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2D0G
Asym. Unit
Info
Asym.Unit (122 KB)
Biol.Unit 1 (116 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 1 (TVAI) MUTANT D356N/E396Q COMPLEXED WITH P5, A PULLULAN MODEL OLIGOSACCHARIDE
Authors
:
A. Abe, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
Date
:
02 Aug 05 (Deposition) - 11 Jul 06 (Release) - 04 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Alpha-Amylase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Abe, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
Complexes Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 And Pullulan Model Oligossacharides Provide New Insight Into The Mechanism For Recognizing Substrates With Alpha-(1, 6) Glycosidic Linkages
Febs J. V. 272 6145 2005
(for further references see the
PDB file header
)
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Hetero Components
(4, 23)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
1d: BETA-D-GLUCOSE (BGCd)
1e: BETA-D-GLUCOSE (BGCe)
1f: BETA-D-GLUCOSE (BGCf)
1g: BETA-D-GLUCOSE (BGCg)
1h: BETA-D-GLUCOSE (BGCh)
1i: BETA-D-GLUCOSE (BGCi)
1j: BETA-D-GLUCOSE (BGCj)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
3a: ALPHA-D-GLUCOSE (GLCa)
3b: ALPHA-D-GLUCOSE (GLCb)
3c: ALPHA-D-GLUCOSE (GLCc)
3d: ALPHA-D-GLUCOSE (GLCd)
3e: ALPHA-D-GLUCOSE (GLCe)
3f: ALPHA-D-GLUCOSE (GLCf)
3g: ALPHA-D-GLUCOSE (GLCg)
3h: ALPHA-D-GLUCOSE (GLCh)
3i: ALPHA-D-GLUCOSE (GLCi)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
10
Ligand/Ion
BETA-D-GLUCOSE
2
CA
3
Ligand/Ion
CALCIUM ION
3
GLC
9
Ligand/Ion
ALPHA-D-GLUCOSE
4
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
[
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
THR A:529 , GLC A:702 , HOH A:2471
BINDING SITE FOR RESIDUE BGC A 701
02
AC2
SOFTWARE
THR A:606 , BGC A:701 , BGC A:703 , HOH A:2159 , HOH A:2200 , HOH A:2471
BINDING SITE FOR RESIDUE GLC A 702
03
AC3
SOFTWARE
TYR A:174 , ALA A:515 , ASP A:516 , PRO A:517 , ASP A:518 , GLC A:702 , BGC A:704 , HOH A:2438
BINDING SITE FOR RESIDUE BGC A 703
04
AC4
SOFTWARE
GLN A:547 , ASN A:577 , GLN A:637 , BGC A:703 , GLC A:705 , HOH A:2198 , HOH A:2244
BINDING SITE FOR RESIDUE BGC A 704
05
AC5
SOFTWARE
PRO A:549 , VAL A:576 , ASN A:577 , BGC A:704 , GLC A:706 , HOH A:2116 , HOH A:2308 , HOH A:2309 , HOH A:2340
BINDING SITE FOR RESIDUE GLC A 705
06
AC6
SOFTWARE
SER A:182 , ASP A:516 , GLC A:705 , GLC A:707 , HOH A:2176 , HOH A:2308
BINDING SITE FOR RESIDUE GLC A 706
07
AC7
SOFTWARE
HIS A:221 , TYR A:223 , ASP A:516 , ARG A:520 , GLC A:706 , GLC A:708 , HOH A:2376
BINDING SITE FOR RESIDUE GLC A 707
08
AC8
SOFTWARE
TYR A:223 , HIS A:267 , PHE A:310 , ARG A:354 , ASN A:356 , GLN A:396 , HIS A:471 , ASP A:472 , GLC A:707 , GLC A:709
BINDING SITE FOR RESIDUE GLC A 708
09
AC9
SOFTWARE
PHE A:310 , TYR A:360 , GLN A:396 , TRP A:398 , GLC A:708 , GLC A:710 , HOH A:2254
BINDING SITE FOR RESIDUE GLC A 709
10
BC1
SOFTWARE
TRP A:398 , GLN A:434 , ASP A:472 , GLC A:709
BINDING SITE FOR RESIDUE GLC A 710
11
BC2
SOFTWARE
ALA A:115 , ASP A:116 , ASP A:117 , TYR A:119 , ASN A:402 , BGC A:802 , HOH A:2084
