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1MYR
Biol. Unit 1
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
(8, 70)
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
4
Ligand/Ion
BETA-D-MANNOSE
2
FUC
4
Ligand/Ion
ALPHA-L-FUCOSE
3
GOL
8
Ligand/Ion
GLYCEROL
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
24
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7
SO4
20
Ligand/Ion
SULFATE ION
8
XYP
4
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 only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
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PROSITE Patterns/Profiles
(2, 4)
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
2
A:29-43
2
GLYCOSYL_HYDROL_F1_1
PS00572
Glycosyl hydrolases family 1 active site.
MYRA_SINAL
405-413
2
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.
(no "Exon" information available for biological units yet)
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)
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Architectures
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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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