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.
4COX
Biol. Unit 1
Info
Asym.Unit (373 KB)
Biol.Unit 1 (185 KB)
Biol.Unit 2 (186 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CYCLOOXYGENASE-2 (PROSTAGLANDIN SYNTHASE-2) COMPLEXED WITH A NON-SELECTIVE INHIBITOR, INDOMETHACIN
Authors
:
R. Kurumbail, W. Stallings
Date
:
18 Dec 96 (Deposition) - 24 Dec 97 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Peroxidase, Dioxygenase, Cyclooxygenase, Nonsteroidal Antiinflammatory Drugs, Inflammation, Arthritis, Prostaglandin, Prostaglandin Synthase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. G. Kurumbail, A. M. Stevens, J. K. Gierse, J. J. Mcdonald, R. A. Stegeman, J. Y. Pak, D. Gildehaus, J. M. Miyashiro, T. D. Penning, K. Seibert, P. C. Isakson, W. C. Stallings
Structural Basis For Selective Inhibition Of Cyclooxygenase-2 By Anti-Inflammatory Agents.
Nature V. 384 644 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
2a: INDOMETHACIN (IMNa)
2b: INDOMETHACIN (IMNb)
2c: INDOMETHACIN (IMNc)
2d: INDOMETHACIN (IMNd)
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)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
IMN
2
Ligand/Ion
INDOMETHACIN
3
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: ACE (UNKNOWN)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: CAT (UNKNOWN)
13: HEM (UNKNOWN)
14: SUB (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:55 , GLU A:67 , ASN A:68 , THR A:70
BINDING SITE FOR RESIDUE NAG A 661
02
AC2
SOFTWARE
GLU A:140 , ASN A:144 , TYR A:147
BINDING SITE FOR RESIDUE NAG A 671
03
AC3
SOFTWARE
ASN A:410 , SER A:412 , ILE A:413
BINDING SITE FOR RESIDUE NAG A 681
04
AC4
SOFTWARE
TYR B:55 , GLU B:67 , ASN B:68 , THR B:70
BINDING SITE FOR RESIDUE NAG B 661
05
AC5
SOFTWARE
GLU B:140 , ASN B:144 , SER B:146 , TYR B:147 , ARG B:216
BINDING SITE FOR RESIDUE NAG B 671
06
AC6
SOFTWARE
TYR B:402 , ASN B:410 , SER B:412 , ILE B:413
BINDING SITE FOR RESIDUE NAG B 681
07
ACE
UNKNOWN
SER A:530
SER 530 IS ACETYLATED BY ASPIRIN (AN ACETYL GROUP IS COVALENTLY ATTACHED TO THE PROTEIN WHEN INHIBITED WITH ASPIRIN). THE ACETYLATED SER PREVENTS THE PROPER BINDING OF THE SUBSTRATE IN THE CYCLOOXYGENASE ACTIVE SITE. IT HAS BEEN RECENTLY SHOWN, HOWEVER, THAT ACETYLATION OF CYCLOOXYGENASE-2 RESULTS IN THE FORMATION OF A DIFFERENT PRODUCT (15-HETE).
08
BC4
SOFTWARE
ALA A:199 , GLN A:203 , HIS A:207 , THR A:212 , VAL A:295 , ASN A:382 , TYR A:385 , HIS A:386 , TRP A:387 , HIS A:388 , LEU A:391 , VAL A:447 , GLN A:454
BINDING SITE FOR RESIDUE HEM A 682
09
BC5
SOFTWARE
ARG A:120 , VAL A:349 , LEU A:352 , SER A:353 , TYR A:355 , LEU A:384 , TYR A:385 , TRP A:387 , MET A:522 , VAL A:523 , GLY A:526 , ALA A:527 , SER A:530 , LEU A:531
BINDING SITE FOR RESIDUE IMN A 701
10
BC6
SOFTWARE
ALA B:199 , GLN B:203 , HIS B:207 , THR B:212 , VAL B:295 , ASN B:382 , TYR B:385 , HIS B:386 , HIS B:388 , LEU B:391 , LEU B:408 , VAL B:447 , ALA B:450
BINDING SITE FOR RESIDUE HEM B 682
11
BC7
SOFTWARE
ARG B:120 , VAL B:349 , LEU B:352 , SER B:353 , TYR B:355 , TYR B:385 , MET B:522 , VAL B:523 , GLY B:526 , ALA B:527 , SER B:530 , LEU B:531
BINDING SITE FOR RESIDUE IMN B 701
12
CAT
UNKNOWN
TYR A:385
TYR 385 IS BELIEVED TO BE THE AMINO ACID THAT ABSTRACTS A HYDROGEN ATOM FROM THE SUBSTRATE. IT IS LOCATED CLOSE TO THE HEME. A TYROSINE RADICAL IS FORMED DURING THE COURSE OF THE REACTION.
13
HEM
UNKNOWN
HIS A:388
HIS 388 IS THE AXIAL LIGAND TO THE HEME.
14
SUB
UNKNOWN
ARG A:120
ARGININE 120 IS BELIEVED TO ANCHOR THE CARBOXYLATE OF THE SUBSTRATE BY FORMING AN ION-PAIR.
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_3 (A:110-583,B:110-583)
;
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:110-583
B:110-583
-
-
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d4coxa1 (A:74-583)
1b: SCOP_d4coxb1 (B:74-583)
1c: SCOP_d4coxc1 (C:74-583)
1d: SCOP_d4coxd1 (D:74-583)
2a: SCOP_d4coxa2 (A:33-73)
2b: SCOP_d4coxb2 (B:33-73)
2c: SCOP_d4coxc2 (C:33-73)
2d: SCOP_d4coxd2 (D:33-73)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme-dependent peroxidases
(402)
Superfamily
:
Heme-dependent peroxidases
(402)
Family
:
Myeloperoxidase-like
(44)
Protein domain
:
Prostaglandin H2 synthase
(34)
Mouse (Mus musculus) [TaxId: 10090]
(11)
1a
d4coxa1
A:74-583
1b
d4coxb1
B:74-583
1c
d4coxc1
C:74-583
1d
d4coxd1
D:74-583
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
Prostaglandin H2 synthase-1, EGF-like module
(34)
Mouse (Mus musculus) [TaxId: 10090]
(11)
2a
d4coxa2
A:33-73
2b
d4coxb2
B:33-73
2c
d4coxc2
C:33-73
2d
d4coxd2
D:33-73
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_4coxA02 (A:74-583)
1b: CATH_4coxB02 (B:74-583)
1c: CATH_4coxC02 (C:74-583)
1d: CATH_4coxD02 (D:74-583)
2a: CATH_4coxA01 (A:33-73)
2b: CATH_4coxB01 (B:33-73)
2c: CATH_4coxC01 (C:33-73)
2d: CATH_4coxD01 (D: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)
House mouse (Mus musculus)
(8)
1a
4coxA02
A:74-583
1b
4coxB02
B:74-583
1c
4coxC02
C:74-583
1d
4coxD02
D:74-583
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
House mouse (Mus musculus)
(18)
2a
4coxA01
A:33-73
2b
4coxB01
B:33-73
2c
4coxC01
C:33-73
2d
4coxD01
D: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 (373 KB)
Header - Asym.Unit
Biol.Unit 1 (185 KB)
Header - Biol.Unit 1
Biol.Unit 2 (186 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
4COX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help