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.
2VHL
Biol. Unit 1
Info
Asym.Unit (140 KB)
Biol.Unit 1 (69 KB)
Biol.Unit 2 (69 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE THREE-DIMENSIONAL STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM BACILLUS SUBTILIS
Authors
:
F. Vincent, D. Yates, E. Garman, G. J. Davies
Date
:
22 Nov 07 (Deposition) - 04 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
N- Acetyleglucosamine-6-Phosphate, Carbohydrate Metabolism, Hydrolase, Deacetylase, Bacillus Subtilis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Vincent, D. Yates, E. Garman, G. J. Davies
The Three-Dimensional Structure Of The N- Acetylglucosamine-6-Phosphate Deacetylase From Bacillus Subtilis
J. Biol. Chem. V. 279 2809 2004
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
1d: FE (III) ION (FEd)
2a: GLUCOSAMINE 6-PHOSPHATE (GLPa)
2b: GLUCOSAMINE 6-PHOSPHATE (GLPb)
3a: TRIETHYLENE GLYCOL (PGEa)
3b: TRIETHYLENE GLYCOL (PGEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
-1
Ligand/Ion
FE (III) ION
2
GLP
1
Ligand/Ion
GLUCOSAMINE 6-PHOSPHATE
3
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:146 , ALA A:147 , HIS A:202 , ASN A:226 , ALA A:227 , HIS A:233 , ARG A:234 , HIS A:258 , ASP A:281 , THR A:313 , LEU A:314 , GLY A:316 , FE A:1398 , HOH A:2199 , HOH A:2318 , HOH A:2319 , HOH A:2320 , HOH A:2321 , HOH A:2322
BINDING SITE FOR RESIDUE GLP A1395
2
AC2
SOFTWARE
ASP A:246 , LYS A:265 , PHE A:331 , THR A:332 , ASN A:333
BINDING SITE FOR RESIDUE PGE A1396
3
AC3
SOFTWARE
HIS A:63 , HIS A:65 , GLU A:136 , ASP A:281 , FE A:1398 , HOH A:2321
BINDING SITE FOR RESIDUE FE A1397
4
AC4
SOFTWARE
GLU A:136 , HIS A:202 , HIS A:223 , GLP A:1395 , FE A:1397 , HOH A:2321
BINDING SITE FOR RESIDUE FE A1398
[
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_d2vhla1 (A:3-57,A:359-394)
1b: SCOP_d2vhlb1 (B:2-57,B:359-394)
2a: SCOP_d2vhla2 (A:58-358)
2b: SCOP_d2vhlb2 (B:58-358)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Composite domain of metallo-dependent hydrolases
(103)
Superfamily
:
Composite domain of metallo-dependent hydrolases
(103)
Family
:
N-acetylglucosamine-6-phosphate deacetylase, NagA
(6)
Protein domain
:
N-acetylglucosamine-6-phosphate deacetylase, NagA
(6)
Bacillus subtilis [TaxId: 1423]
(1)
1a
d2vhla1
A:3-57,A:359-394
1b
d2vhlb1
B:2-57,B:359-394
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain
(6)
Protein domain
:
N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain
(6)
Bacillus subtilis [TaxId: 1423]
(1)
2a
d2vhla2
A:58-358
2b
d2vhlb2
B:58-358
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2vhlA02 (A:58-358)
1b: CATH_2vhlB02 (B:58-358)
2a: CATH_2vhlB01 (B:2-57,B:359-394)
2b: CATH_2vhlA01 (A:3-57,A:359-394)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Bacillus subtilis. Organism_taxid: 1423.
(1)
1a
2vhlA02
A:58-358
1b
2vhlB02
B:58-358
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Urease, subunit C; domain 1
(95)
Homologous Superfamily
:
Urease, subunit C, domain 1
(95)
Bacillus subtilis. Organism_taxid: 1423.
(1)
2a
2vhlB01
B:2-57,B:359-394
2b
2vhlA01
A:3-57,A:359-394
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Amidohydro_1_2vhlB01 (B:54-372)
1b: PFAM_Amidohydro_1_2vhlB02 (B:54-372)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Amidohydrolase
(126)
Family
:
Amidohydro_1
(28)
Bacillus subtilis
(1)
1a
Amidohydro_1-2vhlB01
B:54-372
1b
Amidohydro_1-2vhlB02
B:54-372
[
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 (140 KB)
Header - Asym.Unit
Biol.Unit 1 (69 KB)
Header - Biol.Unit 1
Biol.Unit 2 (69 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
2VHL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
