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.
5HYS
Biol. Unit 1
Info
Asym.Unit (429 KB)
Biol.Unit 1 (215 KB)
Biol.Unit 2 (214 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF IGE COMPLEXED WITH OMALIZUMAB
Authors
:
L. F. Pennington, S. S. Tarchevskaya, K. Sathiyamoorthy, T. S. Jardetz
Date
:
01 Feb 16 (Deposition) - 01 Jun 16 (Release) - 01 Jun 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,G,H,I,L (1x)
Biol. Unit 2: C,D,E,F,J,K (1x)
Keywords
:
Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. F. Pennington, S. Tarchevskaya, D. Brigger, K. Sathiyamoorthy, M. T. Graham, K. C. Nadeau, A. Eggel, T. S. Jardetzky
Structural Basis Of Omalizumab Therapy And Omalizumab-Mediated Ige Exchange.
Nat Commun V. 7 11610 2016
[
close entry info
]
Hetero Components
(4, 32)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
2e: ALPHA-D-MANNOSE (MANe)
2f: ALPHA-D-MANNOSE (MANf)
2g: ALPHA-D-MANNOSE (MANg)
2h: ALPHA-D-MANNOSE (MANh)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4a: SULFATE ION (SO4a)
4aa: SULFATE ION (SO4aa)
4ab: SULFATE ION (SO4ab)
4ac: SULFATE ION (SO4ac)
4ad: SULFATE ION (SO4ad)
4ae: SULFATE ION (SO4ae)
4af: SULFATE ION (SO4af)
4ag: SULFATE ION (SO4ag)
4ah: SULFATE ION (SO4ah)
4ai: SULFATE ION (SO4ai)
4aj: SULFATE ION (SO4aj)
4ak: SULFATE ION (SO4ak)
4al: SULFATE ION (SO4al)
4am: SULFATE ION (SO4am)
4an: SULFATE ION (SO4an)
4ao: SULFATE ION (SO4ao)
4ap: SULFATE ION (SO4ap)
4aq: SULFATE ION (SO4aq)
4ar: SULFATE ION (SO4ar)
4as: SULFATE ION (SO4as)
4at: SULFATE ION (SO4at)
4au: SULFATE ION (SO4au)
4av: SULFATE ION (SO4av)
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)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
4q: SULFATE ION (SO4q)
4r: SULFATE ION (SO4r)
4s: SULFATE ION (SO4s)
4t: SULFATE ION (SO4t)
4u: SULFATE ION (SO4u)
4v: SULFATE ION (SO4v)
4w: SULFATE ION (SO4w)
4x: SULFATE ION (SO4x)
4y: SULFATE ION (SO4y)
4z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
22
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(28, 28)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AE6 (SOFTWARE)
17: AF5 (SOFTWARE)
18: AF6 (SOFTWARE)
19: AF7 (SOFTWARE)
20: AF8 (SOFTWARE)
21: AF9 (SOFTWARE)
22: AG1 (SOFTWARE)
23: AG2 (SOFTWARE)
24: AG3 (SOFTWARE)
25: AG4 (SOFTWARE)
26: AG7 (SOFTWARE)
27: AH2 (SOFTWARE)
28: AH3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG H:72
binding site for residue SO4 H 301
02
AC2
SOFTWARE
SER H:7 , GLY H:8 , GLY H:9 , THR H:115 , LYS H:209
binding site for residue SO4 H 302
03
AC3
SOFTWARE
ARG H:19 , LYS H:76 , TYR H:80
binding site for residue SO4 H 303
04
AC4
SOFTWARE
LYS H:76
binding site for residue SO4 H 304
05
AC5
SOFTWARE
LYS L:43 , LYS L:46 , LYS L:49
binding site for residue SO4 L 301
06
AC6
SOFTWARE
ARG J:427 , SER L:69 , GLY L:70
binding site for residue SO4 L 302
07
AC7
SOFTWARE
ARG L:24
binding site for residue SO4 L 303
08
AC8
SOFTWARE
SER B:12 , LYS B:111 , SER L:9 , SER L:10 , LYS L:107
binding site for residue SO4 L 304
09
AC9
SOFTWARE
SER A:7 , GLY A:8 , GLY A:9 , THR A:115 , LYS A:209
binding site for residue SO4 A 301
10
AD1
SOFTWARE
GLY A:126
binding site for residue SO4 A 302
11
AD2
SOFTWARE
ARG A:19 , LYS A:76 , TYR A:80
binding site for residue SO4 A 303
12
AD3
SOFTWARE
GLN B:41 , LYS B:43 , LYS B:46 , LYS B:49
binding site for residue SO4 B 301
13
AD4
SOFTWARE
SER B:125 , ASP B:126 , GLU B:127 , HIS J:384
binding site for residue SO4 B 302
14
AD5
SOFTWARE
SER B:160 , GLY B:161 , LYS L:149
binding site for residue SO4 B 303
15
AD6
SOFTWARE
SER B:69 , GLY B:70 , ARG G:427
binding site for residue SO4 B 304
16
AE6
SOFTWARE
SER C:140 , VAL D:119 , LYS D:211 , ARG G:408
binding site for residue SO4 D 305
17
AF5
SOFTWARE
GLY G:406 , THR G:407 , ARG G:408
binding site for residue SO4 G 606
18
AF6
SOFTWARE
SER G:344 , SER G:475
binding site for residue SO4 G 607
19
AF7
SOFTWARE
GLY I:406 , THR I:407 , ARG I:408
binding site for residue SO4 I 606
20
AF8
SOFTWARE
THR G:493 , GLN G:494 , ARG G:496 , GLN I:494 , ARG I:496
binding site for residue SO4 I 607
21
AF9
SOFTWARE
SER I:344 , SER I:475
binding site for residue SO4 I 609
22
AG1
SOFTWARE
MET I:430 , ARG I:431 , SER I:432
binding site for residue SO4 I 610
23
AG2
SOFTWARE
LYS B:187 , GLY J:406 , THR J:407 , ARG J:408
binding site for residue SO4 J 606
24
AG3
SOFTWARE
SER A:123 , LYS A:125 , PRO J:486 , ASP J:487 , HOH J:701
binding site for residue SO4 J 607
25
AG4
SOFTWARE
LYS B:130 , ARG J:376 , ASP J:409
binding site for residue SO4 J 608
26
AG7
SOFTWARE
PRO L:63 , SER L:64
binding site for residue SO4 K 607
27
AH2
SOFTWARE
TYR G:339 , LEU G:359 , VAL G:361 , ASP G:362 , GLN G:392 , ASN G:394 , THR G:396 , THR G:398 , GLN G:494
binding site for Poly-Saccharide residues NAG G 601 through MAN G 605 bound to ASN G 394
28
AH3
SOFTWARE
PRO I:333 , TYR I:339 , VAL I:361 , ASP I:362 , GLN I:392 , ASN I:394 , GLN I:494
binding site for Poly-Saccharide residues NAG I 601 through MAN I 605 bound to ASN I 394
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 G
Chain H
Chain I
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 (429 KB)
Header - Asym.Unit
Biol.Unit 1 (215 KB)
Header - Biol.Unit 1
Biol.Unit 2 (214 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
5HYS
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help