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1LK9
Asym. Unit
Info
Asym.Unit (170 KB)
Biol.Unit 1 (163 KB)
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(1)
Title
:
THE THREE-DIMENSIONAL STRUCTURE OF ALLIINASE FROM GARLIC
Authors
:
E. B. Kuettner, R. Hilgenfeld, M. S. Weiss
Date
:
24 Apr 02 (Deposition) - 11 Dec 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.53
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Egf-Like Domain, Plp Type 1, Chloride Binding, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. B. Kuettner, R. Hilgenfeld, M. S. Weiss
The Active Principle Of Garlic At Atomic Resolution
J. Biol. Chem. V. 277 46402 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(8, 28)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: 2-AMINO-ACRYLIC ACID (DHAa)
4a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
5a: ALPHA-L-FUCOSE (FUCa)
5b: ALPHA-L-FUCOSE (FUCb)
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)
7a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
7b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
8a: SULFATE ION (SO4a)
8b: SULFATE ION (SO4b)
8c: SULFATE ION (SO4c)
8d: SULFATE ION (SO4d)
8e: SULFATE ION (SO4e)
8f: SULFATE ION (SO4f)
8g: SULFATE ION (SO4g)
8h: SULFATE ION (SO4h)
8i: SULFATE ION (SO4i)
8j: SULFATE ION (SO4j)
8k: SULFATE ION (SO4k)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CL
2
Ligand/Ion
CHLORIDE ION
3
DHA
1
Ligand/Ion
2-AMINO-ACRYLIC ACID
4
EPE
2
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
6
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
8
SO4
11
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:146 , THR A:148 , ALA A:149 , FUC A:501 , NAG A:502 , HOH A:1202 , HOH A:1309
BINDING SITE FOR RESIDUE NAG A 500
02
AC2
SOFTWARE
NAG A:500 , NAG A:502 , HOH A:1325 , HOH A:1330 , HOH A:1345
BINDING SITE FOR RESIDUE FUC A 501
03
AC3
SOFTWARE
NAG A:500 , FUC A:501 , BMA A:503 , HOH A:1358
BINDING SITE FOR RESIDUE NAG A 502
04
AC4
SOFTWARE
NAG A:502
BINDING SITE FOR RESIDUE BMA A 503
05
AC5
SOFTWARE
ASN A:328 , GLN A:408 , PHE A:411 , NAG A:505 , HOH A:1328
BINDING SITE FOR RESIDUE NAG A 504
06
AC6
SOFTWARE
NAG A:504
BINDING SITE FOR RESIDUE NAG A 505
07
AC7
SOFTWARE
HOH A:1366 , ASN B:146 , THR B:148 , FUC B:501
BINDING SITE FOR RESIDUE NAG B 500
08
AC8
SOFTWARE
GLU A:170 , TYR A:174 , ASN B:276 , LYS B:280 , NAG B:500
BINDING SITE FOR RESIDUE FUC B 501
09
AC9
SOFTWARE
ASN B:328 , GLN B:408 , PHE B:411 , NAG B:503 , HOH B:1374
BINDING SITE FOR RESIDUE NAG B 502
10
BC1
SOFTWARE
NAG B:502
BINDING SITE FOR RESIDUE NAG B 503
11
BC2
SOFTWARE
LYS A:237 , GLU A:348 , ARG B:384
BINDING SITE FOR RESIDUE SO4 A 904
12
BC3
SOFTWARE
ARG A:323 , HOH A:1236 , HOH A:1310
BINDING SITE FOR RESIDUE SO4 A 905
13
BC4
SOFTWARE
ALA A:120 , ALA A:121 , LYS A:122 , LYS A:239 , HOH A:1094
BINDING SITE FOR RESIDUE SO4 A 906
14
BC5
SOFTWARE
THR A:310 , MET A:311 , HOH A:1306
BINDING SITE FOR RESIDUE SO4 A 907
15
BC6
SOFTWARE
GLU A:71 , LYS A:321 , THR A:407 , GLN A:408 , HOH A:1075 , HOH A:1096 , HOH A:1101 , HOH A:1145 , HOH A:1308
BINDING SITE FOR RESIDUE SO4 A 910
16
BC7
SOFTWARE
ARG A:355 , MET A:356 , HOH A:1376
BINDING SITE FOR RESIDUE SO4 A 911
17
BC8
SOFTWARE
PHE A:93 , PHE A:94 , SER A:98 , ASN A:99 , PHE A:100
BINDING SITE FOR RESIDUE CL A 1001
18
BC9
SOFTWARE
LYS B:74 , GLN B:75 , HIS B:76 , LYS B:77 , GLU B:78 , HOH B:1117
BINDING SITE FOR RESIDUE SO4 B 901
