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- PDB-5kir: The Structure of Vioxx Bound to Human COX-2 -

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Basic information

Entry
Database: PDB / ID: 5kir
TitleThe Structure of Vioxx Bound to Human COX-2
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE / cyclooxyrgenase / Vioxx / Rofecoxib / COX
Function / homology
Function and homology information


Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / positive regulation of platelet-derived growth factor production / Biosynthesis of DHA-derived SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / Synthesis of 15-eicosatetraenoic acid derivatives / positive regulation of fibroblast growth factor production / cellular response to non-ionic osmotic stress / lipoxygenase pathway ...Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / positive regulation of platelet-derived growth factor production / Biosynthesis of DHA-derived SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / Synthesis of 15-eicosatetraenoic acid derivatives / positive regulation of fibroblast growth factor production / cellular response to non-ionic osmotic stress / lipoxygenase pathway / positive regulation of transforming growth factor beta production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of prostaglandin biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / regulation of neuroinflammatory response / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / : / response to selenium ion / positive regulation of fever generation / prostaglandin secretion / cellular response to fluid shear stress / response to nematode / nuclear inner membrane / prostaglandin biosynthetic process / positive regulation of cell migration involved in sprouting angiogenesis / long-chain fatty acid biosynthetic process / Interleukin-10 signaling / nuclear outer membrane / positive regulation of vascular endothelial growth factor production / decidualization / brown fat cell differentiation / positive regulation of brown fat cell differentiation / embryo implantation / peroxidase activity / regulation of blood pressure / positive regulation of nitric oxide biosynthetic process / regulation of cell population proliferation / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / response to oxidative stress / neuron projection / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / protein homodimerization activity / metal ion binding / cytosol / 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 ...: / 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
PROTOPORPHYRIN IX CONTAINING CO / AMMONIUM ION / PHOSPHATE ION / Rofecoxib / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.697 Å
AuthorsOrlando, B.J. / Malkowski, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 115386 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of rofecoxib bound to human cyclooxygenase-2.
Authors: Orlando, B.J. / Malkowski, M.G.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_conn_angle / 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.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.pdbx_aromatic_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,00419
Polymers126,8232
Non-polymers4,18117
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-63 kcal/mol
Surface area41530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.989, 149.422, 185.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Prostaglandin G/H synthase 2 / Cyclooxygenase-2 / COX-2 / PHS II / Prostaglandin H2 synthase 2 / PGHS-2 / Prostaglandin- ...Cyclooxygenase-2 / COX-2 / PHS II / Prostaglandin H2 synthase 2 / PGHS-2 / Prostaglandin-endoperoxide synthase 2


Mass: 63411.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTGS2, COX2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P35354, prostaglandin-endoperoxide synthase

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Sugars , 2 types, 4 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 167 molecules

#3: Chemical ChemComp-RCX / Rofecoxib / Vioxx


Mass: 314.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C17H14O4S / Comment: antiinflammatory*YM
#4: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32CoN4O4
#6: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG400, ammonium phosphate, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→30 Å / Num. obs: 48415 / % possible obs: 100 % / Redundancy: 7.1 % / Net I/σ(I): 17.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HS5

