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3A7K
Asym. Unit
Info
Asym.Unit (144 KB)
Biol.Unit 1 (135 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HALORHODOPSIN FROM NATRONOMONAS PHARAONIS
Authors
:
T. Kouyama
Date
:
27 Sep 09 (Deposition) - 15 Dec 09 (Release) - 02 Mar 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,D
Biol. Unit 1: A,B,D (1x)
Keywords
:
Light-Driven Chloride Ion Pump, Trimeric Bacterioruberin- Protein Complex, Retinal Protein, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Kouyama, S. Kanada, Y. Takeguchi, A. Narusawa, M. Murakami, K. Ihara
Crystal Structure Of The Light-Driven Chloride Pump Halorhodopsin From Natronomonas Pharaonis.
J. Mol. Biol. V. 396 564 2010
[
close entry info
]
Hetero Components
(6, 30)
Info
All Hetero Components
1a: BACTERIORUBERIN (22Ba)
1b: BACTERIORUBERIN (22Bb)
1c: BACTERIORUBERIN (22Bc)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYC... (L1Pa)
3b: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYC... (L1Pb)
3c: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYC... (L1Pc)
4a: 2,3-DI-PHYTANYL-GLYCEROL (L2Pa)
4b: 2,3-DI-PHYTANYL-GLYCEROL (L2Pb)
4c: 2,3-DI-PHYTANYL-GLYCEROL (L2Pc)
4d: 2,3-DI-PHYTANYL-GLYCEROL (L2Pd)
4e: 2,3-DI-PHYTANYL-GLYCEROL (L2Pe)
4f: 2,3-DI-PHYTANYL-GLYCEROL (L2Pf)
5a: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pa)
5b: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pb)
5c: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pc)
5d: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pd)
5e: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pe)
5f: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pf)
5g: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pg)
5h: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Ph)
5i: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-P... (L3Pi)
6a: RETINAL (RETa)
6b: RETINAL (RETb)
6c: RETINAL (RETc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
22B
3
Ligand/Ion
BACTERIORUBERIN
2
CL
6
Ligand/Ion
CHLORIDE ION
3
L1P
3
Ligand/Ion
3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
4
L2P
6
Ligand/Ion
2,3-DI-PHYTANYL-GLYCEROL
5
L3P
9
Ligand/Ion
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
6
RET
3
Ligand/Ion
RETINAL
[
close Hetero Component info
]
Sites
(30, 30)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:127 , THR A:131 , MET A:159 , TYR A:180 , SER A:183 , PHE A:187 , TRP A:222 , TYR A:225 , ASP A:252 , LYS A:256
BINDING SITE FOR RESIDUE RET A 292
02
AC2
SOFTWARE
LEU A:29 , GLY A:46 , THR A:56 , LYS A:65 , ILE A:72 , THR D:151 , PHE D:155 , ALA D:185 , GLU D:197
BINDING SITE FOR RESIDUE 22B A 300
03
AC3
SOFTWARE
LEU A:89 , HOH A:552 , SER D:92 , LEU D:94 , TRP D:121 , LEU D:125 , VAL D:161 , LEU D:164 , LEU D:168
BINDING SITE FOR RESIDUE L1P A 293
04
AC4
SOFTWARE
ALA A:146 , PHE A:150 , ILE A:153 , THR A:154 , ILE A:157 , ALA A:158 , L2P A:295 , VAL B:77 , ALA B:80 , L2P B:295
BINDING SITE FOR RESIDUE L2P A 294
05
AC5
SOFTWARE
MET A:133 , LEU A:136 , ILE A:157 , L2P A:294 , L2P D:294
BINDING SITE FOR RESIDUE L2P A 295
06
AC6
SOFTWARE
LEU A:195 , GLN A:200
BINDING SITE FOR RESIDUE L3P A 331
07
AC7
SOFTWARE
ILE A:188 , TYR A:192
BINDING SITE FOR RESIDUE L3P A 296
08
AC8
SOFTWARE
SER A:172 , LEU A:174 , PHE A:178 , PHE B:25 , ASN B:270
BINDING SITE FOR RESIDUE L3P A 297
09
AC9
SOFTWARE
LEU A:29 , LEU D:174
BINDING SITE FOR RESIDUE L3P A 298
10
BC1
SOFTWARE
L2P B:295
BINDING SITE FOR RESIDUE L3P A 299
11
