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.
2CBJ
Asym. Unit
Info
Asym.Unit (397 KB)
Biol.Unit 1 (197 KB)
Biol.Unit 2 (197 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE CLOSTRIDIUM PERFRINGENS NAGJ FAMILY 84 GLYCOSIDE HYDROLASE, A HOMOLOGUE OF HUMAN O-GLCNACASE IN COMPLEX WITH PUGNAC
Authors
:
F. V. Rao, H. C. Dorfmueller, F. Villa, M. Allwood, I. M. Eggleston, D. M. Aalten
Date
:
05 Jan 06 (Deposition) - 13 Feb 06 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
O-Glcnac, Family 84 Glycoside Hydrolases, Glycoside Hydrolase, Hyaluronidases, Carbohydrates, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. V. Rao, H. C. Dorfmueller, F. Villa, M. Allwood, I. M. Eggleston, D. M. F. Van Aalten
Structural Insights Into The Mechanism And Inhibition Of Eukaryotic O-Glcnac Hydrolysis.
Embo J. V. 25 1569 2006
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRA... (OANa)
2b: O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRA... (OANb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
OAN
2
Ligand/Ion
O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE
[
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
PHE B:265
BINDING SITE FOR RESIDUE CL B 1626
2
AC2
SOFTWARE
SER B:64
BINDING SITE FOR RESIDUE CL B 1627
3
AC3
SOFTWARE
GLY A:187 , PHE A:188 , LYS A:218 , ASP A:297 , ASP A:298 , TYR A:335 , VAL A:370 , TRP A:394 , ASN A:396 , ASP A:401 , TYR A:402 , ASN A:429 , TRP A:490 , HOH A:2143 , LEU B:512 , SER B:513 , ASP B:620 , LEU B:621
BINDING SITE FOR RESIDUE OAN A 1625
4
AC4
SOFTWARE
LEU A:512 , SER A:513 , GLY B:187 , TYR B:189 , LYS B:218 , ASP B:297 , ASP B:298 , TYR B:335 , VAL B:370 , TRP B:394 , ASN B:396 , ASP B:401 , TYR B:402 , ASN B:429
BINDING SITE FOR RESIDUE OAN B 1625
[
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2cbja1 (A:496-624)
1b: SCOP_d2cbjb1 (B:496-624)
2a: SCOP_d2cbja3 (A:40-178)
2b: SCOP_d2cbjb3 (B:40-178)
3a: SCOP_d2cbja2 (A:179-495)
3b: SCOP_d2cbjb2 (B:179-495)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Hyaluronidase domain-like
(25)
Superfamily
:
Hyaluronidase post-catalytic domain-like
(20)
Family
:
Hyaluronidase post-catalytic domain-like
(15)
Protein domain
:
Hyaluronidase, post-catalytic domain 3
(7)
Clostridium perfringens [TaxId: 1502]
(7)
1a
d2cbja1
A:496-624
1b
d2cbjb1
B:496-624
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
beta-N-acetylhexosaminidase-like domain
(54)
Family
:
Hyaluronidase N-terminal domain-like
(15)
Protein domain
:
Hyaluronidase N-terminal domain
(7)
Clostridium perfringens [TaxId: 1502]
(7)
2a
d2cbja3
A:40-178
2b
d2cbjb3
B:40-178
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
alpha-D-glucuronidase/Hyaluronidase catalytic domain
(32)
Protein domain
:
Hyaluronidase catalytic domain
(7)
Clostridium perfringens [TaxId: 1502]
(7)
3a
d2cbja2
A:179-495
3b
d2cbjb2
B:179-495
[
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
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 (397 KB)
Header - Asym.Unit
Biol.Unit 1 (197 KB)
Header - Biol.Unit 1
Biol.Unit 2 (197 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
2CBJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
