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- PDB-7jy1: Structure of HbA with compound 19 -

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Basic information

Entry
Database: PDB / ID: 7jy1
TitleStructure of HbA with compound 19
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / hemoglobin
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / 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 / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Chem-VOP / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsJasti, J.
CitationJournal: J.Med.Chem. / Year: 2021
Title: PF-07059013: A Noncovalent Modulator of Hemoglobin for Treatment of Sickle Cell Disease.
Authors: Gopalsamy, A. / Aulabaugh, A.E. / Barakat, A. / Beaumont, K.C. / Cabral, S. / Canterbury, D.P. / Casimiro-Garcia, A. / Chang, J.S. / Chen, M.Z. / Choi, C. / Dow, R.L. / Fadeyi, O.O. / Feng, ...Authors: Gopalsamy, A. / Aulabaugh, A.E. / Barakat, A. / Beaumont, K.C. / Cabral, S. / Canterbury, D.P. / Casimiro-Garcia, A. / Chang, J.S. / Chen, M.Z. / Choi, C. / Dow, R.L. / Fadeyi, O.O. / Feng, X. / France, S.P. / Howard, R.M. / Janz, J.M. / Jasti, J. / Jasuja, R. / Jones, L.H. / King-Ahmad, A. / Knee, K.M. / Kohrt, J.T. / Limberakis, C. / Liras, S. / Martinez, C.A. / McClure, K.F. / Narayanan, A. / Narula, J. / Novak, J.J. / O'Connell, T.N. / Parikh, M.D. / Piotrowski, D.W. / Plotnikova, O. / Robinson, R.P. / Sahasrabudhe, P.V. / Sharma, R. / Thuma, B.A. / Vasa, D. / Wei, L. / Wenzel, A.Z. / Withka, J.M. / Xiao, J. / Yayla, H.G.
History
DepositionAug 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,40221
Polymers62,0814
Non-polymers5,32117
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-119 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.720, 81.390, 64.500
Angle α, β, γ (deg.)90.000, 97.270, 90.000
Int Tables number4
Space group name H-MP1211

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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: Homo sapiens (human) / 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: Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 5 types, 443 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6


Mass: 264.315 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C12H24O6
#6: Chemical ChemComp-VOP / [6-{(1S)-1-[(2-amino-6-fluoroquinolin-3-yl)oxy]ethyl}-5-(1H-pyrazol-1-yl)-1H-indazol-1-yl]acetic acid


Mass: 446.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H19FN6O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M lithium sulfate, 30-32% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→63.98 Å / Num. obs: 64632 / % possible obs: 87.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 12.2 / Num. measured all: 218020
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.59-1.683.50.56835361101430.7340.3540.6722.294.6
5.03-63.983.20.029756023270.9980.0190.03531.896.6

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3WHM

3whm


Resolution: 1.59→63.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.099 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3230 5 %RANDOM
Rwork0.171 ---
obs0.172 64601 87.4 %-
Displacement parametersBiso max: 114.22 Å2 / Biso mean: 26.13 Å2 / Biso min: 8.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.0795 Å20 Å20.9707 Å2
2---2.3745 Å20 Å2
3---0.295 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.59→63.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 372 426 5182
Biso mean--28.57 37.4 -
Num. residues----574
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1650SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes837HARMONIC5
X-RAY DIFFRACTIONt_it4971HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion582SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6078SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4971HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6798HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion16.65
LS refinement shellResolution: 1.59→1.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 243 4.92 %
Rwork0.198 4698 -
all0.2 4941 -
obs--90.77 %
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)
10.9066-0.01840.16170.3715-0.0460.3455-0.0141-0.1057-0.06720.02860.00770.0510.0194-0.08180.0064-0.17320.00650.0095-0.17040.0132-0.14675.1645-8.460425.7929
21.19070.26520.13980.87370.0930.6121-0.0337-0.03420.1528-0.04280.02360.0063-0.04630.01080.0102-0.1780.0056-0.0086-0.1951-0.0085-0.142322.28639.187525.5857
30.9878-0.02720.14250.4996-0.2390.67490.00370.2516-0.0831-0.0892-0.0166-0.00030.10940.1130.0128-0.16480.00640.0112-0.1242-0.0339-0.184519.8752-8.8239-1.3108
41.51750.1774-0.41160.9463-0.20661.3972-0.01270.28990.2820.03220.12430.0711-0.0952-0.1822-0.1115-0.1330.0039-0.0121-0.07480.0695-0.06582.78788.6804-1.3813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 141
2X-RAY DIFFRACTION2{ B|* }B1 - 146
3X-RAY DIFFRACTION3{ C|* }C1 - 141
4X-RAY DIFFRACTION4{ D|* }D1 - 146

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