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.
2JKB
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (131 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANB IN COMPLEX WITH 2,7-ANHYDRO-NEU5AC
Authors
:
H. Gut, S. J. King, M. A. Walsh
Date
:
26 Aug 08 (Deposition) - 16 Sep 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.54
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Intramolecular Trans-Sialidase, Lyase, Glycosidase, Neuraminidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Gut, S. J. King, M. A. Walsh
Structural And Functional Studies Of Streptococcus Pneumoniae Neuraminidase B: An Intramolecular Trans-Sialidase.
Febs Lett. V. 582 3348 2008
[
close entry info
]
Hetero Components
(2, 7)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
2a: 2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETH... (SKDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
2
SKD
1
Ligand/Ion
2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:245 , ILE A:246 , ARG A:264 , ASP A:270 , ILE A:326 , ASP A:327 , ASP A:344 , ASN A:352 , THR A:539 , GLU A:541 , ARG A:557 , ARG A:619 , TYR A:653 , TRP A:674 , HOH A:2457 , HOH A:3012 , HOH A:3013
BINDING SITE FOR RESIDUE SKD A1698
2
AC2
SOFTWARE
LEU A:84 , SER A:103 , GLU A:115 , TYR A:199 , LYS A:335 , HOH A:3014 , HOH A:3015
BINDING SITE FOR RESIDUE EDO A1699
3
AC3
SOFTWARE
TYR A:458 , ILE A:459 , LEU A:477 , PRO A:478 , PHE A:480 , HOH A:3016
BINDING SITE FOR RESIDUE EDO A1700
4
AC4
SOFTWARE
VAL A:385 , ILE A:404 , ASN A:405 , ASP A:406 , TYR A:408 , LYS A:475 , HOH A:2629 , HOH A:3017 , HOH A:3018 , HOH A:3019
BINDING SITE FOR RESIDUE EDO A1701
5
AC5
SOFTWARE
THR A:251 , GLN A:494 , ILE A:596 , THR A:657 , HOH A:2956 , HOH A:3020
BINDING SITE FOR RESIDUE EDO A1702
6
AC6
SOFTWARE
SER A:617 , LYS A:620 , SER A:648 , HOH A:2911 , HOH A:3021 , HOH A:3022
BINDING SITE FOR RESIDUE EDO A1703
7
AC7
SOFTWARE
ARG A:256 , ASN A:466 , ARG A:467 , GLU A:469 , SER A:617 , HOH A:2444 , HOH A:3023 , HOH A:3024
BINDING SITE FOR RESIDUE EDO A1704
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2jkbA02 (A:229-357,A:456-697)
2a: CATH_2jkbA03 (A:358-455)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
6 Propellor
(215)
Topology
:
Neuraminidase
(215)
Homologous Superfamily
:
[code=2.120.10.10, no name defined]
(150)
Streptococcus pneumoniae. Organism_taxid: 170187. Strain: tigr4.
(1)
1a
2jkbA02
A:229-357,A:456-697
Architecture
:
Beta Barrel
(4804)
Topology
:
Intramolecular trans-sialidase; domain 3
(9)
Homologous Superfamily
:
Intramolecular Trans-sialidase; Domain 3
(9)
Streptococcus pneumoniae. Organism_taxid: 170187. Strain: tigr4.
(1)
2a
2jkbA03
A:358-455
[
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 (136 KB)
Header - Asym.Unit
Biol.Unit 1 (131 KB)
Header - Biol.Unit 1
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
2JKB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
