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1MYR
Asym. Unit
Info
Asym.Unit (111 KB)
Biol.Unit 1 (203 KB)
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(1)
Title
:
MYROSINASE FROM SINAPIS ALBA
Authors
:
W. P. Burmeister, R. Iori, S. Palmieri, B. Henrissat
Date
:
23 Mar 97 (Deposition) - 16 Jun 97 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.64
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Family 1 Glycosyl Hydrolase, Glucosinolate, Myrosinase, Tim Barrel, Glycosidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. P. Burmeister, S. Cottaz, H. Driguez, R. Iori, S. Palmieri, B. Henrissat
The Crystal Structures Of Sinapis Alba Myrosinase And A Covalent Glycosyl-Enzyme Intermediate Provide Insights Into The Substrate Recognition And Active-Site Machinery Of An S-Glycosidase.
Structure V. 5 663 1997
[
close entry info
]
Hetero Components
(9, 36)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5l: N-ACETYL-D-GLUCOSAMINE (NAGl)
6a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
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)
7h: SULFATE ION (SO4h)
7i: SULFATE ION (SO4i)
7j: SULFATE ION (SO4j)
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
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
3
GOL
4
Ligand/Ion
GLYCEROL
4
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7
SO4
10
Ligand/Ion
SULFATE ION
8
XYP
2
Ligand/Ion
BETA-D-XYLOPYRANOSE
9
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(38, 38)
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: ASN (AUTHOR)
11: BC1 (SOFTWARE)
12: BC2 (SOFTWARE)
13: BC3 (SOFTWARE)
14: BC4 (SOFTWARE)
15: BC5 (SOFTWARE)
16: BC6 (SOFTWARE)
17: BC7 (SOFTWARE)
18: BC8 (SOFTWARE)
19: BC9 (SOFTWARE)
20: CC1 (SOFTWARE)
21: CC2 (SOFTWARE)
22: CC3 (SOFTWARE)
23: CC4 (SOFTWARE)
24: CC5 (SOFTWARE)
25: CC6 (SOFTWARE)
26: CC7 (SOFTWARE)
27: CC8 (SOFTWARE)
28: CC9 (SOFTWARE)
29: DC1 (SOFTWARE)
30: DC2 (SOFTWARE)
31: DC3 (SOFTWARE)
32: DC4 (SOFTWARE)
33: DC5 (SOFTWARE)
34: DC6 (SOFTWARE)
35: DC7 (SOFTWARE)
36: DC8 (SOFTWARE)
37: DC9 (SOFTWARE)
38: ZNB (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:17 , ASP A:18 , GLY A:19 , ASN A:21 , SER A:24 , HOH A:1008 , HOH A:1153 , HOH A:1404
BINDING SITE FOR RESIDUE NAG A 901
02
AC2
SOFTWARE
ASN A:90 , SER A:500 , MAN A:957 , HOH A:1039 , HOH A:1419
BINDING SITE FOR RESIDUE NAG A 911
03
AC3
SOFTWARE
SER A:207 , ASN A:218 , THR A:221 , NAG A:923 , HOH A:1121 , HOH A:1582 , HOH A:1651
BINDING SITE FOR RESIDUE NAG A 921
04
AC4
SOFTWARE
ARG A:306 , NAG A:921
BINDING SITE FOR RESIDUE NAG A 923
05
AC5
SOFTWARE
LYS A:165 , ASP A:239 , LEU A:240 , ASN A:244
