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1DWF
Biol. Unit 1
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 2: STRUCTURE AFTER IRRADIATION WITH 9.1*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
:
Hydrolase, Glycosidase, Radiation Damage, Radiolysis, Cryo-Cooled
(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
)
[
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Hetero Components
(7, 70)
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
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
28
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 , ASN M:68 , ASP M:70
BINDING SITE FOR RESIDUE ZN M 1524
02
AC2
SOFTWARE
ARG M:106 , ARG M:205 , HOH M:2192 , HOH M:2213 , HOH M:2356 , HOH M:3002 , HOH M:3003 , HOH M:3004
BINDING SITE FOR RESIDUE SO4 M 1525
03
AC3
SOFTWARE
LYS M:108 , ARG M:111 , GLU M:151 , HOH M:2209 , HOH M:2292 , HOH M:3005 , HOH M:3006
BINDING SITE FOR RESIDUE SO4 M 1526
04
AC4
SOFTWARE
GLN M:7 , GLU M:8 , ASN M:9 , HOH M:2004 , HOH M:3010 , HOH M:3011 , HOH M:3012 , HOH M:3013 , HOH M:3014 , HOH M:3015
BINDING SITE FOR RESIDUE SO4 M 1528
05
AC5
SOFTWARE
HIS M:270 , ALA M:273 , ARG M:277 , HOH M:2413 , HOH M:3016 , HOH M:3017
BINDING SITE FOR RESIDUE SO4 M 1529
06
AC6
SOFTWARE
ARG M:109 , VAL M:113 , GLU M:173 , HOH M:2202 , HOH M:3018 , HOH M:3019
BINDING SITE FOR RESIDUE SO4 M 1530
07
AC7
SOFTWARE
ASN M:60 , HIS M:66 , NAG M:1519 , HOH M:3020
BINDING SITE FOR RESIDUE SO4 M 1531
08
AC8
SOFTWARE
ASN M:316 , LEU M:317 , HOH M:1032 , HOH M:2472 , HOH M:3026 , HOH M:3027 , HOH M:3028 , HOH M:3029
BINDING SITE FOR RESIDUE GOL M 1533
09
AC9
SOFTWARE
PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2354 , HOH M:3030 , HOH M:3031
BINDING SITE FOR RESIDUE GOL M 1534
10
BC1
SOFTWARE
HIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:1040 , FUC M:1513 , HOH M:2385 , HOH M:2426 , HOH M:3032 , HOH M:3033 , HOH M:3034
BINDING SITE FOR RESIDUE GOL M 1535
11
BC2
SOFTWARE
GLY M:132 , THR M:134 , NAG M:1514 , BMA M:1515 , HOH M:3035
BINDING SITE FOR RESIDUE GOL M 1536
12
BC3
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 1537
13
BC4
SOFTWARE
THR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:1010 , HOH M:1011 , HOH M:1012
Binding site for Mono-Saccharide NAG M1502 bound to ASN M 21
14
BC5
SOFTWARE
TYR M:58 , ASN M:60 , HOH M:1056 , HOH M:1057 , HOH M:1059 , SO4 M:1531 , HOH M:2085 , HOH M:2106
Binding site for Mono-Saccharide NAG M1519 bound to ASN M 60
15
BC6
SOFTWARE
ASN M:90 , SER M:500 , HOH M:1013 , HOH M:1016 , HOH M:2686
Binding site for Mono-Saccharide NAG M1503 bound to ASN M 90
16
BC7
SOFTWARE
SER M:207 , ASN M:218 , THR M:221 , GLU M:305 , HOH M:1017 , HOH M:1019 , HOH M:1020 , HOH M:1021 , HOH M:1022
Binding site for Poly-Saccharide residues NAG M1504 through NAG M1505 bound to ASN M 218
17
BC8
SOFTWARE
LYS M:165 , LEU M:240 , ASN M:244 , HOH M:1025 , HOH M:2371
Binding site for Mono-Saccharide NAG M1506 bound to ASN M 244
18
BC9
SOFTWARE
ASN M:265 , ASP M:268 , ALA M:362 , HOH M:1026 , HOH M:1027 , HOH M:1028 , HOH M:1029 , HOH M:1030 , HOH M:1031 , HOH M:1032 , HOH M:1033 , HOH M:1034 , HOH M:2410 , HOH M:2613 , HOH M:2615
Binding site for Poly-Saccharide residues NAG M1507 through XYP M1511 bound to ASN M 265
19
CC1
SOFTWARE
THR M:92 , LYS M:180 , ASN M:292 , THR M:294 , GLN M:297 , ILE M:300 , HOH M:1035 , HOH M:1036 , HOH M:1037 , HOH M:1038 , HOH M:1040 , HOH M:1041 , HOH M:1044 , HOH M:1045 , HOH M:1047 , HOH M:1048 , HOH M:1050 , HOH M:1051 , HOH M:1052 , HOH M:1053 , HOH M:1055 , GOL M:1535 , GOL M:1536 , HOH M:2322 , HOH M:2432 , HOH M:3033 , HOH M:3036
Binding site for Poly-Saccharide residues NAG M1512 through MAN M1518 bound to ASN M 292
20
CC2
SOFTWARE
ASN M:346 , HOH M:2504
Binding site for Mono-Saccharide NAG M1520 bound to ASN M 346
21
CC3
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:1060 , HOH M:1061 , HOH M:1062 , HOH M:1063 , HOH M:2025 , HOH M:2400 , HOH M:2404 , HOH M:2406 , HOH M:2485
Binding site for Poly-Saccharide residues NAG M1521 through NAG M1522 bound to ASN M 361
22
CC4
SOFTWARE
ASN M:482 , ASP M:485 , HOH M:2666
Binding site for Mono-Saccharide NAG M1523 bound to ASN M 482
23
CC5
SOFTWARE
ARG M:194 , ARG M:259 , GLN M:333 , HOH M:2332 , HOH M:3007 , HOH M:3009 , HOH M:3021 , HOH M:3022 , HOH M:3023 , HOH M:3024
Binding site for residues SO4 M1527 and SO4 M1532
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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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_d1dwfm_ (M:)
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Classes
(
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(
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Folds
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Superfamilies
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(
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(
)
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
d1dwfm_
M:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1dwfM00 (M:3-501)
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Topologies
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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
1dwfM00
M:3-501
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein & NOT Site
Protein & NOT PROSITE
Chain M
Asymmetric Unit 1
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