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- PDB-7jxt: Ovine COX-1 in complex with the subtype-selective derivative 2a -

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Basic information

Entry
Database: PDB / ID: 7jxt
TitleOvine COX-1 in complex with the subtype-selective derivative 2a
ComponentsProstaglandin G/H synthase 1Cyclooxygenase
KeywordsOXIDOREDUCTASE/INHIBITOR / Cyclooxygenase-1 / oxidoreductase inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / peroxidase activity / regulation of blood pressure / response to oxidative stress / intracellular membrane-bounded organelle / heme binding ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / prostaglandin biosynthetic process / dioxygenase activity / peroxidase activity / regulation of blood pressure / response to oxidative stress / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-W8M / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsKo, Y. / Iaselli, M. / Miciaccia, M. / Friedrich, L. / Schneider, G. / Scilimati, A. / Cingolani, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD017987 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA56036 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD023479 United States
CitationJournal: Adv Sci / Year: 2021
Title: Learning from Nature: From a Marine Natural Product to Synthetic Cyclooxygenase-1 Inhibitors by Automated De Novo Design.
Authors: Friedrich, L. / Cingolani, G. / Ko, Y.H. / Iaselli, M. / Miciaccia, M. / Perrone, M.G. / Neukirch, K. / Bobinger, V. / Merk, D. / Hofstetter, R.K. / Werz, O. / Koeberle, A. / Scilimati, A. / Schneider, G.
History
DepositionAug 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prostaglandin G/H synthase 1
B: Prostaglandin G/H synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,39112
Polymers127,6242
Non-polymers4,76610
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-18 kcal/mol
Surface area42100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.600, 181.600, 103.401
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 32 through 78 or (resid 79...
21(chain B and (resid 32 through 168 or (resid 169...
12chain C
22chain D
13chain E
23chain F
33chain G
43chain H
53chain I
63chain J

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 32 through 78 or (resid 79...A32 - 78
121(chain A and (resid 32 through 78 or (resid 79...A79
131(chain A and (resid 32 through 78 or (resid 79...A32 - 584
141(chain A and (resid 32 through 78 or (resid 79...A32 - 584
151(chain A and (resid 32 through 78 or (resid 79...A32 - 584
161(chain A and (resid 32 through 78 or (resid 79...A32 - 584
211(chain B and (resid 32 through 168 or (resid 169...B32 - 168
221(chain B and (resid 32 through 168 or (resid 169...B169
231(chain B and (resid 32 through 168 or (resid 169...B32 - 584
241(chain B and (resid 32 through 168 or (resid 169...B32 - 584
251(chain B and (resid 32 through 168 or (resid 169...B32 - 584
261(chain B and (resid 32 through 168 or (resid 169...B32 - 584
112chain CC901
212chain DD901
113chain EE1 - 2
213chain FF1 - 2
313chain GG1 - 2
413chain HH1 - 2
513chain II1 - 2
613chain JJ1 - 2

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Prostaglandin G/H synthase 1 / Cyclooxygenase / Cyclooxygenase-1 / COX-1 / Prostaglandin H2 synthase 1 / PHS 1 / Prostaglandin-endoperoxide synthase 1


Mass: 63812.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: PTGS1, COX1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P05979, prostaglandin-endoperoxide synthase
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#4: Chemical ChemComp-W8M / 2-[4,5-bis(2-chlorophenyl)-1H-imidazol-2-yl]-6-(prop-2-en-1-yl)phenyl methoxyacetate


Mass: 493.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H22Cl2N2O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.5-0.9 M LiCl, 0.7 M sodium citrate pH 6.5, 1 mM sodium azide and 0.3 %(w/v) beta-OG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 27285 / % possible obs: 97.8 % / Redundancy: 4.4 % / CC1/2: 0.96 / Rpim(I) all: 0.069 / Rsym value: 0.123 / Net I/σ(I): 31.7
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1397 / CC1/2: 0.33 / Rpim(I) all: 0.436 / Rsym value: 0.844 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WBE

