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1UKO
Asym. Unit
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Asym.Unit (349 KB)
Biol.Unit 1 (90 KB)
Biol.Unit 2 (91 KB)
Biol.Unit 3 (90 KB)
Biol.Unit 4 (89 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SOYBEAN BETA-AMYLASE MUTANT SUBSTITUTED AT SURFACE REGION
Authors
:
Y. N. Kang, M. Adachi, B. Mikami, S. Utsumi
Date
:
30 Aug 03 (Deposition) - 10 Feb 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
(Alpha/Beta)8 Barrel, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. N. Kang, M. Adachi, B. Mikami, S. Utsumi
Change In The Crystal Packing Of Soybean Beta-Amylase Mutants Substituted At A Few Surface Amino Acid Residues
Protein Eng. V. 16 809 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 24)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
1i: SULFATE ION (SO4i)
1j: SULFATE ION (SO4j)
1k: SULFATE ION (SO4k)
1l: SULFATE ION (SO4l)
1m: SULFATE ION (SO4m)
1n: SULFATE ION (SO4n)
1o: SULFATE ION (SO4o)
1p: SULFATE ION (SO4p)
1q: SULFATE ION (SO4q)
1r: SULFATE ION (SO4r)
1s: SULFATE ION (SO4s)
1t: SULFATE ION (SO4t)
1u: SULFATE ION (SO4u)
1v: SULFATE ION (SO4v)
1w: SULFATE ION (SO4w)
1x: SULFATE ION (SO4x)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
24
Ligand/Ion
SULFATE ION
[
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]
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
TYR A:67 , SER A:160 , ASN A:164 , HOH A:1773
BINDING SITE FOR RESIDUE SO4 A 3000
02
AC2
SOFTWARE
ARG A:347 , SER A:349 , HOH A:701 , HOH A:1822
BINDING SITE FOR RESIDUE SO4 A 3001
03
AC3
SOFTWARE
HIS A:336 , ARG A:376 , HOH A:1871
BINDING SITE FOR RESIDUE SO4 A 3002
04
AC4
SOFTWARE
LYS A:291 , ARG A:376 , PHE A:414 , ASN A:455 , HIS A:456 , ALA A:457
BINDING SITE FOR RESIDUE SO4 A 3003
05
AC5
SOFTWARE
TYR B:67 , SER B:160 , ASN B:164 , HOH B:1959
BINDING SITE FOR RESIDUE SO4 B 3004
06
AC6
SOFTWARE
ARG B:347 , SER B:349 , HOH B:1722 , HOH B:1726
BINDING SITE FOR RESIDUE SO4 B 3005
07
AC7
SOFTWARE
HIS B:336 , ARG B:376 , HOH B:1173 , HOH B:1180
BINDING SITE FOR RESIDUE SO4 B 3006
08
AC8
SOFTWARE
LYS B:291 , ARG B:376 , PHE B:414 , ASN B:455 , HIS B:456 , ALA B:457 , HOH B:1325 , HOH B:1704
BINDING SITE FOR RESIDUE SO4 B 3007
09
AC9
SOFTWARE
TYR C:67 , SER C:160 , ASN C:164 , HOH C:1205 , HOH C:1530
BINDING SITE FOR RESIDUE SO4 C 3008
10
BC1
SOFTWARE
ARG C:347 , SER C:349 , HOH C:1266 , HOH C:1588
BINDING SITE FOR RESIDUE SO4 C 3009
11
BC2
SOFTWARE
HIS C:336 , ARG C:376 , HOH C:1263 , HOH C:1584
BINDING SITE FOR RESIDUE SO4 C 3010
12
BC3
SOFTWARE
LYS C:291 , ARG C:376 , PHE C:414 , ASN C:455 , ALA C:457
BINDING SITE FOR RESIDUE SO4 C 3011
13
BC4
SOFTWARE
TYR D:67 , SER D:160 , ASN D:164 , HOH D:1318
BINDING SITE FOR RESIDUE SO4 D 3012
14
BC5
SOFTWARE
ARG D:347 , SER D:349 , HOH D:971
BINDING SITE FOR RESIDUE SO4 D 3013
