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1W9B
Asym. Unit
Info
Asym.Unit (114 KB)
Biol.Unit 1 (107 KB)
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(1)
Title
:
S. ALBA MYROSINASE IN COMPLEX WITH CARBA-GLUCOTROPAEOLIN
Authors
:
A. Bourderioux, M. Lefoix, D. Gueyrard, A. Tatibouet, S. Cottaz, S. Arzt, W. P. Burmeister, P. Rollin
Date
:
08 Oct 04 (Deposition) - 19 May 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : M
Biol. Unit 1: M (1x)
Keywords
:
Thioglucosidase, Thioglycosidase, Myrosinase, Hydrolase, Thio-Glucoside, Thiohydroximate, Glusosinolate, Glucotropaeolin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Bourderioux, M. Lefoix, D. Gueyrard, A. Tatibouet, S. Cottaz, S. Arzt, W. P. Burmeister, P. Rollin
The Glucosinolate-Myrosinase System. New Insights Into Enzyme-Substrate Interactions By Use Of Simplified Inhibitors
Org. Biomol. Chem. V. 3 1872 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(9, 31)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: CARBA-GLUCOTROPAEOLIN (CGTa)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
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)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
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
CGT
1
Ligand/Ion
CARBA-GLUCOTROPAEOLIN
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
GOL
3
Ligand/Ion
GLYCEROL
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SO4
4
Ligand/Ion
SULFATE ION
8
XYP
2
Ligand/Ion
BETA-D-XYLOPYRANOSE
9
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , HOH M:2049 , HOH M:2672 , HOH M:2673
BINDING SITE FOR RESIDUE NAG M 901
02
AC2
SOFTWARE
ASN M:90 , SER M:500 , MAN M:957 , HOH M:2669 , HOH M:2674 , HOH M:2675
BINDING SITE FOR RESIDUE NAG M 911
03
AC3
SOFTWARE
ASN M:218 , THR M:221 , NAG M:923 , HOH M:2676 , HOH M:2677 , HOH M:2678 , HOH M:2679 , HOH M:2680
BINDING SITE FOR RESIDUE NAG M 921
04
AC4
SOFTWARE
GLU M:305 , NAG M:921 , HOH M:2681
BINDING SITE FOR RESIDUE NAG M 923
05
AC5
SOFTWARE
LYS M:165 , LEU M:240 , ASN M:244 , HOH M:2684
BINDING SITE FOR RESIDUE NAG M 931
06
AC6
SOFTWARE
ASN M:265 , ASP M:268 , ALA M:362 , FUC M:942 , NAG M:943 , HOH M:2685 , HOH M:2686 , HOH M:2687 , HOH M:2689
BINDING SITE FOR RESIDUE NAG M 941
07
AC7
SOFTWARE
NAG M:941 , NAG M:943
BINDING SITE FOR RESIDUE FUC M 942
08
AC8
SOFTWARE
ASN M:316 , NAG M:941 , FUC M:942 , BMA M:944 , XYP M:945 , HOH M:2689 , HOH M:2691 , HOH M:2692 , HOH M:2694
BINDING SITE FOR RESIDUE NAG M 943
09
AC9
SOFTWARE
NAG M:943 , XYP M:945
BINDING SITE FOR RESIDUE BMA M 944
10
BC1
SOFTWARE
ASN M:316 , LYS M:319 , NAG M:943 , BMA M:944 , HOH M:2692 , HOH M:2695
BINDING SITE FOR RESIDUE XYP M 945
11
BC2
SOFTWARE
ASN M:292 , THR M:294 , FUC M:952 , NAG M:953 , HOH M:2426 , HOH M:2430 , HOH M:2696 , HOH M:2697 , HOH M:2762
BINDING SITE FOR RESIDUE NAG M 951
12
BC3
SOFTWARE
ILE M:129 , GLN M:297 , NAG M:951 , NAG M:953 , HOH M:2700 , HOH M:2701 , HOH M:2702 , HOH M:2704 , HOH M:2762
BINDING SITE FOR RESIDUE FUC M 952
13
BC4
SOFTWARE
GLN M:297 , NAG M:951 , FUC M:952 , BMA M:954 , XYP M:955 , MAN M:956 , HOH M:2260 , HOH M:2705 , HOH M:2706 , HOH M:2713 , HOH M:2717
BINDING SITE FOR RESIDUE NAG M 953
14
BC5
SOFTWARE
NAG M:953 , XYP M:955 , MAN M:956 , MAN M:957 , HOH M:2708 , HOH M:2711 , HOH M:2713
BINDING SITE FOR RESIDUE BMA M 954
15
BC6
SOFTWARE
