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.
2WXD
Asym. Unit
Info
Asym.Unit (119 KB)
Biol.Unit 1 (213 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
A MICROMOLAR O-SULFATED THIOHYDROXIMATE INHIBITOR BOUND TO PLANT MYROSINASE
Authors
:
A. Besle, W. P. Burmeister
Date
:
09 Nov 09 (Deposition) - 09 Feb 10 (Release) - 04 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : M
Biol. Unit 1: M (2x)
Keywords
:
Vacuole, Hydrolase, Thiohydroximate, Glucosinolate, Family 1 Glycosyl Hydrolase, Glycosidase, Glycoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Besle, X. Brazzolotto, A. Tatibouet, D. Cerniauskaite, E. Gallienne, P. Rollin, W. P. Burmeister
A Micromolar O-Sulfated Thiohydroximate Inhibitor Bound To Plant Myrosinase
Acta Crystallogr. , Sect. F V. 66 152 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(9, 37)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: 2-(DIMETHYLAMINO)ETHYL (1Z)-2-PHEN... (E18a)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6k: N-ACETYL-D-GLUCOSAMINE (NAGk)
6l: N-ACETYL-D-GLUCOSAMINE (NAGl)
6m: N-ACETYL-D-GLUCOSAMINE (NAGm)
6n: N-ACETYL-D-GLUCOSAMINE (NAGn)
6o: N-ACETYL-D-GLUCOSAMINE (NAGo)
6p: N-ACETYL-D-GLUCOSAMINE (NAGp)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
7e: SULFATE ION (SO4e)
7f: SULFATE ION (SO4f)
7g: SULFATE ION (SO4g)
8a: BETA-D-XYLOPYRANOSE (XYPa)
8b: BETA-D-XYLOPYRANOSE (XYPb)
9a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
E18
1
Ligand/Ion
2-(DIMETHYLAMINO)ETHYL (1Z)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
GOL
4
Ligand/Ion
GLYCEROL
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
16
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SO4
7
Ligand/Ion
SULFATE ION
8
XYP
2
Ligand/Ion
BETA-D-XYLOPYRANOSE
9
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG M:194 , ARG M:259 , GLN M:333 , E18 M:1501 , HOH M:3332 , HOH M:3334 , HOH M:3734 , HOH M:3735 , HOH M:3736
BINDING SITE FOR RESIDUE SO4 M1503
02
AC2
SOFTWARE
GLN M:187 , TYR M:189 , SER M:190 , ARG M:194 , ILE M:257 , ARG M:259 , TYR M:330 , PHE M:371 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:473 , SO4 M:1503 , HOH M:3641
BINDING SITE FOR RESIDUE E18 M1501
03
AC3
SOFTWARE
THR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:3683 , HOH M:3684
BINDING SITE FOR RESIDUE NAG M 901
04
AC4
SOFTWARE
LYS M:165 , ASP M:239 , LEU M:240 , ASN M:244 , HOH M:3366 , HOH M:3369
BINDING SITE FOR RESIDUE NAG M 931
05
AC5
SOFTWARE
SER M:344 , ASN M:346 , HOH M:3504
BINDING SITE FOR RESIDUE NAG M 971
06
AC6
SOFTWARE
ASN M:482 , ASP M:485 , HOH M:3661
BINDING SITE FOR RESIDUE NAG M 991
07
AC7
SOFTWARE
HIS M:56 , ASP M:70
BINDING SITE FOR RESIDUE ZN M1502
08
AC8
SOFTWARE
ARG M:205 , HOH M:3210 , HOH M:3739 , HOH M:3740 , HOH M:3741
BINDING SITE FOR RESIDUE SO4 M1504
09
AC9
SOFTWARE
LYS M:108 , ARG M:111 , HOH M:3207 , HOH M:3286 , HOH M:3742 , HOH M:3743
BINDING SITE FOR RESIDUE SO4 M1505
10
BC1
SOFTWARE
GLN M:7 , GLU M:8 , ASN M:9 , HOH M:3008 , HOH M:3744 , HOH M:3746 , HOH M:3747 , HOH M:3748
BINDING SITE FOR RESIDUE SO4 M1506
11
BC2
SOFTWARE
HIS M:270 , ALA M:273 , ARG M:277 , HOH M:3749 , HOH M:3750 , HOH M:3751 , HOH M:3752
BINDING SITE FOR RESIDUE SO4 M1507
12
BC3
SOFTWARE
ARG M:109 , VAL M:113 , GLU M:173 , HOH M:3203 , HOH M:3753 , HOH M:3754
BINDING SITE FOR RESIDUE SO4 M1508
13
BC4
SOFTWARE
ASN M:60 , HIS M:66 , NAG M:961 , HOH M:3755
BINDING SITE FOR RESIDUE SO4 M1509
14
BC5
SOFTWARE
ARG M:269 , HIS M:270 , ASN M:316 , HOH M:3409 , HOH M:3467 , HOH M:3700 , HOH M:3756 , HOH M:3757
