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.
5H2P
Asym. Unit
Info
Asym.Unit (116 KB)
Biol.Unit 1 (316 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
A THREE DIMENSIONAL MOVIE OF STRUCTURAL CHANGES IN BACTERIORHODOPSIN: STRUCTURE OBTAINED 657 US AFTER PHOTOEXCITATION
Authors
:
A. Royant, E. Nango, T. Nakane, T. Tanaka, T. Arima, R. Neutze, S. Iwata
Date
:
15 Oct 16 (Deposition) - 21 Dec 16 (Release) - 01 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (3x)
Keywords
:
Bacteriorhodopsin, Xfel, Time-Resolved Serial Femtosecond Crystallography, Sacla, Proton Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Nango, A. Royant, M. Kubo, T. Nakane, C. Wickstrand, T. Kimura, T. Tanaka, K. Tono, C. Song, R. Tanaka, T. Arima, A. Yamashita, J. Kobayashi, T. Hosaka, E. Mizohata, P. Nogly, M. Sugahara, D. Nam, T. Nomura, T. Shimamura, D. Im, T. Fujiwara, Y. Yamanaka, B. Jeon, T. Nishizawa, K. Oda, M. Fukuda, R. Andersson, P. Bath, R. Dods, J. Davidsson, S. Matsuoka, S. Kawatake, M. Murata, O. Nureki, S. Owada T. Kameshima, T. Hatsui, Y. Joti, G. Schertler, M. Yabashi, A. N. Bondar, J. Standfuss, R. Neutze, S. Iwata
A Three-Dimensional Movie Of Structural Changes In Bacteriorhodopsin
Science V. 354 1552 2016
[
close entry info
]
Hetero Components
(10, 16)
Info
All Hetero Components
01a: TETRADECANE (C14a)
02a: DECANE (D10a)
03a: NONANE (DD9a)
04a: HEPTANE (HP6a)
05a: 2,3-DI-PHYTANYL-GLYCEROL (L2Pa)
05b: 2,3-DI-PHYTANYL-GLYCEROL (L2Pb)
05c: 2,3-DI-PHYTANYL-GLYCEROL (L2Pc)
06a: PENTADECANE (MYSa)
06b: PENTADECANE (MYSb)
07a: N-OCTANE (OCTa)
07b: N-OCTANE (OCTb)
07c: N-OCTANE (OCTc)
08a: RETINAL (RETa)
09a: TRIDECANE (TRDa)
10a: UNDECANE (UNDa)
10b: UNDECANE (UNDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C14
1
Ligand/Ion
TETRADECANE
2
D10
1
Ligand/Ion
DECANE
3
DD9
1
Ligand/Ion
NONANE
4
HP6
1
Ligand/Ion
HEPTANE
5
L2P
3
Ligand/Ion
2,3-DI-PHYTANYL-GLYCEROL
6
MYS
2
Ligand/Ion
PENTADECANE
7
OCT
3
Ligand/Ion
N-OCTANE
8
RET
1
Ligand/Ion
RETINAL
9
TRD
1
Ligand/Ion
TRIDECANE
10
UND
2
Ligand/Ion
UNDECANE
[
close Hetero Component info
]
Sites
(15, 15)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:86 , THR A:89 , THR A:90 , LEU A:93 , MET A:118 , TRP A:138 , SER A:141 , TRP A:182 , TYR A:185 , PRO A:186 , TRP A:189 , ASP A:212 , LYS A:216
binding site for residue RET A 301
02
AC2
SOFTWARE
ALA A:44 , LEU A:48 , PHE A:54 , THR A:107 , TYR A:147 , D10 A:304
binding site for residue L2P A 302
03
AC3
SOFTWARE
LEU A:149
binding site for residue TRD A 303
04
AC4
SOFTWARE
LEU A:22 , L2P A:302 , HP6 A:305
binding site for residue D10 A 304
05
AC5
SOFTWARE
D10 A:304
binding site for residue HP6 A 305
06
AC6
SOFTWARE
LYS A:172 , ASN A:176
binding site for residue OCT A 306
07
AC7
SOFTWARE
MYS A:308
binding site for residue OCT A 307
08
AC8
SOFTWARE
ILE A:191 , OCT A:307 , L2P A:310
binding site for residue MYS A 308
09
AC9
SOFTWARE
L2P A:310
binding site for residue UND A 309
10
AD1
SOFTWARE
TYR A:131 , TRP A:138 , ILE A:203 , MYS A:308 , UND A:309
binding site for residue L2P A 310
11
AD2
SOFTWARE
ILE A:52 , MET A:56 , TYR A:64 , TRP A:80 , ALA A:84 , PHE A:88 , GLY A:116 , ILE A:117 , GLY A:120 , LEU A:123 , VAL A:124 , C14 A:314
binding site for residue L2P A 311
12
AD3
SOFTWARE
TYR A:26
binding site for residue MYS A 312
13
AD4
SOFTWARE
ARG A:225
binding site for residue DD9 A 313
14
AD5
SOFTWARE
LEU A:87 , PRO A:91 , LEU A:95 , L2P A:311
binding site for residue C14 A 314
15
AD6
SOFTWARE
TYR A:26
binding site for residue OCT A 315
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (116 KB)
Header - Asym.Unit
Biol.Unit 1 (316 KB)
Header - Biol.Unit 1
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
5H2P
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help