BINDING SITE FOR RESIDUE NAG A 931
06
AC6
SOFTWARE
ASN A:265 , ASP A:268 , ALA A:362 , FUC A:942 , NAG A:943 , HOH A:1184 , HOH A:1586 , HOH A:1619 , HOH A:1650
BINDING SITE FOR RESIDUE NAG A 941
07
AC7
SOFTWARE
NAG A:941 , NAG A:943 , SO4 A:1002 , HOH A:1619
BINDING SITE FOR RESIDUE FUC A 942
08
AC8
SOFTWARE
ASN A:316 , NAG A:941 , FUC A:942 , BMA A:944 , XYP A:945 , HOH A:1434 , HOH A:1450 , HOH A:1549 , HOH A:1610 , HOH A:1619 , HOH A:1675
BINDING SITE FOR RESIDUE NAG A 943
09
AC9
SOFTWARE
NAG A:943 , XYP A:945 , HOH A:1450
BINDING SITE FOR RESIDUE BMA A 944
10
ASN
AUTHOR
GLU A:409 , GLN A:187
ACTIVE SITE NUCLEOPHILE AT THE POSITION OF THE GENERAL ACID/BASE
11
BC1
SOFTWARE
ASN A:316 , LYS A:319 , NAG A:943 , BMA A:944 , HOH A:1450 , HOH A:1644
BINDING SITE FOR RESIDUE XYP A 945
12
BC2
SOFTWARE
ASN A:292 , THR A:294 , FUC A:952 , NAG A:953 , HOH A:1049 , HOH A:1177 , HOH A:1178 , HOH A:1290
BINDING SITE FOR RESIDUE NAG A 951
13
BC3
SOFTWARE
ILE A:129 , GLN A:297 , NAG A:951 , NAG A:953 , HOH A:1056 , HOH A:1244 , HOH A:1290 , HOH A:1335 , HOH A:1448
BINDING SITE FOR RESIDUE FUC A 952
14
BC4
SOFTWARE
GLN A:297 , NAG A:951 , FUC A:952 , BMA A:954 , XYP A:955 , MAN A:956 , GOL A:1006 , HOH A:1179 , HOH A:1347 , HOH A:1446 , HOH A:1461 , HOH A:1597 , HOH A:1667
BINDING SITE FOR RESIDUE NAG A 953
15
BC5
SOFTWARE
GLY A:132 , NAG A:953 , XYP A:955 , MAN A:956 , MAN A:957 , GOL A:1006 , HOH A:1543 , HOH A:1667 , HOH A:1669
BINDING SITE FOR RESIDUE BMA A 954
16
BC6
SOFTWARE
NAG A:953 , BMA A:954 , MAN A:956 , HOH A:1643 , HOH A:1667 , HOH A:1671
BINDING SITE FOR RESIDUE XYP A 955
17
BC7
SOFTWARE
GLN A:297 , NAG A:953 , BMA A:954 , XYP A:955 , HOH A:1420 , HOH A:1461 , HOH A:1631 , HOH A:1632
BINDING SITE FOR RESIDUE MAN A 956
18
BC8
SOFTWARE
ASN A:90 , THR A:92 , NAG A:911 , BMA A:954 , HOH A:1426
BINDING SITE FOR RESIDUE MAN A 957
19
BC9
SOFTWARE
ASN A:346
BINDING SITE FOR RESIDUE NDG A 971
20
CC1
SOFTWARE
TYR A:264 , ASN A:265 , ASP A:266 , ASN A:361 , SER A:363 , HIS A:365 , NAG A:983 , HOH A:1328 , HOH A:1546 , HOH A:1674
BINDING SITE FOR RESIDUE NAG A 981
21
CC2
SOFTWARE
PRO A:11 , NAG A:981 , HOH A:1674
BINDING SITE FOR RESIDUE NAG A 983
22
CC3
SOFTWARE
ASN A:482 , ASP A:485 , HOH A:1504
BINDING SITE FOR RESIDUE NAG A 991
23
CC4
SOFTWARE
HIS A:56 , ASP A:70
BINDING SITE FOR RESIDUE ZN A 992
24
CC5
SOFTWARE
ARG A:205 , HOH A:1146 , HOH A:1276 , HOH A:1522 , HOH A:1535
BINDING SITE FOR RESIDUE SO4 A 993
25
CC6
SOFTWARE
LYS A:108 , ARG A:111 , HOH A:1144 , HOH A:1519
BINDING SITE FOR RESIDUE SO4 A 994
26
CC7
SOFTWARE
ARG A:259 , GLN A:333 , LEU A:357 , SO4 A:1000 , HOH A:1082 , HOH A:1483 , HOH A:1532
