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1VB9
Biol. Unit 1
Info
Asym.Unit (211 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (105 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE II (TVA II) COMPLEXED WITH TRANSGLYCOSYLATED PRODUCT
Authors
:
M. Mizuno, T. Tonozuka, A. Uechi, A. Ohtaki, K. Ichikawa, S. Kamitori, A. Nishikawa, Y. Sakano
Date
:
25 Feb 04 (Deposition) - 08 Mar 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
(Beta/Alpha)8 Barrel, Gh Family 13, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Mizuno, T. Tonozuka, A. Uechi, A. Ohtaki, K. Ichikawa, S. Kamitori, A. Nishikawa, Y. Sakano
The Crystal Structure Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii (Tva Ii) Complexed With Transglycosylated Product
Eur. J. Biochem. V. 271 2530 2004
(for further references see the
PDB file header
)
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Hetero Components
(1, 6)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: ALPHA-D-GLUCOSE (GLCa)
2b: ALPHA-D-GLUCOSE (GLCb)
2c: ALPHA-D-GLUCOSE (GLCc)
2d: ALPHA-D-GLUCOSE (GLCd)
2e: ALPHA-D-GLUCOSE (GLCe)
2f: ALPHA-D-GLUCOSE (GLCf)
2g: ALPHA-D-GLUCOSE (GLCg)
2h: ALPHA-D-GLUCOSE (GLCh)
2i: ALPHA-D-GLUCOSE (GLCi)
2j: ALPHA-D-GLUCOSE (GLCj)
2k: ALPHA-D-GLUCOSE (GLCk)
2l: ALPHA-D-GLUCOSE (GLCl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GLC
6
Ligand/Ion
ALPHA-D-GLUCOSE
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: BC1 (SOFTWARE)
8: BC2 (SOFTWARE)
9: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:202 , VAL A:290 , MET A:293 , GLC A:702 , HOH A:881
BINDING SITE FOR RESIDUE GLC A 701
2
AC2
SOFTWARE
HIS A:202 , TYR A:204 , MET A:293 , ASP A:465 , ARG A:469 , GLC A:701 , GLC A:703 , HOH A:728 , HOH A:843
BINDING SITE FOR RESIDUE GLC A 702
3
AC3
SOFTWARE
TYR A:204 , HIS A:244 , PHE A:286 , MET A:293 , ARG A:323 , ASN A:325 , VAL A:326 , GLU A:354 , HIS A:420 , ASP A:421 , GLC A:702 , GLC A:704 , HOH A:902
BINDING SITE FOR RESIDUE GLC A 703
4
AC4
SOFTWARE
VAL A:326 , GLU A:354 , ASP A:421 , GLC A:703 , GLC A:705 , GLC A:706 , HOH A:764 , TYR B:45 , HOH B:710
BINDING SITE FOR RESIDUE GLC A 704
5
AC5
SOFTWARE
TRP A:356 , GLC A:704 , HOH A:717 , ARG B:44 , GLN B:112
BINDING SITE FOR RESIDUE GLC A 705
6
AC6
SOFTWARE
GLC A:704 , HOH A:765 , HOH A:835 , HOH A:942
BINDING SITE FOR RESIDUE GLC A 706
7
BC1
SOFTWARE
TYR A:45 , VAL B:326 , GLU B:354 , ASP B:421 , GLC B:703 , GLC B:705 , GLC B:706 , HOH B:711 , HOH B:791
BINDING SITE FOR RESIDUE GLC B 704
8
BC2
SOFTWARE
ARG A:44 , GLN A:112 , TRP B:356 , GLC B:704 , HOH B:708
BINDING SITE FOR RESIDUE GLC B 705
9
BC4
SOFTWARE
ASN A:143 , ASP A:145 , ASN A:148 , ASP A:149 , GLY A:169 , ASP A:171 , HOH A:763
BINDING SITE FOR RESIDUE CA A 601
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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Sorry, no Info available
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1vb9a2 (A:503-585)
1b: SCOP_d1vb9b2 (B:503-585)
2a: SCOP_d1vb9a1 (A:1-120)
2b: SCOP_d1vb9b1 (B:1-120)
3a: SCOP_d1vb9a3 (A:121-502)
3b: SCOP_d1vb9b3 (B:121-502)
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)
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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
:
alpha-Amylases, C-terminal beta-sheet domain
(272)
Protein domain
:
Maltogenic amylase
(22)
Thermoactinomyces vulgaris, TVAII [TaxId: 2026]
(11)
1a
d1vb9a2
A:503-585
1b
d1vb9b2
B:503-585
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, TVAII [TaxId: 2026]
(11)
2a
d1vb9a1
A:1-120
2b
d1vb9b1
B:1-120
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, TVAII [TaxId: 2026]
(11)
3a
d1vb9a3
A:121-502
3b
d1vb9b3
B:121-502
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1vb9A02 (A:122-242,A:298-502)
1b: CATH_1vb9B02 (B:122-242,B:298-502)
2a: CATH_1vb9A04 (A:503-585)
2b: CATH_1vb9B04 (B:503-585)
3a: CATH_1vb9A01 (A:1-121)
3b: CATH_1vb9B01 (B:1-121)
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Topologies
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)
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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)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
1a
1vb9A02
A:122-242,A:298-502
1b
1vb9B02
B:122-242,B:298-502
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
1vb9A04
A:503-585
2b
1vb9B04
B:503-585
Homologous Superfamily
:
Immunoglobulins
(2282)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
3a
1vb9A01
A:1-121
3b
1vb9B01
B:1-121
[
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]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Alpha_amylase_C_1vb9B01 (B:508-583)
1b: PFAM_Alpha_amylase_C_1vb9B02 (B:508-583)
2a: PFAM_Alpha_amylase_1vb9B03 (B:170-466)
2b: PFAM_Alpha_amylase_1vb9B04 (B:170-466)
3a: PFAM_Alpha_amylase_N_1vb9B05 (B:1-117)
3b: PFAM_Alpha_amylase_N_1vb9B06 (B:1-117)
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Clans
(
)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
GHD
(106)
Family
:
Alpha-amylase_C
(82)
Thermoactinomyces vulgaris
(11)
1a
Alpha-amylase_C-1vb9B01
B:508-583
1b
Alpha-amylase_C-1vb9B02
B:508-583
Clan
:
Glyco_hydro_tim
(488)
Family
:
Alpha-amylase
(138)
Thermoactinomyces vulgaris
(15)
2a
Alpha-amylase-1vb9B03
B:170-466
2b
Alpha-amylase-1vb9B04
B:170-466
Clan
:
no clan defined [family: Alpha-amylase_N]
(16)
Family
:
Alpha-amylase_N
(16)
Thermoactinomyces vulgaris
(15)
3a
Alpha-amylase_N-1vb9B05
B:1-117
3b
Alpha-amylase_N-1vb9B06
B:1-117
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Asym.Unit (211 KB)
Header - Asym.Unit
Biol.Unit 1 (105 KB)
Header - Biol.Unit 1
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