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.
3PGU
Asym. Unit
Info
Asym.Unit (158 KB)
Biol.Unit 1 (149 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PHE3GLU MUTANT OF ECFADL
Authors
:
B. W. Lepore, M. Indic, H. Pham, E. Hearn, D. Patel, B. Van Den Berg
Date
:
02 Nov 10 (Deposition) - 25 May 11 (Release) - 07 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Outer Membrane Beta Barrel, Lipid Transport, Outer Membrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. W. Lepore, M. Indic, H. Pham, E. M. Hearn, D. R. Patel, B. Van Den Ber
From The Cover: Ligand-Gated Diffusion Across The Bacterial Outer Membrane.
Proc. Natl. Acad. Sci. Usa V. 108 10121 2011
[
close entry info
]
Hetero Components
(5, 22)
Info
All Hetero Components
1a: NONAETHYLENE GLYCOL (2PEa)
1b: NONAETHYLENE GLYCOL (2PEb)
1c: NONAETHYLENE GLYCOL (2PEc)
2a: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ea)
2b: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eb)
2c: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ec)
2d: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ed)
2e: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ee)
2f: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ef)
2g: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eg)
2h: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Eh)
2i: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ei)
2j: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ej)
2k: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Ek)
2l: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8El)
2m: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8Em)
2n: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTA... (C8En)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
4a: NICKEL (II) ION (NIa)
4b: NICKEL (II) ION (NIb)
5a: OLEIC ACID (OLAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2PE
3
Ligand/Ion
NONAETHYLENE GLYCOL
2
C8E
14
Ligand/Ion
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
3
NA
2
Ligand/Ion
SODIUM ION
4
NI
2
Ligand/Ion
NICKEL (II) ION
5
OLA
1
Ligand/Ion
OLEIC ACID
[
close Hetero Component info
]
Sites
(22, 22)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:225 , TYR A:227 , TRP A:275
BINDING SITE FOR RESIDUE C8E A 428
02
AC2
SOFTWARE
ALA A:96 , SER A:97 , ILE A:98 , ASN A:129 , LEU A:130 , ILE A:289 , C8E A:433
BINDING SITE FOR RESIDUE C8E A 429
03
AC3
SOFTWARE
LEU A:369 , TYR A:389 , C8E A:431
BINDING SITE FOR RESIDUE C8E A 430
04
AC4
SOFTWARE
GLN A:180 , TRP A:411 , PHE A:413 , C8E A:430 , C8E A:432
BINDING SITE FOR RESIDUE C8E A 431
05
AC5
SOFTWARE
THR A:178 , GLN A:180 , GLY A:181 , C8E A:431
BINDING SITE FOR RESIDUE C8E A 432
06
AC6
SOFTWARE
LEU A:128 , PHE A:146 , PHE A:207 , GLY A:208 , TRP A:209 , C8E A:429
BINDING SITE FOR RESIDUE C8E A 433
07
AC7
SOFTWARE
MET A:82 , ILE A:327
BINDING SITE FOR RESIDUE C8E A 434
08
AC8
SOFTWARE
TRP A:339 , 2PE A:437 , C8E A:439
BINDING SITE FOR RESIDUE C8E A 435
09
AC9
SOFTWARE
LEU A:5 , GLY A:48 , ALA A:77 , TRP A:78 , PRO A:80 , ASN A:81 , MET A:82 , THR A:125 , 2PE A:438 , HOH A:456 , HOH A:678
BINDING SITE FOR RESIDUE 2PE A 436
10
BC1
SOFTWARE
TRP A:78 , GLY A:372 , VAL A:385 , PHE A:413 , GLY A:414 , THR A:415 , C8E A:435 , C8E A:443
BINDING SITE FOR RESIDUE 2PE A 437
11
BC2
SOFTWARE
TRP A:140 , TYR A:215 , 2PE A:436
BINDING SITE FOR RESIDUE 2PE A 438
12
BC3
SOFTWARE
VAL A:166 , C8E A:435
BINDING SITE FOR RESIDUE C8E A 439
13
BC4
SOFTWARE
HIS A:423 , HIS A:425 , HOH A:681 , HOH A:682
BINDING SITE FOR RESIDUE NI A 440
14
BC5
SOFTWARE
ASP A:349 , ASP A:365 , HOH A:683
BINDING SITE FOR RESIDUE NI A 441
15
BC6
SOFTWARE
PRO A:54 , ASP A:55 , ASN A:72
BINDING SITE FOR RESIDUE NA A 442
16
BC7
SOFTWARE
TRP A:287 , THR A:331 , TYR A:333 , 2PE A:437
BINDING SITE FOR RESIDUE C8E A 443
17
BC8
SOFTWARE
GLY A:132 , PHE A:142 , GLY A:143 , LEU A:144
BINDING SITE FOR RESIDUE C8E A 444
18
BC9
SOFTWARE
GLY A:60 , SER A:67 , HOH A:516 , HOH A:554
BINDING SITE FOR RESIDUE NA A 445
19
CC1
SOFTWARE
ARG A:282 , GLN A:286 , LYS A:305 , TYR A:334 , TYR A:335 , ASP A:336 , HOH A:545 , HOH A:567
BINDING SITE FOR RESIDUE C8E A 446
20
CC2
SOFTWARE
GLN A:164 , ALA A:167 , GLY A:168 , GLN A:169 , MET A:171 , GLN A:172 , GLN A:182 , ALA A:185 , ASN A:189
BINDING SITE FOR RESIDUE C8E A 447
21
CC3
SOFTWARE
GLN A:4 , ASN A:6 , GLU A:7 , GLN A:364 , ARG A:366 , TRP A:368 , MET A:390 , GLY A:408 , LYS A:409 , HOH A:536 , HOH A:582
BINDING SITE FOR RESIDUE OLA A 448
22
CC4
SOFTWARE
GLU A:273 , SER A:297 , PHE A:321 , TYR A:419
BINDING SITE FOR RESIDUE C8E A 449
[
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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3pgua_ (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
:
Outer membrane protein transport protein
(10)
Protein domain
:
automated matches
(8)
Escherichia coli K-12 [TaxId: 83333]
(5)
1a
d3pgua_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Toluene_X_3pguA01 (A:1-421)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
MBB
(97)
Family
:
Toluene_X
(12)
Escherichia coli (strain K12)
(12)
1a
Toluene_X-3pguA01
A:1-421
[
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 (158 KB)
Header - Asym.Unit
Biol.Unit 1 (149 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
3PGU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
