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.
3RGN
Asym. Unit
Info
Asym.Unit (196 KB)
Biol.Unit 1 (189 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 SPIN-LABELED BTUB W371R1
Authors
:
D. M. Freed, P. S. Horanyi, M. C. Wiener, D. S. Cafiso
Date
:
08 Apr 11 (Deposition) - 26 Oct 11 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Beta-Barrel, Receptor, Transporter, Cobalamins, Tonb, Outer Membrane, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Freed, A. K. Khan, P. S. Horanyi, D. S. Cafiso
Molecular Origin Of Electron Paramagnetic Resonance Line Shapes On β -Barrel Membrane Proteins: The Local Solvation Environment Modulates Spin-Label Configuration
Biochemistry V. 50 8792 2011
[
close entry info
]
Hetero Components
(3, 11)
Info
All Hetero Components
1a: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ea)
1b: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eb)
1c: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ec)
1d: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ed)
1e: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ee)
1f: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ef)
1g: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eg)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
3a: S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5... (MTNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C8E
7
Ligand/Ion
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2
MG
3
Ligand/Ion
MAGNESIUM ION
3
MTN
1
Ligand/Ion
S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE
[
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
ARG A:358 , SER A:359 , ARG A:367 , GLY A:369 , THR A:370 , PHE A:470 , ASP A:471 , THR A:472 , GLY A:473 , HOH A:638
BINDING SITE FOR RESIDUE C8E A 800
02
AC2
SOFTWARE
TRP A:317 , THR A:338 , ASP A:361 , SER A:363 , TYR A:383 , PHE A:422
BINDING SITE FOR RESIDUE C8E A 801
03
AC3
SOFTWARE
TRP A:300 , ASN A:302 , VAL A:304 , ILE A:311 , ALA A:313 , LEU A:342 , ILE A:433 , ALA A:466 , C8E A:804
BINDING SITE FOR RESIDUE C8E A 802
04
AC4
SOFTWARE
ILE A:311 , PHE A:353 , THR A:373 , VAL A:503 , TYR A:505 , C8E A:805
BINDING SITE FOR RESIDUE C8E A 803
05
AC5
SOFTWARE
TYR A:256 , SER A:263 , GLY A:420 , PHE A:422 , ILE A:433 , GLY A:435 , TYR A:436 , GLY A:463 , HOH A:612 , C8E A:802
BINDING SITE FOR RESIDUE C8E A 804
06
AC6
SOFTWARE
GLN A:346 , TYR A:520 , TYR A:522 , C8E A:803
BINDING SITE FOR RESIDUE C8E A 805
07
AC7
SOFTWARE
THR A:472 , GLY A:473 , HIS A:477 , TYR A:505 , MTN A:598
BINDING SITE FOR RESIDUE C8E A 806
08
AC8
SOFTWARE
HIS A:174 , HIS A:176 , HIS A:449
BINDING SITE FOR RESIDUE MG A 595
09
AC9
SOFTWARE
TYR A:256 , GLY A:258 , GLU A:259 , LEU A:260 , ILE A:261
BINDING SITE FOR RESIDUE MG A 596
10
BC1
SOFTWARE
ASP A:411
BINDING SITE FOR RESIDUE MG A 597
11
BC2
SOFTWARE
CYS A:371 , GLN A:372 , TYR A:389 , C8E A:806
BINDING SITE FOR RESIDUE MTN A 598
[
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, 1)
Info
All PROSITE Patterns/Profiles
1: TONB_DEPENDENT_REC_2 (A:577-594)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TONB_DEPENDENT_REC_2
PS01156
TonB-dependent receptor proteins signature 2.
BTUB_ECOLI
597-614
1
A:577-594
[
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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3rgna_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Transmembrane beta-barrels
(143)
Superfamily
:
Porins
(99)
Family
:
Ligand-gated protein channel
(29)
Protein domain
:
Outer membrane cobalamin transporter BtuB
(12)
Escherichia coli [TaxId: 562]
(12)
1a
d3rgna_
A:
[
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 A
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 (196 KB)
Header - Asym.Unit
Biol.Unit 1 (189 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
3RGN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
