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3KK6
Biol. Unit 1
Info
Asym.Unit (570 KB)
Biol.Unit 1 (557 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CYCLOOXYGENASE-1 IN COMPLEX WITH CELECOXIB
Authors
:
R. S. Sidhu
Date
:
04 Nov 09 (Deposition) - 15 Dec 09 (Release) - 13 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Cox-1, Cyclooxygenase, Peroxidase, Prostaglandin, Heme, Celecoxib, Merohedral Twinned, Dioxygenase, Disulfide Bond, Egf-Like Domain, Endoplasmic Reticulum, Fatty Acid Biosynthesis, Glycoprotein, Iron, Lipid Synthesis, Membrane, Metal-Binding, Microsome, Oxidoreductase, Prostaglandin Biosynthesis, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Rimon, R. S. Sidhu, D. A. Lauver, J. Y. Lee, N. P. Sharma, C. Yuan, R. A. Frieler, R. C. Trievel, B. R. Lucchesi, W. L. Smith
Coxibs Interfere With The Action Of Aspirin By Binding Tightly To One Monomer Of Cyclooxygenase-1.
Proc. Natl. Acad. Sci. Usa V. 107 28 2010
[
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Hetero Components
(8, 24)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: B-OCTYLGLUCOSIDE (BOGa)
2b: B-OCTYLGLUCOSIDE (BOGb)
2c: B-OCTYLGLUCOSIDE (BOGc)
2d: B-OCTYLGLUCOSIDE (BOGd)
3a: 4-[5-(4-METHYLPHENYL)-3-(TRIFLUORO... (CELa)
3b: 4-[5-(4-METHYLPHENYL)-3-(TRIFLUORO... (CELb)
4a: CITRATE ANION (FLCa)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
6a: ALPHA-D-MANNOSE (MANa)
6b: ALPHA-D-MANNOSE (MANb)
6c: ALPHA-D-MANNOSE (MANc)
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)
8a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
8b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
8c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
BOG
4
Ligand/Ion
B-OCTYLGLUCOSIDE
3
CEL
2
Ligand/Ion
4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE
4
FLC
1
Ligand/Ion
CITRATE ANION
5
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
MAN
3
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
NDG
3
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
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Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:148 , GLN A:203 , HIS A:207 , PHE A:210 , LYS A:211 , THR A:212 , LEU A:295 , ASN A:382 , TYR A:385 , HIS A:386 , TRP A:387 , HIS A:388 , MET A:391 , VAL A:447 , ASP A:450 , FLC A:900
BINDING SITE FOR RESIDUE HEM A 601
02
AC2
SOFTWARE
ASN A:144 , TYR A:147 , NAG A:672
BINDING SITE FOR RESIDUE NAG A 671
03
AC3
SOFTWARE
NAG A:671 , MAN A:673 , LEU B:238
BINDING SITE FOR RESIDUE NAG A 672
04
AC4
SOFTWARE
NAG A:672 , BMA A:674
BINDING SITE FOR RESIDUE MAN A 673
05
AC5
SOFTWARE
MAN A:673 , MAN A:675
BINDING SITE FOR RESIDUE BMA A 674
06
AC6
SOFTWARE
BMA A:674 , HOH B:592
BINDING SITE FOR RESIDUE MAN A 675
07
AC7
SOFTWARE
TYR A:402 , GLN A:406 , ASN A:410 , MET A:413 , ASP A:416 , NDG A:682 , ILE B:279 , PRO B:281
BINDING SITE FOR RESIDUE NAG A 681
08
AC8
SOFTWARE
GLN A:400 , TYR A:402 , GLN A:406 , ASP A:416 , HOH A:599 , NAG A:681
BINDING SITE FOR RESIDUE NDG A 682
09
AC9
SOFTWARE
HIS A:90 , VAL A:116 , GLN A:192 , VAL A:349 , LEU A:352 , SER A:353 , TYR A:355 , LEU A:359 , TRP A:387 , SER A:516 , ILE A:517 , PHE A:518 , MET A:522 , ILE A:523 , GLY A:526 , ALA A:527
BINDING SITE FOR RESIDUE CEL A 701
10
BC1
SOFTWARE
PRO A:86 , LEU A:115 , VAL A:119 , ARG A:120 , GLU A:524
BINDING SITE FOR RESIDUE BOG A 751
11
BC2
SOFTWARE
PRO A:84 , SER A:85 , SER A:87 , PHE A:88 , PHE A:91
BINDING SITE FOR RESIDUE BOG A 754
12
BC3
SOFTWARE
LYS A:211 , THR A:212 , HEM A:601
BINDING SITE FOR RESIDUE FLC A 900
13
BC4
SOFTWARE
ALA B:199 , GLN B:203 , THR B:206 , HIS B:207 , PHE B:210 , LYS B:211 , THR B:212 , ASN B:382 , TYR B:385 , HIS B:386 , TRP B:387 , HIS B:388 , MET B:391 , VAL B:447 , ASP B:450
BINDING SITE FOR RESIDUE HEM B 601
14
BC5
SOFTWARE
TYR B:55 , ASN B:68 , NDG B:1662
BINDING SITE FOR RESIDUE NAG B 1661
15
BC6
SOFTWARE
HOH B:31 , TYR B:38 , NAG B:1661
BINDING SITE FOR RESIDUE NDG B 1662
16
