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- PDB-3kk6: Crystal Structure of Cyclooxygenase-1 in complex with celecoxib -

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Basic information

Entry
Database: PDB / ID: 3kk6
TitleCrystal Structure of Cyclooxygenase-1 in complex with celecoxib
ComponentsProstaglandin G/H synthase 1Cyclooxygenase
KeywordsOXIDOREDUCTASE / 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 / Prostaglandin biosynthesis / Transmembrane
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
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily ...Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-CEL / CITRATE ANION / PROTOPORPHYRIN IX CONTAINING FE / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsSidhu, R.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Coxibs interfere with the action of aspirin by binding tightly to one monomer of cyclooxygenase-1.
Authors: Rimon, G. / Sidhu, R.S. / Lauver, D.A. / Lee, J.Y. / Sharma, N.P. / Yuan, C. / Frieler, R.A. / Trievel, R.C. / Lucchesi, B.R. / Smith, W.L.
History
DepositionNov 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2013Group: Refinement description
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)133,73516
Polymers127,4482
Non-polymers6,28714
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21710 Å2
ΔGint78 kcal/mol
Surface area38810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.035, 181.035, 102.698
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 32:278 or resseq 282:584 ) and (not element H)
211chain B and (resseq 32:278 or resseq 282:584 ) and (not element H)

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.521844, -0.853041, -4.0E-5), (-0.853023, 0.521834, -0.006415), (0.005493, -0.003314, -0.999979)0.003363, 0.201833, 36.112499

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 63724.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: COX1, PTGS1 / Plasmid: PFASTBAC-HTOCOX-1 / Production host: Spodoptera Frugiperda (fall armyworm) / Strain (production host): SF21
References: UniProt: P05979, prostaglandin-endoperoxide synthase

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Sugars , 4 types, 9 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-3-2/a4-b1_b4-c1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 110 molecules

#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-CEL / 4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE / CELECOXIB / Celecoxib


Mass: 381.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14F3N3O2S / Comment: antiinflammatory, inhibitor*YM
#8: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMET TO LEU CONFLICT IN UNP ENTRY P05979

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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: 3.81 Å3/Da / Density % sol: 67.73 %
Crystal growTemperature: 273 K / Method: vapor diffusion / pH: 6.5
Details: SODIUM CITRATE, LITHIUM CHLORIDE, SODIUM AZIDE, N-OCTYL GLUCOSIDE, pH 6.5, vapor diffusion, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 23.56 / Number: 366365 / Rmerge(I) obs: 0.079 / Χ2: 1.02 / D res high: 2.75 Å / D res low: 50 Å / Num. obs: 49685 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.925099.710.0380.9997.5
4.75.9210010.0621.157.7
4.114.710010.0590.9857.7
3.734.1110010.0640.9477.7
3.463.7310010.081.0987.7
3.263.4610010.1261.0687.7
3.13.2610010.191.0327.7
2.963.110010.2830.9837.7
2.852.9610010.4180.9537.3
2.752.8596.210.5470.9324.9
Reflection twinOperator: h,-h-k,-l / Fraction: 0.501
ReflectionResolution: 2.75→50 Å / Num. obs: 49685 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.75-2.854.90.547196.2
2.85-2.967.30.4181100
2.96-3.17.70.2831100
3.1-3.267.70.191100
3.26-3.467.70.1261100
3.46-3.737.70.081100
3.73-4.117.70.0641100
4.11-4.77.70.0591100
4.7-5.927.70.0621100
5.92-507.50.038199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å10 Å
Translation4 Å10 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q4G

1q4g


Resolution: 2.75→41.415 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: isotropic / σ(F): 0.14 / Phase error: 26.43 / Stereochemistry target values: TWIN_LSQ_F / Details: used twin operator (h,-h-k,-l)
RfactorNum. reflection% reflection
Rfree0.242 1992 4.1 %
Rwork0.2069 --
obs0.2083 48593 97.42 %
all-49685 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.414 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso mean: 70.522 Å2
Baniso -1Baniso -2Baniso -3
1--13.528 Å20 Å2-0 Å2
2---13.528 Å20 Å2
3----13.13 Å2
Refinement stepCycle: LAST / Resolution: 2.75→41.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8742 0 426 105 9273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918307
X-RAY DIFFRACTIONf_angle_d1.01332834
X-RAY DIFFRACTIONf_dihedral_angle_d18.6044574
X-RAY DIFFRACTIONf_chiral_restr0.0921414
X-RAY DIFFRACTIONf_plane_restr0.0072764
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4207X-RAY DIFFRACTIONPOSITIONAL
12B4207X-RAY DIFFRACTIONPOSITIONAL0.238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.79750.379810.3051953X-RAY DIFFRACTION98
2.7975-2.84830.322930.28692154X-RAY DIFFRACTION98
2.8483-2.90310.404910.28042231X-RAY DIFFRACTION98
2.9031-2.96230.32781010.27482300X-RAY DIFFRACTION98
2.9623-3.02670.307970.27432324X-RAY DIFFRACTION98
3.0267-3.09710.2834970.25972319X-RAY DIFFRACTION98
3.0971-3.17450.2693950.25452323X-RAY DIFFRACTION98
3.1745-3.26030.25611010.2582336X-RAY DIFFRACTION98
3.2603-3.35620.2341960.2482371X-RAY DIFFRACTION98
3.3562-3.46450.2875990.2362349X-RAY DIFFRACTION98
3.4645-3.58830.24990.21652378X-RAY DIFFRACTION98
3.5883-3.73190.29031010.19622371X-RAY DIFFRACTION98
3.7319-3.90160.1975970.19432379X-RAY DIFFRACTION98
3.9016-4.10710.2151010.17912385X-RAY DIFFRACTION98
4.1071-4.36420.2068990.15762375X-RAY DIFFRACTION98
4.3642-4.70070.16521030.15942411X-RAY DIFFRACTION98
4.7007-5.17290.2212990.1552402X-RAY DIFFRACTION98
5.1729-5.91960.17921030.18942399X-RAY DIFFRACTION98
5.9196-7.4510.27031030.21572421X-RAY DIFFRACTION98
7.451-41.420.24781030.19772453X-RAY DIFFRACTION98
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)
10.16270.17840.0370.15790.11910.46310.01010.0385-0.1231-0.1581-0.07410.0431-0.2704-0.09700.41330.241-0.06890.2565-0.03250.278-36.017752.0151-1.2038
20.3230.08450.07180.08980.0370.1611-0.0782-0.10170.0670.1530.0906-0.1688-0.086-0.10390.02780.38710.22-0.06520.2278-0.05730.2394-25.839957.322236.8645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 32:584 OR RESID 601:900 ) )A32 - 584
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 32:584 OR RESID 601:900 ) )A601 - 900
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 32:584 OR RESID 601:1752 ) )B32 - 584
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 32:584 OR RESID 601:1752 ) )B601 - 1752

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