PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1J10
Asym. Unit
Info
Asym.Unit (357 KB)
Biol.Unit 1 (93 KB)
Biol.Unit 2 (92 KB)
Biol.Unit 3 (93 KB)
Biol.Unit 4 (94 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES IN COMPLEX WITH GGX
Authors
:
T. Oyama, H. Miyake, M. Kusunoki, Y. Nitta
Date
:
25 Nov 02 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
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
)
[
close entry info
]
Hetero Components
(4, 28)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
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)
3a: BETA-D-XYLOPYRANOSE (XYPa)
3b: BETA-D-XYLOPYRANOSE (XYPb)
3c: BETA-D-XYLOPYRANOSE (XYPc)
3d: BETA-D-XYLOPYRANOSE (XYPd)
3e: BETA-D-XYLOPYRANOSE (XYPe)
3f: BETA-D-XYLOPYRANOSE (XYPf)
3g: BETA-D-XYLOPYRANOSE (XYPg)
4a: XYLOPYRANOSE (XYSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
GLC
16
Ligand/Ion
ALPHA-D-GLUCOSE
3
XYP
7
Ligand/Ion
BETA-D-XYLOPYRANOSE
4
XYS
1
Ligand/Ion
XYLOPYRANOSE
[
close Hetero Component info
]
Sites
(28, 28)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:172 , ARG A:174 , TYR A:178 , GLY A:290 , HIS A:292 , TRP A:293 , THR A:330 , GLC A:604 , HOH A:849
BINDING SITE FOR RESIDUE GLC A 603
02
AC2
SOFTWARE
TYR A:178 , TYR A:186 , HIS A:292 , TRP A:293 , MET A:334 , GLC A:603 , XYP A:605 , HOH A:854
BINDING SITE FOR RESIDUE GLC A 604
03
AC3
SOFTWARE
GLC A:604
BINDING SITE FOR RESIDUE XYP A 605
04
AC4
SOFTWARE
TRP A:221 , ALA A:230 , ILE A:231 , LEU A:232 , PRO A:233 , SER A:235 , TYR A:249 , GLC A:608
BINDING SITE FOR RESIDUE GLC A 607
05
AC5
SOFTWARE
THR A:223 , PRO A:234 , GLN A:239 , PHE A:240 , GLY A:244 , TYR A:249 , GLC A:607 , XYP A:609
BINDING SITE FOR RESIDUE GLC A 608
06
AC6
SOFTWARE
GLN A:239 , ASN A:243 , GLY A:244 , GLC A:608
BINDING SITE FOR RESIDUE XYP A 609
07
AC7
SOFTWARE
GLU B:172 , ARG B:174 , TYR B:178 , GLY B:290 , THR B:330 , GLC B:604
BINDING SITE FOR RESIDUE GLC B 603
08
AC8
SOFTWARE
TYR B:186 , HIS B:292 , MET B:334 , GLC B:603 , XYP B:605
BINDING SITE FOR RESIDUE GLC B 604
09
AC9
SOFTWARE
LEU B:370 , GLC B:604
BINDING SITE FOR RESIDUE XYP B 605
10
BC1
SOFTWARE
TRP B:221 , ALA B:230 , ILE B:231 , LEU B:232 , PRO B:233 , SER B:235 , TYR B:249 , GLC B:608
BINDING SITE FOR RESIDUE GLC B 607
11
BC2
SOFTWARE
THR B:223 , PRO B:234 , GLN B:239 , PHE B:240 , GLY B:244 , TYR B:249 , GLC B:607 , XYP B:609
BINDING SITE FOR RESIDUE GLC B 608
12
BC3
SOFTWARE
GLN B:239 , ASN B:243 , GLY B:244 , GLC B:608 , HOH B:803
BINDING SITE FOR RESIDUE XYP B 609
13
BC4
SOFTWARE
GLU C:172 , ARG C:174 , TYR C:178 , GLY C:290 , HIS C:292 , TRP C:293 , THR C:330 , GLC C:604
BINDING SITE FOR RESIDUE GLC C 603
14
BC5
SOFTWARE
TYR C:186 , HIS C:292 , GLC C:603 , XYS C:605
BINDING SITE FOR RESIDUE GLC C 604
15
BC6
SOFTWARE
GLC C:604
BINDING SITE FOR RESIDUE XYS C 605
16
BC7
SOFTWARE
