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.
4JU0
Asym. Unit
Info
Asym.Unit (990 KB)
Biol.Unit 1 (492 KB)
Biol.Unit 2 (494 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 2009 PANDEMIC INFLUENZA VIRUS HEMAGGLUTININ MUTANT D225E COMPLEXED WITH HUMAN RECEPTOR ANALOGUE LSTC
Authors
:
W. Zhang, Y. Shi, J. Qi, F. Gao, Q. Li, Z. Fan, J. Yan, G. F. Gao
Date
:
24 Mar 13 (Deposition) - 01 May 13 (Release) - 07 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.91
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Virus Attachment, Membrane Fusion, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Zhang, Y. Shi, J. Qi, F. Gao, Q. Li, Z. Fan, J. Yan, G. F. Gao
Molecular Basis Of The Receptor Binding Specificity Switch Of The Hemagglutinins From Both The 1918 And 2009 Pandemic Influenza A Viruses By A D225G Substitution
J. Virol. V. 87 5949 2013
[
close entry info
]
Hetero Components
(3, 29)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
1b: BETA-D-GALACTOSE (GALb)
1c: BETA-D-GALACTOSE (GALc)
1d: BETA-D-GALACTOSE (GALd)
1e: BETA-D-GALACTOSE (GALe)
1f: BETA-D-GALACTOSE (GALf)
1g: BETA-D-GALACTOSE (GALg)
1h: BETA-D-GALACTOSE (GALh)
1i: BETA-D-GALACTOSE (GALi)
1j: BETA-D-GALACTOSE (GALj)
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)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2l: N-ACETYL-D-GLUCOSAMINE (NAGl)
2m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3a: O-SIALIC ACID (SIAa)
3b: O-SIALIC ACID (SIAb)
3c: O-SIALIC ACID (SIAc)
3d: O-SIALIC ACID (SIAd)
3e: O-SIALIC ACID (SIAe)
3f: O-SIALIC ACID (SIAf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
10
Ligand/Ion
BETA-D-GALACTOSE
2
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SIA
6
Ligand/Ion
O-SIALIC ACID
[
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:280 , ASN C:29
BINDING SITE FOR RESIDUE NAG C 601
02
AC2
SOFTWARE
ASN C:70 , GLU C:72 , ASP C:92 , ASN C:93 , PRO C:143 , ARG C:227 , HOH C:713
BINDING SITE FOR RESIDUE NAG C 602
03
AC3
SOFTWARE
ASN G:293
BINDING SITE FOR RESIDUE NAG G 401
04
AC4
SOFTWARE
ASN I:17 , HOH I:702
BINDING SITE FOR RESIDUE NAG I 601
05
AC5
SOFTWARE
ARG C:51 , LYS K:28 , ASN K:29
BINDING SITE FOR RESIDUE NAG K 601
06
AC6
SOFTWARE
LYS K:60 , GLU K:72 , ASN K:93 , PRO K:143 , HOH K:726
BINDING SITE FOR RESIDUE NAG K 602
07
AC7
SOFTWARE
TYR K:97 , LYS K:136 , VAL K:138 , THR K:139 , ALA K:140 , LYS K:148 , TRP K:156 , HIS K:186 , LEU K:197 , GLN K:229
BINDING SITE FOR RESIDUE SIA K 603
08
AC8
SOFTWARE
TYR A:97 , LYS A:136 , VAL A:138 , THR A:139 , ALA A:140 , LYS A:148 , TRP A:156 , HIS A:186 , SER A:196 , LEU A:197 , LYS A:225 , GLU A:228 , GLN A:229 , HOH A:908
BINDING SITE FOR LINKED RESIDUES A 801 to 804
09
AC9
SOFTWARE
GLN B:30 , TYR C:97 , LYS C:136 , VAL C:138 , THR C:139 , ALA C:140 , LYS C:148 , SER C:196 , LEU C:197 , LYS C:225 , GLU C:228 , GLN C:229 , HOH C:704 , HOH C:718
BINDING SITE FOR LINKED RESIDUES C 603 to 606
10
BC1
SOFTWARE
ASN E:70 , GLU E:72 , ASP E:92 , ASN E:93 , CYS E:96 , PRO E:143 , ARG E:227 , HOH E:712 , LYS L:161
BINDING SITE FOR LINKED RESIDUES E 601 to 602
11
BC2
SOFTWARE
TYR E:97 , LYS E:136 , VAL E:138 , THR E:139 , ALA E:140 , LYS E:148 , TRP E:156 , HIS E:186 , LEU E:197 , LYS E:225 , GLU E:228 , GLN E:229
BINDING SITE FOR LINKED RESIDUES E 603 to 606
12
BC3
SOFTWARE
TYR G:97 , LYS G:136 , VAL G:138 , THR G:139 , ALA G:140 , LYS G:148 , TRP G:156 , HIS G:186 , ASP G:193 , SER G:196 , LEU G:197 , LYS G:225 , GLU G:228 , GLN G:229 , HOH G:506 , GLU K:74 , SER K:75 , LYS K:152
BINDING SITE FOR LINKED RESIDUES G 402 to 405
13
BC4
SOFTWARE
TYR I:97 , LYS I:136 , VAL I:138 , THR I:139 , ALA I:140 , LYS I:148 , TRP I:156 , HIS I:186 , SER I:196 , LEU I:197 , LYS I:225 , GLU I:228 , GLN I:229
BINDING SITE FOR LINKED RESIDUES I 602 to 605
[
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, 12)
Info
All SCOP Domains
1a: SCOP_d4ju0a_ (A:)
1b: SCOP_d4ju0c_ (C:)
1c: SCOP_d4ju0e_ (E:)
1d: SCOP_d4ju0g_ (G:)
1e: SCOP_d4ju0i_ (I:)
1f: SCOP_d4ju0k_ (K:)
2a: SCOP_d4ju0b_ (B:)
2b: SCOP_d4ju0d_ (D:)
2c: SCOP_d4ju0f_ (F:)
2d: SCOP_d4ju0h_ (H:)
2e: SCOP_d4ju0j_ (J:)
2f: SCOP_d4ju0l_ (L:)
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
:
Hemagglutinin
(109)
Influenza A virus, different strains [TaxId: 11320]
(97)
1a
d4ju0a_
A:
1b
d4ju0c_
C:
1c
d4ju0e_
E:
1d
d4ju0g_
G:
1e
d4ju0i_
I:
1f
d4ju0k_
K:
Class
:
Coiled coil proteins
(689)
Fold
:
Stalk segment of viral fusion proteins
(231)
Superfamily
:
Influenza hemagglutinin (stalk)
(172)
Family
:
Influenza hemagglutinin (stalk)
(161)
Protein domain
:
Influenza hemagglutinin (stalk)
(102)
Influenza A virus, different strains [TaxId: 11320]
(93)
2a
d4ju0b_
B:
2b
d4ju0d_
D:
2c
d4ju0f_
F:
2d
d4ju0h_
H:
2e
d4ju0j_
J:
2f
d4ju0l_
L:
[
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
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
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 (990 KB)
Header - Asym.Unit
Biol.Unit 1 (492 KB)
Header - Biol.Unit 1
Biol.Unit 2 (494 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
4JU0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
