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.
2BRD
Biol. Unit 1
Info
Asym.Unit (55 KB)
Biol.Unit 1 (137 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 BACTERIORHODOPSIN IN PURPLE MEMBRANE
Authors
:
R. Henderson, N. Grigorieff
Date
:
27 Dec 95 (Deposition) - 10 Jun 96 (Release) - 30 May 12 (Revision)
Method
:
ELECTRON CRYSTALLOGRAPHY
Resolution
:
3.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (3x)
Keywords
:
Proton Pump, Membrane Protein, Retinal Protein, Two-Dimensional Crystal, Photoreceptor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Grigorieff, T. A. Ceska, K. H. Downing, J. M. Baldwin, R. Henderson
Electron-Crystallographic Refinement Of The Structure Of Bacteriorhodopsin.
J. Mol. Biol. V. 259 393 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 33)
Info
All Hetero Components
1a: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGa)
1b: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGb)
1c: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGc)
1d: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGd)
1e: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGe)
1f: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGf)
1g: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGg)
1h: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGh)
1i: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGi)
1j: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15... (DPGj)
2a: RETINAL (RETa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DPG
30
Ligand/Ion
PHOSPHORIC ACID 2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL ESTER 2-HYDROXO-3-PHOSPHONOOXY-PROPYL ESTER
2
RET
3
Ligand/Ion
RETINAL
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:64 , LEU A:66 , MET A:68 , PRO A:70 , TRP A:80 , LEU A:87 , PHE A:88 , VAL A:124 , LYS A:129 , DPG A:266
BINDING SITE FOR RESIDUE DPG A 261
02
AC2
SOFTWARE
SER A:183 , VAL A:187 , ILE A:191 , ALA A:196 , ILE A:198 , LEU A:207 , DPG A:263 , DPG A:267 , DPG A:268
BINDING SITE FOR RESIDUE DPG A 262
03
AC3
SOFTWARE
TRP A:12 , PHE A:135 , TRP A:138 , ALA A:196 , ILE A:203 , LEU A:206 , VAL A:210 , DPG A:262 , DPG A:264 , DPG A:265 , DPG A:268
BINDING SITE FOR RESIDUE DPG A 263
04
AC4
SOFTWARE
ALA A:18 , PHE A:54 , LEU A:58 , LEU A:61 , VAL A:136 , DPG A:263 , DPG A:265 , DPG A:270
BINDING SITE FOR RESIDUE DPG A 264
05
AC5
SOFTWARE
ILE A:11 , LEU A:15 , ALA A:18 , DPG A:263 , DPG A:264
BINDING SITE FOR RESIDUE DPG A 265
06
AC6
SOFTWARE
ILE A:52 , PHE A:88 , LEU A:92 , LEU A:95 , LEU A:99 , ALA A:103 , GLN A:105 , ILE A:108 , LEU A:109 , GLY A:116 , ILE A:117 , DPG A:261
BINDING SITE FOR RESIDUE DPG A 266
07
AC7
SOFTWARE
PHE A:156 , LYS A:172 , ARG A:175 , ASN A:176 , VAL A:180 , ALA A:184 , VAL A:187 , DPG A:262 , DPG A:268
BINDING SITE FOR RESIDUE DPG A 267
08
AC8
SOFTWARE
TRP A:138 , THR A:142 , MET A:145 , LEU A:149 , TYR A:150 , PHE A:153 , THR A:157 , SER A:169 , LYS A:172 , VAL A:173 , VAL A:179 , PRO A:186 , VAL A:210 , SER A:214 , ARG A:225 , DPG A:262 , DPG A:263 , DPG A:267
BINDING SITE FOR RESIDUE DPG A 268
09
AC9
SOFTWARE
LEU A:28 , MET A:32 , GLY A:33 , LYS A:40 , THR A:47 , ALA A:51 , TYR A:147 , PHE A:154 , LEU A:221 , DPG A:270
BINDING SITE FOR RESIDUE DPG A 269
10
BC1
SOFTWARE
LEU A:22 , TYR A:26 , VAL A:29 , LYS A:30 , GLY A:33 , LEU A:224 , ARG A:227 , DPG A:264 , DPG A:269
BINDING SITE FOR RESIDUE DPG A 270
11
BC2
SOFTWARE
TRP A:86 , THR A:89 , THR A:90 , MET A:118 , TRP A:138 , SER A:141 , TRP A:182 , TYR A:185 , TRP A:189 , ASP A:212 , LYS A:216
BINDING SITE FOR RESIDUE RET A 271
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: BACTERIAL_OPSIN_1 (A:82-94)
2: BACTERIAL_OPSIN_RET (A:208-219)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BACTERIAL_OPSIN_1
PS00950
Bacterial rhodopsins signature 1.
BACR_HALSA
95-107
3
A:82-94
2
BACTERIAL_OPSIN_RET
PS00327
Bacterial rhodopsins retinal binding site.
BACR_HALSA
221-232
3
A:208-219
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2brda_ (A:)
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
:
Bacteriorhodopsin-like
(107)
Protein domain
:
Bacteriorhodopsin
(61)
Halobacterium halobium [TaxId: 2242]
(3)
1a
d2brda_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2brdA00 (A:7-228)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Homologous Superfamily
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Halobacterium salinarum. Organism_taxid: 2242. Strain: r1
(2)
1a
2brdA00
A:7-228
[
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
Asymmetric Unit 2
Asymmetric Unit 3
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 (55 KB)
Header - Asym.Unit
Biol.Unit 1 (137 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
2BRD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help