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1VFU
Asym. Unit
Info
Asym.Unit (207 KB)
Biol.Unit 1 (102 KB)
Biol.Unit 2 (102 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 AMYLASE 2/GAMMA-CYCLODEXTRIN COMPLEX
Authors
:
A. Ohtaki, M. Mizuno, T. Tonozuka, Y. Sakano, S. Kamitori
Date
:
19 Apr 04 (Deposition) - 08 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
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)
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)
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
(2, 18)
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)
2m: ALPHA-D-GLUCOSE (GLCm)
2n: ALPHA-D-GLUCOSE (GLCn)
2o: ALPHA-D-GLUCOSE (GLCo)
2p: ALPHA-D-GLUCOSE (GLCp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
GLC
16
Ligand/Ion
ALPHA-D-GLUCOSE
[
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Sites
(18, 18)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:356 , GLC A:802 , GLC A:808 , TYR B:45
BINDING SITE FOR RESIDUE GLC A 801
02
AC2
SOFTWARE
GLC A:801 , GLC A:803 , ALA B:46
BINDING SITE FOR RESIDUE GLC A 802
03
AC3
SOFTWARE
GLC A:802 , GLC A:804 , SER B:47
BINDING SITE FOR RESIDUE GLC A 803
04
AC4
SOFTWARE
GLC A:803 , GLC A:805
BINDING SITE FOR RESIDUE GLC A 804
05
AC5
SOFTWARE
HIS A:164 , ASP A:465 , GLC A:804 , GLC A:806
BINDING SITE FOR RESIDUE GLC A 805
06
AC6
SOFTWARE
HIS A:202 , TYR A:204 , MET A:293 , ASP A:465 , ARG A:469 , GLC A:805 , GLC A:807
BINDING SITE FOR RESIDUE GLC A 806
07
AC7
SOFTWARE
TYR A:204 , PHE A:286 , HIS A:420 , ASN A:421 , GLC A:806 , GLC A:808
BINDING SITE FOR RESIDUE GLC A 807
08
AC8
SOFTWARE
PHE A:286 , TRP A:356 , GLC A:801 , GLC A:807
BINDING SITE FOR RESIDUE GLC A 808
09
AC9
SOFTWARE
TYR B:204 , HIS B:244 , PHE B:286 , ASN B:325 , ASN B:421 , GLC B:902 , GLC B:908
BINDING SITE FOR RESIDUE GLC B 901
10
BC1
SOFTWARE
TYR A:45 , PHE B:286 , GLU B:354 , TRP B:356 , GLC B:901 , GLC B:903
BINDING SITE FOR RESIDUE GLC B 902
11
BC2
SOFTWARE
TYR A:45 , TRP B:356 , GLC B:902 , GLC B:904 , HOH B:1071
BINDING SITE FOR RESIDUE GLC B 903
12
BC3
SOFTWARE
GLC B:903 , GLC B:905
BINDING SITE FOR RESIDUE GLC B 904
13
BC4
SOFTWARE
GLC B:904 , GLC B:906 , HOH B:1024
BINDING SITE FOR RESIDUE GLC B 905
14
BC5
SOFTWARE
THR B:464 , ASP B:465 , GLC B:905 , GLC B:907
BINDING SITE FOR RESIDUE GLC B 906
15
BC6
SOFTWARE
HIS B:164 , ASP B:465 , GLC B:906 , GLC B:908
BINDING SITE FOR RESIDUE GLC B 907
16
BC7
SOFTWARE
HIS B:202 , TYR B:204 , ARG B:469 , GLC B:901 , GLC B:907
BINDING SITE FOR RESIDUE GLC B 908
17
BC8
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
18
BC9
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)
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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Label:
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_d1vfua2 (A:503-585)
1b: SCOP_d1vfub2 (B:503-585)
2a: SCOP_d1vfua1 (A:1-120)
2b: SCOP_d1vfub1 (B:1-120)
3a: SCOP_d1vfua3 (A:121-502)
3b: SCOP_d1vfub3 (B:121-502)
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Protein Domains
(
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(
)
Organisms
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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
d1vfua2
A:503-585
1b
d1vfub2
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
d1vfua1
A:1-120
2b
d1vfub1
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
d1vfua3
A:121-502
3b
d1vfub3
B:121-502
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1vfuA02 (A:122-242,A:298-502)
1b: CATH_1vfuB02 (B:122-242,B:298-502)
2a: CATH_1vfuA04 (A:503-585)
2b: CATH_1vfuB04 (B:503-585)
3a: CATH_1vfuA01 (A:1-121)
3b: CATH_1vfuB01 (B:1-121)
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)
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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
1vfuA02
A:122-242,A:298-502
1b
1vfuB02
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
1vfuA04
A:503-585
2b
1vfuB04
B:503-585
Homologous Superfamily
:
Immunoglobulins
(2282)
Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47.
(23)
3a
1vfuA01
A:1-121
3b
1vfuB01
B:1-121
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Alpha_amylase_C_1vfuB01 (B:508-583)
1b: PFAM_Alpha_amylase_C_1vfuB02 (B:508-583)
2a: PFAM_Alpha_amylase_1vfuB03 (B:170-466)
2b: PFAM_Alpha_amylase_1vfuB04 (B:170-466)
3a: PFAM_Alpha_amylase_N_1vfuB05 (B:1-117)
3b: PFAM_Alpha_amylase_N_1vfuB06 (B:1-117)
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Clans
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Families
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Organisms
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(
)
Clan
:
GHD
(106)
Family
:
Alpha-amylase_C
(82)
Thermoactinomyces vulgaris
(11)
1a
Alpha-amylase_C-1vfuB01
B:508-583
1b
Alpha-amylase_C-1vfuB02
B:508-583
Clan
:
Glyco_hydro_tim
(488)
Family
:
Alpha-amylase
(138)
Thermoactinomyces vulgaris
(15)
2a
Alpha-amylase-1vfuB03
B:170-466
2b
Alpha-amylase-1vfuB04
B:170-466
Clan
:
no clan defined [family: Alpha-amylase_N]
(16)
Family
:
Alpha-amylase_N
(16)
Thermoactinomyces vulgaris
(15)
3a
Alpha-amylase_N-1vfuB05
B:1-117
3b
Alpha-amylase_N-1vfuB06
B:1-117
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