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- PDB-6eha: Heme oxygenase 1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6eha
TitleHeme oxygenase 1 in complex with inhibitor
ComponentsHeme oxygenase 1HMOX1
KeywordsOXIDOREDUCTASE / heme oxygenase
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxidation / smooth muscle hyperplasia / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxidation / smooth muscle hyperplasia / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / heme catabolic process / cellular response to arsenic-containing substance / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / endothelial cell proliferation / Heme degradation / epithelial cell apoptotic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of macroautophagy / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of macroautophagy / The NLRP3 inflammasome / regulation of angiogenesis / Purinergic signaling in leishmaniasis infection / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of chemokine production / cellular response to cadmium ion / negative regulation of smooth muscle cell proliferation / macroautophagy / Iron uptake and transport / positive regulation of smooth muscle cell proliferation / response to nicotine / Heme signaling / response to hydrogen peroxide / Cytoprotection by HMOX1 / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / cellular response to hypoxia / Interleukin-4 and Interleukin-13 signaling / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / response to oxidative stress / mitochondrial outer membrane / intracellular signal transduction / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / extracellular space / nucleoplasm / membrane / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-B5B / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGrudnik, P. / Mieczkowski, M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2019
Title: Development and characterization of a new inhibitor of heme oxygenase activity for cancer treatment.
Authors: Mucha, O. / Podkalicka, P. / Mikulski, M. / Barwacz, S. / Andrysiak, K. / Biela, A. / Mieczkowski, M. / Kachamakova-Trojanowska, N. / Ryszawy, D. / Bialas, A. / Szelazek, B. / Grudnik, P. / ...Authors: Mucha, O. / Podkalicka, P. / Mikulski, M. / Barwacz, S. / Andrysiak, K. / Biela, A. / Mieczkowski, M. / Kachamakova-Trojanowska, N. / Ryszawy, D. / Bialas, A. / Szelazek, B. / Grudnik, P. / Majewska, E. / Michalik, K. / Jakubiec, K. / Bien, M. / Witkowska, N. / Gluza, K. / Ekonomiuk, D. / Sitarz, K. / Galezowski, M. / Brzozka, K. / Dubin, G. / Jozkowicz, A. / Dulak, J. / Loboda, A.
History
DepositionSep 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _entity.formula_weight
Revision 1.2May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme oxygenase 1
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5716
Polymers65,7212
Non-polymers1,8504
Water5,639313
1
A: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7853
Polymers32,8611
Non-polymers9252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7853
Polymers32,8611
Non-polymers9252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.411, 54.566, 72.540
Angle α, β, γ (deg.)90.00, 99.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heme oxygenase 1 / HMOX1 / HO-1


Mass: 32860.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1, HO, HO1 / Production host: Escherichia coli (E. coli)
References: UniProt: P09601, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-B5B / 1-(3-imidazol-1-ylpropyl)-5-(2-methylpropyl)-4-phenyl-imidazole


Mass: 308.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.08 M AmSO4 0.9 % (v/v) 1,6-hexanediol 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2→42.85 Å / Num. obs: 32213 / % possible obs: 100 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.1145 / Net I/σ(I): 5.28
Reflection shellResolution: 2→2.071 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5626 / Mean I/σ(I) obs: 1.65 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.048 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23876 1583 4.9 %RANDOM
Rwork0.1892 ---
obs0.19162 30597 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.538 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-2.26 Å2
2---1.66 Å2-0 Å2
3---1.39 Å2
Refinement stepCycle: 1 / Resolution: 2→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 132 313 3935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193725
X-RAY DIFFRACTIONr_bond_other_d0.0030.023549
X-RAY DIFFRACTIONr_angle_refined_deg1.5992.0095063
X-RAY DIFFRACTIONr_angle_other_deg1.09438140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6325426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31623.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45115635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9411526
X-RAY DIFFRACTIONr_chiral_restr0.1050.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214186
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02908
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.22.2851710
X-RAY DIFFRACTIONr_mcbond_other2.1842.2831709
X-RAY DIFFRACTIONr_mcangle_it3.4083.4162134
X-RAY DIFFRACTIONr_mcangle_other3.4133.4182135
X-RAY DIFFRACTIONr_scbond_it3.0772.6262015
X-RAY DIFFRACTIONr_scbond_other3.0762.6272016
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9563.7872930
X-RAY DIFFRACTIONr_long_range_B_refined7.67719.5174846
X-RAY DIFFRACTIONr_long_range_B_other7.67619.5214847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 123 -
Rwork0.283 2255 -
obs--99.92 %

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