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- PDB-28od: Crystal structure of C35 bound to Hem -

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Basic information

Entry
Database: PDB / ID: 28od
TitleCrystal structure of C35 bound to Hem
Components(Hemoglobin subunit ...) x 2
KeywordsHYDROLASE
Function / homology
Function and homology information


cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / erythrocyte development / oxygen transport ...cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / erythrocyte development / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / oxygen carrier activity / blood vessel diameter maintenance / hydrogen peroxide catabolic process / response to hydrogen peroxide / carbon dioxide transport / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / Late endosomal microautophagy / platelet aggregation / regulation of blood pressure / positive regulation of nitric oxide biosynthetic process / Chaperone Mediated Autophagy / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / inflammatory response / iron ion binding / heme binding / Neutrophil degranulation / : / extracellular exosome / metal ion binding / extracellular region / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
: / ACETATE ION / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / TRIETHYLENE GLYCOL / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsBrear, P. / Marchesani, F. / De Bei, O. / Spyrakis, F. / Lazzarato, L. / Ronda, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: To be published
Title: ACE2 extracellular domain in complex with the macrocyclic peptide GR3.1.2
Authors: Marchesani, F. / De Bei, O. / Brear, P. / Spyrakis, F. / Lazzarato, L. / Ronda, L.
History
DepositionFeb 10, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,84652
Polymers62,0814
Non-polymers6,76548
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21270 Å2
ΔGint-391 kcal/mol
Surface area21720 Å2
Unit cell
Length a, b, c (Å)92.167, 92.167, 142.979
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Hemoglobin subunit ... , 2 types, 4 molecules ACBD

#1: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: P68871

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Non-polymers , 9 types, 396 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-A1ITR / 4-[2-[[5-(1H-indol-3-yl)-1,3,4-oxadiazol-2-yl]sulfanyl]ethanoylamino]benzoic acid / 4-[[2-[[5-(1H-indol-3-yl)-1,3,4-oxadiazol-2-yl]sulfanyl]acetyl]amino]benzoate


Mass: 394.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H14N4O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3.0 M Ammonium sulfate; 1% (wv) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 30, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.73→47.66 Å / Num. obs: 73941 / % possible obs: 100 % / Redundancy: 19.9 % / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.018 / Rrim(I) all: 0.081 / Χ2: 0.91 / Net I/σ(I): 21.1 / Num. measured all: 1474983
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 100 % / Redundancy: 20.2 % / Rmerge(I) obs: 1.332 / Num. measured all: 80482 / Num. unique obs: 3989 / CC1/2: 0.876 / Rpim(I) all: 0.303 / Rrim(I) all: 1.367 / Χ2: 0.77 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→47.66 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.078 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 3697 5 %RANDOM
Rwork0.16856 ---
obs0.17013 70178 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.352 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å2-0 Å2
3----2.28 Å2
Refinement stepCycle: 1 / Resolution: 1.73→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 422 348 5140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124927
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164515
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.8836744
X-RAY DIFFRACTIONr_angle_other_deg0.6341.75310369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3245574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.345552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24910712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021032
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_it2.32.8912306
X-RAY DIFFRACTIONr_mcbond_other2.2942.8912305
X-RAY DIFFRACTIONr_mcangle_it2.8655.1832872
X-RAY DIFFRACTIONr_mcangle_other2.8685.1832873
X-RAY DIFFRACTIONr_scbond_it4.5843.4472621
X-RAY DIFFRACTIONr_scbond_other4.2333.3342542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9975.8833753
X-RAY DIFFRACTIONr_long_range_B_refined7.09431.525727
X-RAY DIFFRACTIONr_long_range_B_other7.03931.295663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 324 -
Rwork0.239 5098 -
obs--99.96 %

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