:222 , TYR D:225 , PRO D:226 , TRP D:229 , LYS D:256
BINDING SITE FOR RESIDUE RET A 301
02
AC2
SOFTWARE
ALA A:98 , GLY A:99 , HIS A:173 , LEU A:174 , TRP A:177 , ASP B:209 , BNG B:302 , ALA D:98 , GLY D:99 , HIS D:173 , BNG D:304 , ASP E:209
BINDING SITE FOR RESIDUE BNG A 302
03
AC3
SOFTWARE
PHE A:25 , GLU A:26 , ASP C:209 , PHE D:25 , GLU D:26 , LEU F:174 , MET F:175
BINDING SITE FOR RESIDUE BNG A 303
04
AC4
SOFTWARE
TYR B:124 , TRP B:127 , THR B:131 , MET B:159 , SER B:183 , PHE B:187 , TRP B:222 , TYR B:225 , PRO B:226 , TRP B:229 , ALA B:255 , LYS B:256 , TRP E:127 , THR E:131 , ILE E:134 , TYR E:225 , PRO E:226 , ASP E:252 , ALA E:255
BINDING SITE FOR RESIDUE RET B 301
05
AC5
SOFTWARE
BNG A:302 , HOH A:525 , PHE B:25 , GLU B:26 , ASP B:209 , SER B:269 , ASN B:270 , HOH B:449 , LEU D:174 , PHE E:25 , ASP E:209 , ASN E:270
BINDING SITE FOR RESIDUE BNG B 302
06
AC6
SOFTWARE
TYR C:124 , TRP C:127 , SER C:130 , THR C:131 , MET C:159 , TYR C:180 , SER C:183 , PHE C:187 , TRP C:222 , TYR C:225 , TRP C:229 , ASP C:252 , ALA C:255 , LYS C:256 , TRP F:127 , THR F:131 , MET F:159 , GLY F:163 , TYR F:180 , SER F:183 , PHE F:187 , TRP F:222 , TYR F:225
BINDING SITE FOR RESIDUE RET C 301
07
AC7
SOFTWARE
ILE A:49 , THR A:56 , THR C:151 , PHE C:155 , ILE C:193 , HOH C:437 , ILE D:49 , VAL D:53 , THR D:56 , THR F:151 , PHE F:155
BINDING SITE FOR RESIDUE 22B C 302
08
AC8
SOFTWARE
VAL C:19 , ALA C:80 , VAL E:161 , LEU E:164 , LEU E:168 , TRP E:179 , ALA F:80 , SER F:92
BINDING SITE FOR RESIDUE L3P C 303
09
AC9
SOFTWARE
ALA A:80 , LEU A:89 , TRP A:121 , LEU A:125 , ALA C:158 , VAL C:161 , LEU C:168 , VAL D:77 , ALA D:80 , LEU D:89 , TRP D:121 , LEU D:125 , LEU D:129 , VAL F:161
BINDING SITE FOR RESIDUE L3P C 304
10
BC1
SOFTWARE
TRP A:127 , SER A:130 , THR A:131 , MET A:159 , GLY A:163 , SER A:183 , PHE A:187 , TRP A:222 , TYR A:225 , ASP A:252 , TRP D:127 , THR D:131 , MET D:159 , TYR D:180 , SER D:183 , CYS D:184 , PHE D:187 , TRP D:222 , TYR D:225 , ASP D:252 , LYS D:256
BINDING SITE FOR RESIDUE RET D 301
11
BC2
SOFTWARE
VAL A:161 , THR D:154 , ALA D:158 , VAL D:161
BINDING SITE FOR RESIDUE L3P D 302
12
BC3
SOFTWARE
SER A:78 , TRP A:127 , SER A:130 , LYS A:256 , SER D:78 , SER D:81 , THR D:126 , TRP D:127 , SER D:130 , LYS D:256 , HOH D:504
BINDING SITE FOR RESIDUE AZI D 303
13
BC4
SOFTWARE
GLY A:99 , HIS A:173 , TRP A:177 , BNG A:302 , GLY D:99 , PHE D:101
BINDING SITE FOR RESIDUE BNG D 304
14
BC5
SOFTWARE
TRP B:127 , SER B:130 , THR B:131 , MET B:159 , GLY B:163 , TYR B:180 , SER B:183 , CYS B:184 , PHE B:187 , TYR B:225 , TRP B:229 , ASP B:252 , TRP E:127 , THR E:131 , MET E:159 , GLY E:163 , TYR E:180 , SER E:183 , TRP E:222 , TYR E:225 , PRO E:226 , ASP E:252 , LYS E:256
