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1J0Z
Asym. Unit
Info
Asym.Unit (352 KB)
Biol.Unit 1 (92 KB)
Biol.Unit 2 (91 KB)
Biol.Unit 3 (92 KB)
Biol.Unit 4 (92 KB)
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(1)
Title
:
BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES IN COMPLEX WITH MALTOSE
Authors
:
T. Oyama, H. Miyake, M. Kusunoki, Y. Nitta
Date
:
25 Nov 02 (Deposition) - 17 Jun 03 (Release) - 28 Jul 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Hydrolase, Beta-Amylase, Raw-Starch Binding Domain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Oyama, H. Miyake, M. Kusunoki, Y. Nitta
Crystal Structures Of Beta-Amylase From Bacillus Cereus Var. Mycoides In Complexes With Substrate Analogs And Affinity-Labeling Reagents
J. Biochem. (Tokyo) V. 133 467 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 20)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
1d: BETA-D-GLUCOSE (BGCd)
1e: BETA-D-GLUCOSE (BGCe)
1f: BETA-D-GLUCOSE (BGCf)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
6
Ligand/Ion
BETA-D-GLUCOSE
2
CA
4
Ligand/Ion
CALCIUM ION
3
GLC
10
Ligand/Ion
ALPHA-D-GLUCOSE
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:16 , ASP A:49 , TRP A:51 , HIS A:89 , ASP A:97 , ALA A:170 , ARG A:397 , BGC A:602 , HOH A:709 , HOH A:715 , HOH A:755 , HOH A:802 , HOH A:846
BINDING SITE FOR RESIDUE GLC A 601
02
AC2
SOFTWARE
VAL A:95 , ALA A:170 , GLU A:172 , LYS A:287 , THR A:330 , GLU A:367 , ALA A:369 , GLC A:601 , HOH A:723 , HOH A:755 , HOH A:758 , HOH A:843
BINDING SITE FOR RESIDUE BGC A 602
03
AC3
SOFTWARE
ALA A:230 , ILE A:231 , LEU A:232 , PRO A:233 , SER A:235 , TYR A:249 , BGC A:608
BINDING SITE FOR RESIDUE GLC A 607
04
AC4
SOFTWARE
THR A:223 , PRO A:234 , GLN A:239 , PHE A:240 , GLY A:244 , SER A:247 , TYR A:249 , GLC A:607
BINDING SITE FOR RESIDUE BGC A 608
05
AC5
SOFTWARE
GLU A:56 , ASP A:60 , GLN A:61 , GLU A:141 , GLU A:144
BINDING SITE FOR RESIDUE CA A 701
06
AC6
SOFTWARE
ASP B:49 , TRP B:51 , HIS B:89 , ASN B:94 , ASP B:97 , ARG B:397 , BGC B:602 , HOH B:703 , HOH B:737
BINDING SITE FOR RESIDUE GLC B 601
07
AC7
SOFTWARE
VAL B:95 , ALA B:170 , GLU B:172 , LYS B:287 , THR B:330 , GLU B:367 , ALA B:369 , GLC B:601 , HOH B:790 , HOH B:794
BINDING SITE FOR RESIDUE BGC B 602
08
AC8
SOFTWARE
TRP B:221 , ALA B:230 , ILE B:231 , LEU B:232 , PRO B:233 , PRO B:234 , SER B:235 , TYR B:249 , BGC B:608
BINDING SITE FOR RESIDUE GLC B 607
09
AC9
SOFTWARE
PRO B:234 , GLN B:239 , PHE B:240 , GLY B:244 , TYR B:249 , GLC B:607 , HOH B:714
BINDING SITE FOR RESIDUE BGC B 608
10
BC1
SOFTWARE
GLU B:56 , ASP B:60 , GLN B:61 , GLU B:141 , GLU B:144 , HOH B:730
BINDING SITE FOR RESIDUE CA B 701
11
BC2
SOFTWARE
LEU C:19 , ASP C:49 , TRP C:51 , HIS C:89 , ASP C:97 , ALA C:170 , ARG C:397 , GLC C:602 , HOH C:702 , HOH C:703 , HOH C:705 , HOH C:831
BINDING SITE FOR RESIDUE GLC C 601
12
BC3
SOFTWARE
VAL C:95 , ALA C:170 , GLU C:172 , LYS C:287 , THR C:330 , GLU C:367 , ALA C:369 , LEU C:396 , GLC C:601
BINDING SITE FOR RESIDUE GLC C 602
13
BC4
SOFTWARE
TRP C:221 , ALA C:230 , ILE C:231 , LEU C:232 , PRO C:233 , SER C:235 , TYR C:249 , BGC C:608
BINDING SITE FOR RESIDUE GLC C 607
14
BC5
SOFTWARE
THR C:223 , PRO C:234 , GLN C:239 , PHE C:240 , GLY C:244 , SER C:247 , TYR C:249 , GLC C:607 , HOH C:716