BC2
SOFTWARE
TRP A:177 , TYR A:180 , CYS A:184
BINDING SITE FOR RESIDUE L3P A 301
12
BC3
SOFTWARE
SER A:36 , VAL A:238 , LEU A:239 , TYR A:243 , TRP A:246 , ALA A:250
BINDING SITE FOR RESIDUE L3P A 333
13
BC4
SOFTWARE
THR A:126 , SER A:130 , LYS A:256
BINDING SITE FOR RESIDUE CL A 401
14
BC5
SOFTWARE
ASN A:145 , PRO B:62 , HOH B:527 , HOH B:531
BINDING SITE FOR RESIDUE CL A 402
15
BC6
SOFTWARE
THR A:147 , THR A:151 , PHE A:155 , ALA A:185 , VAL A:189 , ALA B:43 , GLY B:46 , ILE B:49 , VAL B:53 , THR B:56 , ILE B:72 , VAL B:273 , HOH B:531
BINDING SITE FOR RESIDUE 22B B 300
16
BC7
SOFTWARE
TYR B:180 , PHE D:54
BINDING SITE FOR RESIDUE L3P B 331
17
BC8
SOFTWARE
TRP B:127 , THR B:131 , MET B:159 , TYR B:180 , SER B:183 , PHE B:187 , TRP B:222 , TYR B:225 , PRO B:226 , ASP B:252 , LYS B:256
BINDING SITE FOR RESIDUE RET B 292
18
BC9
SOFTWARE
THR B:126 , SER B:130 , LYS B:256 , HOH B:502
BINDING SITE FOR RESIDUE CL B 401
19
CC1
SOFTWARE
VAL A:19 , SER A:92 , VAL A:93 , LEU A:125 , VAL A:161 , ALA A:165 , VAL B:19 , ALA B:80 , LEU B:89 , THR B:90 , LEU B:125
BINDING SITE FOR RESIDUE L1P B 293
20
CC2
SOFTWARE
ASN B:145
BINDING SITE FOR RESIDUE CL B 402
21
CC3
SOFTWARE
SER B:92 , LEU B:94 , TRP B:121 , LEU B:125 , ILE B:157 , VAL B:161 , ALA B:165 , HOH B:541 , ALA D:80 , LEU D:89 , LEU D:125 , THR D:126
BINDING SITE FOR RESIDUE L1P B 294
22
CC4
SOFTWARE
PHE B:101 , THR B:147 , LYS B:148 , THR B:151 , PHE B:155 , ILE B:182 , ILE B:193 , GLU B:197 , ILE D:49 , THR D:56 , LYS D:65 , VAL D:69 , ILE D:72 , VAL D:76 , ILE D:79
BINDING SITE FOR RESIDUE 22B D 300
23
CC5
SOFTWARE
ALA A:146 , PHE A:150 , L2P A:294 , L3P A:299 , ALA B:128 , LEU B:129 , MET B:133 , LEU B:136 , ILE B:153 , ILE B:157 , L2P B:296
BINDING SITE FOR RESIDUE L2P B 295
24
CC6
SOFTWARE
ALA B:146 , PHE B:150 , ILE B:153 , THR B:154 , ILE B:157 , ALA B:158 , VAL B:161 , L2P B:295
BINDING SITE FOR RESIDUE L2P B 296
25
CC7
SOFTWARE
LEU D:174
BINDING SITE FOR RESIDUE L3P D 330
26
CC8
SOFTWARE
TRP D:127 , THR D:131 , MET D:159 , GLY D:163 , TYR D:180 , SER D:183 , TRP D:222 , TYR D:225 , PRO D:226 , TRP D:229 , ASP D:252 , LYS D:256
BINDING SITE FOR RESIDUE RET D 292
27
CC9
SOFTWARE
THR D:126 , TRP D:127 , SER D:130 , LYS D:256 , HOH D:502
BINDING SITE FOR RESIDUE CL D 401
28
DC1
SOFTWARE
PRO A:62 , LYS A:65 , ASN D:145 , LYS D:148
BINDING SITE FOR RESIDUE CL D 402
29
DC2
SOFTWARE
PHE B:150 , LEU D:66 , ALA D:128 , MET D:133 , LEU D:136 , ILE D:157
BINDING SITE FOR RESIDUE L2P D 293
30
DC3
SOFTWARE
L2P A:295 , SER D:144 , ALA D:146 , LEU D:149 , ILE D:153 , THR D:154 , ILE D:157
BINDING SITE FOR RESIDUE L2P D 294
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3a7ka_ (A:)
1b: SCOP_d3a7kb_ (B:)
1c: SCOP_d3a7kd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
automated matches
(15)
Protein domain
:
automated matches
(15)
Natronomonas pharaonis [TaxId: 348780]
(2)
1a
d3a7ka_
A:
1b
d3a7kb_
B:
1c
d3a7kd_
D:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_3a7kB00 (B:19-276)
1b: CATH_3a7kA00 (A:19-277)
1c: CATH_3a7kD00 (D:19-277)
View:
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Classes
(
)
(
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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)
Natronomonas pharaonis dsm 2160. Organism_taxid: 348780.
(1)
1a
3a7kB00
B:19-276
1b
3a7kA00
A:19-277
1c
3a7kD00
D:19-277
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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