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.
2YP5
Asym. Unit
Info
Asym.Unit (185 KB)
Biol.Unit 1 (523 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HAEMAGGLUTININ OF 2004 HUMAN H3N2 VIRUS IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3SLN
Authors
:
X. Xiong, Y. P. Lin, S. A. Wharton, S. R. Martin, P. J. Coombs, S. G. Vachie E. Christodoulou, P. A. Walker, J. Liu, J. J. Skehel, S. J. Gamblin, A. J R. S. Daniels, J. W. Mccauley
Date
:
29 Oct 12 (Deposition) - 07 Nov 12 (Release) - 16 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.79
Chains
:
Asym. Unit : A
Biol. Unit 1: A (3x)
Keywords
:
Viral Protein, Receptor Binding, Membrane Fusion, Influenza Virus Evolution, Glycoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. P. Lin, X. Xiong, S. A. Wharton, S. R. Martin, P. J. Coombs, S. G. Vachieri, E. Christodoulou, P. A. Walker, J. Liu, J. J. Skehel, S. J. Gamblin, A. J. Hay, R. S. Daniels, J. W. Mccauley
Evolution Of The Receptor Binding Properties Of The Influenza A(H3N2) Hemagglutinin.
Proc. Natl. Acad. Sci. Usa V. 109 21474 2012
[
close entry info
]
Hetero Components
(6, 16)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEb)
1c: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEc)
2a: BETA-D-GALACTOSE (GALa)
3a: ALPHA-D-MANNOSE (MANa)
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)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5a: O-SIALIC ACID (SIAa)
6a: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
3
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
3
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
9
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SIA
1
Ligand/Ion
O-SIALIC ACID
6
TAM
1
Ligand/Ion
TRIS(HYDROXYETHYL)AMINOMETHANE
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:77 , GLN A:80 , ARG A:141 , ARG A:142 , SER A:146 , PHE A:147 , PHE A:148 , LEU A:151 , ARG A:255 , NAG A:805 , HOH A:2109 , HOH A:2183
BINDING SITE FOR RESIDUE EPE A1504
02
AC2
SOFTWARE
SER A:95 , PRO A:99 , TYR A:100 , TYR A:105 , ARG A:208 , ARG A:224 , HOH A:2131 , HOH A:2531
BINDING SITE FOR RESIDUE EPE A1505
03
AC3
SOFTWARE
ASN A:81 , GLU A:119 , PHE A:120 , ASN A:121 , ASN A:122 , GLU A:280 , GLU A:390 , HOH A:2076
BINDING SITE FOR RESIDUE EPE A1506
04
AC4
SOFTWARE
HOH A:2345 , HOH A:2396 , HOH A:2458 , HOH A:2532
BINDING SITE FOR RESIDUE TAM A1509
05
AC5
SOFTWARE
ASN A:38 , THR A:318 , LEU A:381
BINDING SITE FOR RESIDUE SIA A1507
06
AC6
SOFTWARE
GLU A:62 , ASN A:63 , TYR A:94 , HOH A:2093
BINDING SITE FOR RESIDUE CMO A1508
07
AC7
SOFTWARE
ASN A:133 , EPE A:1504
BINDING SITE FOR MONO-SACCHARIDE NAG A 801 BOUND TO ASN A 38
08
AC8
SOFTWARE
ASN A:165 , SER A:219 , PRO A:221 , ARG A:222 , ASP A:225 , NAG A:809 , HOH A:2211 , HOH A:2260 , HOH A:2524 , HOH A:2525 , HOH A:2526
BINDING SITE FOR MONO-SACCHARIDE NAG A 804 BOUND TO ASN A 63
09
AC9
SOFTWARE
ALA A:163 , LEU A:164 , ASN A:165 , ARG A:201 , ASN A:246 , SER A:247 , THR A:248 , NAG A:806 , HOH A:2527 , HOH A:2528
BINDING SITE FOR MONO-SACCHARIDE NAG A 805 BOUND TO ASN A 133
10
BC1
SOFTWARE
SER A:45 , ASN A:285 , VAL A:297 , HOH A:2311 , HOH A:2322
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 165 RESIDUES 806 TO 808
11
BC2
SOFTWARE
GLY A:479 , SER A:480 , ASN A:483 , THR A:485 , HOH A:2505
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 246 RESIDUES 809 TO 810
12
BC3
SOFTWARE
TYR A:98 , GLY A:134 , THR A:135 , SER A:136 , SER A:137 , TRP A:153 , ASP A:190 , LEU A:194 , SER A:228 , HOH A:2185 , HOH A:2232 , HOH A:2264
BINDING SITE FOR MONO-SACCHARIDE NAG A 812 BOUND TO ASN A 285
13
BC4
SOFTWARE
[no residue information available]
BINDING SITE FOR MONO-SACCHARIDE NAG A 813 BOUND TO ASN A 483
[
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, 1)
Info
All SCOP Domains
1a: SCOP_d2yp5a1 (A:8-328)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Viral protein domain
(195)
Superfamily
:
Viral protein domain
(195)
Family
:
Influenza hemagglutinin headpiece
(152)
Protein domain
:
automated matches
(43)
Influenza A virus [TaxId: 11320]
(15)
1a
d2yp5a1
A:8-328
[
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 (185 KB)
Header - Asym.Unit
Biol.Unit 1 (523 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
2YP5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
