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.
4WKT
Asym. Unit
Info
Asym.Unit (255 KB)
Biol.Unit 1 (247 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
N-ALKYLBORONIC ACID INHIBITORS REVEAL DETERMINANTS OF LIGAND SPECIFICITY IN THE QUORUM-QUENCHING AND SIDEROPHORE BIOSYNTHETIC ENZYME PVDQ
Authors
:
R. Wu, K. D. Clevenger, W. Fast, D. Liu
Date
:
03 Oct 14 (Deposition) - 12 Nov 14 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.78
Chains
:
Asym. Unit : A,C
Biol. Unit 1: A,C (1x)
Keywords
:
N-Alkylboronic Acid Inhibitors Of Pvdq, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. D. Clevenger, R. Wu, D. Liu, W. Fast
N-Alkylboronic Acid Inhibitors Reveal Determinants Of Ligan Specificity In The Quorum-Quenching And Siderophore Biosynthetic Enzyme Pvdq.
Biochemistry V. 53 6679 2014
[
close entry info
]
Hetero Components
(2, 19)
Info
All Hetero Components
1a: 1-BUTANE BORONIC ACID (BUBa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BUB
1
Ligand/Ion
1-BUTANE BORONIC ACID
2
GOL
18
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(19, 19)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER C:217 , HIS C:239 , THR C:285 , VAL C:286 , ASN C:485
binding site for residue BUB C 801
02
AC2
SOFTWARE
LEU C:259 , ASP C:260 , ASN C:382 , ALA C:384 , GOL C:808
binding site for residue GOL C 802
03
AC3
SOFTWARE
ILE A:101 , GLU C:336 , HIS C:337 , HOH C:901 , HOH C:907 , HOH C:1051
binding site for residue GOL C 803
04
AC4
SOFTWARE
GOL A:205 , TYR C:344 , GLY C:345 , LEU C:364 , ARG C:365 , ASP C:366 , LEU C:369 , HOH C:1072 , HOH C:1149
binding site for residue GOL C 804
05
AC5
SOFTWARE
ARG C:365 , TRP C:455 , ALA C:464 , GLY C:465 , HOH C:904
binding site for residue GOL C 805
06
AC6
SOFTWARE
THR C:372 , ARG C:373 , ALA C:462 , HOH C:1067 , HOH C:1080 , HOH C:1093 , HOH C:1324
binding site for residue GOL C 806
07
AC7
SOFTWARE
PHE C:596 , ALA C:597 , LEU C:599 , ASP C:600 , GLY C:601 , ALA C:602 , TRP C:603
binding site for residue GOL C 807
08
AC8
SOFTWARE
GLY C:257 , ARG C:258 , ASP C:260 , GOL C:802
binding site for residue GOL C 808
09
AC9
SOFTWARE
ALA C:470 , GLN C:498 , GLY C:499 , PHE C:500 , HOH C:1295
binding site for residue GOL C 809
10
AD1
SOFTWARE
ASN C:485 , ASP C:486 , GLY C:511
binding site for residue GOL C 810
11
AD2
SOFTWARE
LEU C:580 , ASP C:581 , ARG C:651 , ASP C:654 , ALA C:666
binding site for residue GOL C 811
12
AD3
SOFTWARE
PRO C:459 , ALA C:461 , HOH C:1290 , HOH C:1324 , HOH C:1375
binding site for residue GOL C 812
13
AD4
SOFTWARE
ARG C:591 , ARG C:684 , HOH C:1104
binding site for residue GOL C 813
14
AD5
SOFTWARE
GLU A:172 , GLY A:173 , HOH A:462 , VAL C:286 , TRP C:402
binding site for residue GOL A 201
15
AD6
SOFTWARE
LYS A:48 , ASP A:49 , LYS A:89 , GLU A:93 , LEU A:94 , ASP A:95 , ASP A:180
binding site for residue GOL A 202
16
AD7
SOFTWARE
TRP A:116 , THR A:159 , ASP A:160 , HOH A:301 , HOH A:316 , HOH A:329 , LYS C:643
binding site for residue GOL A 203
17
AD8
SOFTWARE
PHE A:137 , ALA A:141 , ASP A:142 , GLY A:143 , LYS A:144 , THR A:145 , THR A:146 , HOH A:416
binding site for residue GOL A 204
18
AD9
SOFTWARE
TRP A:105 , LEU A:106 , GLN A:108 , ARG A:167 , HOH A:446 , GOL C:804
binding site for residue GOL A 205
19
AE1
SOFTWARE
GLN A:177 , HOH A:404 , HOH A:457 , GLY C:442 , LEU C:443
binding site for residue GOL A 206
[
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 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 (255 KB)
Header - Asym.Unit
Biol.Unit 1 (247 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
4WKT
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
