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1E6S
Asym. Unit
Info
Asym.Unit (216 KB)
Biol.Unit 1 (410 KB)
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(1)
Title
:
MYROSINASE FROM SINAPIS ALBA WITH BOUND GLUCO-HYDROXIMOLACTAM AND SULFATE
Authors
:
W. P. Burmeister
Date
:
23 Aug 00 (Deposition) - 06 Sep 00 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.35
Chains
:
Asym. Unit : M
Biol. Unit 1: M (2x)
Keywords
:
Hydrolase, Family 1 Glycosyl Hydrolase, Glucosinolate, Tim Barrel, Inhibitor, Transition State Analogue
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. P. Burmeister, S. Cottaz, P. Rollin, A. Vasella, B. Henrissat
High Resolution X-Ray Crystallography Shows That Ascorbate Is A Cofactor For Myrosinase And Substitutes For The Function Of The Catalytic Base
J. Biol. Chem. V. 275 39385 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(9, 34)
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: (2S,3S,4R,5R)-6-(HYDROXYAMINO)-2-(... (GOXa)
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)
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)
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
GOX
1
Ligand/Ion
(2S,3S,4R,5R)-6-(HYDROXYAMINO)-2-(HYDROXYMETHYL)-2,3,4,5-TETRAHYDROPYRIDINE-3,4,5-TRIOL
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SO4
8
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
GLN M:39 , HIS M:141 , ASN M:186 , GLN M:187 , TYR M:330 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , PHE M:473 , SO4 M:934 , HOH M:1336 , HOH M:1432
BINDING SITE FOR RESIDUE GOX M 999
02
AC2
SOFTWARE
HIS M:56 , ASP M:70
BINDING SITE FOR RESIDUE ZN M 1502
03
AC3
SOFTWARE
ARG M:205 , HOH M:1501 , HOH M:1091 , HOH M:1224 , HOH M:1048 , HOH M:1411
BINDING SITE FOR RESIDUE SO4 M 1503
04
AC4
SOFTWARE
LYS M:108 , ARG M:111 , HOH M:1250 , HOH M:1279 , HOH M:1150 , HOH M:1292
BINDING SITE FOR RESIDUE SO4 M 1504
05
AC5
SOFTWARE
ARG M:259 , GLN M:333 , HOH M:1107 , HOH M:1047 , HOH M:1543
BINDING SITE FOR RESIDUE SO4 M 1505
06
AC6
SOFTWARE
GLN M:7 , GLU M:8 , ASN M:9 , HOH M:1208 , HOH M:1030 , HOH M:1092 , HOH M:1360 , HOH M:1162 , HOH M:1312
BINDING SITE FOR RESIDUE SO4 M 1506
07
AC7
SOFTWARE
HIS M:270 , ARG M:277 , HOH M:1132 , HOH M:1032 , HOH M:1033 , HOH M:1557
BINDING SITE FOR RESIDUE SO4 M 1507
08
AC8
SOFTWARE
ARG M:109 , VAL M:113 , GLU M:173 , HOH M:1325 , HOH M:1100 , HOH M:1285
BINDING SITE FOR RESIDUE SO4 M 1508
09
AC9
SOFTWARE
ASN M:60 , HIS M:66 , NAG M:918
BINDING SITE FOR RESIDUE SO4 M 1509
10
BC1
SOFTWARE
PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:1202 , HOH M:1349 , HOH M:1269
BINDING SITE FOR RESIDUE GOL M 1510
11
BC2
SOFTWARE
HIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:1509 , HOH M:1313 , HOH M:1192 , HOH M:1154 , HOH M:1098
BINDING SITE FOR RESIDUE GOL M 1511
12
BC3
SOFTWARE
GLY M:132 , THR M:134 , NAG M:913 , BMA M:914 , HOH M:1398
BINDING SITE FOR RESIDUE GOL M 1512
13
BC4
SOFTWARE
ASP M:239 , ASN M:316 , LEU M:317 , HOH M:1009 , HOH M:1263 , HOH M:1007 , HOH M:1296 , HOH M:1023
BINDING SITE FOR RESIDUE GOL M 1513
14
BC5
SOFTWARE
GLN M:187 , ILE M:257 , ARG M:259 , GOX M:921 , HOH M:1239 , HOH M:1182 , HOH M:1311 , HOH M:1152 , HOH M:1432
BINDING SITE FOR RESIDUE SO4 M 1533
15
BC6
SOFTWARE
THR M:17 , ASP M:18 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:1126 , HOH M:1522
Binding site for Mono-Saccharide NAG M 901 bound to ASN M 21
16
BC7
SOFTWARE
TYR M:58 , ASN M:60 , SO4 M:929 , HOH M:1120 , HOH M:1431 , HOH M:1337
Binding site for Mono-Saccharide NAG M 961 bound to ASN M 60
17
BC8
SOFTWARE
ASN M:90 , SER M:500 , HOH M:1262 , HOH M:1483 , HOH M:1273
Binding site for Mono-Saccharide NAG M 911 bound to ASN M 90
18
BC9
SOFTWARE
SER M:207 , ASN M:218 , THR M:221 , HOH M:1430 , HOH M:1520 , HOH M:1487 , HOH M:1139 , HOH M:1029 , HOH M:1075
Binding site for Poly-Saccharide residues NAG M 921 through NAG M 923 bound to ASN M 218
19
CC1
SOFTWARE
LYS M:165 , LEU M:240 , ASN M:244 , HOH M:1310
Binding site for Mono-Saccharide NAG M 931 bound to ASN M 244
20
CC2
SOFTWARE
ASN M:265 , ASP M:268 , ASN M:316 , LYS M:319 , ALA M:362 , HOH M:1381 , HOH M:1232 , HOH M:1559 , HOH M:1408 , HOH M:1046 , HOH M:1393 , HOH M:1366 , HOH M:1342 , HOH M:1170 , HOH M:1314 , HOH M:1013
Binding site for Poly-Saccharide residues NAG M 941 through XYP M 945 bound to ASN M 265
21
CC3
SOFTWARE
THR M:92 , ILE M:129 , GLY M:132 , ASN M:292 , THR M:294 , GLN M:297 , ILE M:300 , GOL M:932 , HOH M:1226 , HOH M:1058 , HOH M:1169 , HOH M:1147 , HOH M:1453 , HOH M:1178 , HOH M:1540 , HOH M:1254 , HOH M:1040 , HOH M:1625 , HOH M:1380 , HOH M:1563 , HOH M:1321 , HOH M:1005 , HOH M:1556 , HOH M:1308 , HOH M:1068 , HOH M:1203 , HOH M:1060 , HOH M:1238 , HOH M:1435 , HOH M:1011 , HOH M:1020 , HOH M:1006 , HOH M:1313 , HOH M:1192
Binding site for Poly-Saccharide residues NAG M 951 through MAN M 957 bound to ASN M 292
22
CC4
SOFTWARE
SER M:344 , ASN M:346
Binding site for Mono-Saccharide NAG M 971 bound to ASN M 346
23
CC5
SOFTWARE
ASN M:482 , ASP M:485 , HOH M:1270
Binding site for Mono-Saccharide NAG M 991 bound to ASN M 482
[
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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
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All Exon Boundaries
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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_d1e6sm_ (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
d1e6sm_
M:
[
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]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1e6sM00 (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
1e6sM00
M:3-501
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain M
Asymmetric Unit 1
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Asym.Unit (216 KB)
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