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.
4BSD
Asym. Unit
Info
Asym.Unit (179 KB)
Biol.Unit 1 (503 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN H7N9 INFLUENZA VIRUS HAEMAGGLUTININ (WITH ASN-133 GLYCOSYLATION) IN COMPLEX WITH AVIAN RECEPTOR ANALOGUE 3'-SLN
Authors
:
X. Xiong, L. F. Haire, S. R. Martin, S. A. Wharton, R. S. Daniels, M. S. Ben J. W. Mccauley, P. J. Collins, P. A. Walker, J. J. Skehel, S. J. Gamblin
Date
:
10 Jun 13 (Deposition) - 03 Jul 13 (Release) - 07 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Viral Protein, Fowl Plague Virus, Sialyllactosamine
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Xiong, S. R. Martin, L. F. Haire, S. A. Wharton, R. S. Daniels, M. S. Bennett, J. W. Mccauley, P. J. Collins, P. A. Walker, J. J. Skehel, S. J. Gamblin
Receptor Binding By An H7N9 Influenza Virus From Humans
Nature V. 499 496 2013
[
close entry info
]
Hetero Components
(4, 23)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3a: O-SIALIC ACID (SIAa)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
2
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SIA
1
Ligand/Ion
O-SIALIC ACID
4
SO4
14
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(20, 20)
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: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:117 , SER A:118 , GLY A:119 , ILE A:120
BINDING SITE FOR RESIDUE SO4 A1324
02
AC2
SOFTWARE
ASN A:37 , HOH A:2014
BINDING SITE FOR RESIDUE SO4 A1325
03
AC3
SOFTWARE
GLN A:302 , ARG A:303 , SER A:304
BINDING SITE FOR RESIDUE SO4 A1326
04
AC4
SOFTWARE
ILE A:38 , ARG A:40
BINDING SITE FOR RESIDUE SO4 A1327
05
AC5
SOFTWARE
SER A:84 , ASP A:85 , VAL A:86 , HOH A:2039
BINDING SITE FOR RESIDUE SO4 A1328
06
AC6
SOFTWARE
ARG A:163 , LYS A:164 , SER A:165
BINDING SITE FOR RESIDUE SO4 A1329
07
AC7
SOFTWARE
GLU A:111 , ALA A:112 , ARG A:247
BINDING SITE FOR RESIDUE SO4 A1330
08
AC8
SOFTWARE
PHE A:92 , ASN A:94 , GLU A:95 , HOH A:2043
BINDING SITE FOR RESIDUE SO4 A1331
09
AC9
SOFTWARE
THR A:20 , GLU A:21 , ARG A:22 , ASN B:53
BINDING SITE FOR RESIDUE SO4 A1332
10
BC1
SOFTWARE
ALA A:150 , SER A:178 , THR A:179 , ALA A:180
BINDING SITE FOR RESIDUE SO4 A1333
11
BC2
SOFTWARE
GLU A:316 , TRP B:14 , GLU B:15 , GLY B:16 , ARG B:25
BINDING SITE FOR RESIDUE SO4 B1173
12
BC3
SOFTWARE
ASN A:199 , ASN A:229 , ASN B:71 , GLU B:72
BINDING SITE FOR RESIDUE SO4 B1174
13
BC4
SOFTWARE
GLN A:302 , GLU B:90 , SER B:93 , TYR B:94
BINDING SITE FOR RESIDUE SO4 B1175
14
BC5
SOFTWARE
LYS B:123 , GLU B:132
BINDING SITE FOR RESIDUE SO4 B1176
15
BC6
SOFTWARE
ASN A:12 , GLY A:13 , HOH A:2099
BINDING SITE FOR MONO-SACCHARIDE NAG A1319 BOUND TO ASN A 12
16
BC7
SOFTWARE
ASN A:28 , THR A:30 , HOH A:2009 , HOH A:2010 , HOH A:2096 , HOH A:2097
BINDING SITE FOR MONO-SACCHARIDE NAG A1317 BOUND TO ASN A 28
17
BC8
SOFTWARE
ASN A:123 , HOH A:2100 , HOH A:2101
BINDING SITE FOR MONO-SACCHARIDE NAG A1320 BOUND TO ASN A 123
18
BC9
SOFTWARE
ASN A:231 , HOH A:2098
BINDING SITE FOR MONO-SACCHARIDE NAG A1318 BOUND TO ASN A 231
19
CC1
SOFTWARE
GLU B:72 , LYS B:75 , ASN B:79 , ASN B:82 , HOH B:2016
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1171 THROUGH NAG B1172 BOUND TO ASN B 82
20
CC2
SOFTWARE
TYR A:88 , GLY A:124 , THR A:125 , THR A:126 , SER A:127 , LEU A:185 , GLN A:213 , GLY A:216 , LEU A:217 , HOH A:2059
BINDING SITE FOR POLY-SACCHARIDE RESIDUES SIA A1321 THROUGH NAG A1323
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d4bsda_ (A:)
2a: SCOP_d4bsdb_ (B:)
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
:
automated matches
(37)
Protein domain
:
automated matches
(37)
Influenza virus a/anhui/1/2013 (h7n9) [TaxId: 11320]
(6)
1a
d4bsda_
A:
Class
:
Coiled coil proteins
(689)
Fold
:
Stalk segment of viral fusion proteins
(231)
Superfamily
:
Influenza hemagglutinin (stalk)
(172)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Influenza virus a/anhui/1/2013 (h7n9) [TaxId: 11320]
(6)
2a
d4bsdb_
B:
[
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 (179 KB)
Header - Asym.Unit
Biol.Unit 1 (503 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
4BSD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