BINDING SITE FOR RESIDUE RET E 301
15
BC6
SOFTWARE
LYS A:148 , THR A:151 , PHE A:155 , VAL A:189 , ILE B:49 , THR B:56 , VAL B:69 , ILE B:72 , LYS D:148 , PHE D:155 , ALA D:185 , TYR D:192 , GLU D:197 , ILE E:49 , LEU E:50 , VAL E:53 , THR E:56 , LYS E:65 , HOH E:536
BINDING SITE FOR RESIDUE 22B E 302
16
BC7
SOFTWARE
PHE E:150 , ILE E:153 , ILE E:157 , ALA E:158 , VAL E:161 , LEU F:129 , MET F:133
BINDING SITE FOR RESIDUE L3P E 303
17
BC8
SOFTWARE
TRP B:127 , SER B:130 , LYS B:256 , SER E:78 , SER E:81 , THR E:126 , TRP E:127 , SER E:130 , LYS E:256
BINDING SITE FOR RESIDUE AZI E 304
18
BC9
SOFTWARE
TRP C:127 , SER C:130 , THR C:131 , MET C:159 , TYR C:180 , SER C:183 , CYS C:184 , PHE C:187 , TRP C:222 , TYR C:225 , PRO C:226 , TRP C:229 , ASP C:252 , TRP F:127 , THR F:131 , MET F:159 , TYR F:180 , SER F:183 , PHE F:187 , TRP F:222 , TYR F:225 , LYS F:256
BINDING SITE FOR RESIDUE RET F 301
19
CC1
SOFTWARE
SER C:78 , TYR C:82 , TRP C:127 , SER C:130 , LYS C:256 , SER F:78 , SER F:81 , THR F:126 , TRP F:127 , SER F:130 , LYS F:256 , HOH F:404
BINDING SITE FOR RESIDUE AZI F 302
[
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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, 12)
Info
All PROSITE Patterns/Profiles
1: BACTERIAL_OPSIN_1 (A:123-135,B:123-135,C:123-135,D:12...)
2: BACTERIAL_OPSIN_RET (A:248-259,B:248-259,C:248-259,D:24...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BACTERIAL_OPSIN_1
PS00950
Bacterial rhodopsins signature 1.
BACH_NATPH
123-135
6
A:123-135
B:123-135
C:123-135
D:123-135
E:123-135
F:123-135
2
BACTERIAL_OPSIN_RET
PS00327
Bacterial rhodopsins retinal binding site.
BACH_NATPH
248-259
6
A:248-259
B:248-259
C:248-259
D:248-259
E:248-259
F:248-259
[
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Exons
(0, 0)
Info
All Exons
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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, 6)
Info
All SCOP Domains
1a: SCOP_d3vvka_ (A:)
1b: SCOP_d3vvkb_ (B:)
1c: SCOP_d3vvkc_ (C:)
1d: SCOP_d3vvkd_ (D:)
1e: SCOP_d3vvke_ (E:)
1f: SCOP_d3vvkf_ (F:)
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Protein Domains
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Organisms
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)
(
)
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
:
automated matches
(15)
Protein domain
:
automated matches
(15)
Natronomonas pharaonis [TaxId: 2257]
(5)
1a
d3vvka_
A:
1b
d3vvkb_
B:
1c
d3vvkc_
C:
1d
d3vvkd_
D:
1e
d3vvke_
E:
1f
d3vvkf_
F:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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