5wbe


Resolution: 3.35→14.99 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 2.25 / Phase error: 33.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1163 5.04 %
Rwork0.2097 21925 -
obs0.2117 23088 83.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 220.14 Å2 / Biso mean: 126.1022 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.35→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8947 0 520 0 9467
Biso mean--137.67 --
Num. residues----1106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039570
X-RAY DIFFRACTIONf_angle_d0.63513029
X-RAY DIFFRACTIONf_dihedral_angle_d16.9983419
X-RAY DIFFRACTIONf_chiral_restr0.0391376
X-RAY DIFFRACTIONf_plane_restr0.0051657
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5467X-RAY DIFFRACTION4.44TORSIONAL
12B5467X-RAY DIFFRACTION4.44TORSIONAL
21A14X-RAY DIFFRACTION4.44TORSIONAL
22B14X-RAY DIFFRACTION4.44TORSIONAL
31E0X-RAY DIFFRACTION4.44TORSIONAL
32F0X-RAY DIFFRACTION4.44TORSIONAL
33G0X-RAY DIFFRACTION4.44TORSIONAL
34H0X-RAY DIFFRACTION4.44TORSIONAL
35I0X-RAY DIFFRACTION4.44TORSIONAL
36J0X-RAY DIFFRACTION4.44TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.35-3.50.4241080.39271980208861
3.5-3.680.34871290.33742317244671
3.68-3.910.34861300.29642559268978
3.91-4.210.24271540.24652856301087
4.21-4.620.2571560.19793036319292
4.62-5.260.24171580.20083054321293
5.26-6.530.25211690.22773130329994
6.53-14.990.20161590.15212993315289
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.18930.1010.02090.0956-0.0593-0.0388-0.16150.62010.556-0.15930.2281-1.03540.44460.65030.00061.0069-0.0221-0.08551.08570.07050.936637.1948134.145520.3241
20.057-0.0517-0.0337-0.0144-0.0071-0.1382-0.2533-0.04890.02061.21020.2837-0.09240.4146-0.60160.00021.1879-0.0742-0.13071.57720.03842.039152.387161.42127.9694
30.44070.02440.20430.31090.32770.62470.0175-0.2491-0.22180.5161-0.2037-0.03480.228-0.3824-0.00051.112-0.13130.04191.12530.00151.198630.7688150.189117.4394
40.0807-0.7752-0.85191.1232-0.11650.8893-0.0047-0.00180.1418-0.0689-0.12660.66840.0933-0.4193-0.00160.8597-0.02450.03891.10470.03430.994419.5954164.314825.0281
50.356-0.1573-0.33260.04980.10490.19630.02070.30680.6880.14430.06660.2062-0.7186-0.5705-0.00010.98270.14840.04121.3963-0.1231.18397.4094178.339920.9637
60.7612-0.00250.50720.90880.15530.23660.08960.4150.2697-0.355-0.35880.4013-0.3975-0.4274-0.00010.81010.11920.01531.0950.04731.018624.1222180.288811.2105
70.66330.45710.78921.3372-1.05932.14560.0466-0.2866-0.2520.3439-0.1321-0.02130.1715-0.223500.9521-0.040.04441.22990.00581.153627.1649161.8532.6831
81.6103-0.57330.28330.12110.04710.39960.14320.1543-0.02090.207-0.0266-0.2298-0.4744-0.1588-00.9441-0.01730.08591.0806-0.05961.076133.8141172.975920.7907
90.4845-0.643-0.80710.9127-0.22720.57430.08580.0577-0.6767-0.2513-0.1818-0.26480.1997-0.0803-0.00011.18010.0356-0.01881.3999-0.04171.412141.2874165.4305-10.9755
101.10290.03590.01611.9102-0.3431.7984-0.00060.0857-0.0065-0.23980.0040.0702-0.0032-0.2803-00.7742-0.0068-0.04091.0792-0.02090.954424.3372147.5523-15.0324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 73 )A32 - 73
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 107 )A74 - 107
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 163 )A108 - 163
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 253 )A164 - 253
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 295 )A254 - 295
6X-RAY DIFFRACTION6chain 'A' and (resid 296 through 346 )A296 - 346
7X-RAY DIFFRACTION7chain 'A' and (resid 347 through 509 )A347 - 509
8X-RAY DIFFRACTION8chain 'A' and (resid 510 through 584 )A510 - 584
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 143 )B32 - 143
10X-RAY DIFFRACTION10chain 'B' and (resid 144 through 584 )B144 - 584

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