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.
5LSE
Asym. Unit
Info
Asym.Unit (298 KB)
Biol.Unit 1 (287 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PHOTOSYNTHETIC REACTION CENTER MUTANT WITH GLU L212 REPLACED WITH ALA (CHAIN L, EL212W), ASP L213 REPLACED WITH ALA (CHAIN L, DL213A) AND LEU M215 REPLACED WITH ALA (CHAIN M, LM215A)
Authors
:
P. K. Fyfe, M. R. Jones
Date
:
25 Aug 16 (Deposition) - 09 Nov 16 (Release) - 09 Nov 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Transmembrane, Electron Transport, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. M. Friebe, D. J. Swainsbury, P. K. Fyfe, W. Van Der Heijden, M. R. Jones, R. N. Frese
On The Mechanism Of Ubiquinone Mediated Photocurrent Generation By A Reaction Center Based Photocathode.
Biochim. Biophys. Acta V. 1857 1925 2016
[
close entry info
]
Hetero Components
(9, 20)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL A (BCLa)
1b: BACTERIOCHLOROPHYLL A (BCLb)
1c: BACTERIOCHLOROPHYLL A (BCLc)
1d: BACTERIOCHLOROPHYLL A (BCLd)
2a: BACTERIOPHEOPHYTIN A (BPHa)
2b: BACTERIOPHEOPHYTIN A (BPHb)
3a: CARDIOLIPIN (CDLa)
4a: DODECANE (D12a)
4b: DODECANE (D12b)
4c: DODECANE (D12c)
4d: DODECANE (D12d)
4e: DODECANE (D12e)
5a: FE (III) ION (FEa)
6a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
6b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
6c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
7a: PHOSPHATE ION (PO4a)
8a: SPEROIDENONE (SPNa)
9a: UBIQUINONE-10 (U10a)
9b: UBIQUINONE-10 (U10b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
4
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
2
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
CDL
1
Ligand/Ion
CARDIOLIPIN
4
D12
5
Ligand/Ion
DODECANE
5
FE
1
Ligand/Ion
FE (III) ION
6
LDA
3
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
7
PO4
1
Ligand/Ion
PHOSPHATE ION
8
SPN
1
Ligand/Ion
SPEROIDENONE
9
U10
2
Ligand/Ion
UBIQUINONE-10
[
close Hetero Component info
]
Sites
(19, 19)
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)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE L:97 , ALA L:124 , ILE L:125 , ALA L:127 , LEU L:131 , VAL L:157 , TYR L:162 , ASN L:166 , PHE L:167 , HIS L:168 , HIS L:173 , ALA L:176 , ILE L:177 , PHE L:180 , SER L:244 , CYS L:247 , MET L:248 , BCL L:302 , BPH L:303 , TYR M:210 , BCL M:402
binding site for residue BCL L 301
02
AC2
SOFTWARE
ILE L:46 , TYR L:128 , LEU L:131 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , BCL L:301 , BPH L:303 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , LDA M:406 , HOH M:515
binding site for residue BCL L 302
03
AC3
SOFTWARE
ALA L:93 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , ALA L:120 , PHE L:121 , ALA L:124 , VAL L:241 , BCL L:301 , BCL L:302 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256 , U10 M:404
binding site for residue BPH L 303
04
AC4
SOFTWARE
HIS L:190 , LEU L:193 , PHE L:216 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , THR L:226 , ILE L:229 , TRP L:263
binding site for residue U10 L 304
05
AC5
SOFTWARE
HOH H:501
binding site for residue D12 L 305
06
AC6
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
binding site for residue FE L 306
07
AC7
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , HOH L:408 , MET M:122 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:402 , BPH M:403 , SPN M:405
binding site for residue BCL M 401
08
AC8
SOFTWARE
VAL L:157 , TYR L:162 , PHE L:181 , BCL L:301 , LEU M:156 , LEU M:160 , THR M:186 , ASN M:187 , SER M:190 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , TYR M:210 , VAL M:276 , GLY M:280 , ILE M:284 , BCL M:401 , BPH M:403
binding site for residue BCL M 402
09
AC9
SOFTWARE
PHE L:181 , ALA L:184 , LEU L:185 , LEU L:189 , LEU L:219 , LEU M:60 , GLY M:63 , PHE M:67 , ALA M:125 , VAL M:126 , TRP M:129 , THR M:133 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:153 , THR M:277 , BCL M:401 , BCL M:402
binding site for residue BPH M 403
10
AD1
SOFTWARE
GLY L:35 , BPH L:303 , MET M:218 , HIS M:219 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , THR M:261 , ILE M:265 , TRP M:268
binding site for residue U10 M 404
11
AD2
SOFTWARE
PHE M:67 , PHE M:68 , ILE M:70 , GLY M:71 , TRP M:75 , TRP M:115 , SER M:119 , TRP M:157 , MET M:158 , GLY M:161 , TRP M:171 , HIS M:182 , BCL M:401
binding site for residue SPN M 405
12
AD3
SOFTWARE
TRP H:21 , LDA H:301 , HOH H:501 , BCL L:302 , PRO M:200 , GLY M:203 , LEU M:204
binding site for residue LDA M 406
13
AD4
SOFTWARE
LDA H:301 , PRO L:28 , GLY M:257
binding site for residue LDA M 407
14
AD5
SOFTWARE
ASN M:28 , GLY M:53 , SER M:54 , HOH M:508 , HOH M:545
binding site for residue PO4 M 408
15
AD6
SOFTWARE
TYR H:30 , ASN L:199 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , ARG M:267 , TRP M:271 , VAL M:274 , HOH M:562
binding site for residue CDL M 409
16
AD7
SOFTWARE
GLN H:32 , TYR H:40 , ARG M:253 , PHE M:258 , LDA M:406 , LDA M:407
binding site for residue LDA H 301
17
AD8
SOFTWARE
ALA H:25 , D12 H:303 , D12 H:305
binding site for residue D12 H 302
18
AD9
SOFTWARE
D12 H:302
binding site for residue D12 H 303
19
AE1
SOFTWARE
D12 H:302
binding site for residue D12 H 305
[
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 H
Chain L
Chain M
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 (298 KB)
Header - Asym.Unit
Biol.Unit 1 (287 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
5LSE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
