PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4HYJ
Asym. Unit
Info
Asym.Unit (167 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (80 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF EXIGUOBACTERIUM SIBIRICUM RHODOPSIN
Authors
:
I. Gushchin, P. Chervakov, P. Kuzmichev, A. Popov, E. Round, V. Borshch D. Dolgikh, M. Kirpichnikov, L. Petrovskaya, V. Chupin, A. Arseniev, V. Gordeliy
Date
:
13 Nov 12 (Deposition) - 17 Jul 13 (Release) - 11 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Seven-Helical Transmembrane Protein, Proton Pump, Membrane, Proton Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Gushchin, P. Chervakov, P. Kuzmichev, A. N. Popov, E. Round, V. Borshchevskiy, A. Ishchenko, L. Petrovskaya, V. Chupin, D. A. Dolgikh, A. A. Arseniev, M. Kirpichnikov, V. Gordeliy
Structural Insights Into The Proton Pumping By Unusual Proteorhodopsin From Nonmarine Bacteria.
Proc. Natl. Acad. Sci. Usa V. 110 12631 2013
[
close entry info
]
Hetero Components
(2, 32)
Info
All Hetero Components
1a: EICOSANE (LFAa)
1aa: EICOSANE (LFAaa)
1ab: EICOSANE (LFAab)
1ac: EICOSANE (LFAac)
1ad: EICOSANE (LFAad)
1b: EICOSANE (LFAb)
1c: EICOSANE (LFAc)
1d: EICOSANE (LFAd)
1e: EICOSANE (LFAe)
1f: EICOSANE (LFAf)
1g: EICOSANE (LFAg)
1h: EICOSANE (LFAh)
1i: EICOSANE (LFAi)
1j: EICOSANE (LFAj)
1k: EICOSANE (LFAk)
1l: EICOSANE (LFAl)
1m: EICOSANE (LFAm)
1n: EICOSANE (LFAn)
1o: EICOSANE (LFAo)
1p: EICOSANE (LFAp)
1q: EICOSANE (LFAq)
1r: EICOSANE (LFAr)
1s: EICOSANE (LFAs)
1t: EICOSANE (LFAt)
1u: EICOSANE (LFAu)
1v: EICOSANE (LFAv)
1w: EICOSANE (LFAw)
1x: EICOSANE (LFAx)
1y: EICOSANE (LFAy)
1z: EICOSANE (LFAz)
2a: RETINAL (RETa)
2b: RETINAL (RETb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LFA
30
Ligand/Ion
EICOSANE
2
RET
2
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
TYR A:83 , TRP A:86 , MET A:122 , GLY A:126 , TYR A:147 , GLY A:150 , CYS A:151 , TRP A:154 , TRP A:191 , TYR A:194 , PRO A:195 , TYR A:198 , LYS A:225
BINDING SITE FOR RESIDUE RET A 301
02
AC2
SOFTWARE
LFA A:308
BINDING SITE FOR RESIDUE LFA A 302
03
AC3
SOFTWARE
PRO A:38 , THR A:45 , LEU A:49 , LFA A:305 , VAL B:53 , PHE B:60 , ILE B:81 , ILE B:84
BINDING SITE FOR RESIDUE LFA A 304
04
AC4
SOFTWARE
VAL A:88 , LFA A:304 , LEU B:49
BINDING SITE FOR RESIDUE LFA A 305
05
AC5
SOFTWARE
LYS A:114 , ILE A:117 , PHE A:152 , TYR A:156 , LFA A:312
BINDING SITE FOR RESIDUE LFA A 306
06
AC6
SOFTWARE
PHE A:186
BINDING SITE FOR RESIDUE LFA A 307
07
AC7
SOFTWARE
VAL A:212 , LFA A:302
BINDING SITE FOR RESIDUE LFA A 308
08
AC8
SOFTWARE
LYS A:62
BINDING SITE FOR RESIDUE LFA A 310
09
AC9
SOFTWARE
VAL A:124 , LFA B:317
BINDING SITE FOR RESIDUE LFA A 311
10
BC1
SOFTWARE
LFA A:306
BINDING SITE FOR RESIDUE LFA A 312
11
BC2
SOFTWARE
ILE A:193 , ILE A:216
BINDING SITE FOR RESIDUE LFA A 313
12
BC3
SOFTWARE
TYR B:83 , TRP B:86 , THR B:90 , MET B:122 , GLY B:126 , TYR B:147 , GLY B:150 , CYS B:151 , TRP B:191 , TYR B:194 , ASP B:221 , LYS B:225
BINDING SITE FOR RESIDUE RET B 301
13
BC4
SOFTWARE
LEU A:92 , VAL A:95 , GLU B:80 , ILE B:84
BINDING SITE FOR RESIDUE LFA B 302
14
BC5
SOFTWARE
THR B:45
BINDING SITE FOR RESIDUE LFA B 303
15
BC6
SOFTWARE
LYS B:62
BINDING SITE FOR RESIDUE LFA B 304
16
BC7
SOFTWARE
ILE A:158 , PHE A:162 , THR A:163 , LFA B:319
BINDING SITE FOR RESIDUE LFA B 305
17
BC8
SOFTWARE
LEU B:27
BINDING SITE FOR RESIDUE LFA B 306
18
BC9
SOFTWARE
PHE A:203 , LFA B:308 , LFA B:310
BINDING SITE FOR RESIDUE LFA B 307
19
CC1
SOFTWARE
PHE A:139 , PHE A:203 , LFA B:307
BINDING SITE FOR RESIDUE LFA B 308
20
CC2
SOFTWARE
GLU A:80 , TYR A:127 , VAL B:95 , LEU B:103 , ARG B:109
BINDING SITE FOR RESIDUE LFA B 309
21
CC3
SOFTWARE
LEU B:185 , LFA B:307
BINDING SITE FOR RESIDUE LFA B 310
22
CC4
SOFTWARE
THR B:223
BINDING SITE FOR RESIDUE LFA B 311
23
CC5
SOFTWARE
GLN B:141 , TRP B:145
BINDING SITE FOR RESIDUE LFA B 312
24
CC6
SOFTWARE
PHE A:152 , GLN B:141 , TRP B:145
BINDING SITE FOR RESIDUE LFA B 313
25
CC7
SOFTWARE
PHE B:52 , TYR B:59
BINDING SITE FOR RESIDUE LFA B 314
26
CC8
SOFTWARE
TYR B:156
BINDING SITE FOR RESIDUE LFA B 315
27
CC9
SOFTWARE
PHE A:234 , TYR B:13 , LFA B:318
BINDING SITE FOR RESIDUE LFA B 316
28
DC1
SOFTWARE
LFA A:311 , ILE B:121
BINDING SITE FOR RESIDUE LFA B 317
29
DC2
SOFTWARE
TYR A:28 , LEU A:230 , TRP B:16 , VAL B:20 , LFA B:316
BINDING SITE FOR RESIDUE LFA B 318
30
DC3
SOFTWARE
LFA B:305
BINDING SITE FOR RESIDUE LFA B 319
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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, 2)
Info
All SCOP Domains
1a: SCOP_d4hyja_ (A:)
1b: SCOP_d4hyjb_ (B:)
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)
Exiguobacterium sibiricum [TaxId: 332410]
(1)
1a
d4hyja_
A:
1b
d4hyjb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (167 KB)
Header - Asym.Unit
Biol.Unit 1 (82 KB)
Header - Biol.Unit 1
Biol.Unit 2 (80 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4HYJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help