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.
4POV
Asym. Unit
Info
Asym.Unit (135 KB)
Biol.Unit 1 (67 KB)
Biol.Unit 2 (65 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THIT WITH LMG135 BOUND
Authors
:
L. J. Y. M. Swier, A. Guskov, D. J. Slotboom
Date
:
26 Feb 14 (Deposition) - 17 Sep 14 (Release) - 01 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
S-Component, Thiamine-Binding Protein, Ecf Module, Membrane, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. J. Swier, L. Monjas, A. Guskov, A. R. De Voogd, G. B. Erkens, D. J. Slotboom, A. K. Hirsch
Structure-Based Design Of Potent Small-Molecule Binders To The S-Component Of The Ecf Transporter For Thiamine.
Chembiochem V. 16 819 2015
[
close entry info
]
Hetero Components
(9, 37)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
2a: 4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL... (2VYa)
2b: 4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL... (2VYb)
3a: B-NONYLGLUCOSIDE (BNGa)
3b: B-NONYLGLUCOSIDE (BNGb)
3c: B-NONYLGLUCOSIDE (BNGc)
3d: B-NONYLGLUCOSIDE (BNGd)
3e: B-NONYLGLUCOSIDE (BNGe)
3f: B-NONYLGLUCOSIDE (BNGf)
4a: CHLORIDE ION (CLa)
5a: HEXAETHYLENE GLYCOL (P6Ga)
6a: DI(HYDROXYETHYL)ETHER (PEGa)
6b: DI(HYDROXYETHYL)ETHER (PEGb)
6c: DI(HYDROXYETHYL)ETHER (PEGc)
6d: DI(HYDROXYETHYL)ETHER (PEGd)
6e: DI(HYDROXYETHYL)ETHER (PEGe)
6f: DI(HYDROXYETHYL)ETHER (PEGf)
6g: DI(HYDROXYETHYL)ETHER (PEGg)
6h: DI(HYDROXYETHYL)ETHER (PEGh)
6i: DI(HYDROXYETHYL)ETHER (PEGi)
6j: DI(HYDROXYETHYL)ETHER (PEGj)
7a: 2-(2-METHOXYETHOXY)ETHANOL (PG0a)
7b: 2-(2-METHOXYETHOXY)ETHANOL (PG0b)
8a: TETRAETHYLENE GLYCOL (PG4a)
8b: TETRAETHYLENE GLYCOL (PG4b)
8c: TETRAETHYLENE GLYCOL (PG4c)
8d: TETRAETHYLENE GLYCOL (PG4d)
8e: TETRAETHYLENE GLYCOL (PG4e)
8f: TETRAETHYLENE GLYCOL (PG4f)
8g: TETRAETHYLENE GLYCOL (PG4g)
8h: TETRAETHYLENE GLYCOL (PG4h)
8i: TETRAETHYLENE GLYCOL (PG4i)
9a: TRIETHYLENE GLYCOL (PGEa)
9b: TRIETHYLENE GLYCOL (PGEb)
9c: TRIETHYLENE GLYCOL (PGEc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
3
Ligand/Ion
PENTAETHYLENE GLYCOL
2
2VY
2
Ligand/Ion
4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHENE-2-CARBALDEHYDE
3
BNG
6
Ligand/Ion
B-NONYLGLUCOSIDE
4
CL
1
Ligand/Ion
CHLORIDE ION
5
P6G
1
Ligand/Ion
HEXAETHYLENE GLYCOL
6
PEG
10
Ligand/Ion
DI(HYDROXYETHYL)ETHER
7
PG0
2
Ligand/Ion
2-(2-METHOXYETHOXY)ETHANOL
8
PG4
9
Ligand/Ion
TETRAETHYLENE GLYCOL
9
PGE
3
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(36, 36)
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)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:34 , GLU A:84 , TYR A:85 , TYR A:122 , HIS A:125 , GLY A:129 , TRP A:133 , TYR A:146 , ASN A:151 , HOH A:306
BINDING SITE FOR RESIDUE 2VY A 201
02
AC2
SOFTWARE
PRO A:104 , LEU A:105 , GLY A:140 , VAL A:170 , LYS A:171 , PRO A:174 , LYS A:175 , HOH A:330 , HOH A:332
BINDING SITE FOR RESIDUE PG0 A 202
03
AC3
SOFTWARE
LEU A:20 , ILE A:24 , PHE A:169
BINDING SITE FOR RESIDUE PG4 A 203
04
AC4
SOFTWARE
THR A:30 , VAL A:37 , PG4 B:206
BINDING SITE FOR RESIDUE PG4 A 204
05
AC5
SOFTWARE
1PE A:216 , PG4 B:204
BINDING SITE FOR RESIDUE PG4 A 206
06
AC6
SOFTWARE