BC7
SOFTWARE
ASN B:144 , TYR B:147 , NAG B:1672
BINDING SITE FOR RESIDUE NAG B 1671
17
BC8
SOFTWARE
MET B:216 , HOH B:588 , NAG B:1671 , MAN B:1673
BINDING SITE FOR RESIDUE NAG B 1672
18
BC9
SOFTWARE
HOH B:589 , NAG B:1672 , BMA B:1674
BINDING SITE FOR RESIDUE MAN B 1673
19
CC1
SOFTWARE
MAN B:1673
BINDING SITE FOR RESIDUE BMA B 1674
20
CC2
SOFTWARE
PRO A:281 , TYR B:402 , GLN B:406 , ASN B:410 , MET B:413 , ASP B:416 , NDG B:1682
BINDING SITE FOR RESIDUE NAG B 1681
21
CC3
SOFTWARE
HOH B:4 , TYR B:402 , NAG B:1681
BINDING SITE FOR RESIDUE NDG B 1682
22
CC4
SOFTWARE
HIS B:90 , VAL B:116 , GLN B:192 , VAL B:349 , LEU B:352 , SER B:353 , TYR B:355 , LEU B:359 , TRP B:387 , SER B:516 , ILE B:517 , PHE B:518 , MET B:522 , ILE B:523 , GLY B:526 , ALA B:527 , SER B:530
BINDING SITE FOR RESIDUE CEL B 1701
23
CC5
SOFTWARE
ARG B:83 , ILE B:89 , ARG B:120 , GLY B:471 , GLU B:524 , HOH B:617
BINDING SITE FOR RESIDUE BOG B 1751
24
CC6
SOFTWARE
TRP B:77 , GLY B:96 , ARG B:97 , TRP B:98
BINDING SITE FOR RESIDUE BOG B 1752
[
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]
SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_PGH1_SHEEP_001 (R97H, chain A/B, )
2: VAR_PGH1_SHEEP_002 (G164G, chain A/B, )
3: VAR_PGH1_SHEEP_003 (R456Q, chain A/B, )
4: VAR_PGH1_SHEEP_004 (E520K, chain A/B, )
5: VAR_PGH1_SHEEP_005 (E520Q, chain A/B, )
6: VAR_PGH1_SHEEP_006 (M525I, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_PGH1_SHEEP_001
*
R
97
H
PGH1_SHEEP
---
---
A/B
R
97
H
2
UniProt
VAR_PGH1_SHEEP_002
*
D
164
G
PGH1_SHEEP
---
---
A/B
G
164
G
3
UniProt
VAR_PGH1_SHEEP_003
*
R
456
Q
PGH1_SHEEP
---
---
A/B
R
456
Q
4
UniProt
VAR_PGH1_SHEEP_004
*
E
520
K
PGH1_SHEEP
---
---
A/B
E
520
K
5
UniProt
VAR_PGH1_SHEEP_005
*
E
520
Q
PGH1_SHEEP
---
---
A/B
E
520
Q
6
UniProt
VAR_PGH1_SHEEP_006
*
M
525
I
PGH1_SHEEP
---
---
A/B
M
525
I
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: EGF_3 (A:32-70,B:32-70)
2: PEROXIDASE_3 (A:110-584,B:110-584)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_3
PS50026
EGF-like domain profile.
PGH1_SHEEP
32-70
2
A:32-70
B:32-70
2
PEROXIDASE_3
PS50292
Animal heme peroxidase superfamily profile.
PGH1_SHEEP
110-600
2
A:110-584
B:110-584
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
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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, 4)
Info
All SCOP Domains
1a: SCOP_d3kk6a2 (A:74-584)
1b: SCOP_d3kk6b2 (B:74-584)
2a: SCOP_d3kk6a1 (A:32-73)
2b: SCOP_d3kk6b1 (B:32-73)
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(
)
(
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(
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(
)
Superfamilies
(
)
(
)
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(
)
(
)
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)
Sheep (Ovis aries) [TaxId: 9940]
(23)
1a
d3kk6a2
A:74-584
1b
d3kk6b2
B:74-584
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)
Sheep (Ovis aries) [TaxId: 9940]
(23)
2a
d3kk6a1
A:32-73
2b
d3kk6b1
B:32-73
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3kk6A02 (A:74-583)
1b: CATH_3kk6B02 (B:74-583)
2a: CATH_3kk6A01 (A:33-73)
2b: CATH_3kk6B01 (B:33-73)
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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)
Domestic sheep,lambs,wild sheep (Ovis aries)
(1)
1a
3kk6A02
A:74-583
1b
3kk6B02
B:74-583
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Domestic sheep,lambs,wild sheep (Ovis aries)
(1)
2a
3kk6A01
A:33-73
2b
3kk6B01
B:33-73
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_An_peroxidase_3kk6B01 (B:142-582)
1b: PFAM_An_peroxidase_3kk6B02 (B:142-582)
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Clans
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: An_peroxidase]
(45)
Family
:
An_peroxidase
(45)
Ovis aries (Sheep)
(15)
1a
An_peroxidase-3kk6B01
B:142-582
1b
An_peroxidase-3kk6B02
B:142-582
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