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.
2DRD
Asym. Unit
Info
Asym.Unit (486 KB)
Biol.Unit 1 (469 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 A MULTIDRUG TRANSPORTER REVEAL A FUNCTIONALLY ROTATING MECHANISM
Authors
:
S. Murakami, R. Nakashima, E. Yamashita, T. Matsumoto
Date
:
08 Jun 06 (Deposition) - 22 Aug 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Membrane Transporter, Membrane Protein, Multidrug Efflux, Drug Resistance, Transporter, Exporter, Antiporter
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Murakami, R. Nakashima, E. Yamashita, T. Matsumoto, A. Yamaguchi
Crystal Structures Of A Multidrug Transporter Reveal A Functionally Rotating Mechanism
Nature V. 443 173 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYL... (MIYa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MIY
1
Ligand/Ion
(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE A:178 , GLY A:179 , ASN A:274 , ILE A:277 , ALA A:279 , PHE A:615
BINDING SITE FOR RESIDUE MIY A 2001
[
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
(6, 24)
Info
all CATH domains
1a: CATH_2drdA02 (A:38-132,A:813-820)
1b: CATH_2drdA06 (A:569-673)
1c: CATH_2drdB06 (B:569-673)
1d: CATH_2drdC06 (C:569-673)
1e: CATH_2drdB02 (B:38-132,B:813-820)
1f: CATH_2drdC02 (C:38-132,C:813-820)
2a: CATH_2drdA03 (A:133-179,A:276-328)
2b: CATH_2drdB03 (B:133-179,B:276-328)
2c: CATH_2drdC03 (C:133-179,C:276-328)
3a: CATH_2drdA07 (A:674-723,A:821-867)
3b: CATH_2drdC07 (C:674-723,C:821-864)
3c: CATH_2drdB07 (B:674-723,B:821-869)
4a: CATH_2drdA08 (A:724-812)
4b: CATH_2drdA04 (A:180-275)
4c: CATH_2drdB04 (B:180-275)
4d: CATH_2drdC04 (C:180-275)
4e: CATH_2drdB08 (B:724-812)
4f: CATH_2drdC08 (C:724-812)
5a: CATH_2drdB05 (B:522-568,B:870-1036)
5b: CATH_2drdA05 (A:513-568,A:868-1036)
5c: CATH_2drdC05 (C:515-568,C:865-1036)
6a: CATH_2drdC01 (C:1-37,C:329-514)
6b: CATH_2drdA01 (A:1-37,A:329-498)
6c: CATH_2drdB01 (B:1-37,B:329-521)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
Multidrug efflux transporter AcrB pore domain
(27)
Escherichia coli. Organism_taxid: 562.
(4)
1a
2drdA02
A:38-132,A:813-820
1b
2drdA06
A:569-673
1c
2drdB06
B:569-673
1d
2drdC06
C:569-673
1e
2drdB02
B:38-132,B:813-820
1f
2drdC02
C:38-132,C:813-820
Homologous Superfamily
:
Multidrug efflux transporter AcrB pore domain like
(27)
Escherichia coli. Organism_taxid: 562.
(4)
2a
2drdA03
A:133-179,A:276-328
2b
2drdB03
B:133-179,B:276-328
2c
2drdC03
C:133-179,C:276-328
Homologous Superfamily
:
Multidrug efflux transporter AcrB pore domain
(27)
Escherichia coli. Organism_taxid: 562.
(4)
3a
2drdA07
A:674-723,A:821-867
3b
2drdC07
C:674-723,C:821-864
3c
2drdB07
B:674-723,B:821-869
Topology
:
Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
(27)
Homologous Superfamily
:
Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
(27)
Escherichia coli. Organism_taxid: 562.
(4)
4a
2drdA08
A:724-812
4b
2drdA04
A:180-275
4c
2drdB04
B:180-275
4d
2drdC04
C:180-275
4e
2drdB08
B:724-812
4f
2drdC08
C:724-812
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
(27)
Homologous Superfamily
:
Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
(27)
Escherichia coli. Organism_taxid: 562.
(4)
5a
2drdB05
B:522-568,B:870-1036
5b
2drdA05
A:513-568,A:868-1036
5c
2drdC05
C:515-568,C:865-1036
Architecture
:
Up-down Bundle
(3216)
Topology
:
Multidrug efflux transporter AcrB transmembrane fold
(27)
Homologous Superfamily
:
Multidrug efflux transporter AcrB transmembrane domain
(27)
Escherichia coli. Organism_taxid: 562.
(4)
6a
2drdC01
C:1-37,C:329-514
6b
2drdA01
A:1-37,A:329-498
6c
2drdB01
B:1-37,B:329-521
[
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 (486 KB)
Header - Asym.Unit
Biol.Unit 1 (469 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
2DRD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help