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1D3C
Asym. Unit
Info
Asym.Unit (135 KB)
Biol.Unit 1 (128 KB)
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(1)
Title
:
MICHAELIS COMPLEX OF BACILLUS CIRCULANS STRAIN 251 CYCLODEXTRIN GLYCOSYLTRANSFERASE WITH GAMMA-CYCLODEXTRIN
Authors
:
J. C. M. Uitdehaag, K. H. Kalk, B. A. Van Der Veen, L. Dijkhuizen, B. W. Dijkstra
Date
:
29 Sep 99 (Deposition) - 22 Dec 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.78
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Alpha-Amylase, Product Complex, Oligosaccharide, Family 13 Glycosyl Hydrolase, Transglycosylation, Induced Fit, Catalysis, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. C. Uitdehaag, K. H. Kalk, B. A. Van Der Veen, L. Dijkhuizen, B. W. Dijkstra
The Cyclization Mechanism Of Cyclodextrin Glycosyltransferase (Cgtase) As Revealed By A Gamma-Cyclodextrin-Cgtase Complex At 1. 8-A Resolution.
J. Biol. Chem. V. 274 34868 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 30)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
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)
2q: ALPHA-D-GLUCOSE (GLCq)
2r: ALPHA-D-GLUCOSE (GLCr)
2s: ALPHA-D-GLUCOSE (GLCs)
2t: ALPHA-D-GLUCOSE (GLCt)
2u: ALPHA-D-GLUCOSE (GLCu)
2v: ALPHA-D-GLUCOSE (GLCv)
2w: ALPHA-D-GLUCOSE (GLCw)
2x: ALPHA-D-GLUCOSE (GLCx)
2y: ALPHA-D-GLUCOSE (GLCy)
2z: ALPHA-D-GLUCOSE (GLCz)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
3
Ligand/Ion
CALCIUM ION
2
GLC
26
Ligand/Ion
ALPHA-D-GLUCOSE
3
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
[
close Hetero Component info
]
Sites
(30, 30)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:413 , ILE A:414 , SER A:445 , GLY A:446 , ALA A:539 , ASP A:540 , GLC A:691 , HOH A:770 , HOH A:951
BINDING SITE FOR RESIDUE GLC A 690
02
AC2
SOFTWARE
GLU A:411 , ARG A:412 , GLY A:446 , GLC A:690 , HOH A:923 , HOH A:1113 , HOH A:1165 , HOH A:1289
BINDING SITE FOR RESIDUE GLC A 691
03
AC3
SOFTWARE
GLC A:693 , GLC A:699 , HOH A:1259
BINDING SITE FOR RESIDUE GLC A 692
04
AC4
SOFTWARE
PHE A:183 , LYS A:232 , PHE A:259 , GLC A:692 , GLC A:694 , HOH A:754 , HOH A:854 , HOH A:1195
BINDING SITE FOR RESIDUE GLC A 693
05
AC5
SOFTWARE
TYR A:195 , ALA A:230 , LYS A:232 , HIS A:233 , GLN A:257 , GLC A:693 , GLC A:695 , HOH A:1130
BINDING SITE FOR RESIDUE GLC A 694
06
AC6
SOFTWARE
TYR A:100 , HIS A:140 , ARG A:227 , ASN A:229 , GLN A:257 , HIS A:327 , ASP A:328 , GLC A:694 , GLC A:696
BINDING SITE FOR RESIDUE GLC A 695
07
AC7
SOFTWARE
HIS A:98 , TYR A:100 , TRP A:101 , ASP A:371 , ARG A:375 , GLC A:695 , GLC A:697 , HOH A:984
BINDING SITE FOR RESIDUE GLC A 696
08
AC8
SOFTWARE
ARG A:47 , ASP A:371 , GLC A:696 , GLC A:698 , HOH A:984 , HOH A:1171 , HOH A:1221
BINDING SITE FOR RESIDUE GLC A 697
09
AC9
SOFTWARE
GLC A:697 , GLC A:699
BINDING SITE FOR RESIDUE GLC A 698
10
BC1
SOFTWARE
GLC A:692 , GLC A:698
BINDING SITE FOR RESIDUE GLC A 699
11
BC2
SOFTWARE
TRP A:616 , GLC A:701 , GLC A:707 , HOH A:995
BINDING SITE FOR RESIDUE GLC A 700
12
BC3
SOFTWARE
GLC A:700 , GLC A:702
BINDING SITE FOR RESIDUE GLC A 701
13
BC4
SOFTWARE
GLC A:701 , GLC A:703
BINDING SITE FOR RESIDUE GLC A 702
14
BC5
SOFTWARE
GLC A:702 , GLC A:704
BINDING SITE FOR RESIDUE GLC A 703
15
BC6
SOFTWARE
ARG A:339 , GLU A:343 , GLC A:703 , GLC A:705 , HOH A:1262
BINDING SITE FOR RESIDUE GLC A 704
16
BC7
SOFTWARE
THR A:385 , GLC A:704 , GLC A:706 , HOH A:869 , HOH A:990 , HOH A:1170 , HOH A:1262 , HOH A:1276 , HOH A:1352
BINDING SITE FOR RESIDUE GLC A 705
17
BC8
