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.
2BNP
Asym. Unit
Info
Asym.Unit (151 KB)
Biol.Unit 1 (140 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
LIPIDIC CUBIC PHASE GROWN REACTION CENTRE FROM RHODOBACTER SPHAEROIDES, GROUND STATE
Authors
:
G. Katona, A. Snijder, P. Gourdon, U. Andreasson, O. Hansson, L. E. Andreasson, R. Neutze
Date
:
31 Mar 05 (Deposition) - 27 May 05 (Release) - 20 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Photosynthesis, Membrane Protein, Intermediate Trapping, Bacteriochlorophyll, Chromophore, Electront Transport, Reaction Centre
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Katona, A. Snijder, P. Gourdon, U. Andreasson, O. Hansson, L. E. Andreasson, R. Neutze
Conformational Regulation Of Charge Recombination Reactions In A Photosynthetic Bacterial Reaction Centre
Nat. Struct. Mol. Biol. V. 12 630 2005
[
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 (BPHa)
2b: BACTERIOPHEOPHYTIN (BPHb)
3a: CHLORIDE ION (CLa)
4a: FE (II) ION (FE2a)
5a: 2-T-BUTYLAMINO-4-ETHYLAMINO-6-METH... (MSTa)
6a: PHOSPHATE ION (PO4a)
6b: PHOSPHATE ION (PO4b)
7a: UBIQUINONE-10 (U10a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
4
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
2
Ligand/Ion
BACTERIOPHEOPHYTIN
3
CL
1
Ligand/Ion
CHLORIDE ION
4
FE2
1
Ligand/Ion
FE (II) ION
5
MST
1
Ligand/Ion
2-T-BUTYLAMINO-4-ETHYLAMINO-6-METHYLTHIO-S-TRIAZINE
6
PO4
2
Ligand/Ion
PHOSPHATE ION
7
U10
1
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 A:190 , HIS A:230 , HIS B:219 , GLU B:234 , HIS B:266
BINDING SITE FOR RESIDUE FE2 B1305
02
AC2
SOFTWARE
ASN A:199 , LYS A:202 , HIS B:145 , ARG B:267 , PO4 B:1309
BINDING SITE FOR RESIDUE PO4 B1308
03
AC3
SOFTWARE
LYS A:202 , GLY B:143 , LYS B:144 , TRP B:148 , PO4 B:1308 , HOH B:2022
BINDING SITE FOR RESIDUE PO4 B1309
04
AC4
SOFTWARE
GLY B:56 , ARG B:136
BINDING SITE FOR RESIDUE CL B1307
05
AC5
SOFTWARE
PHE A:97 , ALA A:127 , LEU A:131 , VAL A:157 , THR A:160 , TYR A:162 , ASN A:166 , HIS A:168 , HIS A:173 , ILE A:177 , PHE A:180 , SER A:244 , CYS A:247 , MET A:248 , BCL A:1283 , BPH A:1284 , BCL B:1302 , BCL B:1303
BINDING SITE FOR RESIDUE BCL A1282
06
AC6
SOFTWARE
ILE A:49 , TYR A:128 , LEU A:131 , PHE A:146 , ILE A:150 , HIS A:153 , LEU A:154 , BCL A:1282 , BPH A:1284 , PHE B:197 , GLY B:203 , ILE B:206 , ALA B:207 , TYR B:210 , LEU B:214
BINDING SITE FOR RESIDUE BCL A1283
07
AC7
SOFTWARE
PHE A:97 , TRP A:100 , GLU A:104 , ILE A:117 , PHE A:121 , ALA A:124 , TYR A:148 , VAL A:241 , BCL A:1282 , BCL A:1283 , TYR B:210 , ALA B:213 , LEU B:214 , TRP B:252 , MET B:256
BINDING SITE FOR RESIDUE BPH A1284
08
AC8
SOFTWARE
HIS A:190 , LEU A:193 , ASP A:213 , PHE A:216 , TYR A:222 , SER A:223 , ILE A:224 , GLY A:225 , ILE A:229
BINDING SITE FOR RESIDUE MST A1285
09
AC9
SOFTWARE
HIS A:168 , MET A:174 , ILE A:177 , SER A:178 , THR A:182 , LEU A:185 , BCL A:1282 , HOH A:2012 , TRP B:157 , ILE B:179 , HIS B:182 , LEU B:183 , THR B:186 , BCL B:1303 , BPH B:1304
BINDING SITE FOR RESIDUE BCL B1302
10
BC1
SOFTWARE
VAL A:157 , TYR A:162 , PHE A:181 , BCL A:1282 , ALA B:153 , LEU B:156 , LEU B:160 , THR B:186 , ASN B:187 , PHE B:189 , LEU B:196 , PHE B:197 , HIS B:202 , SER B:205 , ILE B:206 , TYR B:210 , VAL B:276 , GLY B:280 , ILE B:284 , BCL B:1302 , BPH B:1304
BINDING SITE FOR RESIDUE BCL B1303
11
BC2
SOFTWARE
PHE A:181 , LEU A:185 , LEU A:189 , LEU A:219 , GLY B:63 , ALA B:125 , TRP B:129 , THR B:146 , PHE B:150 , ALA B:273 , THR B:277 , BCL B:1302 , BCL B:1303
BINDING SITE FOR RESIDUE BPH B1304
12
BC3
SOFTWARE
HIS B:219 , THR B:222 , ALA B:248 , ALA B:249 , TRP B:252 , MET B:256 , PHE B:258 , ASN B:259 , ALA B:260 , THR B:261 , ILE B:265 , TRP B:268
BINDING SITE FOR RESIDUE U10 B1306
[
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 (A:166-192,A:166-192,B:195-221,B:19...)
;
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_RHOS4
167-193
1
A:166-192
RCEL_RHOSH
167-193
1
A:166-192
RCEM_RHOS4
196-222
1
B:195-221
RCEM_RHOSH
196-222
1
B: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_d2bnpc2 (C:36-247)
2a: SCOP_d2bnpa_ (A:)
2b: SCOP_d2bnpb_ (B:)
3a: SCOP_d2bnpc1 (C: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
:
Photosynthetic reaction centre
(98)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
1a
d2bnpc2
C:36-247
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
d2bnpa_
A:
2b
d2bnpb_
B:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Photosystem II reaction centre subunit H, transmembrane region
(108)
Family
:
Photosystem II reaction centre subunit H, transmembrane region
(98)
Protein domain
:
Photosystem II reaction centre subunit H, transmembrane region
(98)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
3a
d2bnpc1
C:11-35
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2bnpC02 (C:117-247)
2a: CATH_2bnpC01 (C:12-116)
3a: CATH_2bnpB01 (B:1-143)
3b: CATH_2bnpB02 (B:144-302)
3c: CATH_2bnpA01 (A:1-163)
3d: CATH_2bnpA02 (A: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. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(5)
1a
2bnpC02
C:117-247
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. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(5)
2a
2bnpC01
C:12-116
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. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(5)
3a
2bnpB01
B:1-143
3b
2bnpB02
B:144-302
3c
2bnpA01
A:1-163
3d
2bnpA02
A: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 A
Chain B
Chain C
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 (151 KB)
Header - Asym.Unit
Biol.Unit 1 (140 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
2BNP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
