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.
2X8R
Asym. Unit
Info
Asym.Unit (228 KB)
Biol.Unit 1 (41 KB)
Biol.Unit 2 (41 KB)
Biol.Unit 3 (41 KB)
Biol.Unit 4 (39 KB)
Biol.Unit 5 (39 KB)
Biol.Unit 6 (39 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURE OF A FAMILY GH25 LYSOZYME FROM ASPERGILLUS FUMIGATUS
Authors
:
J. E. Korczynska, S. Danielsen, U. Schagerlof, J. P. Turkenburg, G. J. D K. S. Wilson, E. J. Taylor
Date
:
11 Mar 10 (Deposition) - 08 Sep 10 (Release) - 18 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
Peptidoglycan Cleavage, Endo-N-Acetylmuramidases, Hydrolase, Dxe Motif
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. E. Korczynska, S. Danielsen, U. Schagerlof, J. P. Turkenburg, G. J. Davies, K. S. Wilson, E. J. Taylor
The Structure Of A Family Gh25 Lysozyme From Aspergillus Fumigatus
Acta Crystallogr. , Sect. F V. 66 973 2010
[
close entry info
]
Hetero Components
(1, 6)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
6
Ligand/Ion
CHLORIDE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:109 , CYS A:115 , TRP A:150 , THR D:50
BINDING SITE FOR RESIDUE CL A1219
2
AC2
SOFTWARE
ASN B:109 , CYS B:115 , TRP B:150 , THR E:50
BINDING SITE FOR RESIDUE CL B1219
3
AC3
SOFTWARE
THR B:50 , ASN C:109 , CYS C:115 , TRP C:150
BINDING SITE FOR RESIDUE CL C1219
4
AC4
SOFTWARE
ASN D:109 , CYS D:115 , TRP D:150 , HOH F:2036
BINDING SITE FOR RESIDUE CL D1219
5
AC5
SOFTWARE
HOH C:2052 , TYR E:108 , ASN E:109 , CYS E:115 , TRP E:150
BINDING SITE FOR RESIDUE CL E1219
6
AC6
SOFTWARE
THR A:50 , ASN F:109 , CYS F:115 , TRP F:150
BINDING SITE FOR RESIDUE CL F1219
[
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
(0, 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.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2x8ra_ (A:)
1b: SCOP_d2x8rb_ (B:)
1c: SCOP_d2x8rc_ (C:)
1d: SCOP_d2x8rd_ (D:)
1e: SCOP_d2x8re_ (E:)
1f: SCOP_d2x8rf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
automated matches
(180)
Protein domain
:
automated matches
(180)
Aspergillus fumigatus [TaxId: 330879]
(1)
1a
d2x8ra_
A:
1b
d2x8rb_
B:
1c
d2x8rc_
C:
1d
d2x8rd_
D:
1e
d2x8re_
E:
1f
d2x8rf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2x8rB00 (B:9-218)
1b: CATH_2x8rC00 (C:9-218)
1c: CATH_2x8rE00 (E:9-218)
1d: CATH_2x8rA00 (A:10-218)
1e: CATH_2x8rD00 (D:10-218)
1f: CATH_2x8rF00 (F:10-218)
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 fumigatus. Organism_taxid: 330879. Strain: af293
(1)
1a
2x8rB00
B:9-218
1b
2x8rC00
C:9-218
1c
2x8rE00
E:9-218
1d
2x8rA00
A:10-218
1e
2x8rD00
D:10-218
1f
2x8rF00
F:10-218
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_25_2x8rF01 (F:15-201)
1b: PFAM_Glyco_hydro_25_2x8rF02 (F:15-201)
1c: PFAM_Glyco_hydro_25_2x8rF03 (F:15-201)
1d: PFAM_Glyco_hydro_25_2x8rF04 (F:15-201)
1e: PFAM_Glyco_hydro_25_2x8rF05 (F:15-201)
1f: PFAM_Glyco_hydro_25_2x8rF06 (F:15-201)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_25
(2)
Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (Aspergillus fumigatus
(1)
1a
Glyco_hydro_25-2x8rF01
F:15-201
1b
Glyco_hydro_25-2x8rF02
F:15-201
1c
Glyco_hydro_25-2x8rF03
F:15-201
1d
Glyco_hydro_25-2x8rF04
F:15-201
1e
Glyco_hydro_25-2x8rF05
F:15-201
1f
Glyco_hydro_25-2x8rF06
F:15-201
[
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
Chain E
Chain F
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 (228 KB)
Header - Asym.Unit
Biol.Unit 1 (41 KB)
Header - Biol.Unit 1
Biol.Unit 2 (41 KB)
Header - Biol.Unit 2
Biol.Unit 3 (41 KB)
Header - Biol.Unit 3
Biol.Unit 4 (39 KB)
Header - Biol.Unit 4
Biol.Unit 5 (39 KB)
Header - Biol.Unit 5
Biol.Unit 6 (39 KB)
Header - Biol.Unit 6
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
2X8R
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