SOFTWARE
LYS A:651 , TRP A:662 , GLU A:663 , GLC A:705 , GLC A:707 , HOH A:820 , HOH A:1219 , HOH A:1270 , HOH A:1352
BINDING SITE FOR RESIDUE GLC A 706
18
BC9
SOFTWARE
TRP A:662 , ASN A:667 , GLC A:700 , GLC A:706 , HOH A:1025
BINDING SITE FOR RESIDUE GLC A 707
19
CC1
SOFTWARE
ALA A:599 , LEU A:600 , GLY A:601 , GLN A:602 , ASN A:603 , ASN A:627 , GLN A:628 , GLC A:709 , GLC A:715
BINDING SITE FOR RESIDUE GLC A 708
20
CC2
SOFTWARE
GLN A:628 , GLC A:708 , GLC A:710 , HOH A:994 , HOH A:1308
BINDING SITE FOR RESIDUE GLC A 709
21
CC3
SOFTWARE
THR A:185 , GLC A:709 , GLC A:711 , HOH A:1278
BINDING SITE FOR RESIDUE GLC A 710
22
CC4
SOFTWARE
GLC A:710 , GLC A:712
BINDING SITE FOR RESIDUE GLC A 711
23
CC5
SOFTWARE
GLC A:711 , GLC A:713
BINDING SITE FOR RESIDUE GLC A 712
24
CC6
SOFTWARE
GLC A:712 , GLC A:714
BINDING SITE FOR RESIDUE GLC A 713
25
CC7
SOFTWARE
GLC A:713 , GLC A:715
BINDING SITE FOR RESIDUE GLC A 714
26
CC8
SOFTWARE
THR A:598 , ALA A:599 , LEU A:600 , TYR A:633 , GLC A:708 , GLC A:714
BINDING SITE FOR RESIDUE GLC A 715
27
CC9
SOFTWARE
ASP A:27 , ASN A:29 , ASN A:32 , ASN A:33 , GLY A:51 , ASP A:53 , HOH A:950
BINDING SITE FOR RESIDUE CA A 687
28
DC1
SOFTWARE
ASN A:139 , ILE A:190 , ASP A:199 , HIS A:233 , HOH A:866 , HOH A:867 , HOH A:915
BINDING SITE FOR RESIDUE CA A 688
29
DC2
SOFTWARE
ALA A:315 , ASP A:577 , HOH A:806 , HOH A:927 , HOH A:978 , HOH A:1057 , HOH A:1344
BINDING SITE FOR RESIDUE CA A 689
30
DC3
SOFTWARE
ILE A:378 , HOH A:814 , HOH A:1207
BINDING SITE FOR RESIDUE MPD A 716
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: CBM20 (A:581-686)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CBM20
PS51166
CBM20 (carbohydrate binding type-20) domain profile.
CDGT2_BACCI
608-713
1
A:581-686
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d1d3ca3 (A:407-496)
2a: SCOP_d1d3ca1 (A:497-583)
3a: SCOP_d1d3ca2 (A:584-686)
4a: SCOP_d1d3ca4 (A:1-406)
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
Families
(
)
(
)
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 circulans, different strains [TaxId: 1397]
(36)
1a
d1d3ca3
A: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 circulans, different strains [TaxId: 1397]
(36)
2a
d1d3ca1
A:497-583
Fold
:
Prealbumin-like
(433)
Superfamily
:
Starch-binding domain-like
(84)
Family
:
Starch-binding domain
(67)
Protein domain
:
Cyclodextrin glycosyltransferase, C-terminal domain
(51)
Bacillus circulans, different strains [TaxId: 1397]
(36)
3a
d1d3ca2
A:584-686
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 circulans, different strains [TaxId: 1397]
(36)
4a
d1d3ca4
A:1-406
[
close SCOP info
]
CATH Domains
(3, 4)
Info
all CATH domains
1a: CATH_1d3cA01 (A:1-400)
2a: CATH_1d3cA02 (A:401-495)
3a: CATH_1d3cA04 (A:583-685)
3b: CATH_1d3cA03 (A:496-582)
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)
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)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Bacillus circulans. Organism_taxid: 1397. Strain: 251.
(4)
1a
1d3cA01
A:1-400
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Bacillus circulans. Organism_taxid: 1397. Strain: 251.
(4)
2a
1d3cA02
A:401-495
Homologous Superfamily
:
Immunoglobulins
(2282)
Bacillus circulans. Organism_taxid: 1397. Strain: 251.
(4)
3a
1d3cA04
A:583-685
3b
1d3cA03
A:496-582
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain A
Asymmetric Unit 1
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Asym.Unit (135 KB)
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