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.
1RV0
Asym. Unit
Info
Asym.Unit (249 KB)
Biol.Unit 1 (244 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
1930 SWINE H1 HEMAGGLUTININ COMPLEXED WITH LSTA
Authors
:
J. J. Skehel, S. J. Gamblin, L. F. Haire, R. J. Russell, D. J. Stevens, B. Xiao, Y. Ha, N. Vasisht, D. A. Steinhauer, R. S. Daniels
Date
:
12 Dec 03 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : H,I,J,K,L,M
Biol. Unit 1: H,I,J,K,L,M (1x)
Keywords
:
Hemagglutinin, Influenza A Virus, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. J. Gamblin, L. F. Haire, R. J. Russell, D. J. Stevens, B. Xiao, Y. Ha, N. Vasisht, D. A. Steinhauer, R. S. Daniels, A. Elliot, D. C. Wiley, J. J. Skehel
The Structure And Receptor Binding Properties Of The 1918 Influenza Hemagglutinin.
Science V. 303 1838 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURA... (DANa)
2a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
2b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
2c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DAN
1
Ligand/Ion
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2
NDG
3
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN J:68 , GLU J:70 , ASN J:91 , CYS J:94 , ARG J:224 , HOH J:748
BINDING SITE FOR RESIDUE NDG J 640
2
AC2
SOFTWARE
ASN H:68 , GLU H:70 , ASN H:91 , CYS H:94 , CYS H:139 , PRO H:140 , ARG H:224 , HOH H:697
BINDING SITE FOR RESIDUE NDG H 642
3
AC3
SOFTWARE
ASN L:68 , GLU L:70 , ASN L:91 , CYS L:94 , ARG L:224
BINDING SITE FOR RESIDUE NDG L 644
4
AC4
SOFTWARE
TYR L:95 , ARG L:133A , GLY L:134 , VAL L:135 , THR L:136 , ALA L:137 , HIS L:183 , PRO L:186 , LEU L:194 , GLN L:226 , HOH L:731 , HOH L:743
BINDING SITE FOR RESIDUE DAN L 701
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d1rv0h_ (H:)
1b: SCOP_d1rv0j_ (J:)
1c: SCOP_d1rv0l_ (L:)
2a: SCOP_d1rv0i_ (I:)
2b: SCOP_d1rv0k_ (K:)
2c: SCOP_d1rv0m_ (M:)
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
d1rv0h_
H:
1b
d1rv0j_
J:
1c
d1rv0l_
L:
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
d1rv0i_
I:
2b
d1rv0k_
K:
2c
d1rv0m_
M:
[
close SCOP info
]
CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_1rv0H02 (H:47-276)
1b: CATH_1rv0J02 (J:47-276)
1c: CATH_1rv0L02 (L:47-276)
2a: CATH_1rv0I00 (I:501-660)
2b: CATH_1rv0K00 (K:501-660)
2c: CATH_1rv0M00 (M:501-660)
3a: CATH_1rv0H01 (H:5-46,H:277-327)
3b: CATH_1rv0J01 (J:5-46,J:277-327)
3c: CATH_1rv0L01 (L:5-46,L:277-327)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Hemagglutinin (Ha1 Chain); Chain: A; domain 1
(59)
Homologous Superfamily
:
[code=3.90.209.20, no name defined]
(59)
Influenza a virus. Organism_taxid: 11320. Strain: a-swine-iowa-30.
(1)
1a
1rv0H02
H:47-276
1b
1rv0J02
J:47-276
1c
1rv0L02
L:47-276
Topology
:
Hemagglutinin Ectodomain; Chain B
(70)
Homologous Superfamily
:
[code=3.90.20.10, no name defined]
(69)
Influenza a virus. Organism_taxid: 11320. Strain: a-swine-iowa-30.
(1)
2a
1rv0I00
I:501-660
2b
1rv0K00
K:501-660
2c
1rv0M00
M:501-660
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Hemagglutinin; Chain A, domain 2
(27)
Homologous Superfamily
:
Hemagglutinin Chain A, Domain 2
(27)
Influenza a virus. Organism_taxid: 11320. Strain: a-swine-iowa-30.
(1)
3a
1rv0H01
H:5-46,H:277-327
3b
1rv0J01
J:5-46,J:277-327
3c
1rv0L01
L:5-46,L:277-327
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Hemagglutinin_1rv0M01 (M:501-660)
1b: PFAM_Hemagglutinin_1rv0M02 (M:501-660)
1c: PFAM_Hemagglutinin_1rv0M03 (M:501-660)
1d: PFAM_Hemagglutinin_1rv0M04 (M:501-660)
1e: PFAM_Hemagglutinin_1rv0M05 (M:501-660)
1f: PFAM_Hemagglutinin_1rv0M06 (M:501-660)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Hemagglutinin]
(58)
Family
:
Hemagglutinin
(58)
Influenza A virus (A/swine/St-Hyacinthe/148/1990(H1N1))
(2)
1a
Hemagglutinin-1rv0M01
M:501-660
1b
Hemagglutinin-1rv0M02
M:501-660
1c
Hemagglutinin-1rv0M03
M:501-660
1d
Hemagglutinin-1rv0M04
M:501-660
1e
Hemagglutinin-1rv0M05
M:501-660
1f
Hemagglutinin-1rv0M06
M:501-660
[
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 H
Chain I
Chain J
Chain K
Chain L
Chain M
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 (249 KB)
Header - Asym.Unit
Biol.Unit 1 (244 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
1RV0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
