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3N8X
Asym. Unit
Info
Asym.Unit (395 KB)
Biol.Unit 1 (385 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CYCLOOXYGENASE-1 IN COMPLEX WITH NIMESULIDE
Authors
:
J. Y. Lee
Date
:
28 May 10 (Deposition) - 28 Jul 10 (Release) - 01 Sep 10 (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, Nimesulide, Merohedral Twinned, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. S. Sidhu, J. Y. Lee, C. Yuan, W. L. Smith
Comparison Of Cyclooxygenase-1 Crystal Structures: Cross-Talk Between Monomers Comprising Cyclooxygenase-1 Homodimers
Biochemistry V. 49 7069 2010
[
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Hetero Components
(5, 19)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: B-OCTYLGLUCOSIDE (BOGa)
2b: B-OCTYLGLUCOSIDE (BOGb)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
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)
5a: 4-NITRO-2-PHENOXYMETHANESULFONANIL... (NIMa)
5b: 4-NITRO-2-PHENOXYMETHANESULFONANIL... (NIMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
BOG
2
Ligand/Ion
B-OCTYLGLUCOSIDE
3
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NIM
2
Ligand/Ion
4-NITRO-2-PHENOXYMETHANESULFONANILIDE
[
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]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:202 , GLN A:203 , THR A:206 , HIS A:207 , PHE A:210 , LYS A:211 , THR A:212 , ASN A:382 , TYR A:385 , HIS A:386 , HIS A:388 , MET A:391 , ILE A:444 , VAL A:447
BINDING SITE FOR RESIDUE HEM A 601
02
AC2
SOFTWARE
ASN A:68 , ASP A:584 , NAG A:662
BINDING SITE FOR RESIDUE NAG A 661
03
AC3
SOFTWARE
NAG A:661
BINDING SITE FOR RESIDUE NAG A 662
04
AC4
SOFTWARE
ASN A:144 , TYR A:147 , NAG A:672 , LEU B:238 , GLU B:239
BINDING SITE FOR RESIDUE NAG A 671
05
AC5
SOFTWARE
MET A:216 , NAG A:671 , BMA A:673 , LEU B:238 , TYR B:242
BINDING SITE FOR RESIDUE NAG A 672
06
AC6
SOFTWARE
NAG A:672 , BMA A:674
BINDING SITE FOR RESIDUE BMA A 673
07
AC7
SOFTWARE
BMA A:673 , BMA A:675
BINDING SITE FOR RESIDUE BMA A 674
08
AC8
SOFTWARE
BMA A:674 , GLN B:243
BINDING SITE FOR RESIDUE BMA A 675
09
AC9
SOFTWARE
TYR A:402 , GLN A:406 , ASN A:410 , MET A:413 , ASP A:416
BINDING SITE FOR RESIDUE NAG A 681
10
BC1
SOFTWARE
HOH A:14 , ARG A:120 , VAL A:349 , LEU A:352 , SER A:353 , TYR A:355 , PHE A:518 , ILE A:523 , GLY A:526 , ALA A:527 , SER A:530 , LEU A:531
BINDING SITE FOR RESIDUE NIM A 701
11
BC2
SOFTWARE
ALA B:199 , GLN B:203 , HIS B:207 , PHE B:210 , THR B:212 , LEU B:295 , ASN B:382 , TYR B:385 , HIS B:386 , TRP B:387 , HIS B:388 , MET B:391 , ASP B:450 , HOH B:597
BINDING SITE FOR RESIDUE HEM B 601
12
BC3
SOFTWARE
TYR B:55 , ASN B:68 , ASP B:584 , HOH B:618
BINDING SITE FOR RESIDUE NAG B 1661
13
BC4
SOFTWARE
GLY A:278 , ILE A:279 , PRO A:281 , TYR B:402 , GLN B:406 , ASN B:410 , MET B:413 , ASP B:416 , NAG B:1682
BINDING SITE FOR RESIDUE NAG B 1681
14
BC5
SOFTWARE
GLN A:282 , HOH B:5 , GLN B:400 , TYR B:402 , HOH B:610 , NAG B:1681
BINDING SITE FOR RESIDUE NAG B 1682
15
BC6
SOFTWARE
LEU A:238 , GLU B:140 , ASN B:144 , TYR B:147 , PHE B:220 , HOH B:613 , NAG B:1672
BINDING SITE FOR RESIDUE NAG B 1671
16
BC7
SOFTWARE
MET B:216 , NAG B:1671
BINDING SITE FOR RESIDUE NAG B 1672
17
BC8
SOFTWARE
HIS B:90 , ARG B:120 , VAL B:349 , LEU B:352 , SER B:353 , TYR B:355 , PHE B:518 , MET B:522 , ILE B:523 , GLY B:526 , ALA B:527 , LEU B:531
BINDING SITE FOR RESIDUE NIM B 1701
18
BC9
SOFTWARE
ARG B:83 , PRO B:86 , ILE B:89 , LEU B:112 , LEU B:115 , ARG B:120 , LEU B:123 , GLU B:524
BINDING SITE FOR RESIDUE BOG B 1751
19
CC1
SOFTWARE
PRO B:84 , SER B:85 , SER B:87 , PHE B:88 , PHE B:91
BINDING SITE FOR RESIDUE BOG B 1752
[
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]
SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are not available)
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:
Select:
Label:
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
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3n8xa2 (A:74-584)
1b: SCOP_d3n8xb2 (B:74-584)
2a: SCOP_d3n8xa1 (A:32-73)
2b: SCOP_d3n8xb1 (B:32-73)
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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
d3n8xa2
A:74-584
1b
d3n8xb2
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
d3n8xa1
A:32-73
2b
d3n8xb1
B:32-73
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_An_peroxidase_3n8xB01 (B:142-582)
1b: PFAM_An_peroxidase_3n8xB02 (B:142-582)
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Clans
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(
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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-3n8xB01
B:142-582
1b
An_peroxidase-3n8xB02
B:142-582
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]
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