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1VB9
Asym. Unit
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:
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Gene Ontology, PubMed, Web (Google)
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)
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
(2, 14)
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
2
Ligand/Ion
CALCIUM ION
2
GLC
12
Ligand/Ion
ALPHA-D-GLUCOSE
[
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Sites
(14, 14)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:202 , VAL A:290 , MET A:293 , GLC A:702 , HOH A:881
BINDING SITE FOR RESIDUE GLC A 701
02
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
03
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
04
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
05
AC5
SOFTWARE
TRP A:356 , GLC A:704 , HOH A:717 , ARG B:44 , GLN B:112
BINDING SITE FOR RESIDUE GLC A 705
06
AC6
SOFTWARE
GLC A:704 , HOH A:765 , HOH A:835 , HOH A:942
BINDING SITE FOR RESIDUE GLC A 706
07
AC7
SOFTWARE
HIS B:164 , HIS B:202 , VAL B:290 , MET B:293 , GLC B:702 , HOH B:829 , HOH B:863
BINDING SITE FOR RESIDUE GLC B 701
08
AC8
SOFTWARE
HIS B:202 , TYR B:204 , MET B:293 , ASP B:465 , ARG B:469 , GLC B:701 , GLC B:703
BINDING SITE FOR RESIDUE GLC B 702
09
AC9
SOFTWARE
TYR B:204 , HIS B:244 , PHE B:286 , ASN B:325 , VAL B:326 , GLU B:354 , HIS B:420 , ASP B:421 , GLC B:702 , GLC B:704
BINDING SITE FOR RESIDUE GLC B 703
10
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
11
BC2
SOFTWARE
ARG A:44 , GLN A:112 , TRP B:356 , GLC B:704 , HOH B:708
BINDING SITE FOR RESIDUE GLC B 705
12
BC3
SOFTWARE
GLC B:704 , HOH B:761
BINDING SITE FOR RESIDUE GLC B 706
13
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
14
BC5
SOFTWARE
ASN B:143 , ASP B:145 , ASN B:148 , ASP B:149 , GLY B:169 , ASP B:171 , HOH B:757
BINDING SITE FOR RESIDUE CA B 602
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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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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, 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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)
(
)
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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)
(
)
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
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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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