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1E4M
Biol. Unit 1
Info
Asym.Unit (219 KB)
Biol.Unit 1 (418 KB)
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(1)
Title
:
MYROSINASE FROM SINAPIS ALBA
Authors
:
W. P. Burmeister
Date
:
10 Jul 00 (Deposition) - 25 May 01 (Release) - 09 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : M
Biol. Unit 1: M (2x)
Keywords
:
Hydrolase, Family 1 Glycosyl Hydrolase, Glucosinolate, Tim Barrel
(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
(7, 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)
3e: GLYCEROL (GOLe)
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: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
7a: BETA-D-XYLOPYRANOSE (XYPa)
7b: BETA-D-XYLOPYRANOSE (XYPb)
8a: 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
10
Ligand/Ion
GLYCEROL
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
24
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SO4
16
Ligand/Ion
SULFATE ION
7
XYP
4
Ligand/Ion
BETA-D-XYLOPYRANOSE
8
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
HIS M:56 , ASP M:70
BINDING SITE FOR RESIDUE ZN M1502
02
AC2
SOFTWARE
ARG M:205 , HOH M:2370 , HOH M:2763 , HOH M:2764 , HOH M:2765 , HOH M:2766
BINDING SITE FOR RESIDUE SO4 M1503
03
AC3
SOFTWARE
LYS M:108 , ARG M:111 , HOH M:2213 , HOH M:2291 , HOH M:2767 , HOH M:2768
BINDING SITE FOR RESIDUE SO4 M1504
04
AC4
SOFTWARE
ARG M:259 , GLN M:333 , SO4 M:1510 , HOH M:2769 , HOH M:2771 , HOH M:2783
BINDING SITE FOR RESIDUE SO4 M1505
05
AC5
SOFTWARE
GLN M:7 , GLU M:8 , ASN M:9 , HOH M:2009 , HOH M:2772 , HOH M:2773 , HOH M:2774 , HOH M:2775 , HOH M:2776
BINDING SITE FOR RESIDUE SO4 M1506
06
AC6
SOFTWARE
HIS M:270 , ALA M:273 , ARG M:277 , HOH M:2429 , HOH M:2432 , HOH M:2777 , HOH M:2778
BINDING SITE FOR RESIDUE SO4 M1507
07
AC7
SOFTWARE
ARG M:109 , VAL M:113 , GLU M:173 , HOH M:2205 , HOH M:2779 , HOH M:2780
BINDING SITE FOR RESIDUE SO4 M1508
08
AC8
SOFTWARE
ASN M:60 , HIS M:66 , NAG M:961 , HOH M:2781
BINDING SITE FOR RESIDUE SO4 M1509
09
AC9
SOFTWARE
ARG M:194 , ARG M:259 , SO4 M:1505 , HOH M:2769 , HOH M:2782 , HOH M:2783 , HOH M:2784 , HOH M:2785
BINDING SITE FOR RESIDUE SO4 M1510
10
BC1
SOFTWARE
ASN M:316 , LEU M:317 , HOH M:2385 , HOH M:2487 , HOH M:2730 , HOH M:2786 , HOH M:2787 , HOH M:2788 , HOH M:2789
BINDING SITE FOR RESIDUE GOL M1511
11
BC2
SOFTWARE
ILE M:50 , PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2288 , HOH M:2295 , HOH M:2790
BINDING SITE FOR RESIDUE GOL M1512
12
BC3
SOFTWARE
HIS M:247 , GLN M:248 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:2791 , HOH M:2792 , HOH M:2793 , HOH M:2794 , HOH M:2795
BINDING SITE FOR RESIDUE GOL M1513
13
BC4
SOFTWARE
GLY M:132 , THR M:134 , NAG M:953 , BMA M:954 , HOH M:2796
BINDING SITE FOR RESIDUE GOL M1514
14
BC5
SOFTWARE
GLN M:39 , HIS M:141 , ASN M:186 , GLN M:187 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , HOH M:2500
BINDING SITE FOR RESIDUE GOL M1515
15
BC6
SOFTWARE
THR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:2709 , HOH M:2710 , HOH M:2711
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:2108 , HOH M:2760 , HOH M:2761
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:2712 , HOH M:2713 , HOH M:2715
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:2716 , HOH M:2717 , HOH M:2718 , HOH M:2719 , HOH M:2721 , HOH M:2723
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:2384 , HOH M:2724
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 , HOH M:2428 , HOH M:2725 , HOH M:2726 , HOH M:2728 , HOH M:2729 , HOH M:2730 , HOH M:2731 , HOH M:2732 , HOH M:2733 , HOH M:2734 , HOH M:2735
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 265 RESIDUES 941 TO 945
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:1514 , HOH M:2256 , HOH M:2268 , HOH M:2336 , HOH M:2448 , HOH M:2737 , HOH M:2738 , HOH M:2739 , HOH M:2740 , HOH M:2741 , HOH M:2742 , HOH M:2743 , HOH M:2744 , HOH M:2745 , HOH M:2746 , HOH M:2748 , HOH M:2751 , HOH M:2752 , HOH M:2753 , HOH M:2754 , HOH M:2755 , HOH M:2756 , HOH M:2757 , HOH M:2758 , HOH M:2759 , HOH M:2792 , HOH M:2793
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 292 RESIDUES 951 TO 957
22
CC4
SOFTWARE
ASN M:346
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:2684
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 482 RESIDUES 991 TO 991
[
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
]
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
View:
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Label:
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_d1e4mm_ (M:)
View:
Select:
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
d1e4mm_
M:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1e4mM00 (M:3-501)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
1e4mM00
M:3-501
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
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all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain M
Asymmetric Unit 1
Asymmetric Unit 2
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select chains 'A' and 'C'
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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'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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