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.
2VQI
Asym. Unit
Info
Asym.Unit (163 KB)
Biol.Unit 1 (156 KB)
Biol.Unit 2 (155 KB)
Biol.Unit 3 (157 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE P PILUS USHER (PAPC) TRANSLOCATION PORE
Authors
:
H. Remaut, C. Tang, N. S. Henderson, J. S. Pinkner, T. Wang, S. J. Hultgren, D. G. Thanassi, H. Li, G. Waksman
Date
:
16 Mar 08 (Deposition) - 27 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A (2x)
Biol. Unit 3: B (2x)
Keywords
:
Transmembrane, Outer Membrane, Transport, Usher, P Pilus, Membrane, Fimbrium, Om Translocation Pore, Pilus Assembly Platform
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Remaut, C. Tang, N. S. Henderson, J. S. Pinkner, T. Wang, S. J. Hultgren, D. G. Thanassi, G. Waksman, H. Li
Fiber Formation Across The Bacterial Outer Membrane By The Chaperone/Usher Pathway.
Cell(Cambridge, Mass. ) V. 133 640 2008
[
close entry info
]
Hetero Components
(3, 20)
Info
All Hetero Components
1a: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ea)
1b: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eb)
2a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
2b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C8E
2
Ligand/Ion
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2
LDA
2
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
3
MSE
16
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU B:399 , LEU B:423 , ARG B:510 , LEU B:524
BINDING SITE FOR RESIDUE C8E B1637
2
AC2
SOFTWARE
ILE A:615 , LEU B:340 , LEU B:378
BINDING SITE FOR RESIDUE C8E B1638
3
AC3
SOFTWARE
PHE A:573 , TYR A:580 , LEU B:224 , LEU B:246 , SER B:342 , GLY B:343 , VAL B:356 , PHE B:357
BINDING SITE FOR RESIDUE LDA B1639
4
AC4
SOFTWARE
LEU A:340 , SER A:342 , GLY A:343 , VAL A:356 , PHE A:357 , PHE B:573 , TYR B:580
BINDING SITE FOR RESIDUE LDA A1638
[
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: FIMBRIAL_USHER (A:288-298,B:288-298)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FIMBRIAL_USHER
PS01151
Fimbrial biogenesis outer membrane usher protein signature.
PAPC_ECOLX
315-325
2
A:288-298
B:288-298
[
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
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Usher_2vqiB01 (B:169-636)
1b: PFAM_Usher_2vqiB02 (B:169-636)
2a: PFAM_PapC_N_2vqiB03 (B:146-155)
2b: PFAM_PapC_N_2vqiB04 (B:146-155)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
MBB
(97)
Family
:
Usher
(2)
Escherichia coli
(1)
1a
Usher-2vqiB01
B:169-636
1b
Usher-2vqiB02
B:169-636
Clan
:
no clan defined [family: PapC_N]
(4)
Family
:
PapC_N
(4)
Escherichia coli
(1)
2a
PapC_N-2vqiB03
B:146-155
2b
PapC_N-2vqiB04
B:146-155
[
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
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 (163 KB)
Header - Asym.Unit
Biol.Unit 1 (156 KB)
Header - Biol.Unit 1
Biol.Unit 2 (155 KB)
Header - Biol.Unit 2
Biol.Unit 3 (157 KB)
Header - Biol.Unit 3
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
2VQI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help