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1VFO
Asym. Unit
Info
Asym.Unit (207 KB)
Biol.Unit 1 (103 KB)
Biol.Unit 2 (103 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 2/BETA-CYCLODEXTRIN COMPLEX
Authors
:
A. Ohtaki, M. Mizuno, T. Tonozuka, Y. Sakano, S. Kamitori
Date
:
16 Apr 04 (Deposition) - 08 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.81
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Amylase, Complex, Cyclodextrin, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Ohtaki, M. Mizuno, T. Tonozuka, Y. Sakano, S. Kamitori
Complex Structures Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 2 With Acarbose And Cyclodextrins Demonstrate The Multiple Substrate Recognition Mechanism
J. Biol. Chem. V. 279 31033 2004
(for further references see the
PDB file header
)
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Hetero Components
(3, 16)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
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)
3j: ALPHA-D-GLUCOSE (GLCj)
3k: ALPHA-D-GLUCOSE (GLCk)
3l: ALPHA-D-GLUCOSE (GLCl)
3m: ALPHA-D-GLUCOSE (GLCm)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
1
Ligand/Ion
BETA-D-GLUCOSE
2
CA
2
Ligand/Ion
CALCIUM ION
3
GLC
13
Ligand/Ion
ALPHA-D-GLUCOSE
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Sites
(16, 16)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:356 , GLC A:602 , GLC A:607
BINDING SITE FOR RESIDUE GLC A 601
02
AC2
SOFTWARE
GLC A:601 , GLC A:603
BINDING SITE FOR RESIDUE GLC A 602
03
AC3
SOFTWARE
GLC A:602 , GLC A:604 , HOH A:1068 , HOH A:1099
BINDING SITE FOR RESIDUE GLC A 603
04
AC4
SOFTWARE
HIS A:164 , ASP A:465 , GLC A:603 , GLC A:605 , HOH A:1097
BINDING SITE FOR RESIDUE GLC A 604
05
AC5
SOFTWARE
HIS A:202 , TYR A:204 , MET A:293 , ASP A:465 , ARG A:469 , GLC A:604 , GLC A:606
BINDING SITE FOR RESIDUE GLC A 605
06
AC6
SOFTWARE
TYR A:204 , HIS A:244 , PHE A:286 , ASN A:325 , GLU A:354 , HIS A:420 , ASN A:421 , GLC A:605 , GLC A:607
BINDING SITE FOR RESIDUE GLC A 606
07
AC7
SOFTWARE
PHE A:286 , VAL A:326 , GLU A:354 , ASN A:421 , GLC A:601 , GLC A:606
BINDING SITE FOR RESIDUE GLC A 607
08
AC8
SOFTWARE
VAL B:326 , GLU B:354 , TRP B:356 , ASN B:421 , GLC B:702 , GLC B:707
BINDING SITE FOR RESIDUE GLC B 701
09
AC9
SOFTWARE
ARG A:44 , TRP B:356 , GLC B:701 , BGC B:703
BINDING SITE FOR RESIDUE GLC B 702
10
BC1
SOFTWARE
TYR A:45 , GLC B:702 , GLC B:704
BINDING SITE FOR RESIDUE BGC B 703
11
BC2
SOFTWARE
BGC B:703 , GLC B:705
BINDING SITE FOR RESIDUE GLC B 704
12
BC3
SOFTWARE
HIS B:164 , ASP B:465 , GLC B:704 , GLC B:706
BINDING SITE FOR RESIDUE GLC B 705
13
BC4
SOFTWARE
TYR B:204 , MET B:293 , ASP B:465 , ARG B:469 , GLC B:705 , GLC B:707
BINDING SITE FOR RESIDUE GLC B 706
14
BC5
SOFTWARE
TYR B:204 , HIS B:244 , PHE B:286 , ASN B:325 , GLU B:354 , HIS B:420 , ASN B:421 , GLC B:701 , GLC B:706
BINDING SITE FOR RESIDUE GLC B 707
15
BC6
SOFTWARE
ASN A:143 , ASP A:145 , ASN A:148 , ASP A:149 , GLY A:169 , ASP A:171
BINDING SITE FOR RESIDUE CA A 1001
16
BC7
SOFTWARE
ASN B:143 , ASP B:145 , ASN B:148 , ASP B:149 , GLY B:169 , ASP B:171
BINDING SITE FOR RESIDUE CA B 1002
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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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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_d1vfoa2 (A:503-585)
1b: SCOP_d1vfob2 (B:503-585)
2a: SCOP_d1vfoa1 (A:1-120)
2b: SCOP_d1vfob1 (B:1-120)
3a: SCOP_d1vfoa3 (A:121-502)
3b: SCOP_d1vfob3 (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
:
automated matches
(85)
Protein domain
:
automated matches
(85)
Thermoactinomyces vulgaris [TaxId: 2026]
(6)
1a
d1vfoa2
A:503-585
1b
d1vfob2
B:503-585
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
d1vfoa1
A:1-120
2b
d1vfob1
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
:
automated matches
(71)
Thermoactinomyces vulgaris [TaxId: 2026]
(6)
3a
d1vfoa3
A:121-502
3b
d1vfob3
B:121-502
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1vfoA02 (A:122-242,A:298-502)
1b: CATH_1vfoB02 (B:122-242,B:298-502)
2a: CATH_1vfoA04 (A:503-585)
2b: CATH_1vfoB04 (B:503-585)
3a: CATH_1vfoA01 (A:1-121)
3b: CATH_1vfoB01 (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
1vfoA02
A:122-242,A:298-502
1b
1vfoB02
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
1vfoA04
A:503-585
2b
1vfoB04
B:503-585
Homologous Superfamily
:
Immunoglobulins
(2282)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
3a
1vfoA01
A:1-121
3b
1vfoB01
B:1-121
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Alpha_amylase_C_1vfoB01 (B:508-583)
1b: PFAM_Alpha_amylase_C_1vfoB02 (B:508-583)
2a: PFAM_Alpha_amylase_1vfoB03 (B:170-466)
2b: PFAM_Alpha_amylase_1vfoB04 (B:170-466)
3a: PFAM_Alpha_amylase_N_1vfoB05 (B:1-117)
3b: PFAM_Alpha_amylase_N_1vfoB06 (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-1vfoB01
B:508-583
1b
Alpha-amylase_C-1vfoB02
B:508-583
Clan
:
Glyco_hydro_tim
(488)
Family
:
Alpha-amylase
(138)
Thermoactinomyces vulgaris
(15)
2a
Alpha-amylase-1vfoB03
B:170-466
2b
Alpha-amylase-1vfoB04
B:170-466
Clan
:
no clan defined [family: Alpha-amylase_N]
(16)
Family
:
Alpha-amylase_N
(16)
Thermoactinomyces vulgaris
(15)
3a
Alpha-amylase_N-1vfoB05
B:1-117
3b
Alpha-amylase_N-1vfoB06
B:1-117
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