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.
4HLZ
Asym. Unit
Info
Asym.Unit (945 KB)
Biol.Unit 1 (936 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 FAB C179 IN COMPLEX WITH A H2N2 INFLUENZA VIRUS HEMAGGLUTININ
Authors
:
C. Dreyfus, I. A. Wilson
Date
:
17 Oct 12 (Deposition) - 17 Apr 13 (Release) - 24 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Neutralizing Antibodies, Antibody Affinity, Antigens, Epitopes, Glycosylation, Hemagglutinin Glycoproteins, Immunoglobulin Fab Fragments, H2N2 Subtype, Influenza Vaccines, Avian Flu, Envelope Protein, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Dreyfus, D. C. Ekiert, I. A. Wilson
Structure Of A Classical Broadly Neutralizing Stem Antibody In Complex With A Pandemic H2 Influenza Virus Hemagglutinin
J. Virol. V. 87 7149 2013
[
close entry info
]
Hetero Components
(5, 27)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: 1,2-ETHANEDIOL (EDOa)
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)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4n: N-ACETYL-D-GLUCOSAMINE (NAGn)
4o: N-ACETYL-D-GLUCOSAMINE (NAGo)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
15
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(27, 27)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:169 , TRP A:240 , THR A:242
BINDING SITE FOR RESIDUE NAG A 401
02
AC2
SOFTWARE
LYS A:280 , ASN A:289 , NAG A:403 , SER G:74
BINDING SITE FOR RESIDUE NAG A 402
03
AC3
SOFTWARE
NAG A:402 , BMA A:404 , THR G:24 , GLN G:75 , SER G:76
BINDING SITE FOR RESIDUE NAG A 403
04
AC4
SOFTWARE
NAG A:403
BINDING SITE FOR RESIDUE BMA A 404
05
AC5
SOFTWARE
ASN A:21
BINDING SITE FOR RESIDUE NAG A 405
06
AC6
SOFTWARE
LYS B:38 , GLU B:39 , THR H:33
BINDING SITE FOR RESIDUE SO4 B 201
07
AC7
SOFTWARE
GLU B:147 , ASN B:154 , THR B:156
BINDING SITE FOR RESIDUE NAG B 202
08
AC8
SOFTWARE
GLU C:278 , ASN C:289 , NAG C:402 , SER I:74 , GLN I:75
BINDING SITE FOR RESIDUE NAG C 401
09
AC9
SOFTWARE
NAG C:401 , BMA C:403 , GLY I:23 , GLN I:75
BINDING SITE FOR RESIDUE NAG C 402
10
BC1
SOFTWARE
NAG C:402 , MAN C:404 , GLN I:75
BINDING SITE FOR RESIDUE BMA C 403
11
BC2
SOFTWARE
ASN A:276 , BMA C:403
BINDING SITE FOR RESIDUE MAN C 404
12
BC3
SOFTWARE
ASN C:169 , TRP C:240 , NAG C:406
BINDING SITE FOR RESIDUE NAG C 405
13
BC4
SOFTWARE
NAG C:405
BINDING SITE FOR RESIDUE NAG C 406
14
BC5
SOFTWARE
ALA D:36 , ASP D:37 , LYS D:38 , GLU D:39 , THR J:33
BINDING SITE FOR RESIDUE SO4 D 201
15
BC6
SOFTWARE
ASN E:169 , THR E:242
BINDING SITE FOR RESIDUE NAG E 401
16
BC7
SOFTWARE
ASN E:48 , CYS E:277
BINDING SITE FOR RESIDUE SO4 E 402
17
BC8
SOFTWARE
ASN E:289 , NAG E:404 , GLN K:75
BINDING SITE FOR RESIDUE NAG E 403
18
BC9
SOFTWARE
NAG E:403 , BMA E:405 , GLY K:23 , ILE K:77
BINDING SITE FOR RESIDUE NAG E 404
19
CC1
SOFTWARE
NAG E:404
BINDING SITE FOR RESIDUE BMA E 405
20
CC2
SOFTWARE
ASN E:21 , NAG E:407
BINDING SITE FOR RESIDUE NAG E 406
21
CC3
SOFTWARE
NAG E:406
BINDING SITE FOR RESIDUE NAG E 407
22
CC4
SOFTWARE
ALA F:36 , LYS F:38 , GLU F:39 , THR L:33
BINDING SITE FOR RESIDUE SO4 F 201
23
CC5
SOFTWARE
GLU F:147 , ASN F:154 , THR F:156
BINDING SITE FOR RESIDUE NAG F 202
24
CC6
SOFTWARE
ALA B:35 , TRP H:34 , TYR H:94
BINDING SITE FOR RESIDUE SO4 H 301
25
CC7
SOFTWARE
TRP J:34 , TYR J:94
BINDING SITE FOR RESIDUE SO4 J 301
26
CC8
SOFTWARE
ALA J:11 , SER J:12
BINDING SITE FOR RESIDUE EDO J 302
27
CC9
SOFTWARE
ALA F:35 , TRP L:34 , TYR L:94
BINDING SITE FOR RESIDUE SO4 L 301
[
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
(4, 12)
Info
All SCOP Domains
1a: SCOP_d4hlzh1 (H:3-109)
1b: SCOP_d4hlzj1 (J:3-109)
1c: SCOP_d4hlzl1 (L:3-109)
2a: SCOP_d4hlzh2 (H:110-213)
2b: SCOP_d4hlzj2 (J:110-214)
2c: SCOP_d4hlzl2 (L:110-214)
3a: SCOP_d4hlza_ (A:)
3b: SCOP_d4hlzc_ (C:)
3c: SCOP_d4hlze_ (E:)
4a: SCOP_d4hlzb_ (B:)
4b: SCOP_d4hlzd_ (D:)
4c: SCOP_d4hlzf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d4hlzh1
H:3-109
1b
d4hlzj1
J:3-109
1c
d4hlzl1
L:3-109
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d4hlzh2
H:110-213
2b
d4hlzj2
J:110-214
2c
d4hlzl2
L:110-214
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)
3a
d4hlza_
A:
3b
d4hlzc_
C:
3c
d4hlze_
E:
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)
4a
d4hlzb_
B:
4b
d4hlzd_
D:
4c
d4hlzf_
F:
[
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 (945 KB)
Header - Asym.Unit
Biol.Unit 1 (936 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
4HLZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
