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3QDC
Asym. Unit
Info
Asym.Unit (89 KB)
Biol.Unit 1 (80 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NATRONOMONAS PHARAONIS SENSORY RHODOPSIN II IN THE ACTIVE STATE
Authors
:
I. Gushchin, A. Reshetnyak, V. Borshchevskiy, A. Ishchenko, E. Round, S. Grudinin, M. Engelhard, G. Buldt, V. Gordeliy
Date
:
18 Jan 11 (Deposition) - 14 Sep 11 (Release) - 28 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Phototaxis, Nphtrii, Membrane, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Gushchin, A. Reshetnyak, V. Borshchevskiy, A. Ishchenko, E. Round S. Grudinin, M. Engelhard, G. Buldt, V. Gordeliy
Active State Of Sensory Rhodopsin Ii: Structural Determinants For Signal Transfer And Proton Pumping.
J. Mol. Biol. V. 412 591 2011
[
close entry info
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Hetero Components
(4, 33)
Info
All Hetero Components
1a: B-OCTYLGLUCOSIDE (BOGa)
2a: 2,3-DI-PHYTANYL-GLYCEROL (L2Pa)
2b: 2,3-DI-PHYTANYL-GLYCEROL (L2Pb)
3a: EICOSANE (LFAa)
3aa: EICOSANE (LFAaa)
3ab: EICOSANE (LFAab)
3ac: EICOSANE (LFAac)
3b: EICOSANE (LFAb)
3c: EICOSANE (LFAc)
3d: EICOSANE (LFAd)
3e: EICOSANE (LFAe)
3f: EICOSANE (LFAf)
3g: EICOSANE (LFAg)
3h: EICOSANE (LFAh)
3i: EICOSANE (LFAi)
3j: EICOSANE (LFAj)
3k: EICOSANE (LFAk)
3l: EICOSANE (LFAl)
3m: EICOSANE (LFAm)
3n: EICOSANE (LFAn)
3o: EICOSANE (LFAo)
3p: EICOSANE (LFAp)
3q: EICOSANE (LFAq)
3r: EICOSANE (LFAr)
3s: EICOSANE (LFAs)
3t: EICOSANE (LFAt)
3u: EICOSANE (LFAu)
3v: EICOSANE (LFAv)
3w: EICOSANE (LFAw)
3x: EICOSANE (LFAx)
3y: EICOSANE (LFAy)
3z: EICOSANE (LFAz)
4a: RETINAL (RETa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BOG
1
Ligand/Ion
B-OCTYLGLUCOSIDE
2
L2P
2
Ligand/Ion
2,3-DI-PHYTANYL-GLYCEROL
3
LFA
29
Ligand/Ion
EICOSANE
4
RET
1
Ligand/Ion
RETINAL
[
close Hetero Component info
]
Sites
(32, 32)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:76 , THR A:79 , THR A:80 , VAL A:108 , MET A:109 , GLY A:112 , PHE A:127 , PHE A:134 , TRP A:171 , TYR A:174 , PRO A:175 , ASP A:201 , THR A:204 , LYS A:205
BINDING SITE FOR RESIDUE RET A 240
02
AC2
SOFTWARE
GLY A:3 , VAL A:132 , GLY A:136 , TYR A:139 , PRO A:144 , THR A:191 , VAL A:192 , ALA A:195 , HOH A:291 , HOH A:301
BINDING SITE FOR RESIDUE BOG A 241
03
AC3
SOFTWARE
TYR A:36 , TYR A:37 , LEU A:40 , LEU A:90 , ILE A:156 , LEU A:159 , ALA A:212 , ALA A:216
BINDING SITE FOR RESIDUE LFA A 242
04
AC4
SOFTWARE
LEU A:110 , PHE A:113 , ALA A:114 , MET A:117 , LFA A:247
BINDING SITE FOR RESIDUE LFA A 243
05
AC5
SOFTWARE
L2P A:257 , LFA A:266 , LFA A:272
BINDING SITE FOR RESIDUE LFA A 244
06
AC6
SOFTWARE
THR A:106 , L2P A:257
BINDING SITE FOR RESIDUE LFA A 245
07
AC7
SOFTWARE
VAL A:138 , TYR A:139 , VAL A:142
BINDING SITE FOR RESIDUE LFA A 246
08
AC8
SOFTWARE
ALA A:114 , ILE A:169 , LFA A:243
BINDING SITE FOR RESIDUE LFA A 247
09
AC9
SOFTWARE
ARG A:35 , THR A:39 , LFA A:264
BINDING SITE FOR RESIDUE LFA A 248
10
BC1
SOFTWARE
LEU A:110 , ALA A:111 , ALA A:114 , LEU A:126 , MET A:129 , LFA A:251
BINDING SITE FOR RESIDUE LFA A 249
11
BC2
SOFTWARE
TRP A:24 , PHE A:210 , LEU A:213 , ASP A:214 , LFA A:267 , HOH A:307
BINDING SITE FOR RESIDUE LFA A 250
12
BC3
SOFTWARE
THR A:103 , THR A:106 , VAL A:107 , PHE A:176 , LEU A:180 , LEU A:187 , LFA A:249 , LFA A:271
BINDING SITE FOR RESIDUE LFA A 251
13
BC4
SOFTWARE
