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.
2GVY
Biol. Unit 1
Info
Asym.Unit (173 KB)
Biol.Unit 1 (86 KB)
Biol.Unit 2 (86 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MONOCLINIC CRYSTAL FORM OF ASPERGILLUS NIGER ALPHA-AMYLASE IN COMPLEX WITH MALTOSE AT 1.8 A RESOLUTION
Authors
:
A. Vujicic-Zagar, B. W. Dijkstra
Date
:
03 May 06 (Deposition) - 15 Aug 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
(Beta-Alpha)8 Barrel, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Vujicic-Zagar, B. W. Dijkstra
Monoclinic Crystal Form Of Aspergillus Niger Alpha-Amylase In Complex With Maltose At 1. 8 Angstroms Resolution.
Acta Crystallogr. , Sect. F V. 62 716 2006
[
close entry info
]
Hetero Components
(3, 9)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
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)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
2
Ligand/Ion
BETA-D-GLUCOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
GLC
6
Ligand/Ion
ALPHA-D-GLUCOSE
4
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
-1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:88 , TRP A:190 , SER A:193 , LEU A:194 , ASN A:197 , HOH A:1180
BINDING SITE FOR RESIDUE NAG A 500
02
AC2
SOFTWARE
TYR A:155 , LYS A:209 , GLC A:1001 , HOH A:1309
BINDING SITE FOR RESIDUE BGC A 1002
03
AC3
SOFTWARE
TYR A:155 , LEU A:166 , HIS A:210 , GLC A:1000 , BGC A:1002 , HOH A:1066 , HOH A:1069 , HOH A:1168 , HOH A:1312 , HOH A:1327 , HOH A:1372
BINDING SITE FOR RESIDUE GLC A 1001
04
AC4
SOFTWARE
TYR A:82 , HIS A:122 , ARG A:204 , ASP A:206 , THR A:207 , GLU A:230 , HIS A:296 , ASP A:297 , ARG A:344 , GLC A:999 , GLC A:1001 , HOH A:1069 , HOH A:1372
BINDING SITE FOR RESIDUE GLC A 1000
05
AC5
SOFTWARE
HIS A:80 , TYR A:82 , TRP A:83 , LEU A:173 , ASP A:340 , ARG A:344 , GLC A:1000 , HOH A:1030 , HOH A:1069 , HOH A:1310 , HOH A:1311 , HOH A:1312 , HOH A:1313
BINDING SITE FOR RESIDUE GLC A 999
06
AC6
SOFTWARE
GLY A:234 , ASP A:235 , PRO A:236 , GLC A:1004 , HOH A:1141 , HOH A:1194 , HOH A:1376
BINDING SITE FOR RESIDUE BGC A 1003
07
AC7
SOFTWARE
ASP A:233 , GLY A:234 , ASP A:235 , TYR A:256 , BGC A:1003 , HOH A:1374
BINDING SITE FOR RESIDUE GLC A 1004
08
AC8
SOFTWARE
LYS A:280 , GLC A:1012 , HOH A:1333
BINDING SITE FOR RESIDUE GLC A 1011
09
AC9
SOFTWARE
TYR A:382 , LYS A:383 , GLC A:1011 , HOH A:1146 , HOH A:1344
BINDING SITE FOR RESIDUE GLC A 1012
10
BC1
SOFTWARE
ASN A:121 , GLU A:162 , ASP A:175 , HIS A:210 , HOH A:1013 , HOH A:1083 , HOH A:1211
BINDING SITE FOR RESIDUE CA A 801
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2gvya1 (A:382-476)
1b: SCOP_d2gvyb1 (B:382-476)
2a: SCOP_d2gvya2 (A:1-381)
2b: SCOP_d2gvyb2 (B:1-381)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
:
Fungal alpha-amylase
(9)
Aspergillus oryzae, Taka-amylase [TaxId: 5062]
(8)
1a
d2gvya1
A:382-476
1b
d2gvyb1
B:382-476
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
:
Fungal alpha-amylases
(9)
Aspergillus oryzae, Taka-amylase [TaxId: 5062]
(8)
2a
d2gvya2
A:1-381
2b
d2gvyb2
B:1-381
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2gvyA01 (A:1-374)
1b: CATH_2gvyB01 (B:1-374)
2a: CATH_2gvyA02 (A:375-476)
2b: CATH_2gvyB02 (B:375-476)
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)
Aspergillus oryzae. Organism_taxid: 5062.
(1)
1a
2gvyA01
A:1-374
1b
2gvyB01
B:1-374
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Aspergillus oryzae. Organism_taxid: 5062.
(1)
2a
2gvyA02
A:375-476
2b
2gvyB02
B:375-476
[
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
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 (173 KB)
Header - Asym.Unit
Biol.Unit 1 (86 KB)
Header - Biol.Unit 1
Biol.Unit 2 (86 KB)
Header - Biol.Unit 2
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
2GVY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
