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2D0F
Asym. Unit
Info
Asym.Unit (118 KB)
Biol.Unit 1 (113 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 1 (TVAI) MUTANT D356N COMPLEXED WITH P2, 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
:
2.08
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, 15)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
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)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
4b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
4c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
4d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
2
Ligand/Ion
BETA-D-GLUCOSE
2
CA
3
Ligand/Ion
CALCIUM ION
3
GLC
6
Ligand/Ion
ALPHA-D-GLUCOSE
4
MPD
4
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
[
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]
Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:546 , GLN A:547 , PRO A:549 , GLC A:702 , HOH A:2444
BINDING SITE FOR RESIDUE GLC A 701
02
AC2
SOFTWARE
ASP A:180 , SER A:182 , GLC A:701 , GLC A:703 , HOH A:2126 , HOH A:2147
BINDING SITE FOR RESIDUE GLC A 702
03
AC3
SOFTWARE
SER A:182 , THR A:219 , HIS A:221 , SER A:315 , GLC A:702 , GLC A:704 , HOH A:2085 , HOH A:2248 , HOH A:2404
BINDING SITE FOR RESIDUE GLC A 703
04
AC4
SOFTWARE
HIS A:221 , TYR A:223 , ASP A:516 , ARG A:520 , GLC A:703 , BGC A:705 , HOH A:2404 , HOH A:2437
BINDING SITE FOR RESIDUE GLC A 704
05
AC5
SOFTWARE
TYR A:223 , HIS A:267 , PHE A:310 , ASN A:356 , GLU A:396 , HIS A:471 , ASP A:472 , GLC A:704 , HOH A:2010
BINDING SITE FOR RESIDUE BGC A 705
06
AC6
SOFTWARE
ASN A:3 , GLC A:802 , HOH A:2097
BINDING SITE FOR RESIDUE GLC A 801
07
AC7
SOFTWARE
GLY A:41 , ILE A:43 , TRP A:65 , ASP A:75 , GLC A:801 , BGC A:803
BINDING SITE FOR RESIDUE GLC A 802
08
AC8
SOFTWARE
LYS A:40 , TRP A:65 , ASN A:68 , ASP A:75 , GLC A:802
BINDING SITE FOR RESIDUE BGC A 803
09
AC9
SOFTWARE
ALA A:2 , ASP A:4 , ASN A:6 , ASP A:42 , ASP A:96 , HOH A:2019
BINDING SITE FOR RESIDUE CA A 2001
10
BC1
SOFTWARE
ASN A:145 , ASP A:147 , ASN A:150 , ASP A:151 , GLY A:187 , ASP A:189 , HOH A:2037
BINDING SITE FOR RESIDUE CA A 2002
11
BC2
SOFTWARE
ASP A:276 , ASN A:279 , PHE A:281 , SER A:283 , GLU A:288 , HOH A:2013
BINDING SITE FOR RESIDUE CA A 2003
12
BC3
SOFTWARE
ASN A:10 , LEU A:12 , MET A:557 , THR A:558 , LEU A:559 , GLN A:598 , HOH A:2255
BINDING SITE FOR RESIDUE MPD A 1001
13
BC4
SOFTWARE
GLY A:170 , SER A:171 , SER A:533 , ALA A:536 , LEU A:537 , LYS A:540 , TYR A:631
BINDING SITE FOR RESIDUE MPD A 1002
14
BC5
SOFTWARE
THR A:73 , PRO A:347 , TRP A:597 , ASN A:620
BINDING SITE FOR RESIDUE MPD A 1003
15
BC6
SOFTWARE
GLU A:165 , TRP A:485 , SER A:587 , GLY A:629 , HOH A:2442
BINDING SITE FOR RESIDUE MPD A 1004
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d2d0fa2 (A:555-637)
2a: SCOP_d2d0fa1 (A:1-122)
3a: SCOP_d2d0fa3 (A:123-554)
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Classes
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Folds
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Superfamilies
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Families
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Glycosyl hydrolase domain
(397)
Superfamily
:
Glycosyl hydrolase domain
(397)
Family
:
automated matches
(85)
Protein domain
:
automated matches
(85)
Thermoactinomyces vulgaris [TaxId: 2026]
(6)
1a
d2d0fa2
A:555-637
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
automated matches
(93)
Protein domain
:
automated matches
(93)
Thermoactinomyces vulgaris [TaxId: 2026]
(6)
2a
d2d0fa1
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
:
automated matches
(71)
Thermoactinomyces vulgaris [TaxId: 2026]
(6)
3a
d2d0fa3
A:123-554
[
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]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2d0fA02 (A:125-547)
2a: CATH_2d0fA03 (A:548-637)
3a: CATH_2d0fA01 (A:1-124)
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)
Organisms
(
)
(
)
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
2d0fA02
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
2d0fA03
A:548-637
Homologous Superfamily
:
Immunoglobulins
(2282)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
3a
2d0fA01
A:1-124
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Pfam Domains
(0, 0)
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all PFAM domains
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Atom Selection
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Protein
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Sidechain
Hetero
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
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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select non-helix/non-sheet protein parts
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (118 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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