19
CC1
SOFTWARE
TRP B:370 , GLU B:371 , ARG B:426 , HOH B:1166 , HOH B:1269 , HOH B:1408 , HOH B:1409
BINDING SITE FOR RESIDUE SO4 B 902
20
CC2
SOFTWARE
HIS B:161 , ALA B:187 , LYS B:308 , ARG B:354 , HOH B:1017 , HOH B:1103 , HOH B:1157 , HOH B:1208
BINDING SITE FOR RESIDUE SO4 B 903
21
CC3
SOFTWARE
GLU B:114 , ALA B:120 , ALA B:121 , LYS B:122 , LYS B:239 , HOH B:1246
BINDING SITE FOR RESIDUE SO4 B 908
22
CC4
SOFTWARE
LYS B:367 , TYR B:399 , HOH B:1165 , HOH B:1334
BINDING SITE FOR RESIDUE SO4 B 909
23
CC5
SOFTWARE
PHE B:93 , PHE B:94 , SER B:98 , ASN B:99 , PHE B:100
BINDING SITE FOR RESIDUE CL B 1002
24
CC6
SOFTWARE
GLY A:131 , VAL A:132 , THR A:133 , TYR A:165 , THR A:203 , ASN A:207 , ASP A:225 , VAL A:227 , TYR A:228 , THR A:248 , SER A:250 , LYS A:251 , ARG A:259 , TYR B:92
BINDING SITE FOR RESIDUE PLP A 600
25
CC7
SOFTWARE
TYR A:92 , THR A:279 , GLU A:283 , HOH A:1371 , SER B:63 , GLY B:64 , TYR B:165 , GLU B:170 , GLN B:388 , ARG B:401
BINDING SITE FOR RESIDUE EPE A 851
26
CC8
SOFTWARE
SER A:63 , GLY A:64 , TYR A:165 , GLU A:170 , GLN A:388 , ARG A:401 , HOH A:1274 , HOH A:1363 , HOH A:1374 , TYR B:92 , THR B:279 , GLU B:283
BINDING SITE FOR RESIDUE EPE A 852
27
CC9
SOFTWARE
TYR A:92 , GLY B:131 , VAL B:132 , THR B:133 , TYR B:165 , THR B:203 , ASN B:207 , ASP B:225 , VAL B:227 , TYR B:228 , THR B:248 , SER B:250 , LYS B:251 , ARG B:259 , DHA B:850
BINDING SITE FOR RESIDUE PLP B 600
28
DC1
SOFTWARE
TYR A:92 , GLY B:64 , TYR B:165 , ASN B:207 , TYR B:228 , LYS B:251 , TYR B:363 , ARG B:401 , PLP B:600 , HOH B:1380
BINDING SITE FOR RESIDUE DHA B 850
[
close Site info
]
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: EGF_1 (A:39-50,B:39-50)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_1
PS00022
EGF-like domain signature 1.
ALLN1_ALLSA
77-88
2
A:39-50
B:39-50
[
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1lk9a_ (A:)
1b: SCOP_d1lk9b_ (B:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
AAT-like
(184)
Protein domain
:
Alliinase
(1)
Garlic (Allium sativum) [TaxId: 4682]
(1)
1a
d1lk9a_
A:
1b
d1lk9b_
B:
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1lk9A02 (A:101-310)
1b: CATH_1lk9B02 (B:101-310)
2a: CATH_1lk9A03 (A:311-423)
2b: CATH_1lk9B03 (B:311-423)
3a: CATH_1lk9A01 (A:2-100)
3b: CATH_1lk9B01 (B:2-100)
View:
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Classes
(
)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Garlic (Allium sativum)
(3)
1a
1lk9A02
A:101-310
1b
1lk9B02
B:101-310
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Garlic (Allium sativum)
(3)
2a
1lk9A03
A:311-423
2b
1lk9B03
B:311-423
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Alliin lyase; domain 1
(3)
Garlic (Allium sativum)
(3)
3a
1lk9A01
A:2-100
3b
1lk9B01
B:2-100
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_EGF_alliinase_1lk9B01 (B:2-57)
1b: PFAM_EGF_alliinase_1lk9B02 (B:2-57)
2a: PFAM_Alliinase_C_1lk9B03 (B:59-422)
2b: PFAM_Alliinase_C_1lk9B04 (B:59-422)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
EGF
(60)
Family
:
EGF_alliinase
(1)
Allium sativum (Garlic)
(1)
1a
EGF_alliinase-1lk9B01
B:2-57
1b
EGF_alliinase-1lk9B02
B:2-57
Clan
:
PLP_aminotran
(240)
Family
:
Alliinase_C
(1)
Allium sativum (Garlic)
(1)
2a
Alliinase_C-1lk9B03
B:59-422
2b
Alliinase_C-1lk9B04
B:59-422
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]
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