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.
2YL9
Biol. Unit 1
Info
Asym.Unit (294 KB)
Biol.Unit 1 (76 KB)
Biol.Unit 2 (75 KB)
Biol.Unit 3 (75 KB)
Biol.Unit 4 (75 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
Authors
:
B. Pluvinage, M. A. Higgins, D. W. Abbott, C. Robb, A. B. Dalia, L. Deng, J. N. Weiser, T. B. Parsons, A. J. Fairbanks, D. J. Vocadlo, A. B. Borast
Date
:
01 Jun 11 (Deposition) - 21 Sep 11 (Release) - 23 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
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
:
Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Pluvinage, M. A. Higgins, D. W. Abbott, C. Robb, A. B. Dalia, L. Deng, J. N. Weiser, T. B. Parsons, A. J. Fairbanks, D. J. Vocadlo, A. B. Boraston
Inhibition Of The Pneumococcal Virulence Factor Strh And Molecular Insights Into N-Glycan Recognition And Hydrolysis
Structure V. 19 1603 2011
[
close entry info
]
Hetero Components
(4, 21)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2ag: 1,2-ETHANEDIOL (EDOag)
2ah: 1,2-ETHANEDIOL (EDOah)
2ai: 1,2-ETHANEDIOL (EDOai)
2aj: 1,2-ETHANEDIOL (EDOaj)
2ak: 1,2-ETHANEDIOL (EDOak)
2al: 1,2-ETHANEDIOL (EDOal)
2am: 1,2-ETHANEDIOL (EDOam)
2an: 1,2-ETHANEDIOL (EDOan)
2ao: 1,2-ETHANEDIOL (EDOao)
2ap: 1,2-ETHANEDIOL (EDOap)
2aq: 1,2-ETHANEDIOL (EDOaq)
2ar: 1,2-ETHANEDIOL (EDOar)
2as: 1,2-ETHANEDIOL (EDOas)
2at: 1,2-ETHANEDIOL (EDOat)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
EDO
17
Ligand/Ion
1,2-ETHANEDIOL
3
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(17, 17)
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: DC3 (SOFTWARE)
17: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:751
BINDING SITE FOR RESIDUE EDO A2044
02
AC2
SOFTWARE
ALA A:888 , GLY A:891
BINDING SITE FOR RESIDUE EDO A2045
03
AC3
SOFTWARE
GLU A:724
BINDING SITE FOR RESIDUE EDO A2046
04
AC4
SOFTWARE
ASP A:790 , ALA A:793 , ARG A:842 , GLN D:885 , SER D:933 , THR D:934 , LYS D:935 , GLU D:938 , VAL D:939
BINDING SITE FOR RESIDUE EDO A2047
05
AC5
SOFTWARE
TRP A:876 , TRP A:877 , EDO A:2052 , HOH A:3220 , GLN D:845
BINDING SITE FOR RESIDUE EDO A2048
06
AC6
SOFTWARE
GLN A:885 , SER A:933 , THR A:934 , LYS A:935 , VAL A:939 , ALA D:793 , ARG D:842 , HOH D:3075
BINDING SITE FOR RESIDUE EDO A2049
07
AC7
SOFTWARE
THR A:645 , ARG A:651
BINDING SITE FOR RESIDUE EDO A2050
08
AC8
SOFTWARE
ASP A:809 , HOH A:3102
BINDING SITE FOR RESIDUE EDO A2051
09
AC9
SOFTWARE
LYS A:874 , TRP A:876 , ASN A:880 , LEU A:881 , EDO A:2048 , EDO D:2044
BINDING SITE FOR RESIDUE EDO A2052
10
BC1
SOFTWARE
LYS A:918 , ASN A:922 , HOH A:3167
BINDING SITE FOR RESIDUE EDO A2053
11
BC2
SOFTWARE
ARG A:954 , SER A:956
BINDING SITE FOR RESIDUE EDO A2054
12
BC3
SOFTWARE
ASN A:898 , ASP A:900 , THR A:926 , GLN A:930 , SER A:933
BINDING SITE FOR RESIDUE EDO A2055
13
BC4
SOFTWARE
ASP A:730 , ARG A:980 , GLU D:856 , LYS D:858
BINDING SITE FOR RESIDUE EDO A2056
14
BC5
SOFTWARE
LYS A:633 , GLY A:660 , TYR A:661 , SER A:662 , ASP A:730 , ARG A:980
BINDING SITE FOR RESIDUE EDO A2057
15
BC6
SOFTWARE
GLU A:830
BINDING SITE FOR RESIDUE EDO A2058
16
DC3
SOFTWARE
ASP A:857 , LEU A:881 , SER A:883 , EDO A:2052 , THR D:796
BINDING SITE FOR RESIDUE EDO D2044
17
EC8
SOFTWARE
ARG A:641 , ASP A:804 , GLN A:805 , ASN A:808 , ALA A:813 , TRP A:872 , TRP A:876 , TYR A:902 , ILE A:904 , TRP A:951 , ASP A:953 , HOH A:3025 , HOH A:3219 , ASP D:866
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 2040 TO 2043
[
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
(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
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 (294 KB)
Header - Asym.Unit
Biol.Unit 1 (76 KB)
Header - Biol.Unit 1
Biol.Unit 2 (75 KB)
Header - Biol.Unit 2
Biol.Unit 3 (75 KB)
Header - Biol.Unit 3
Biol.Unit 4 (75 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
2YL9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