TRP C:221 , ALA C:230 , ILE C:231 , LEU C:232 , PRO C:233 , SER C:235 , TYR C:249 , GLC C:608
BINDING SITE FOR RESIDUE GLC C 607
17
BC8
SOFTWARE
THR C:223 , PRO C:234 , GLN C:239 , PHE C:240 , GLY C:244 , TYR C:249 , GLC C:607 , XYP C:609 , HOH C:705
BINDING SITE FOR RESIDUE GLC C 608
18
BC9
SOFTWARE
GLN C:239 , ASN C:243 , GLY C:244 , GLC C:608
BINDING SITE FOR RESIDUE XYP C 609
19
CC1
SOFTWARE
GLU D:172 , ARG D:174 , TYR D:178 , GLY D:290 , HIS D:292 , THR D:330 , GLC D:604 , HOH D:842
BINDING SITE FOR RESIDUE GLC D 603
20
CC2
SOFTWARE
TYR D:186 , HIS D:292 , MET D:334 , LEU D:370 , GLC D:603 , XYP D:605
BINDING SITE FOR RESIDUE GLC D 604
21
CC3
SOFTWARE
GLC D:604
BINDING SITE FOR RESIDUE XYP D 605
22
CC4
SOFTWARE
TRP D:221 , ALA D:230 , LEU D:232 , PRO D:233 , SER D:235 , TYR D:249 , GLC D:608
BINDING SITE FOR RESIDUE GLC D 607
23
CC5
SOFTWARE
THR D:223 , PRO D:234 , GLN D:239 , PHE D:240 , GLY D:244 , TYR D:249 , GLC D:607 , XYP D:609
BINDING SITE FOR RESIDUE GLC D 608
24
CC6
SOFTWARE
GLN D:239 , ASN D:243 , GLY D:244 , GLC D:608
BINDING SITE FOR RESIDUE XYP D 609
25
CC7
SOFTWARE
GLU A:56 , ASP A:60 , GLN A:61 , GLU A:141 , GLU A:144 , HOH A:802
BINDING SITE FOR RESIDUE CA A 701
26
CC8
SOFTWARE
GLU B:56 , ASP B:60 , GLN B:61 , GLU B:141 , GLU B:144 , HOH B:752
BINDING SITE FOR RESIDUE CA B 701
27
CC9
SOFTWARE
GLU C:56 , ASP C:60 , GLN C:61 , GLU C:141 , GLU C:144 , HOH C:765
BINDING SITE FOR RESIDUE CA C 701
28
DC1
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:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1j10a1 (A:418-516)
1b: SCOP_d1j10b1 (B:418-516)
1c: SCOP_d1j10c1 (C:418-516)
1d: SCOP_d1j10d1 (D:418-516)
2a: SCOP_d1j10a2 (A:1-417)
2b: SCOP_d1j10b2 (B:1-417)
2c: SCOP_d1j10c2 (C:1-417)
2d: SCOP_d1j10d2 (D:1-417)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
d1j10a1
A:418-516
1b
d1j10b1
B:418-516
1c
d1j10c1
C:418-516
1d
d1j10d1
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
d1j10a2
A:1-417
2b
d1j10b2
B:1-417
2c
d1j10c2
C:1-417
2d
d1j10d2
D:1-417
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1j10A01 (A:1-416)
1b: CATH_1j10C01 (C:1-416)
1c: CATH_1j10D01 (D:1-416)
1d: CATH_1j10B01 (B:1-416)
2a: CATH_1j10A02 (A:417-516)
2b: CATH_1j10C02 (C:417-516)
2c: CATH_1j10D02 (D:417-516)
2d: CATH_1j10B02 (B:417-516)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
1j10A01
A:1-416
1b
1j10C01
C:1-416
1c
1j10D01
D:1-416
1d
1j10B01
B: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
1j10A02
A:417-516
2b
1j10C02
C:417-516
2c
1j10D02
D:417-516
2d
1j10B02
B:417-516
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (357 KB)
Header - Asym.Unit
Biol.Unit 1 (93 KB)
Header - Biol.Unit 1
Biol.Unit 2 (92 KB)
Header - Biol.Unit 2
Biol.Unit 3 (93 KB)
Header - Biol.Unit 3
Biol.Unit 4 (94 KB)
Header - Biol.Unit 4
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1J10
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help