SER A:25 , ASN A:29 , THR A:30 , GLY A:33 , TRP A:34 , ILE A:36 , TYR A:74 , HOH A:305 , HOH A:311
BINDING SITE FOR RESIDUE PG4 A 207
07
AC7
SOFTWARE
LYS A:139 , TRP A:141 , GLY A:142 , ALA A:145
BINDING SITE FOR RESIDUE BNG A 208
08
AC8
SOFTWARE
ILE A:75 , SER A:77 , LEU A:78 , LEU A:86 , BNG A:210
BINDING SITE FOR RESIDUE BNG A 209
09
AC9
SOFTWARE
ILE A:65 , BNG A:209
BINDING SITE FOR RESIDUE BNG A 210
10
BC1
SOFTWARE
PHE A:22
BINDING SITE FOR RESIDUE PEG A 211
11
BC2
SOFTWARE
ILE A:168
BINDING SITE FOR RESIDUE PEG A 212
12
BC3
SOFTWARE
MET A:17 , ARG A:50
BINDING SITE FOR RESIDUE PEG A 213
13
BC4
SOFTWARE
LEU A:57 , VAL A:58
BINDING SITE FOR RESIDUE PEG A 214
14
BC5
SOFTWARE
LYS A:106 , LEU A:107 , ALA A:108 , HOH A:326 , VAL B:31 , TYR B:32
BINDING SITE FOR RESIDUE PEG A 215
15
BC6
SOFTWARE
LEU A:148 , PG4 A:206 , PG4 B:204
BINDING SITE FOR RESIDUE 1PE A 216
16
BC7
SOFTWARE
PRO A:109 , LEU A:112 , PGE A:219 , TYR B:32
BINDING SITE FOR RESIDUE PGE A 217
17
BC8
SOFTWARE
LEU A:10 , THR A:54 , ARG A:99 , HOH A:316 , HOH A:317
BINDING SITE FOR RESIDUE PGE A 218
18
BC9
SOFTWARE
LEU A:97 , PHE A:98 , ARG A:99 , PGE A:217 , 1PE B:215
BINDING SITE FOR RESIDUE PGE A 219
19
CC1
SOFTWARE
ALA A:15
BINDING SITE FOR RESIDUE P6G A 220
20
CC2
SOFTWARE
TRP B:34 , GLU B:84 , TYR B:85 , HIS B:125 , GLY B:129 , TRP B:133 , TYR B:146 , ASN B:151 , HOH B:313 , HOH B:316
BINDING SITE FOR RESIDUE 2VY B 201
21
CC3
SOFTWARE
THR B:30 , GLY B:33 , TRP B:34 , ILE B:36 , TYR B:74 , HOH B:305
BINDING SITE FOR RESIDUE PG0 B 202
22
CC4
SOFTWARE
LEU B:10 , ALA B:55 , HOH B:311
BINDING SITE FOR RESIDUE PG4 B 203
23
CC5
SOFTWARE
PG4 A:206 , 1PE A:216 , LEU B:119
BINDING SITE FOR RESIDUE PG4 B 204
24
CC6
SOFTWARE
MET B:68 , ILE B:69 , PEG B:213
BINDING SITE FOR RESIDUE PG4 B 205
25
CC7
SOFTWARE
VAL A:31 , PG4 A:204 , BNG B:209
BINDING SITE FOR RESIDUE PG4 B 206
26
CC8
SOFTWARE
ALA B:15 , ALA B:19 , PHE B:22 , ILE B:69
BINDING SITE FOR RESIDUE BNG B 207
27
CC9
SOFTWARE
LEU B:97 , PHE B:98 , ARG B:99 , PRO B:109 , VAL B:116 , BNG B:209
BINDING SITE FOR RESIDUE BNG B 208
28
DC1
SOFTWARE
PHE B:98 , ALA B:108 , LEU B:112 , PG4 B:206 , BNG B:208
BINDING SITE FOR RESIDUE BNG B 209
29
DC2
SOFTWARE
ILE B:160
BINDING SITE FOR RESIDUE PEG B 210
30
DC3
SOFTWARE
ILE A:153 , LEU B:112 , PHE B:115 , PEG B:212
BINDING SITE FOR RESIDUE PEG B 211
31
DC4
SOFTWARE
PEG B:211
BINDING SITE FOR RESIDUE PEG B 212
32
DC5
SOFTWARE
MET B:68 , LEU B:78 , LEU B:86 , PG4 B:205
BINDING SITE FOR RESIDUE PEG B 213
33
DC6
SOFTWARE
PHE B:173 , PRO B:174 , LYS B:175
BINDING SITE FOR RESIDUE PEG B 214
34
DC7
SOFTWARE
PGE A:219 , LYS B:139 , GLY B:140 , TRP B:141 , ALA B:145
BINDING SITE FOR RESIDUE 1PE B 215
35
DC8
SOFTWARE
THR B:30 , ILE B:165
BINDING SITE FOR RESIDUE 1PE B 216
36
DC9
SOFTWARE
TRP B:34 , TYR B:146
BINDING SITE FOR RESIDUE CL B 217
[
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
(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
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 (135 KB)
Header - Asym.Unit
Biol.Unit 1 (67 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
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
4POV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
