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1E6X
Asym. Unit
Info
Asym.Unit (216 KB)
Biol.Unit 1 (412 KB)
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(1)
Title
:
MYROSINASE FROM SINAPIS ALBA WITH A BOUND TRANSITION STATE ANALOGUE,D-GLUCONO-1,5-LACTONE
Authors
:
W. P. Burmeister
Date
:
23 Aug 00 (Deposition) - 05 Jan 01 (Release) - 19 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : M
Biol. Unit 1: M (2x)
Keywords
:
Family 1 Glycosyl Hydrolase, Glucosinolate, Tim Barrel, Hydrolase
(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, 33)
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: (3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(... (LGCa)
5a: ALPHA-D-MANNOSE (MANa)
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
LGC
1
Ligand/Ion
(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
5
MAN
1
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 , ASN M:328 , TYR M:330 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , PHE M:473 , HOH M:2763 , HOH M:2764 , HOH M:2765
BINDING SITE FOR RESIDUE LGC M 999
02
AC2
SOFTWARE
HIS M:56 , ASP M:70
BINDING SITE FOR RESIDUE ZN M1502
03
AC3
SOFTWARE
ARG M:205 , HOH M:2375 , HOH M:2767 , HOH M:2768 , HOH M:2769 , HOH M:2770
BINDING SITE FOR RESIDUE SO4 M1503
04
AC4
SOFTWARE
LYS M:108 , ARG M:111 , HOH M:2225 , HOH M:2303 , HOH M:2771 , HOH M:2772
BINDING SITE FOR RESIDUE SO4 M1504
05
AC5
SOFTWARE
ARG M:259 , GLN M:333 , SO4 M:1510 , HOH M:2773 , HOH M:2775 , HOH M:2792
BINDING SITE FOR RESIDUE SO4 M1505
06
AC6
SOFTWARE
GLN M:7 , GLU M:8 , ASN M:9 , HOH M:2009 , HOH M:2776 , HOH M:2777 , HOH M:2778 , HOH M:2779 , HOH M:2780
BINDING SITE FOR RESIDUE SO4 M1506
07
AC7
SOFTWARE
HIS M:270 , ALA M:273 , ARG M:277 , HOH M:2782 , HOH M:2783 , HOH M:2784 , HOH M:2785
BINDING SITE FOR RESIDUE SO4 M1507
08
AC8
SOFTWARE
ARG M:109 , VAL M:113 , GLU M:173 , HOH M:2786 , HOH M:2787 , HOH M:2788
BINDING SITE FOR RESIDUE SO4 M1508
09
AC9
SOFTWARE
ASN M:60 , HIS M:66 , NAG M:961
BINDING SITE FOR RESIDUE SO4 M1509
10
BC1
SOFTWARE
ARG M:194 , ARG M:259 , SO4 M:1505 , HOH M:2352 , HOH M:2773 , HOH M:2791 , HOH M:2792 , HOH M:2793 , HOH M:2794
BINDING SITE FOR RESIDUE SO4 M1510
11
BC2
SOFTWARE
ASN M:316 , LEU M:317 , HOH M:2385 , HOH M:2389 , HOH M:2486 , HOH M:2795 , HOH M:2796 , HOH M:2797 , HOH M:2798
BINDING SITE FOR RESIDUE GOL M1511
12
BC3
SOFTWARE
ILE M:50 , PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2301 , HOH M:2307 , HOH M:2799
BINDING SITE FOR RESIDUE GOL M1512
13
BC4
SOFTWARE
HIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:2409 , HOH M:2453 , HOH M:2800 , HOH M:2801 , HOH M:2802
BINDING SITE FOR RESIDUE GOL M1513
14
BC5
SOFTWARE
GLY M:132 , THR M:134 , NAG M:953 , BMA M:954 , HOH M:2276 , HOH M:2803 , HOH M:2804
BINDING SITE FOR RESIDUE GOL M1514
15
BC6
SOFTWARE
THR M:17 , ASP M:18 , ASN M:21 , SER M:24 , HOH M:2712 , HOH M:2713 , HOH M:2714
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 21 RESIDUES 901 TO 901
16
BC7
SOFTWARE
TYR M:58 , ASN M:60 , SER M:213 , SO4 M:1509 , HOH M:2119 , HOH M:2371 , HOH M:2759 , HOH M:2760
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 60 RESIDUES 961 TO 961
17
BC8
SOFTWARE
ASN M:90 , SER M:500 , HOH M:2715 , HOH M:2718 , HOH M:2719
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 90 RESIDUES 911 TO 911
18
BC9
SOFTWARE
SER M:207 , ASN M:218 , THR M:221 , GLU M:305 , HOH M:2720 , HOH M:2721 , HOH M:2722 , HOH M:2723 , HOH M:2724 , HOH M:2726
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 218 RESIDUES 921 TO 923
19
CC1
SOFTWARE
LYS M:165 , LEU M:240 , ASN M:244 , HOH M:2390 , HOH M:2399
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 244 RESIDUES 931 TO 931
20
CC2
SOFTWARE
ASN M:265 , ASP M:268 , ASN M:316 , LYS M:319 , ALA M:362 , SER M:363 , HOH M:2433 , HOH M:2487 , HOH M:2729 , HOH M:2731 , HOH M:2733 , HOH M:2734 , HOH M:2735 , HOH M:2736 , HOH M:2738 , HOH M:2739
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 265 RESIDUES 941 TO 945
21
CC3
SOFTWARE
ILE M:129 , ASN M:292 , THR M:294 , GLN M:297 , ILE M:300 , GOL M:1514 , HOH M:2269 , HOH M:2344 , HOH M:2452 , HOH M:2453 , HOH M:2455 , HOH M:2740 , HOH M:2741 , HOH M:2742 , HOH M:2744 , HOH M:2745 , HOH M:2747 , HOH M:2749 , HOH M:2750 , HOH M:2752 , HOH M:2753 , HOH M:2755 , HOH M:2756 , HOH M:2757 , HOH M:2758 , HOH M:2800
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 292 RESIDUES 951 TO 956
22
CC4
SOFTWARE
ASN M:346 , HOH M:2528
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 346 RESIDUES 971 TO 971
23
CC5
SOFTWARE
ASN M:482 , ASP M:485 , HOH M:2692 , HOH M:2761
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 482 RESIDUES 991 TO 991
[
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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
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_d1e6xm_ (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
d1e6xm_
M:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1e6xM00 (M:3-501)
View:
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Classes
(
)
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)
Architectures
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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
1e6xM00
M:3-501
[
close CATH info
]
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
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain M
Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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