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1V3L
Biol. Unit 1
Info
Asym.Unit (234 KB)
Biol.Unit 1 (118 KB)
Biol.Unit 2 (116 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF F283L MUTANT CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH A PSEUDO-TETRAOSE DERIVED FROM ACARBOSE
Authors
:
R. Kanai, K. Haga, T. Akiba, K. Yamane, K. Harata
Date
:
03 Nov 03 (Deposition) - 03 Aug 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Cgtase, Cyclodextrin, Acarbose, Transferase
(Keyword Search:
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Reference
:
R. Kanai, K. Haga, T. Akiba, K. Yamane, K. Harata
Role Of Phe283 In Enzymatic Reaction Of Cyclodextrin Glycosyltransferase From Alkalophilic Bacillus Sp. 1011: Substrate Binding And Arrangement Of The Catalytic Site
Protein Sci. V. 13 457 2004
(for further references see the
PDB file header
)
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Hetero Components
(4, 4)
Info
All Hetero Components
1a: 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4... (ACIa)
1b: 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4... (ACIb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: BETA-D-GALACTOSE (GALa)
4a: ALPHA-D-GLUCOSE (GLCa)
4b: ALPHA-D-GLUCOSE (GLCb)
4c: ALPHA-D-GLUCOSE (GLCc)
5a: 4,6-DIDEOXYGLUCOSE (GLDa)
5b: 4,6-DIDEOXYGLUCOSE (GLDb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ACI
1
Ligand/Ion
6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
2
CA
-1
Ligand/Ion
CALCIUM ION
3
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
4
GLC
1
Ligand/Ion
ALPHA-D-GLUCOSE
5
GLD
1
Ligand/Ion
4,6-DIDEOXYGLUCOSE
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:100 , TRP A:101 , LEU A:197 , ASP A:371 , ARG A:375 , ACI A:702 , HOH A:1150 , HOH A:1367
BINDING SITE FOR RESIDUE GLC A 701
2
AC2
SOFTWARE
LEU A:197 , ASP A:229 , GLU A:257 , HIS A:327 , ASP A:328 , ARG A:375 , GLC A:701 , GLD A:703 , HOH A:1420
BINDING SITE FOR RESIDUE ACI A 702
3
AC3
SOFTWARE
TYR A:195 , LYS A:232 , HIS A:233 , GLU A:257 , PHE A:259 , ACI A:702 , GAL A:704 , HOH A:1171 , HOH A:1420
BINDING SITE FOR RESIDUE GLD A 703
4
AC4
SOFTWARE
TYR A:195 , PHE A:259 , ASP A:328 , GLD A:703
BINDING SITE FOR RESIDUE GAL A 704
5
AC9
SOFTWARE
ASP A:27 , ASN A:29 , ASN A:32 , ASN A:33 , GLY A:51 , ASP A:53 , HOH A:1281
BINDING SITE FOR RESIDUE CA A 687
6
BC1
SOFTWARE
ASN A:139 , ILE A:190 , ASP A:199 , HIS A:233 , HOH A:1295 , HOH A:1358 , HOH A:1421
BINDING SITE FOR RESIDUE CA A 688
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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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: CBM20 (A:581-686)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CBM20
PS51166
CBM20 (carbohydrate binding type-20) domain profile.
CDGT_BACS0
608-713
1
A:581-686
-
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Exons
(0, 0)
Info
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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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1v3la3 (A:407-496)
1b: SCOP_d1v3lb3 (B:407-496)
2a: SCOP_d1v3la1 (A:497-582)
2b: SCOP_d1v3lb1 (B:497-582)
3a: SCOP_d1v3la2 (A:583-686)
3b: SCOP_d1v3lb2 (B:583-686)
4a: SCOP_d1v3la4 (A:1-406)
4b: SCOP_d1v3lb4 (B:1-406)
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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
:
Cyclodextrin glycosyltransferase
(51)
Bacillus sp., strain 1011 [TaxId: 1409]
(8)
1a
d1v3la3
A:407-496
1b
d1v3lb3
B:407-496
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
E-set domains of sugar-utilizing enzymes
(147)
Protein domain
:
Cyclomaltodextrin glycanotransferase, domain D
(49)
Bacillus sp., strain 1011 [TaxId: 1409]
(8)
2a
d1v3la1
A:497-582
2b
d1v3lb1
B:497-582
Fold
:
Prealbumin-like
(433)
Superfamily
:
Starch-binding domain-like
(84)
Family
:
Starch-binding domain
(67)
Protein domain
:
Cyclodextrin glycosyltransferase, C-terminal domain
(51)
Bacillus sp., strain 1011 [TaxId: 1409]
(8)
3a
d1v3la2
A:583-686
3b
d1v3lb2
B:583-686
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
:
Cyclodextrin glycosyltransferase
(51)
Bacillus sp. 1011, alkaliphilic [TaxId: 1410]
(8)
4a
d1v3la4
A:1-406
4b
d1v3lb4
B:1-406
[
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1v3lA01 (A:1-400)
1b: CATH_1v3lB01 (B:1-400)
2a: CATH_1v3lA02 (A:401-495)
2b: CATH_1v3lB02 (B:401-495)
3a: CATH_1v3lA04 (A:583-685)
3b: CATH_1v3lB04 (B:583-685)
3c: CATH_1v3lA03 (A:496-582)
3d: CATH_1v3lB03 (B:496-582)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
1011 (Bacillus sp)
(10)
1a
1v3lA01
A:1-400
1b
1v3lB01
B:1-400
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
1011 (Bacillus sp)
(10)
2a
1v3lA02
A:401-495
2b
1v3lB02
B:401-495
Homologous Superfamily
:
Immunoglobulins
(2282)
1011 (Bacillus sp)
(10)
3a
1v3lA04
A:583-685
3b
1v3lB04
B:583-685
3c
1v3lA03
A:496-582
3d
1v3lB03
B:496-582
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Pfam Domains
(4, 8)
Info
all PFAM domains
1a: PFAM_TIG_1v3lB01 (B:499-581)
1b: PFAM_TIG_1v3lB02 (B:499-581)
2a: PFAM_Alpha_amylase_C_1v3lB03 (B:413-494)
2b: PFAM_Alpha_amylase_C_1v3lB04 (B:413-494)
3a: PFAM_CBM_20_1v3lB05 (B:586-682)
3b: PFAM_CBM_20_1v3lB06 (B:586-682)
4a: PFAM_Alpha_amylase_1v3lB07 (B:52-372)
4b: PFAM_Alpha_amylase_1v3lB08 (B:52-372)
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Clans
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)
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
E-set
(290)
Family
:
TIG
(28)
Bacillus sp. (strain 1011)
(8)
1a
TIG-1v3lB01
B:499-581
1b
TIG-1v3lB02
B:499-581
Clan
:
GHD
(106)
Family
:
Alpha-amylase_C
(82)
Bacillus sp. (strain 1011)
(8)
2a
Alpha-amylase_C-1v3lB03
B:413-494
2b
Alpha-amylase_C-1v3lB04
B:413-494
Family
:
CBM_20
(20)
Bacillus sp. (strain 1011)
(8)
3a
CBM_20-1v3lB05
B:586-682
3b
CBM_20-1v3lB06
B:586-682
Clan
:
Glyco_hydro_tim
(488)
Family
:
Alpha-amylase
(138)
Bacillus sp. (strain 1011)
(8)
4a
Alpha-amylase-1v3lB07
B:52-372
4b
Alpha-amylase-1v3lB08
B:52-372
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Asym.Unit (234 KB)
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