BINDING SITE FOR RESIDUE BGC A 801
12
BC3
SOFTWARE
PHE A:58 , TYR A:89 , ARG A:91 , ASP A:117 , BGC A:801
BINDING SITE FOR RESIDUE BGC A 802
13
BC4
SOFTWARE
ASP A:418 , TRP A:448
BINDING SITE FOR RESIDUE GLC A 810
14
BC5
SOFTWARE
ASP A:66 , SER A:67 , BGC A:902 , HOH A:2337
BINDING SITE FOR RESIDUE GLC A 901
15
BC6
SOFTWARE
TRP A:65 , ASP A:66 , GLC A:901 , BGC A:903
BINDING SITE FOR RESIDUE BGC A 902
16
BC7
SOFTWARE
BGC A:902 , BGC A:904 , HOH A:2172
BINDING SITE FOR RESIDUE BGC A 903
17
BC8
SOFTWARE
GLY A:41 , ILE A:43 , TRP A:65 , ASP A:75 , BGC A:903 , BGC A:905 , HOH A:2184 , HOH A:2241 , HOH A:2364
BINDING SITE FOR RESIDUE BGC A 904
18
BC9
SOFTWARE
LYS A:40 , TRP A:65 , ASN A:68 , ASP A:75 , BGC A:904
BINDING SITE FOR RESIDUE BGC A 905
19
CC1
SOFTWARE
ASP A:483 , TRP A:485 , GLY A:629 , HIS A:630
BINDING SITE FOR RESIDUE BGC A 910
20
CC2
SOFTWARE
ALA A:2 , ASP A:4 , ASN A:6 , ASP A:42 , ASP A:96 , HOH A:2474
BINDING SITE FOR RESIDUE CA A 2001
21
CC3
SOFTWARE
ASN A:145 , ASP A:147 , ASN A:150 , ASP A:151 , GLY A:187 , ASP A:189 , HOH A:2118
BINDING SITE FOR RESIDUE CA A 2002
22
CC4
SOFTWARE
ASP A:276 , ASN A:279 , PHE A:281 , SER A:283 , GLU A:288 , HOH A:2263
BINDING SITE FOR RESIDUE CA A 2003
23
CC5
SOFTWARE
ASP A:446 , LEU A:559 , THR A:561 , HOH A:2058
BINDING SITE FOR RESIDUE MPD A 1001
[
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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
(0, 0)
Info
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;
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Exons
(0, 0)
Info
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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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2d0ga2 (A:555-637)
2a: SCOP_d2d0ga1 (A:1-122)
3a: SCOP_d2d0ga3 (A:123-554)
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Glycosyl hydrolase domain
(397)
Superfamily
:
Glycosyl hydrolase domain
(397)
Family
:
alpha-Amylases, C-terminal beta-sheet domain
(272)
Protein domain
:
Maltogenic amylase
(22)
Thermoactinomyces vulgaris, TVAI [TaxId: 2026]
(8)
1a
d2d0ga2
A:555-637
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
E-set domains of sugar-utilizing enzymes
(147)
Protein domain
:
Maltogenic amylase, N-terminal domain N
(22)
Thermoactinomyces vulgaris, TVAI [TaxId: 2026]
(8)
2a
d2d0ga1
A:1-122
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
:
Maltogenic amylase, central domain
(22)
Thermoactinomyces vulgaris, TVAI [TaxId: 2026]
(8)
3a
d2d0ga3
A:123-554
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2d0gA02 (A:125-547)
2a: CATH_2d0gA03 (A:548-637)
3a: CATH_2d0gA01 (A:1-124)
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Organisms
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
1a
2d0gA02
A:125-547
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
2a
2d0gA03
A:548-637
Homologous Superfamily
:
Immunoglobulins
(2282)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
3a
2d0gA01
A:1-124
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain A
Asymmetric Unit 1
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