3hs5


Resolution: 2.697→30.029 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 2219 4.89 %
Rwork0.1781 --
obs0.1801 45368 93.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.697→30.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8916 0 274 154 9344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059485
X-RAY DIFFRACTIONf_angle_d1.27512901
X-RAY DIFFRACTIONf_dihedral_angle_d14.6563488
X-RAY DIFFRACTIONf_chiral_restr0.1331354
X-RAY DIFFRACTIONf_plane_restr0.0051658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6968-2.75540.26371000.21031709X-RAY DIFFRACTION60
2.7554-2.81940.22861000.21981995X-RAY DIFFRACTION70
2.8194-2.88990.3055970.22812252X-RAY DIFFRACTION78
2.8899-2.9680.25761270.22262487X-RAY DIFFRACTION87
2.968-3.05520.26711510.21862717X-RAY DIFFRACTION95
3.0552-3.15370.26991430.22382826X-RAY DIFFRACTION99
3.1537-3.26630.3071520.21892888X-RAY DIFFRACTION100
3.2663-3.39690.23621510.20472872X-RAY DIFFRACTION100
3.3969-3.55130.22141410.1842910X-RAY DIFFRACTION100
3.5513-3.73820.20711400.17432892X-RAY DIFFRACTION100
3.7382-3.97190.20311610.1592867X-RAY DIFFRACTION100
3.9719-4.27780.20171530.15572879X-RAY DIFFRACTION100
4.2778-4.70680.19681450.14082924X-RAY DIFFRACTION100
4.7068-5.38450.18751590.13992913X-RAY DIFFRACTION100
5.3845-6.7710.22061580.18122959X-RAY DIFFRACTION100
6.771-30.03070.18641410.17613059X-RAY DIFFRACTION100
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)
12.9137-0.6248-0.47012.1189-0.95580.64040.0596-0.11740.07390.69990.20790.9914-0.3098-0.5411-0.04530.44750.15860.17620.46280.10410.56547.101727.329239.8511
21.3350.6627-0.31032.1769-0.21242.2322-0.07430.3979-0.5106-0.3330.13470.24380.3078-0.1668-0.04370.2494-0.0691-0.07390.4282-0.17920.5512.35180.332325.6085
31.3584-0.0294-0.09751.8339-0.19050.8895-0.0516-0.0597-0.42090.25090.0266-0.52090.07630.12070.02160.22480.061-0.0540.1936-0.07050.440139.555310.24633.3473
41.1659-0.6201-0.83831.5643-0.20440.9875-0.2413-0.2617-0.67690.46520.1204-0.41730.11050.18840.00870.36150.015-0.1680.30410.05430.719839.41182.667939.7198
51.32680.0435-0.32292.2122-0.35241.4724-0.0201-0.1655-0.77550.4592-0.0108-0.08720.0678-0.0940.0830.27540.0181-0.06070.1917-0.07490.432527.79114.156338.8979
60.39560.35820.26381.36640.05321.0223-0.04850.5451-0.3179-0.7905-0.0477-0.13510.10670.0361-0.93770.8957-0.09750.10480.7615-0.36090.367536.171913.6108-3.135
72.2103-0.7780.68810.9102-0.71350.577-0.25650.34310.115-0.62960.1470.1080.0413-0.1546-0.11750.477-0.0457-0.20480.5253-0.07530.391522.439229.7766.0668
82.334-1.3292-0.61632.55931.69473.1842-0.20620.65640.1339-1.0301-0.0745-0.83770.02270.55340.29810.6813-0.12490.19550.7662-0.00990.471647.821434.5749-1.3182
91.45710.12-0.4172.4775-0.03071.4559-0.0940.16720.3858-0.04920.20590.0291-0.34690.0443-0.08430.3630.0231-0.12650.2291-0.00470.284629.917848.426121.48
100.8182-0.08170.25441.8595-0.25660.8701-0.09360.5510.2338-0.72580.08780.0777-0.19750.05350.02810.53-0.0715-0.07570.50690.02670.266830.525740.9285.1204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 34:73)
2X-RAY DIFFRACTION2(chain A and resid 74:122)
3X-RAY DIFFRACTION3(chain A and resid 123:367)
4X-RAY DIFFRACTION4(chain A and resid 368:419)
5X-RAY DIFFRACTION5(chain A and resid 420:583)
6X-RAY DIFFRACTION6(chain B and resid 34:78)
7X-RAY DIFFRACTION7(chain B and resid 79:147)
8X-RAY DIFFRACTION8(chain B and resid 148:183)
9X-RAY DIFFRACTION9(chain B and resid 184:429)
10X-RAY DIFFRACTION10(chain B and resid 430:583)

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