NAG M:953 , BMA M:954 , MAN M:956 , HOH M:2713 , HOH M:2714
BINDING SITE FOR RESIDUE XYP M 955
16
BC7
SOFTWARE
GLN M:297 , ILE M:300 , NAG M:953 , BMA M:954 , XYP M:955 , HOH M:2716 , HOH M:2717 , HOH M:2718 , HOH M:2719
BINDING SITE FOR RESIDUE MAN M 956
17
BC8
SOFTWARE
THR M:92 , NAG M:911 , BMA M:954 , HOH M:2711 , HOH M:2721 , HOH M:2722 , HOH M:2723 , HOH M:2724
BINDING SITE FOR RESIDUE MAN M 957
18
BC9
SOFTWARE
ASN M:60 , HOH M:2111 , HOH M:2119 , HOH M:2728 , HOH M:2729
BINDING SITE FOR RESIDUE NAG M 961
19
CC1
SOFTWARE
ASN M:346 , MET M:351 , HOH M:2498
BINDING SITE FOR RESIDUE NAG M 971
20
CC2
SOFTWARE
ASN M:265 , ASP M:266 , ASN M:361 , SER M:363 , HIS M:365 , NAG M:983 , HOH M:2395 , HOH M:2399 , HOH M:2478
BINDING SITE FOR RESIDUE NAG M 981
21
CC3
SOFTWARE
PRO M:11 , NAG M:981 , HOH M:2005 , HOH M:2735 , HOH M:2736
BINDING SITE FOR RESIDUE NAG M 983
22
CC4
SOFTWARE
ASN M:482 , ASP M:485 , HOH M:2737 , HOH M:2738
BINDING SITE FOR RESIDUE NAG M 991
23
CC5
SOFTWARE
HIS M:56 , ASP M:70
BINDING SITE FOR RESIDUE ZN M1502
24
CC6
SOFTWARE
GLU M:153 , ARG M:205 , HOH M:2744 , HOH M:2745 , HOH M:2746 , HOH M:2747
BINDING SITE FOR RESIDUE SO4 M1503
25
CC7
SOFTWARE
LYS M:108 , ARG M:111 , HOH M:2222 , HOH M:2749 , HOH M:2750 , HOH M:2751
BINDING SITE FOR RESIDUE SO4 M1504
26
CC8
SOFTWARE
ARG M:259 , GLN M:333 , LEU M:357 , HOH M:2333 , HOH M:2752
BINDING SITE FOR RESIDUE SO4 M1505
27
CC9
SOFTWARE
GLN M:7 , GLU M:8 , ASN M:9 , HOH M:2754 , HOH M:2755 , HOH M:2756 , HOH M:2757 , HOH M:2758 , HOH M:2759
BINDING SITE FOR RESIDUE SO4 M1506
28
DC1
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:465 , PHE M:473 , GOL M:1000 , HOH M:2532 , HOH M:2636 , HOH M:2739 , HOH M:2740 , HOH M:2741 , HOH M:2742 , HOH M:2743
BINDING SITE FOR RESIDUE CGT M 999
29
DC2
SOFTWARE
GLN M:39 , HIS M:141 , ASN M:186 , GLN M:187 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , CGT M:999 , HOH M:2742 , HOH M:2743
BINDING SITE FOR RESIDUE GOL M1000
30
DC3
SOFTWARE
PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2296 , HOH M:2760
BINDING SITE FOR RESIDUE GOL M1512
31
DC4
SOFTWARE
THR M:246 , HIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:2701 , HOH M:2761 , HOH M:2762 , HOH M:2763 , HOH M:2764
BINDING SITE FOR RESIDUE GOL M1513
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
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
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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_d1w9bm_ (M:)
View:
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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
d1w9bm_
M:
[
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]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1w9bM00 (M:3-501)
View:
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(
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(
)
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
1w9bM00
M:3-501
[
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]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_1_1w9bM01 (M:21-501)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_1
(36)
Sinapis alba (White mustard) (Brassica hirta)
(4)
1a
Glyco_hydro_1-1w9bM01
M:21-501
[
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]
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Asymmetric Unit 1
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