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.
3HS6
Asym. Unit
Info
Asym.Unit (331 KB)
Biol.Unit 1 (318 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF EICOSAPENTAENOIC ACID BOUND TO THE CYCLOOXYGENASE CHANNEL OF CYCLOOXYGENASE-2
Authors
:
A. J. Vecchio, D. M. Simmons, M. G. Malkowski
Date
:
10 Jun 09 (Deposition) - 12 May 10 (Release) - 04 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase, Dioxygenase, Disulfide Bond, Endoplasmic Reticulum, Fatty Acid Biosynthesis, Glycoprotein, Heme, Iron, Lipid Synthesis, Membrane, Metal-Binding, Microsome, Peroxidase, Phosphoprotein, Prostaglandin Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. J. Vecchio, D. M. Simmons, M. G. Malkowski
Structural Basis Of Fatty Acid Substrate Binding To Cyclooxygenase-2.
J. Biol. Chem. V. 285 22152 2010
[
close entry info
]
Hetero Components
(8, 29)
Info
All Hetero Components
1a: ACRYLIC ACID (AKRa)
1b: ACRYLIC ACID (AKRb)
1c: ACRYLIC ACID (AKRc)
1d: ACRYLIC ACID (AKRd)
2a: B-OCTYLGLUCOSIDE (BOGa)
2b: B-OCTYLGLUCOSIDE (BOGb)
3a: PROTOPORPHYRIN IX CONTAINING CO (COHa)
3b: PROTOPORPHYRIN IX CONTAINING CO (COHb)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
4e: 1,2-ETHANEDIOL (EDOe)
4f: 1,2-ETHANEDIOL (EDOf)
4g: 1,2-ETHANEDIOL (EDOg)
4h: 1,2-ETHANEDIOL (EDOh)
5a: 5,8,11,14,17-EICOSAPENTAENOIC ACID (EPAa)
5b: 5,8,11,14,17-EICOSAPENTAENOIC ACID (EPAb)
6a: ALPHA-D-MANNOSE (MANa)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
8a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AKR
4
Ligand/Ion
ACRYLIC ACID
2
BOG
2
Ligand/Ion
B-OCTYLGLUCOSIDE
3
COH
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING CO
4
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
5
EPA
2
Ligand/Ion
5,8,11,14,17-EICOSAPENTAENOIC ACID
6
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
9
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(29, 29)
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)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:205 , TYR A:348 , TYR A:355 , TYR A:385 , TRP A:387 , GLY A:526 , ALA A:527 , SER A:530 , HOH A:736
BINDING SITE FOR RESIDUE EPA A 1
02
AC2
SOFTWARE
SER A:477 , PHE A:478 , GLU A:479 , LYS A:492
BINDING SITE FOR RESIDUE AKR A 2
03
AC3
SOFTWARE
THR A:237 , ARG A:240 , LYS A:243 , VAL A:271 , GLU A:272
BINDING SITE FOR RESIDUE AKR A 3
04
AC4
SOFTWARE
ALA A:199 , GLN A:203 , HIS A:207 , PHE A:210 , THR A:212 , HIS A:214 , VAL A:295 , ASN A:382 , TYR A:385 , HIS A:386 , HIS A:388 , VAL A:447 , HOH A:878
BINDING SITE FOR RESIDUE COH A 619
05
AC5
SOFTWARE
TYR A:55 , GLU A:67 , ASN A:68 , NAG A:662
BINDING SITE FOR RESIDUE NAG A 661
06
AC6
SOFTWARE
NAG A:661
BINDING SITE FOR RESIDUE NAG A 662
07
AC7
SOFTWARE
GLU A:140 , ASN A:144 , TYR A:147 , ARG A:216 , HOH A:649 , NAG A:672 , HOH A:682 , HOH A:720
BINDING SITE FOR RESIDUE NAG A 671
08
AC8
SOFTWARE
ARG A:216 , NAG A:671 , MAN A:673 , HOH A:851 , ASP B:239
BINDING SITE FOR RESIDUE NAG A 672
09
AC9
SOFTWARE
NAG A:672
BINDING SITE FOR RESIDUE MAN A 673
10
BC1
SOFTWARE
GLN A:406 , ASN A:410 , SER A:412 , ILE A:413 , GLU A:416
BINDING SITE FOR RESIDUE NAG A 681
11
BC2
SOFTWARE
LYS A:180 , ARG A:184 , ARG A:185 , ARG A:438 , GLU A:486 , GLU A:490 , GLU B:179 , ARG B:185 , ILE B:442 , GLN B:445 , BOG B:703
