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- PDB-6xdt: Carbonmonoxy hemoglobin in complex with the antisickling agent me... -

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Basic information

Entry
Database: PDB / ID: 6xdt
TitleCarbonmonoxy hemoglobin in complex with the antisickling agent methyl 5-((2-formyl-4-methoxyphenoxy)methyl)picolinate
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Hemoglobin / Aromatic aldehyde / Antisickling / Allosteric effector
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid 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 / Chem-V1M / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPagare, P.P. / Safo, M.K. / Musayev, F.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)RO1MD009124 United States
National Institutes of Health/Office of the DirectorS10OD021756 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Exploration of Structure-Activity Relationship of Aromatic Aldehydes Bearing Pyridinylmethoxy-Methyl Esters as Novel Antisickling Agents.
Authors: Pagare, P.P. / Ghatge, M.S. / Chen, Q. / Musayev, F.N. / Venitz, J. / Abdulmalik, O. / Zhang, Y. / Safo, M.K.
History
DepositionJun 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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)65,23414
Polymers62,0814
Non-polymers3,15310
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-120 kcal/mol
Surface area23380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.681, 82.977, 105.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 natural source / Source: (natural) 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 553 molecules

#3: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-V1M / methyl 5-[(4-methoxy-2-methylphenoxy)methyl]pyridine-2-carboxylate


Mass: 287.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.4 / Details: 25% PEG 6000, 100 mM HEPES buffer

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.9→29.32 Å / Num. obs: 40600 / % possible obs: 92.5 % / Redundancy: 4.27 % / Biso Wilson estimate: 29.53 Å2 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.062 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4331 / Rrim(I) all: 0.427 / % possible all: 86.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
CrystalClear2data collection
CrystalClear2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BBB

1bbb


Resolution: 1.9→29.319 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 2063 5.08 %
Rwork0.1881 38510 -
obs0.1909 40573 92.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.62 Å2 / Biso mean: 31.9909 Å2 / Biso min: 17.44 Å2
Refinement stepCycle: final / Resolution: 1.9→29.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 222 546 5152
Biso mean--29.52 36.9 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064758
X-RAY DIFFRACTIONf_angle_d0.9696508
X-RAY DIFFRACTIONf_chiral_restr0.035700
X-RAY DIFFRACTIONf_plane_restr0.005812
X-RAY DIFFRACTIONf_dihedral_angle_d15.9461626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.94420.37521240.2951233285
1.9442-1.99280.30741140.2656249792
1.9928-2.04670.31111220.2313250191
2.0467-2.10690.28781340.2188252492
2.1069-2.17490.25171370.1992251191
2.1749-2.25260.29131380.2005246991
2.2526-2.34270.271240.2031251891
2.3427-2.44930.24531560.204247891
2.4493-2.57840.26621350.2102251791
2.5784-2.73980.27371310.2062257492
2.7398-2.95110.22641260.2002259093
2.9511-3.24780.25191470.194264995
3.2478-3.71690.21931570.1768272197
3.7169-4.67990.20351620.1565277999
4.6799-29.3190.20981560.1643285096

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