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1DWH
Asym. Unit
Info
Asym.Unit (119 KB)
Biol.Unit 1 (213 KB)
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(1)
Title
:
STUDY ON RADIATION DAMAGE ON A CRYOCOOLED CRYSTAL. PART 4: STRUCTURE AFTER IRRADIATION WITH 27.2*10E15 PHOTONS/MM2
Authors
:
W. P. Burmeister
Date
:
05 Dec 99 (Deposition) - 03 Mar 00 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : M
Biol. Unit 1: M (2x)
Keywords
:
Glycosidase, Radiation Damage, Radiolysis, Cryo-Cooled, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. P. Burmeister
Structural Changes In A Cryo-Cooled Protein Crystal Due To Radiation Damage
Acta Crystallogr. , Sect. D V. 56 328 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(8, 36)
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)
5m: N-ACETYL-D-GLUCOSAMINE (NAGm)
5n: N-ACETYL-D-GLUCOSAMINE (NAGn)
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
2
Ligand/Ion
BETA-D-MANNOSE
2
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
3
GOL
5
Ligand/Ion
GLYCEROL
4
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SO4
8
Ligand/Ion
SULFATE ION
7
XYP
2
Ligand/Ion
BETA-D-XYLOPYRANOSE
8
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS M:56 , ASN M:68 , ASP M:70
BINDING SITE FOR RESIDUE ZN M 1001
02
AC2
SOFTWARE
ARG M:106 , ARG M:205 , HOH M:2192 , HOH M:2213 , HOH M:2356 , HOH M:3065 , HOH M:3066 , HOH M:3067
BINDING SITE FOR RESIDUE SO4 M 1002
03
AC3
SOFTWARE
LYS M:108 , ARG M:111 , GLU M:151 , HOH M:2209 , HOH M:2292 , HOH M:3068 , HOH M:3069
BINDING SITE FOR RESIDUE SO4 M 1003
04
AC4
SOFTWARE
ARG M:259 , GLN M:333 , SO4 M:1009 , HOH M:3070 , HOH M:3072 , HOH M:3085
BINDING SITE FOR RESIDUE SO4 M 1004
05
AC5
SOFTWARE
ARG M:194 , ARG M:259 , SO4 M:1004 , HOH M:2332 , HOH M:3070 , HOH M:3084 , HOH M:3085 , HOH M:3086 , HOH M:3087
BINDING SITE FOR RESIDUE SO4 M 1009
06
AC6
SOFTWARE
GLN M:7 , GLU M:8 , ASN M:9 , HOH M:2004 , HOH M:3073 , HOH M:3074 , HOH M:3075 , HOH M:3076 , HOH M:3077 , HOH M:3078
BINDING SITE FOR RESIDUE SO4 M 1005
07
AC7
SOFTWARE
HIS M:270 , ALA M:273 , ARG M:277 , HOH M:2413 , HOH M:3079 , HOH M:3080
BINDING SITE FOR RESIDUE SO4 M 1006
08
AC8
SOFTWARE
ARG M:109 , VAL M:113 , GLU M:173 , HOH M:2202 , HOH M:3081 , HOH M:3082
BINDING SITE FOR RESIDUE SO4 M 1007
09
AC9
SOFTWARE
ASN M:60 , HIS M:66 , NAG M:961 , HOH M:3083
BINDING SITE FOR RESIDUE SO4 M 1008
10
BC1
SOFTWARE
ASN M:316 , LEU M:317 , HOH M:2472 , HOH M:3032 , HOH M:3089 , HOH M:3090 , HOH M:3091 , HOH M:3092
BINDING SITE FOR RESIDUE GOL M 1010
11
BC2
SOFTWARE
PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2354 , HOH M:3093 , HOH M:3094
BINDING SITE FOR RESIDUE GOL M 1020
12
BC3
SOFTWARE
HIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , FUC M:952 , HOH M:2385 , HOH M:2426 , HOH M:3040 , HOH M:3095 , HOH M:3096 , HOH M:3097
BINDING SITE FOR RESIDUE GOL M 1021
13
BC4
SOFTWARE
GLY M:132 , THR M:134 , NAG M:953 , BMA M:954 , HOH M:3098
BINDING SITE FOR RESIDUE GOL M 1023
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:2482
BINDING SITE FOR RESIDUE GOL M 1024
15
BC6
SOFTWARE
THR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:3010 , HOH M:3011 , HOH M:3012
Binding site for Mono-Saccharide NAG M 901 bound to ASN M 21
16
BC7
SOFTWARE
TYR M:58 , ASN M:60 , SO4 M:1008 , HOH M:2085 , HOH M:2106 , HOH M:3056 , HOH M:3057 , HOH M:3059
Binding site for Mono-Saccharide NAG M 961 bound to ASN M 60
17
BC8
SOFTWARE
ASN M:90 , SER M:500 , HOH M:2686 , HOH M:3013 , HOH M:3016
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 , GLU M:305 , HOH M:3017 , HOH M:3019 , HOH M:3020 , HOH M:3021 , HOH M:3022
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:2371 , HOH M:3025
Binding site for Mono-Saccharide NAG M 931 bound to ASN M 244
20
CC2
SOFTWARE
ASN M:265 , ASP M:268 , ALA M:362 , HOH M:2410 , HOH M:2613 , HOH M:2615 , HOH M:3026 , HOH M:3027 , HOH M:3028 , HOH M:3029 , HOH M:3030 , HOH M:3031 , HOH M:3032 , HOH M:3033 , HOH M:3034
Binding site for Poly-Saccharide residues NAG M 941 through XYP M 945 bound to ASN M 265
21
CC3
SOFTWARE
THR M:92 , LYS M:180 , ASN M:292 , THR M:294 , GLN M:297 , ILE M:300 , GOL M:1021 , GOL M:1023 , HOH M:2322 , HOH M:2432 , HOH M:3035 , HOH M:3036 , HOH M:3037 , HOH M:3038 , HOH M:3040 , HOH M:3041 , HOH M:3044 , HOH M:3045 , HOH M:3047 , HOH M:3048 , HOH M:3050 , HOH M:3051 , HOH M:3052 , HOH M:3053 , HOH M:3055 , HOH M:3096 , HOH M:3099
Binding site for Poly-Saccharide residues NAG M 951 through MAN M 957 bound to ASN M 292
22
CC4
SOFTWARE
ASN M:346 , HOH M:2504
Binding site for Mono-Saccharide NAG M 971 bound to ASN M 346
23
CC5
SOFTWARE
PRO M:11 , PHE M:12 , THR M:13 , ASN M:265 , ASP M:266 , ASN M:361 , SER M:363 , HIS M:365 , HOH M:2025 , HOH M:2400 , HOH M:2404 , HOH M:2406 , HOH M:2485 , HOH M:3060 , HOH M:3061 , HOH M:3062 , HOH M:3063
Binding site for Poly-Saccharide residues NAG M 981 through NAG M 983 bound to ASN M 361
24
CC6
SOFTWARE
ASN M:482 , ASP M:485 , HOH M:2666
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
[
close SNP/Variant info
]
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
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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1dwhm_ (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
d1dwhm_
M:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1dwhM00 (M:3-501)
View:
Select:
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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
1dwhM00
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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