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1DWA
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 1: STRUCTURE PRIOR TO IRRADIATION
Authors
:
W. P. Burmeister
Date
:
05 Dec 99 (Deposition) - 03 Mar 00 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : M
Biol. Unit 1: M (2x)
Keywords
:
Glycosidase, 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
(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
(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
THR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:1535 , HOH M:1122 , HOH M:1548
BINDING SITE FOR RESIDUE NAG M 901
02
AC2
SOFTWARE
ASN M:90 , SER M:500 , HOH M:1205 , HOH M:1331 , HOH M:1451
BINDING SITE FOR RESIDUE NAG M 911
03
AC3
SOFTWARE
LYS M:165 , LEU M:240 , ASN M:244 , HOH M:1360 , HOH M:1549
BINDING SITE FOR RESIDUE NAG M 931
04
AC4
SOFTWARE
TYR M:58 , ASN M:60 , SER M:213 , SO4 M:930 , HOH M:1180 , HOH M:1097 , HOH M:1622 , HOH M:1555 , HOH M:1458
BINDING SITE FOR RESIDUE NAG M 961
05
AC5
SOFTWARE
ASN M:346 , HOH M:1277
BINDING SITE FOR RESIDUE NAG M 971
06
AC6
SOFTWARE
ASN M:482 , ASP M:485 , HOH M:1274
BINDING SITE FOR RESIDUE NAG M 991
07
AC7
SOFTWARE
HIS M:56 , ASN M:68 , ASP M:70
BINDING SITE FOR RESIDUE ZN M1001
08
AC8
SOFTWARE
ARG M:106 , ARG M:205 , HOH M:1036 , HOH M:1017 , HOH M:1468 , HOH M:1413 , HOH M:1066 , HOH M:1071
BINDING SITE FOR RESIDUE SO4 M1002
09
AC9
SOFTWARE
LYS M:108 , ARG M:111 , GLU M:151 , HOH M:1186 , HOH M:1031 , HOH M:1142 , HOH M:1016
BINDING SITE FOR RESIDUE SO4 M1003
10
BC1
SOFTWARE
ARG M:259 , GLN M:333 , SO4 M:931 , HOH M:1168 , HOH M:1512 , HOH M:1041
BINDING SITE FOR RESIDUE SO4 M1004
11
BC2
SOFTWARE
ARG M:194 , ARG M:259 , SO4 M:926 , HOH M:1481 , HOH M:1168 , HOH M:1082 , HOH M:1041 , HOH M:1049 , HOH M:1010
BINDING SITE FOR RESIDUE SO4 M1009
12
BC3
SOFTWARE
GLN M:7 , GLU M:8 , ASN M:9 , HOH M:1251 , HOH M:1173 , HOH M:1137 , HOH M:1380 , HOH M:1118 , HOH M:1497 , HOH M:1294
BINDING SITE FOR RESIDUE SO4 M1005
13
BC4
SOFTWARE
HIS M:270 , ALA M:273 , ARG M:277 , HOH M:1221 , HOH M:1054 , HOH M:1492
BINDING SITE FOR RESIDUE SO4 M1006
14
BC5
SOFTWARE
ARG M:109 , VAL M:113 , GLU M:173 , HOH M:1269 , HOH M:1469 , HOH M:1084
BINDING SITE FOR RESIDUE SO4 M1007
15
BC6
SOFTWARE
ASN M:60 , HIS M:66 , NAG M:918 , HOH M:1554
BINDING SITE FOR RESIDUE SO4 M1008
16
BC7
SOFTWARE
ASN M:316 , LEU M:317 , HOH M:1259 , HOH M:1409 , HOH M:1011 , HOH M:1117 , HOH M:1293 , HOH M:1035
BINDING SITE FOR RESIDUE GOL M1010
17
BC8
SOFTWARE
PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:1047 , HOH M:1329 , HOH M:1050
BINDING SITE FOR RESIDUE GOL M1020
18
BC9
SOFTWARE
HIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , FUC M:912 , HOH M:1075 , HOH M:1046 , HOH M:1012 , HOH M:1464 , HOH M:1052 , HOH M:1123
BINDING SITE FOR RESIDUE GOL M1021
19
CC1
SOFTWARE
GLY M:132 , THR M:134 , NAG M:913 , BMA M:914 , HOH M:1359
BINDING SITE FOR RESIDUE GOL M1023
20
CC2
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:1525
BINDING SITE FOR RESIDUE GOL M1024
21
CC3
SOFTWARE
SER M:207 , ASN M:218 , THR M:221 , GLU M:305 , HOH M:1443 , HOH M:1013 , HOH M:1256 , HOH M:1502 , HOH M:1260
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 218 RESIDUES 921 TO 923
22
CC4
SOFTWARE
ASN M:265 , ASP M:268 , ALA M:362 , HOH M:1353 , HOH M:1575 , HOH M:1039 , HOH M:1537 , HOH M:1369 , HOH M:1550 , HOH M:1418 , HOH M:1204 , HOH M:1364 , HOH M:1409 , HOH M:1326 , HOH M:1072
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 265 RESIDUES 941 TO 945
23
CC5
SOFTWARE
THR M:92 , LYS M:180 , ASN M:292 , THR M:294 , GLN M:297 , ILE M:300 , GOL M:934 , GOL M:935 , HOH M:1094 , HOH M:1200 , HOH M:1437 , HOH M:1189 , HOH M:1282 , HOH M:1480 , HOH M:1012 , HOH M:1267 , HOH M:1321 , HOH M:1454 , HOH M:1160 , HOH M:1276 , HOH M:1207 , HOH M:1065 , HOH M:1416 , HOH M:1023 , HOH M:1006 , HOH M:1052 , HOH M:1592
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 292 RESIDUES 951 TO 957
24
CC6
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:1001 , HOH M:1235 , HOH M:1076 , HOH M:1062 , HOH M:1317 , HOH M:1389 , HOH M:1495 , HOH M:1578 , HOH M:1095
BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 361 RESIDUES 981 TO 983
[
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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
[
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
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1dwam_ (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
d1dwam_
M:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1dwaM00 (M:3-501)
View:
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Classes
(
)
(
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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
1dwaM00
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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)
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Nucleic
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Sidechain
Hetero
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain M
Asymmetric Unit 1
Asymmetric Unit 2
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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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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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