BINDING SITE FOR RESIDUE GOL M2511
15
BC6
SOFTWARE
ILE M:50 , PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:3288 , HOH M:3758
BINDING SITE FOR RESIDUE GOL M2512
16
BC7
SOFTWARE
HIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , FUC M:952 , HOH M:3710 , HOH M:3759 , HOH M:3760 , HOH M:3761
BINDING SITE FOR RESIDUE GOL M2513
17
BC8
SOFTWARE
GLY M:132 , THR M:134 , FUC M:952 , NAG M:953 , BMA M:954 , HOH M:3763 , HOH M:3764
BINDING SITE FOR RESIDUE GOL M2514
18
BC9
SOFTWARE
ASN M:60 , SER M:213 , SO4 M:1509 , HOH M:3089 , HOH M:3108 , HOH M:3725 , HOH M:3726 , HOH M:3727 , HOH M:3728
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 60 RESIDUES 961 TO 963
19
CC1
SOFTWARE
ASN M:90 , SER M:500 , MAN M:957 , HOH M:3481 , HOH M:3685 , HOH M:3686 , HOH M:3687 , HOH M:3688
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 90 RESIDUES 911 TO 913
20
CC2
SOFTWARE
SER M:207 , ASN M:218 , THR M:221 , GLU M:305 , HOH M:3354 , HOH M:3448 , HOH M:3689 , HOH M:3690 , HOH M:3691 , HOH M:3692 , HOH M:3693
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 218 RESIDUES 921 TO 923
21
CC3
SOFTWARE
ASN M:265 , ASP M:268 , ASN M:316 , LYS M:319 , ALA M:362 , HOH M:3409 , HOH M:3695 , HOH M:3696 , HOH M:3698 , HOH M:3699 , HOH M:3700 , HOH M:3701 , HOH M:3702 , HOH M:3703 , HOH M:3704 , HOH M:3705 , HOH M:3706
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 265 RESIDUES 941 TO 945
22
CC4
SOFTWARE
SER M:27 , ASP M:28 , ASN M:90 , ALA M:91 , THR M:92 , ILE M:129 , LYS M:131 , GLY M:132 , ASN M:292 , THR M:294 , GLN M:297 , NAG M:911 , GOL M:2513 , GOL M:2514 , HOH M:3165 , HOH M:3171 , HOH M:3252 , HOH M:3430 , HOH M:3707 , HOH M:3708 , HOH M:3709 , HOH M:3710 , HOH M:3711 , HOH M:3712 , HOH M:3713 , HOH M:3714 , HOH M:3716 , HOH M:3717 , HOH M:3718 , HOH M:3719 , HOH M:3720 , HOH M:3722 , HOH M:3723 , HOH M:3760
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 292 RESIDUES 951 TO 957
23
CC5
SOFTWARE
PRO M:11 , ASN M:265 , ASP M:266 , ASN M:361 , SER M:363 , HIS M:365 , HOH M:3399 , HOH M:3403 , HOH M:3405 , HOH M:3485 , HOH M:3729 , HOH M:3730 , HOH M:3731
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 361 RESIDUES 981 TO 983
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F1_2 (M:29-43)
2: GLYCOSYL_HYDROL_F1_1 (M:405-413)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F1_2
PS00653
Glycosyl hydrolases family 1 N-terminal signature.
MYRA_SINAL
29-43
1
M:29-43
2
GLYCOSYL_HYDROL_F1_1
PS00572
Glycosyl hydrolases family 1 active site.
MYRA_SINAL
405-413
1
M:405-413
[
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_d2wxdm_ (M:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
Family 1 of glycosyl hydrolase
(102)
Protein domain
:
Plant beta-glucosidase (myrosinase)
(30)
White mustard (Sinapis alba) [TaxId: 3728]
(18)
1a
d2wxdm_
M:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2wxdM00 (M:3-501)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
White mustard (Sinapis alba)
(18)
1a
2wxdM00
M:3-501
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_1_2wxdM01 (M:21-501)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_1
(36)
Sinapis alba (White mustard) (Brassica hirta)
(4)
1a
Glyco_hydro_1-2wxdM01
M:21-501
[
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 M
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 (119 KB)
Header - Asym.Unit
Biol.Unit 1 (213 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
2WXD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
