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3DDL
Asym. Unit
Info
Asym.Unit (96 KB)
Biol.Unit 1 (46 KB)
Biol.Unit 2 (48 KB)
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(1)
Title
:
CRYSTALLOGRAPHIC STRUCTURE OF XANTHORHODOPSIN, A LIGHT-DRIVEN ION PUMP WITH DUAL CHROMOPHORE
Authors
:
J. Stagno, H. Luecke, B. Schobert, J. K. Lanyi, E. S. Imasheva, J. M. Wang S. P. Balashov
Date
:
05 Jun 08 (Deposition) - 14 Oct 08 (Release) - 08 Jun 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Rhodopsin, Carotenoid, Ion Pump, Light-Harvesting, Antenna, Retinal, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Luecke, B. Schobert, J. Stagno, E. S. Imasheva, J. M. Wang, S. P. Balashov, J. K. Lanyi
Crystallographic Structure Of Xanthorhodopsin, The Light-Driven Proton Pump With A Dual Chromophore.
Proc. Natl. Acad. Sci. Usa V. 105 16561 2008
[
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Hetero Components
(5, 27)
Info
All Hetero Components
1a: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOC... (PCWa)
2a: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSP... (PX4a)
3a: RETINAL (RETa)
3b: RETINAL (RETb)
4a: SALINIXANTHIN (SXNa)
4b: SALINIXANTHIN (SXNb)
5a: UNKNOWN LIGAND (UNLa)
5b: UNKNOWN LIGAND (UNLb)
5c: UNKNOWN LIGAND (UNLc)
5d: UNKNOWN LIGAND (UNLd)
5e: UNKNOWN LIGAND (UNLe)
5f: UNKNOWN LIGAND (UNLf)
5g: UNKNOWN LIGAND (UNLg)
5h: UNKNOWN LIGAND (UNLh)
5i: UNKNOWN LIGAND (UNLi)
5j: UNKNOWN LIGAND (UNLj)
5k: UNKNOWN LIGAND (UNLk)
5l: UNKNOWN LIGAND (UNLl)
5m: UNKNOWN LIGAND (UNLm)
5n: UNKNOWN LIGAND (UNLn)
5o: UNKNOWN LIGAND (UNLo)
5p: UNKNOWN LIGAND (UNLp)
5q: UNKNOWN LIGAND (UNLq)
5r: UNKNOWN LIGAND (UNLr)
5s: UNKNOWN LIGAND (UNLs)
5t: UNKNOWN LIGAND (UNLt)
5u: UNKNOWN LIGAND (UNLu)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PCW
1
Ligand/Ion
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
2
PX4
1
Ligand/Ion
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3
RET
2
Ligand/Ion
RETINAL
4
SXN
2
Ligand/Ion
SALINIXANTHIN
5
UNL
21
Ligand/Ion
UNKNOWN LIGAND
[
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]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:148 , GLY A:156 , THR A:160 , ARG A:184 , ASN A:191 , LEU A:194 , ALA A:198 , TYR A:207 , MET A:208 , MET A:211 , UNL A:1408
BINDING SITE FOR RESIDUE SXN A1401
02
AC2
SOFTWARE
MET A:19 , ILE A:234
BINDING SITE FOR RESIDUE UNL A1402
03
AC3
SOFTWARE
PRO A:139
BINDING SITE FOR RESIDUE UNL A1403
04
AC4
SOFTWARE
LEU A:36 , LEU B:154
BINDING SITE FOR RESIDUE UNL A1404
05
AC5
SOFTWARE
SER A:21 , PHE A:22 , UNL B:1403
BINDING SITE FOR RESIDUE UNL A1405
06
AC6
SOFTWARE
PHE A:202
BINDING SITE FOR RESIDUE UNL A1406
07
AC7
SOFTWARE
TYR A:168 , PHE A:171
BINDING SITE FOR RESIDUE UNL A1407
08
AC8
SOFTWARE
GLY A:242 , ASN A:249 , SXN A:1401
BINDING SITE FOR RESIDUE UNL A1408
09
AC9
SOFTWARE
VAL A:164 , TYR A:168
BINDING SITE FOR RESIDUE UNL A1409
10
BC1
SOFTWARE
TRP A:97 , VAL A:101 , MET A:133 , SER A:159 , PHE A:163 , TRP A:200 , TYR A:203 , ASP A:236 , ALA A:239 , LYS A:240
BINDING SITE FOR RESIDUE RET A1301
11
BC2
SOFTWARE
LEU B:148 , GLY B:156 , THR B:160 , ARG B:184 , ASN B:191 , LEU B:194 , ALA B:198 , TYR B:207 , MET B:211 , PCW B:1416
BINDING SITE FOR RESIDUE SXN B1401
12
BC3
SOFTWARE
GLY A:11 , PRO B:102 , PHE B:128
BINDING SITE FOR RESIDUE UNL B1402
13
BC4
SOFTWARE
UNL A:1405 , LYS B:125 , TRP B:165
BINDING SITE FOR RESIDUE UNL B1403
14
BC5
SOFTWARE
THR B:28 , GLY B:60
BINDING SITE FOR RESIDUE UNL B1404
15
BC6
SOFTWARE
LEU B:148 , GLY B:153 , LEU B:154
BINDING SITE FOR RESIDUE UNL B1405
16
BC7
SOFTWARE
PHE B:202
BINDING SITE FOR RESIDUE UNL B1406
17
BC8
SOFTWARE
LEU B:197
BINDING SITE FOR RESIDUE UNL B1408
18
BC9
SOFTWARE
LEU A:136 , VAL B:32 , UNL B:1412
BINDING SITE FOR RESIDUE UNL B1409
19
CC1
SOFTWARE
VAL B:164 , TRP B:165
BINDING SITE FOR RESIDUE UNL B1410
20
CC2
SOFTWARE
PX4 B:1415
BINDING SITE FOR RESIDUE UNL B1411
21
CC3
SOFTWARE
VAL B:24 , THR B:67 , GLU B:71 , UNL B:1409
BINDING SITE FOR RESIDUE UNL B1412
22
CC4
SOFTWARE
MET B:50 , PHE B:57
BINDING SITE FOR RESIDUE UNL B1413
23
CC5
SOFTWARE
TRP B:97 , VAL B:101 , MET B:133 , SER B:159 , TRP B:200 , TYR B:203 , ASP B:236 , ALA B:239 , LYS B:240
BINDING SITE FOR RESIDUE RET B1301
24
CC6
SOFTWARE
VAL A:106 , GLY A:120 , ALA A:123 , PHE A:128 , THR B:9 , GLY B:11 , UNL B:1411 , PCW B:1416
BINDING SITE FOR RESIDUE PX4 B1415
25
CC7
SOFTWARE
GLY B:242 , LEU B:246 , SXN B:1401 , PX4 B:1415
BINDING SITE FOR RESIDUE PCW B1416
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
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;
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Sorry, no Info available
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Exons
(0, 0)
Info
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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_d3ddla_ (A:)
1b: SCOP_d3ddlb_ (B:)
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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)
Salinibacter ruber [TaxId: 146919]
(1)
1a
d3ddla_
A:
1b
d3ddlb_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3ddlB00 (B:5-261)
1b: CATH_3ddlA00 (A:4-261)
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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)
Salinibacter ruber. Organism_taxid: 146919
(1)
1a
3ddlB00
B:5-261
1b
3ddlA00
A:4-261
[
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Pfam Domains
(0, 0)
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all PFAM domains
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