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- PDB-1qxe: Structural Basis for the Potent Antisickling Effect of a Novel Cl... -

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Basic information

Entry
Database: PDB / ID: 1qxe
TitleStructural Basis for the Potent Antisickling Effect of a Novel Class of 5-Membered Heterocyclic Aldehydic Compounds
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / allosteric / antisickling / relaxed state / hemoglobin / sickle cell / 5-hydroxymethyl-2-furfural / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / 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 / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / 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 / blood microparticle / ficolin-1-rich granule lumen / 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 / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5-HYDROXYMETHYL-FURFURAL / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / isomorphous refinement / Resolution: 1.85 Å
AuthorsSafo, M.K. / Abdulmalik, O. / Danso-Danquah, R. / Nokuri, S. / Joshi, G.S. / Musayev, F.N. / Asakura, T. / Abraham, D.J.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Structural basis for the potent antisickling effect of a novel class of five-membered heterocyclic aldehydic compounds
Authors: Safo, M.K. / Abdulmalik, O. / Danso-Danquah, R. / Burnett, J.C. / Nokuri, S. / Joshi, G.S. / Musayev, F.N. / Asakura, T. / Abraham, D.J.
History
DepositionSep 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,60021
Polymers62,0814
Non-polymers3,51917
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12840 Å2
ΔGint-191 kcal/mol
Surface area23480 Å2
MethodPISA
2
A: Hemoglobin alpha chain
B: Hemoglobin beta chain
C: Hemoglobin alpha chain
D: Hemoglobin beta chain
hetero molecules

A: Hemoglobin alpha chain
B: Hemoglobin beta chain
C: Hemoglobin alpha chain
D: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,19942
Polymers124,1628
Non-polymers7,03734
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area28260 Å2
ΔGint-444 kcal/mol
Surface area44770 Å2
MethodPISA
3
A: Hemoglobin alpha chain
B: Hemoglobin beta chain
hetero molecules

A: Hemoglobin alpha chain
B: Hemoglobin beta chain
hetero molecules

C: Hemoglobin alpha chain
D: Hemoglobin beta chain
hetero molecules

C: Hemoglobin alpha chain
D: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,19942
Polymers124,1628
Non-polymers7,03734
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation3_665-x+y+1,-x+1,z+1/31
crystal symmetry operation6_665-x+1,-x+y+1,-z+2/31
Buried area23720 Å2
ΔGint-406 kcal/mol
Surface area49310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.857, 91.857, 143.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11D-1001-

SO4

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2 / Fragment: alpha chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: erythrocytes / Organ: blood / References: UniProt: P69905
#2: Protein Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2 / Fragment: beta chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: erythrocytes / Organ: blood / References: UniProt: P68871

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Non-polymers , 5 types, 554 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-FUX / 5-HYDROXYMETHYL-FURFURAL / Hydroxymethylfurfural


Mass: 126.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.5
Details: ammonium phosphate and sulfate, pH 6.5, LIQUID DIFFUSION, temperature 298K
Crystal grow
*PLUS
pH: 6.4 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130-50 mg/mlprotein11
23.2-3.4 Msodium potassium phosphate11pH6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 4, 2002 / Details: mirrors
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→70 Å / Num. all: 56802 / Num. obs: 56802 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.5
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2940 / % possible all: 64.2
Reflection
*PLUS
Lowest resolution: 69.57 Å / Num. measured all: 286747
Reflection shell
*PLUS
% possible obs: 64.2 % / Num. unique obs: 2940 / Num. measured obs: 6589

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Processing

Software
NameClassification
bioteXdata collection
bioteXdata reduction
CNSrefinement
bioteXdata scaling
CNSphasing
RefinementMethod to determine structure: isomorphous refinement
Starting model: PDB entry 1QXD

1qxd


Resolution: 1.85→69.58 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2859 5 %RANDOM
Rwork0.184 ---
all0.19 56780 --
obs0.184 56780 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.7707 Å2 / ksol: 0.369354 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å22.02 Å20 Å2
2--2.8 Å20 Å2
3----5.59 Å2
Refine analyzeLuzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.85→69.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 231 537 5152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d1.4
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 342 4.8 %
Rwork0.293 6741 -
obs-6741 71.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM19X_JKNAP.HTOPH19X_JKNAP_O2
X-RAY DIFFRACTION4HMF_COV2.PARHMF_COV2.TOP
X-RAY DIFFRACTION5SULFATE.PARPROTEIN.LINK
Refinement
*PLUS
Lowest resolution: 69.57 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.89
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.4
LS refinement shell
*PLUS
Num. reflection Rwork: 698 / Num. reflection obs: 698

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