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.
3LK6
Asym. Unit
Info
Asym.Unit (794 KB)
Biol.Unit 1 (202 KB)
Biol.Unit 2 (201 KB)
Biol.Unit 3 (203 KB)
Biol.Unit 4 (201 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
BETA-N-HEXOSAMINIDASE N318D MUTANT (YBBD_N318D) FROM BACILLUS SUBTILIS
Authors
:
M. Krug
Date
:
27 Jan 10 (Deposition) - 25 May 11 (Release) - 25 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.88
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
:
Bacillus Subtilis, Hexosaminidase, Cell Membrane, Glycosidase, Hydrolase, Lipoprotein, Membrane, Palmitate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Krug, S. Fischer, K. Diederichs, W. Boos, C. Mayer
Beta-N-Hexosaminidase N318D Mutant (Ybbd_n318D) From Bacillus Subtilis
To Be Published
[
close entry info
]
Hetero Components
(2, 23)
Info
All Hetero Components
1a: SODIUM ION (NAa)
1b: SODIUM ION (NAb)
1c: SODIUM ION (NAc)
1d: SODIUM ION (NAd)
2a: DI(HYDROXYETHYL)ETHER (PEGa)
2b: DI(HYDROXYETHYL)ETHER (PEGb)
2c: DI(HYDROXYETHYL)ETHER (PEGc)
2d: DI(HYDROXYETHYL)ETHER (PEGd)
2e: DI(HYDROXYETHYL)ETHER (PEGe)
2f: DI(HYDROXYETHYL)ETHER (PEGf)
2g: DI(HYDROXYETHYL)ETHER (PEGg)
2h: DI(HYDROXYETHYL)ETHER (PEGh)
2i: DI(HYDROXYETHYL)ETHER (PEGi)
2j: DI(HYDROXYETHYL)ETHER (PEGj)
2k: DI(HYDROXYETHYL)ETHER (PEGk)
2l: DI(HYDROXYETHYL)ETHER (PEGl)
2m: DI(HYDROXYETHYL)ETHER (PEGm)
2n: DI(HYDROXYETHYL)ETHER (PEGn)
2o: DI(HYDROXYETHYL)ETHER (PEGo)
2p: DI(HYDROXYETHYL)ETHER (PEGp)
2q: DI(HYDROXYETHYL)ETHER (PEGq)
2r: DI(HYDROXYETHYL)ETHER (PEGr)
2s: DI(HYDROXYETHYL)ETHER (PEGs)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
4
Ligand/Ion
SODIUM ION
2
PEG
19
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:479 , ILE A:481 , LYS A:482
BINDING SITE FOR RESIDUE PEG A 643
02
AC2
SOFTWARE
ASN A:152 , GLN A:155 , LYS A:429 , LYS A:433
BINDING SITE FOR RESIDUE PEG A 644
03
AC3
SOFTWARE
HIS A:222 , ASN A:318
BINDING SITE FOR RESIDUE PEG A 645
04
AC4
SOFTWARE
ARG A:148 , SER A:149 , ARG A:150 , ILE A:151
BINDING SITE FOR RESIDUE PEG A 646
05
AC5
SOFTWARE
THR A:106 , ASP A:107 , LEU A:167 , GLY A:168 , LYS A:410
BINDING SITE FOR RESIDUE NA A 647
06
AC6
SOFTWARE
LYS B:479 , ILE B:481 , LYS B:482
BINDING SITE FOR RESIDUE PEG B 643
07
AC7
SOFTWARE
ARG B:148 , SER B:149 , ARG B:150 , ILE B:151 , ARG B:202
BINDING SITE FOR RESIDUE PEG B 644
08
AC8
SOFTWARE
ILE B:151
BINDING SITE FOR RESIDUE PEG B 645
09
AC9
SOFTWARE
HIS B:222 , ASN B:318
BINDING SITE FOR RESIDUE PEG B 648
10
BC1
SOFTWARE
ASN B:182 , ASP B:184 , ASP B:230
BINDING SITE FOR RESIDUE PEG B 649
11
BC2
SOFTWARE
ASN B:152 , GLN B:155 , LYS B:429 , LYS B:433
BINDING SITE FOR RESIDUE PEG B 650
12
BC3
SOFTWARE
THR B:106 , ASP B:107 , LEU B:167 , GLY B:168 , LYS B:410
BINDING SITE FOR RESIDUE NA B 651
13
BC4
SOFTWARE
THR C:280
BINDING SITE FOR RESIDUE PEG C 647
14
BC5
SOFTWARE
LYS C:479 , ILE C:481 , LYS C:482
BINDING SITE FOR RESIDUE PEG C 643
15
BC6
SOFTWARE
ARG C:148 , SER C:149 , ARG C:150 , ILE C:151 , ARG C:202
BINDING SITE FOR RESIDUE PEG C 644
16
BC7
SOFTWARE
ASN C:152 , GLN C:155 , ALA C:426 , LYS C:429 , LYS C:433
BINDING SITE FOR RESIDUE PEG C 645
17
BC8
SOFTWARE
HIS C:222
BINDING SITE FOR RESIDUE PEG C 646
18
BC9
SOFTWARE
THR C:106 , ASP C:107 , GLY C:168 , LYS C:410
BINDING SITE FOR RESIDUE NA C 648
19
CC1
SOFTWARE
HIS D:222 , HIS D:226
BINDING SITE FOR RESIDUE PEG D 643
20
CC2
SOFTWARE
ASN D:152 , GLN D:155 , LYS D:429 , LYS D:433
BINDING SITE FOR RESIDUE PEG D 644
21
CC3
SOFTWARE
ARG D:148 , SER D:149 , ARG D:150 , ILE D:151 , ARG D:202
BINDING SITE FOR RESIDUE PEG D 645
22
CC4
SOFTWARE
LYS D:479 , LYS D:482
BINDING SITE FOR RESIDUE PEG D 646
23
CC5
SOFTWARE
THR D:106 , ASP D:107 , LEU D:167 , GLY D:168 , LYS D:410
BINDING SITE FOR RESIDUE NA D 647
[
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F3 (A:304-321,B:304-321,C:304-321,D:30...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F3
PS00775
Glycosyl hydrolases family 3 active site.
NAGZ_BACSU
304-321
4
A:304-321
B:304-321
C:304-321
D:304-321
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 (794 KB)
Header - Asym.Unit
Biol.Unit 1 (202 KB)
Header - Biol.Unit 1
Biol.Unit 2 (201 KB)
Header - Biol.Unit 2
Biol.Unit 3 (203 KB)
Header - Biol.Unit 3
Biol.Unit 4 (201 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
3LK6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
