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- PDB-5u3i: CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE C... -

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Basic information

Entry
Database: PDB / ID: 5u3i
TitleCRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE CELL HEMOGLOBIN) COMPLEXED WITH GBT compound 31
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / R2 QUATERNARY STATE
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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 / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7SJ / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPartridge, J.R. / Choy, R.M. / Li, Z. / Metcalf, B.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin.
Authors: Metcalf, B. / Chuang, C. / Dufu, K. / Patel, M.P. / Silva-Garcia, A. / Johnson, C. / Lu, Q. / Partridge, J.R. / Patskovska, L. / Patskovsky, Y. / Almo, S.C. / Jacobson, M.P. / Hua, L. / Xu, ...Authors: Metcalf, B. / Chuang, C. / Dufu, K. / Patel, M.P. / Silva-Garcia, A. / Johnson, C. / Lu, Q. / Partridge, J.R. / Patskovska, L. / Patskovsky, Y. / Almo, S.C. / Jacobson, M.P. / Hua, L. / Xu, Q. / Gwaltney, S.L. / Yee, C. / Harris, J. / Morgan, B.P. / James, J. / Xu, D. / Hutchaleelaha, A. / Paulvannan, K. / Oksenberg, D. / Li, Z.
History
DepositionDec 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Nov 27, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)64,95213
Polymers62,0214
Non-polymers2,9309
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-109 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.385, 59.040, 172.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 15860.216 Da / Num. of mol.: 2 / Mutation: E6V / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 64 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Chemical ChemComp-7SJ / 2-methoxy-5-({2-[1-(propan-2-yl)-1H-pyrazol-5-yl]pyridin-3-yl}methoxy)pyridine-4-carbaldehyde


Mass: 352.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 100 mM Hepes pH 7.4 20 mM NaCl 30 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 43683 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 48.57 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.018 / Rsym value: 0.06 / Net I/σ(I): 17.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.7 / Mean I/σ(I) obs: 1.7 / Rpim(I) all: 0.503 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+83 / Resolution: 1.95→29.805 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 2003 4.59 %
Rwork0.2062 --
obs0.2084 43667 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→29.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 205 55 4633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094739
X-RAY DIFFRACTIONf_angle_d0.9716506
X-RAY DIFFRACTIONf_dihedral_angle_d15.5342690
X-RAY DIFFRACTIONf_chiral_restr0.045705
X-RAY DIFFRACTIONf_plane_restr0.006811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.38021450.34692918X-RAY DIFFRACTION100
1.9988-2.05280.43491410.33982969X-RAY DIFFRACTION100
2.0528-2.11320.3711370.31522935X-RAY DIFFRACTION100
2.1132-2.18140.32831380.2842902X-RAY DIFFRACTION100
2.1814-2.25930.32091350.27492922X-RAY DIFFRACTION100
2.2593-2.34970.33181490.26782966X-RAY DIFFRACTION100
2.3497-2.45660.28311440.24852945X-RAY DIFFRACTION100
2.4566-2.58610.29151390.24382961X-RAY DIFFRACTION100
2.5861-2.7480.321480.25532949X-RAY DIFFRACTION100
2.748-2.960.28141380.24672978X-RAY DIFFRACTION100
2.96-3.25750.27571480.24312975X-RAY DIFFRACTION100
3.2575-3.72810.26261430.20693014X-RAY DIFFRACTION100
3.7281-4.69410.21111450.16583035X-RAY DIFFRACTION100
4.6941-29.80830.2031530.16073195X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.8883 Å / Origin y: -2.5457 Å / Origin z: -21.664 Å
111213212223313233
T0.2906 Å2-0.0402 Å20.0953 Å2-0.2821 Å20.0456 Å2--0.4237 Å2
L2.1171 °20.6146 °20.8858 °2-3.7542 °23.8759 °2--9.9408 °2
S0.0555 Å °-0.1106 Å °0.2133 Å °0.5324 Å °-0.2851 Å °0.3433 Å °0.897 Å °-0.2368 Å °0.0889 Å °
Refinement TLS groupSelection details: all

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