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1E6S
Biol. Unit 1
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
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Hetero Components
(8, 66)
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
4
Ligand/Ion
BETA-D-MANNOSE
2
FUC
4
Ligand/Ion
ALPHA-L-FUCOSE
3
GOL
8
Ligand/Ion
GLYCEROL
4
GOX
2
Ligand/Ion
(2S,3S,4R,5R)-6-(HYDROXYAMINO)-2-(HYDROXYMETHYL)-2,3,4,5-TETRAHYDROPYRIDINE-3,4,5-TRIOL
5
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
24
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SO4
16
Ligand/Ion
SULFATE ION
8
XYP
4
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 only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 4)
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
2
M:29-43
2
GLYCOSYL_HYDROL_F1_1
PS00572
Glycosyl hydrolases family 1 active site.
MYRA_SINAL
405-413
2
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1e6sm_ (M:)
View:
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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
d1e6sm_
M:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1e6sM00 (M:3-501)
View:
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(
)
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Architectures
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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
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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
Asymmetric Unit 2
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