BINDING SITE FOR RESIDUE BGC C 608
15
BC6
SOFTWARE
GLU C:56 , ASP C:60 , GLN C:61 , GLU C:141 , GLU C:144 , HOH C:763
BINDING SITE FOR RESIDUE CA C 701
16
BC7
SOFTWARE
ASP D:49 , TRP D:51 , HIS D:89 , ASP D:97 , ALA D:170 , ARG D:397 , GLC D:602 , HOH D:704 , HOH D:793
BINDING SITE FOR RESIDUE GLC D 601
17
BC8
SOFTWARE
VAL D:95 , ALA D:170 , GLU D:172 , LYS D:287 , THR D:330 , GLU D:367 , ALA D:369 , GLC D:601
BINDING SITE FOR RESIDUE GLC D 602
18
BC9
SOFTWARE
TRP D:221 , ALA D:230 , ILE D:231 , LEU D:232 , PRO D:233 , SER D:235 , TYR D:249 , BGC D:608
BINDING SITE FOR RESIDUE GLC D 607
19
CC1
SOFTWARE
THR D:223 , PRO D:234 , GLN D:239 , GLY D:244 , SER D:247 , TYR D:249 , GLC D:607
BINDING SITE FOR RESIDUE BGC D 608
20
CC2
SOFTWARE
GLU D:56 , ASP D:60 , GLN D:61 , GLU D:141 , GLU D:144
BINDING SITE FOR RESIDUE CA D 701
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: BETA_AMYLASE_1 (A:89-97,B:89-97,C:89-97,D:89-97)
2: BETA_AMYLASE_2 (A:168-178,B:168-178,C:168-178,D:16...)
3: CBM20 (A:414-516,B:414-516,C:414-516,D:41...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BETA_AMYLASE_1
PS00506
Beta-amylase active site 1.
AMYB_BACCE
119-127
4
A:89-97
B:89-97
C:89-97
D:89-97
2
BETA_AMYLASE_2
PS00679
Beta-amylase active site 2.
AMYB_BACCE
198-208
4
A:168-178
B:168-178
C:168-178
D:168-178
3
CBM20
PS51166
CBM20 (carbohydrate binding type-20) domain profile.
AMYB_BACCE
444-546
4
A:414-516
B:414-516
C:414-516
D:414-516
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1j0za1 (A:418-516)
1b: SCOP_d1j0zb1 (B:418-516)
1c: SCOP_d1j0zc1 (C:418-516)
1d: SCOP_d1j0zd1 (D:418-516)
2a: SCOP_d1j0za2 (A:1-417)
2b: SCOP_d1j0zb2 (B:1-417)
2c: SCOP_d1j0zc2 (C:1-417)
2d: SCOP_d1j0zd2 (D:1-417)
View:
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Classes
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)
(
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)
(
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Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Prealbumin-like
(433)
Superfamily
:
Starch-binding domain-like
(84)
Family
:
Starch-binding domain
(67)
Protein domain
:
beta-amylase
(12)
Bacillus cereus [TaxId: 1396]
(12)
1a
d1j0za1
A:418-516
1b
d1j0zb1
B:418-516
1c
d1j0zc1
C:418-516
1d
d1j0zd1
D:418-516
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
:
Bacterial beta-amylase
(11)
Bacillus cereus [TaxId: 1396]
(11)
2a
d1j0za2
A:1-417
2b
d1j0zb2
B:1-417
2c
d1j0zc2
C:1-417
2d
d1j0zd2
D:1-417
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1j0zA01 (A:1-416)
1b: CATH_1j0zB01 (B:1-416)
1c: CATH_1j0zC01 (C:1-416)
1d: CATH_1j0zD01 (D:1-416)
2a: CATH_1j0zA02 (A:417-516)
2b: CATH_1j0zB02 (B:417-516)
2c: CATH_1j0zC02 (C:417-516)
2d: CATH_1j0zD02 (D:417-516)
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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 cereus. Organism_taxid: 1396. Strain: var. Mycoides
(5)
1a
1j0zA01
A:1-416
1b
1j0zB01
B:1-416
1c
1j0zC01
C:1-416
1d
1j0zD01
D:1-416
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Bacillus cereus. Organism_taxid: 1396. Strain: var. Mycoides
(5)
2a
1j0zA02
A:417-516
2b
1j0zB02
B:417-516
2c
1j0zC02
C:417-516
2d
1j0zD02
D:417-516
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (352 KB)
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