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1WDS
Asym. Unit
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Asym.Unit (102 KB)
Biol.Unit 1 (97 KB)
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(1)
Title
:
THE ROLE OF AN INNER LOOP IN THE CATALYTIC MECHANISM OF SOYBEAN BETA-AMYLASE
Authors
:
Y. N. Kang, M. Adachi, S. Utsumi, B. Mikami
Date
:
17 May 04 (Deposition) - 05 Apr 05 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.64
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
(Beta/Alpha)8 Barrel, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. N. Kang, A. Tanabe, M. Adachi, S. Utsumi, B. Mikami
Structural Analysis Of Threonine 342 Mutants Of Soybean Beta-Amylase: Role Of A Conformational Change Of The Inner Loop In The Catalytic Mechanism.
Biochemistry V. 44 5106 2005
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Hetero Components
(3, 11)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
2a: ALPHA-D-GLUCOSE (GLCa)
2b: ALPHA-D-GLUCOSE (GLCb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
1
Ligand/Ion
BETA-D-GLUCOSE
2
GLC
2
Ligand/Ion
ALPHA-D-GLUCOSE
3
SO4
8
Ligand/Ion
SULFATE ION
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Sites
(11, 11)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:53 , TRP A:55 , HIS A:93 , ASP A:101 , ARG A:420 , BGC A:497 , HOH A:596 , HOH A:629 , HOH A:716 , HOH A:779
BINDING SITE FOR RESIDUE GLC A 496
02
AC2
SOFTWARE
ALA A:184 , GLU A:186 , LYS A:295 , ALA A:342 , GLU A:380 , ALA A:382 , LEU A:419 , GLC A:496 , HOH A:758 , HOH A:779 , HOH A:1029 , HOH A:1282 , HOH A:1284
BINDING SITE FOR RESIDUE BGC A 497
03
AC3
SOFTWARE
VAL A:99 , TRP A:198 , HIS A:300 , MET A:346 , LEU A:383 , HOH A:631 , HOH A:887 , HOH A:1077 , HOH A:1240 , HOH A:1282 , HOH A:1285
BINDING SITE FOR RESIDUE GLC A 499
04
AC4
SOFTWARE
HIS A:146 , ARG A:326 , ARG A:330 , ARG A:372 , HOH A:966 , HOH A:1242
BINDING SITE FOR RESIDUE SO4 A 2000
05
AC5
SOFTWARE
HIS A:119 , ARG A:130 , HOH A:1066
BINDING SITE FOR RESIDUE SO4 A 2001
06
AC6
SOFTWARE
GLY A:225 , LYS A:304 , LYS A:453 , HOH A:1035 , HOH A:1036 , HOH A:1171
BINDING SITE FOR RESIDUE SO4 A 2002
07
AC7
SOFTWARE
ARG A:347 , SER A:349 , HOH A:611 , HOH A:765 , HOH A:1006 , HOH A:1064
BINDING SITE FOR RESIDUE SO4 A 2003
08
AC8
SOFTWARE
GLN A:77 , ARG A:372 , THR A:480 , LEU A:481 , HOH A:627 , HOH A:628 , HOH A:733 , HOH A:872
BINDING SITE FOR RESIDUE SO4 A 2004
09
AC9
SOFTWARE
THR A:256 , GLU A:257 , HOH A:610 , HOH A:954 , HOH A:1141
BINDING SITE FOR RESIDUE SO4 A 2005
10
BC1
SOFTWARE
ASN A:125 , SER A:127 , GLU A:205 , LYS A:237 , HOH A:784 , HOH A:832 , HOH A:838 , HOH A:1001 , HOH A:1032
BINDING SITE FOR RESIDUE SO4 A 2006
11
BC2
SOFTWARE
PRO A:352 , SER A:353 , HOH A:788
BINDING SITE FOR RESIDUE SO4 A 2007
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: BETA_AMYLASE_1 (A:93-101)
2: BETA_AMYLASE_2 (A:182-192)
;
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
1
A:93-101
2
BETA_AMYLASE_2
PS00679
Beta-amylase active site 2.
AMYB_SOYBN
183-193
1
A: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, 1)
Info
All SCOP Domains
1a: SCOP_d1wdsa1 (A:5-495)
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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
d1wdsa1
A:5-495
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1wdsA00 (A:4-495)
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Soybean (Glycine max)
(20)
1a
1wdsA00
A:4-495
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_14_1wdsA01 (A: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_14-1wdsA01
A:15-437
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Chain A
Asymmetric Unit 1
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