15
BC6
SOFTWARE
HIS D:336 , ARG D:376 , HOH D:969 , HOH D:1346
BINDING SITE FOR RESIDUE SO4 D 3014
16
BC7
SOFTWARE
HOH B:1154 , LYS D:291 , ARG D:376 , PHE D:414 , ASN D:455 , ALA D:457
BINDING SITE FOR RESIDUE SO4 D 3015
17
BC8
SOFTWARE
ARG A:70
BINDING SITE FOR RESIDUE SO4 A 3016
18
BC9
SOFTWARE
ARG B:70
BINDING SITE FOR RESIDUE SO4 B 3017
19
CC1
SOFTWARE
ARG C:70
BINDING SITE FOR RESIDUE SO4 C 3018
20
CC2
SOFTWARE
ARG D:70
BINDING SITE FOR RESIDUE SO4 D 3019
21
CC3
SOFTWARE
ASN A:98 , PRO A:193 , GLN A:194 , HOH A:675 , HOH A:1794 , HOH A:1855
BINDING SITE FOR RESIDUE SO4 A 3020
22
CC4
SOFTWARE
ASN B:98 , TYR B:192 , PRO B:193 , GLN B:194 , HOH B:1148 , HOH B:1638 , HOH B:1639 , HOH B:1656
BINDING SITE FOR RESIDUE SO4 B 3021
23
CC5
SOFTWARE
ASN C:98 , PRO C:193 , GLN C:194 , HOH C:1405 , HOH C:1406 , HOH C:1407
BINDING SITE FOR RESIDUE SO4 C 3022
24
CC6
SOFTWARE
ASN D:98 , PRO D:193 , GLN D:194 , HOH D:1298 , HOH D:1307 , HOH D:1319
BINDING SITE FOR RESIDUE SO4 D 3023
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: BETA_AMYLASE_1 (A:93-101,B:93-101,C:93-101,D:93-10...)
2: BETA_AMYLASE_2 (A:182-192,B:182-192,C:182-192,D:18...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BETA_AMYLASE_1
PS00506
Beta-amylase active site 1.
AMYB_SOYBN
94-102
4
A:93-101
B:93-101
C:93-101
D:93-101
2
BETA_AMYLASE_2
PS00679
Beta-amylase active site 2.
AMYB_SOYBN
183-193
4
A:182-192
B:182-192
C:182-192
D:182-192
[
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1ukoa_ (A:)
1b: SCOP_d1ukob_ (B:)
1c: SCOP_d1ukoc_ (C:)
1d: SCOP_d1ukod_ (D:)
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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
:
Amylase, catalytic domain
(385)
Protein domain
:
beta-Amylase
(20)
Soybean (Glycine max) [TaxId: 3847]
(18)
1a
d1ukoa_
A:
1b
d1ukob_
B:
1c
d1ukoc_
C:
1d
d1ukod_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1ukoA00 (A:6-495)
1b: CATH_1ukoB00 (B:6-495)
1c: CATH_1ukoC00 (C:6-495)
1d: CATH_1ukoD00 (D:6-495)
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Homologous Superfamilies
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Soybean (Glycine max)
(20)
1a
1ukoA00
A:6-495
1b
1ukoB00
B:6-495
1c
1ukoC00
C:6-495
1d
1ukoD00
D:6-495
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_14_1ukoD01 (D:15-437)
1b: PFAM_Glyco_hydro_14_1ukoD02 (D:15-437)
1c: PFAM_Glyco_hydro_14_1ukoD03 (D:15-437)
1d: PFAM_Glyco_hydro_14_1ukoD04 (D:15-437)
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Clans
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Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_14
(16)
Glycine max (Soybean) (Glycine hispida)
(12)
1a
Glyco_hydro_14-1ukoD01
D:15-437
1b
Glyco_hydro_14-1ukoD02
D:15-437
1c
Glyco_hydro_14-1ukoD03
D:15-437
1d
Glyco_hydro_14-1ukoD04
D:15-437
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