BINDING SITE FOR RESIDUE SO4 A 995
27
CC8
SOFTWARE
GLN A:7 , GLU A:8 , ASN A:9 , HOH A:1316 , HOH A:1401 , HOH A:1412 , HOH A:1621 , HOH A:1661
BINDING SITE FOR RESIDUE SO4 A 996
28
CC9
SOFTWARE
HIS A:270 , ALA A:273 , ARG A:277 , HOH A:1045 , HOH A:1424 , HOH A:1555
BINDING SITE FOR RESIDUE SO4 A 997
29
DC1
SOFTWARE
ARG A:109 , VAL A:113 , LEU A:170 , GLU A:173 , HOH A:1510 , HOH A:1571 , HOH A:1576
BINDING SITE FOR RESIDUE SO4 A 998
30
DC2
SOFTWARE
ASP A:60 , HIS A:66
BINDING SITE FOR RESIDUE SO4 A 999
31
DC3
SOFTWARE
ARG A:194 , ARG A:259 , SO4 A:995 , HOH A:1094 , HOH A:1344 , HOH A:1483 , HOH A:1532 , HOH A:1589
BINDING SITE FOR RESIDUE SO4 A 1000
32
DC4
SOFTWARE
ASP A:239 , ARG A:269 , ASN A:316 , LEU A:317 , HOH A:1026 , HOH A:1339
BINDING SITE FOR RESIDUE SO4 A 1001
33
DC5
SOFTWARE
TYR A:427 , LYS A:490 , FUC A:942
BINDING SITE FOR RESIDUE SO4 A 1002
34
DC6
SOFTWARE
PHE A:54 , ARG A:57 , GLN A:146 , GLN A:149 , PRO A:203 , TYR A:215 , HOH A:1277 , HOH A:1308
BINDING SITE FOR RESIDUE GOL A 1003
35
DC7
SOFTWARE
HIS A:247 , GLY A:249 , GLN A:280 , GLN A:297 , ILE A:298 , HOH A:1035 , HOH A:1290 , HOH A:1335 , HOH A:1453
BINDING SITE FOR RESIDUE GOL A 1004
36
DC8
SOFTWARE
GLN A:39 , HIS A:141 , ASN A:186 , GLN A:187 , GLU A:409 , TRP A:457 , GLU A:464 , PHE A:465 , HOH A:1478
BINDING SITE FOR RESIDUE GOL A 1005
37
DC9
SOFTWARE
GLY A:132 , THR A:134 , NAG A:953 , BMA A:954 , HOH A:1166 , HOH A:1338 , HOH A:1446 , HOH A:1593
BINDING SITE FOR RESIDUE GOL A 1006
38
ZNB
AUTHOR
HIS A:56 , ASP A:70
ZN BINDING SITE TOGETHER WITH THE SYMMETRY- RELATED EQUIVALENTS.
[
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 (A:29-43)
2: GLYCOSYL_HYDROL_F1_1 (A: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
A:29-43
2
GLYCOSYL_HYDROL_F1_1
PS00572
Glycosyl hydrolases family 1 active site.
MYRA_SINAL
405-413
1
A:405-413
[
close PROSITE info
]
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_d1myra_ (A:)
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
d1myra_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1myrA00 (A:3-501)
View:
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Topologies
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)
(
)
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
1myrA00
A:3-501
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_1_1myrA01 (A: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_1-1myrA01
A:21-501
[
close Pfam info
]
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Chain A
Asymmetric Unit 1
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Asym.Unit (111 KB)
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