TRP A:9 , LEU A:16 , VAL A:52 , LFA A:258 , LFA A:261 , LFA A:266
BINDING SITE FOR RESIDUE LFA A 252
14
BC5
SOFTWARE
TRP A:9 , ALA A:55 , GLY A:57 , LFA A:261
BINDING SITE FOR RESIDUE LFA A 253
15
BC6
SOFTWARE
ILE A:121 , TYR A:124 , ALA A:125 , GLY A:128 , VAL A:132 , TYR A:199 , ILE A:211 , LFA A:255 , L2P A:260 , LFA A:261 , LFA A:262 , LFA A:268
BINDING SITE FOR RESIDUE LFA A 254
16
BC7
SOFTWARE
TRP A:24 , ILE A:121 , TYR A:199 , LEU A:202 , VAL A:203 , GLY A:207 , PHE A:210 , ASP A:214 , LFA A:254 , LFA A:267
BINDING SITE FOR RESIDUE LFA A 255
17
BC8
SOFTWARE
VAL A:49 , ALA A:50 , VAL A:58 , GLY A:59 , PRO A:71 , ILE A:74 , ASP A:75 , LEU A:78 , PHE A:113 , LFA A:244 , LFA A:245 , LFA A:258 , LFA A:264 , LFA A:272 , HOH A:332
BINDING SITE FOR RESIDUE L2P A 257
18
BC9
SOFTWARE
LEU A:16 , VAL A:49 , LFA A:252 , L2P A:257
BINDING SITE FOR RESIDUE LFA A 258
19
CC1
SOFTWARE
THR A:6 , TRP A:9 , LFA A:261
BINDING SITE FOR RESIDUE LFA A 259
20
CC2
SOFTWARE
ALA A:131 , PHE A:134 , PHE A:176 , LEU A:179 , LFA A:254 , LFA A:262
BINDING SITE FOR RESIDUE L2P A 260
21
CC3
SOFTWARE
TRP A:9 , ILE A:13 , LFA A:252 , LFA A:253 , LFA A:254 , LFA A:259
BINDING SITE FOR RESIDUE LFA A 261
22
CC4
SOFTWARE
LEU A:20 , LFA A:254 , L2P A:260
BINDING SITE FOR RESIDUE LFA A 262
23
CC5
SOFTWARE
ARG A:35 , PRO A:81 , LEU A:82 , TYR A:85 , LFA A:265
BINDING SITE FOR RESIDUE LFA A 263
24
CC6
SOFTWARE
ALA A:23 , GLY A:26 , VAL A:41 , GLY A:42 , LFA A:248 , L2P A:257
BINDING SITE FOR RESIDUE LFA A 264
25
CC7
SOFTWARE
LEU A:93 , ASP A:94 , SER A:95 , PHE A:98 , ILE A:102 , LFA A:263
BINDING SITE FOR RESIDUE LFA A 265
26
CC8
SOFTWARE
LEU A:56 , VAL A:58 , LFA A:244 , LFA A:252 , LFA A:272
BINDING SITE FOR RESIDUE LFA A 266
27
CC9
SOFTWARE
LEU A:7 , LEU A:10 , GLY A:14 , VAL A:132 , LEU A:135 , ALA A:195 , VAL A:198 , TYR A:199 , LEU A:202 , LFA A:250 , LFA A:255 , LFA A:268
BINDING SITE FOR RESIDUE LFA A 267
28
DC1
SOFTWARE
GLY A:3 , LEU A:7 , LEU A:10 , LFA A:254 , LFA A:267 , LFA A:269
BINDING SITE FOR RESIDUE LFA A 268
29
DC2
SOFTWARE
TYR A:139 , LFA A:268
BINDING SITE FOR RESIDUE LFA A 269
30
DC3
SOFTWARE
SER A:95 , ARG A:96
BINDING SITE FOR RESIDUE LFA A 270
31
DC4
SOFTWARE
PHE A:176 , LEU A:180 , VAL A:185 , LEU A:187 , LFA A:251
BINDING SITE FOR RESIDUE LFA A 271
32
DC5
SOFTWARE
VAL A:58 , LFA A:244 , L2P A:257 , LFA A:266
BINDING SITE FOR RESIDUE LFA A 272
[
close Site info
]
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: BACTERIAL_OPSIN_1 (A:72-84)
2: BACTERIAL_OPSIN_RET (A:197-208)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BACTERIAL_OPSIN_1
PS00950
Bacterial rhodopsins signature 1.
BACS2_NATPH
72-84
1
A:72-84
2
BACTERIAL_OPSIN_RET
PS00327
Bacterial rhodopsins retinal binding site.
BACS2_NATPH
197-208
1
A:197-208
[
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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, 1)
Info
All SCOP Domains
1a: SCOP_d3qdca_ (A:)
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Classes
(
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(
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Folds
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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
:
Sensory rhodopsin II
(10)
Natronobacterium pharaonis [TaxId: 2257]
(10)
1a
d3qdca_
A:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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