BINDING SITE FOR RESIDUE BOG A 703
12
BC3
SOFTWARE
HIS A:90 , GLN A:192 , LEU A:352 , ARG A:513 , ALA A:516 , ILE A:517 , PHE A:518 , VAL A:523
BINDING SITE FOR RESIDUE EDO A 620
13
BC4
SOFTWARE
EDO A:5 , PRO A:162 , SER A:455 , ARG A:456 , LYS A:459 , TYR A:460 , HOH A:877
BINDING SITE FOR RESIDUE EDO A 4
14
BC5
SOFTWARE
EDO A:4 , ALA A:156 , ASP A:157 , CYS A:159 , THR A:161 , PRO A:162 , LYS A:459
BINDING SITE FOR RESIDUE EDO A 5
15
BC6
SOFTWARE
ASP A:58 , CYS A:59
BINDING SITE FOR RESIDUE EDO A 6
16
BC7
SOFTWARE
HOH A:855 , LEU B:178 , GLN B:445 , LYS B:449
BINDING SITE FOR RESIDUE EDO A 8
17
BC8
SOFTWARE
PHE B:205 , PHE B:209 , TYR B:348 , TYR B:355 , ILE B:377 , PHE B:381 , TYR B:385 , VAL B:523 , GLY B:526 , ALA B:527 , SER B:530 , GLY B:533 , LEU B:534
BINDING SITE FOR RESIDUE EPA B 1
18
BC9
SOFTWARE
SER B:477 , PHE B:478 , GLU B:479 , LYS B:492
BINDING SITE FOR RESIDUE AKR B 2
19
CC1
SOFTWARE
ARG B:240 , LYS B:243 , GLN B:270 , GLU B:272
BINDING SITE FOR RESIDUE AKR B 3
20
CC2
SOFTWARE
ALA B:199 , GLN B:203 , HIS B:207 , PHE B:210 , THR B:212 , VAL B:295 , ASN B:382 , TYR B:385 , HIS B:386 , HIS B:388 , LEU B:391
BINDING SITE FOR RESIDUE COH B 619
21
CC3
SOFTWARE
TYR B:55 , GLU B:67 , ASN B:68 , NDG B:662
BINDING SITE FOR RESIDUE NAG B 661
22
CC4
SOFTWARE
NAG B:661
BINDING SITE FOR RESIDUE NDG B 662
23
CC5
SOFTWARE
GLU B:140 , ASN B:144 , TYR B:147 , ARG B:216 , PHE B:220 , HOH B:627 , NAG B:672 , HOH B:815
BINDING SITE FOR RESIDUE NAG B 671
24
CC6
SOFTWARE
ASP A:239 , ARG B:216 , NAG B:671 , HOH B:804 , HOH B:834
BINDING SITE FOR RESIDUE NAG B 672
25
CC7
SOFTWARE
HOH B:20 , ASN B:410 , ILE B:413 , GLU B:416
BINDING SITE FOR RESIDUE NAG B 681
26
CC8
SOFTWARE
GLU A:179 , ARG A:185 , ARG A:438 , GLU A:486 , GLU A:490 , BOG A:703 , LYS B:175 , GLU B:179 , ARG B:184 , ARG B:185 , ILE B:442 , GLN B:445
BINDING SITE FOR RESIDUE BOG B 703
27
CC9
SOFTWARE
HIS B:90 , GLN B:192 , LEU B:352 , ARG B:513 , ALA B:516 , ILE B:517 , PHE B:518 , VAL B:523
BINDING SITE FOR RESIDUE EDO B 620
28
DC1
SOFTWARE
LYS B:251 , TYR B:254 , VAL B:261 , ASN B:310
BINDING SITE FOR RESIDUE EDO B 621
29
DC2
SOFTWARE
PRO B:162 , ARG B:456 , LYS B:459 , TYR B:460 , HOH B:729
BINDING SITE FOR RESIDUE EDO B 7
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_3 (A:110-582,B:110-582)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEROXIDASE_3
PS50292
Animal heme peroxidase superfamily profile.
PGH2_MOUSE
96-598
2
A:110-582
B:110-582
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3hs6A02 (A:74-582)
1b: CATH_3hs6B02 (B:74-582)
2a: CATH_3hs6A01 (A:33-73)
2b: CATH_3hs6B01 (B:33-73)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Myeloperoxidase, subunit C
(39)
Homologous Superfamily
:
Myeloperoxidase, subunit C
(39)
Mouse (Mus musculus)
(4)
1a
3hs6A02
A:74-582
1b
3hs6B02
B:74-582
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Mouse (Mus musculus)
(6)
2a
3hs6A01
A:33-73
2b
3hs6B01
B:33-73
[
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 (331 KB)
Header - Asym.Unit
Biol.Unit 1 (318 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
3HS6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help