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- PDB-9hba: Crystal structure of C35 bound to Hem -

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Basic information

Entry
Database: PDB / ID: 9hba
TitleCrystal structure of C35 bound to Hem
Components(Hemoglobin subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / Inhibitor / drug discovery
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / platelet aggregation / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / 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
: / ACETIC ACID / 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: 1.51 Å
AuthorsBrear, P. / Marchesani, F. / De Bei, O. / Spyrakis, F. / Lazzarato, L. / Ronda, L.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal structure of C35 bound to Hem
Authors: Marchesani, F. / De Bei, O. / Brear, P. / Spyrakis, F. / Lazzarato, L. / Ronda, L.
History
DepositionNov 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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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)68,82748
Polymers62,0814
Non-polymers6,74644
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19380 Å2
ΔGint-323 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.178, 92.178, 142.973
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 BL21(DE3) (bacteria) / References: UniProt: P68871

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Non-polymers , 9 types, 367 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.: 6 / Source method: obtained synthetically / 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.: 3 / Source method: obtained synthetically / Formula: C19H14N4O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / 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.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 56.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.0 M Ammonium sulfate; 1% (w/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.51→53.255 Å / Num. obs: 110596 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.022 / Rrim(I) all: 0.097 / Net I/σ(I): 14.5
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 14.6 % / Rmerge(I) obs: 4.399 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 5481 / CC1/2: 0.324 / Rpim(I) all: 1.178 / Rrim(I) all: 4.559

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→53.255 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.481 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2149 5451 4.961 %
Rwork0.1844 104424 -
all0.186 --
obs-109875 99.403 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.315 Å20 Å2
2--0.63 Å2-0 Å2
3----2.043 Å2
Refinement stepCycle: LAST / Resolution: 1.51→53.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 0 412 323 5098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124929
X-RAY DIFFRACTIONr_bond_other_d0.0090.0154445
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.7076743
X-RAY DIFFRACTIONr_angle_other_deg0.5481.62510273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2865576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.615512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68610712
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0110182
X-RAY DIFFRACTIONr_chiral_restr0.080.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025616
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02998
X-RAY DIFFRACTIONr_nbd_refined0.2560.21167
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24122
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22364
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.22417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2209
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2510.243
X-RAY DIFFRACTIONr_nbd_other0.2650.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.222
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0570.21
X-RAY DIFFRACTIONr_mcbond_it2.3113.042309
X-RAY DIFFRACTIONr_mcbond_other2.2673.0392308
X-RAY DIFFRACTIONr_mcangle_it2.6544.5472878
X-RAY DIFFRACTIONr_mcangle_other2.6554.5472879
X-RAY DIFFRACTIONr_scbond_it4.163.5472620
X-RAY DIFFRACTIONr_scbond_other4.163.5492621
X-RAY DIFFRACTIONr_scangle_it5.725.1293865
X-RAY DIFFRACTIONr_scangle_other5.7195.133866
X-RAY DIFFRACTIONr_lrange_it6.82248.6645714
X-RAY DIFFRACTIONr_lrange_other6.82248.6695715
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.51-1.5490.4723680.43770330.43880510.4820.57191.92650.433
1.549-1.5920.3963730.39475420.39479180.8670.86599.96210.395
1.592-1.6380.3423850.35372760.35376620.8880.87899.98690.357
1.638-1.6880.3434070.32370400.32474470.8870.8981000.325
1.688-1.7440.3063630.28768740.28872370.9210.9291000.285
1.744-1.8050.2853250.24966620.25169870.9330.9511000.238
1.805-1.8730.2493260.21664370.21767640.9570.96699.98520.197
1.873-1.9490.2253160.19162260.19365420.9650.9741000.169
1.949-2.0360.2113090.17358990.17562090.9730.9899.98390.148
2.036-2.1350.2162990.16357170.16660170.9720.98399.98340.139
2.135-2.250.2073000.15254120.15557120.9740.9851000.128
2.25-2.3860.1762580.14951310.1553890.980.9861000.125
2.386-2.5510.1782480.14548630.14751110.980.9881000.122
2.551-2.7550.2032550.16144870.16347420.9730.9841000.139
2.755-3.0170.1992250.15841630.1643880.9740.9851000.14
3.017-3.3710.2011730.1738110.17139840.9730.9821000.154
3.371-3.890.1841830.16233690.16335520.980.9841000.157
3.89-4.7580.181430.16228840.16330270.9810.9841000.165
4.758-6.7030.261160.21222670.21523830.9710.9761000.219
6.703-53.2550.19790.17913310.1814100.980.9791000.202

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