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.
2GNU
Asym. Unit
Info
Asym.Unit (152 KB)
Biol.Unit 1 (142 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE CRYSTALLIZATION OF REACTION CENTER FROM RHODOBACTER SPHAEROIDES OCCURS VIA A NEW ROUTE
Authors
:
P. Wadsten, A. B. Woehri, A. Snijder, G. Katona, A. T. Gardiner, R. J. Cog R. Neutze, S. Engstroem
Date
:
11 Apr 06 (Deposition) - 07 Nov 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Reaction Centre, Ubiquinone B, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Wadsten, A. B. Woehri, A. Snijder, G. Katona, A. T. Gardiner, R. J. Cogdell, R. Neutze, S. Engstroem
Lipidic Sponge Phase Crystallization Of Membrane Proteins
J. Mol. Biol. V. 364 44 2006
[
close entry info
]
Hetero Components
(7, 12)
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: CHLORIDE ION (CLa)
5a: FE (II) ION (FE2a)
6a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
7a: UBIQUINONE-10 (U10a)
7b: 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
CL
1
Ligand/Ion
CHLORIDE ION
5
FE2
1
Ligand/Ion
FE (II) ION
6
LDA
1
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
7
U10
2
Ligand/Ion
UBIQUINONE-10
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE2 M 1307
02
AC2
SOFTWARE
GLY M:53 , GLY M:56 , ARG M:132 , HOH M:1352
BINDING SITE FOR RESIDUE CL M 1308
03
AC3
SOFTWARE
PHE L:97 , ALA L:124 , ALA L:127 , LEU L:131 , VAL L:157 , THR L:160 , TYR L:162 , ASN L:166 , HIS L:168 , HIS L:173 , ILE L:177 , PHE L:180 , SER L:244 , ALA L:245 , CYS L:247 , MET L:248 , BCL L:1283 , TYR M:210 , BPH M:1284 , BCL M:1302 , BCL M:1303
BINDING SITE FOR RESIDUE BCL L 1282
04
AC4
SOFTWARE
ILE L:46 , TYR L:128 , LEU L:131 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , BCL L:1282 , HOH L:1308 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , GLY M:211 , BPH M:1284
BINDING SITE FOR RESIDUE BCL L 1283
05
AC5
SOFTWARE
THR L:38 , ALA L:93 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , PHE L:121 , ALA L:124 , GLY L:149 , HIS L:153 , VAL L:241 , BCL L:1282 , BCL L:1283 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256
BINDING SITE FOR RESIDUE BPH M 1284
06
AC6
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , BCL L:1282 , TRP M:157 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:1303 , BPH M:1304 , HOH M:1323
BINDING SITE FOR RESIDUE BCL M 1302
07
AC7
SOFTWARE
VAL L:157 , TYR L:162 , BCL L:1282 , ALA M:153 , LEU M:156 , LEU M:160 , THR M:186 , ASN M:187 , PHE M:189 , 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:1302 , BPH M:1304
BINDING SITE FOR RESIDUE BCL M 1303
08
AC8
SOFTWARE
PHE L:181 , LEU L:185 , LEU L:189 , GLY M:63 , LEU M:64 , PHE M:67 , ALA M:125 , TRP M:129 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:153 , THR M:277 , BCL M:1302 , BCL M:1303
BINDING SITE FOR RESIDUE BPH M 1304
09
AC9
SOFTWARE
PHE L:29 , GLY L:35 , TRP L:100 , ARG L:103 , 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 , ILE M:265 , TRP M:268 , MET M:272
BINDING SITE FOR RESIDUE U10 M 1305
10
BC1
SOFTWARE
LEU L:189 , HIS L:190 , LEU L:193 , ASP L:213 , PHE L:216 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , THR L:226 , ILE L:229 , HOH L:1327
BINDING SITE FOR RESIDUE U10 L 1306
11
BC2
SOFTWARE
ASN L:199 , LYS L:202 , GLY M:143 , LYS M:144 , HIS M:145 , ARG M:267 , HOH M:1353 , HOH M:1356
BINDING SITE FOR RESIDUE CDL M 1309
12
BC3
SOFTWARE
GLN H:32 , TYR H:40 , GLY H:54 , ARG M:253 , GLY M:257
BINDING SITE FOR RESIDUE LDA H 1310
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: REACTION_CENTER (L:166-192,M:195-221)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_RHOSH
167-193
1
L:166-192
RCEM_RHOSH
196-222
1
M:195-221
[
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
(3, 4)
Info
All SCOP Domains
1a: SCOP_d2gnuh2 (H:36-245)
2a: SCOP_d2gnul_ (L:)
2b: SCOP_d2gnum_ (M:)
3a: SCOP_d2gnuh1 (H:11-35)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PRC-barrel domain
(113)
Superfamily
:
PRC-barrel domain
(113)
Family
:
Photosynthetic reaction centre, H-chain, cytoplasmic domain
(108)
Protein domain
:
automated matches
(10)
Rhodobacter sphaeroides [TaxId: 1063]
(6)
1a
d2gnuh2
H:36-245
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Superfamily
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Family
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Protein domain
:
automated matches
(44)
Rhodobacter sphaeroides [TaxId: 1063]
(31)
2a
d2gnul_
L:
2b
d2gnum_
M:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Photosystem II reaction centre subunit H, transmembrane region
(108)
Family
:
automated matches
(10)
Protein domain
:
automated matches
(10)
Rhodobacter sphaeroides [TaxId: 1063]
(6)
3a
d2gnuh1
H:11-35
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2gnuH02 (H:117-245)
2a: CATH_2gnuH01 (H:11-116)
3a: CATH_2gnuM01 (M:2-143)
3b: CATH_2gnuM02 (M:144-301)
3c: CATH_2gnuL01 (L:1-163)
3d: CATH_2gnuL02 (L:164-263)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 2
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 2
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(1)
1a
2gnuH02
H:117-245
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 1
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 1
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(1)
2a
2gnuH01
H:11-116
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Photosynthetic Reaction Center, subunit M; domain 1
(93)
Homologous Superfamily
:
Membrane spanning alpha-helix pairs
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(1)
3a
2gnuM01
M:2-143
3b
2gnuM02
M:144-301
3c
2gnuL01
L:1-163
3d
2gnuL02
L:164-263
[
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 (152 KB)
Header - Asym.Unit
Biol.Unit 1 (142 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
2GNU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
