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- PDB-5ufj: Crystal Structure of Carbonmonoxy Hemoglobin S (Liganded Sickle C... -

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Basic information

Entry
Database: PDB / ID: 5ufj
TitleCrystal Structure of Carbonmonoxy Hemoglobin S (Liganded Sickle Cell Hemoglobin) Complexed with GBT Compound 6
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-86M / 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: 2.05 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
DepositionJan 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Atomic model / Database references
Revision 1.2Oct 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 / struct_conn_type
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

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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)65,16614
Polymers62,0214
Non-polymers3,14510
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-112 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.411, 58.881, 174.386
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, 40 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-86M / 5-[(imidazo[1,2-a]pyridin-8-yl)methoxy]-2-methoxypyridine-4-carbaldehyde


Mass: 283.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13N3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Hepes pH 7.4, 40 mM NaCl, 29 % PEG3350

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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: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 37327 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 47.25 Å2 / CC1/2: 0.99 / Net I/σ(I): 14.27

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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: 2.05→29.764 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 1994 5.34 %
Rwork0.2108 --
obs0.2132 37317 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→29.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 220 30 4630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094765
X-RAY DIFFRACTIONf_angle_d1.0536543
X-RAY DIFFRACTIONf_dihedral_angle_d14.6262703
X-RAY DIFFRACTIONf_chiral_restr0.046707
X-RAY DIFFRACTIONf_plane_restr0.006812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10130.32671440.31692507X-RAY DIFFRACTION100
2.1013-2.15810.37651400.30262477X-RAY DIFFRACTION100
2.1581-2.22150.28761440.27622444X-RAY DIFFRACTION100
2.2215-2.29320.30871340.2712518X-RAY DIFFRACTION100
2.2932-2.37510.31151350.26552481X-RAY DIFFRACTION100
2.3751-2.47020.34391500.26032509X-RAY DIFFRACTION100
2.4702-2.58260.31851270.26382483X-RAY DIFFRACTION100
2.5826-2.71860.30651560.2632517X-RAY DIFFRACTION100
2.7186-2.88880.28711350.24412493X-RAY DIFFRACTION100
2.8888-3.11170.28171480.24942542X-RAY DIFFRACTION100
3.1117-3.42440.25691450.23242506X-RAY DIFFRACTION100
3.4244-3.9190.24151430.19422562X-RAY DIFFRACTION100
3.919-4.93380.23421410.17782578X-RAY DIFFRACTION100
4.9338-29.76690.2041520.16732706X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -16.6528 Å / Origin y: -3.143 Å / Origin z: 21.9907 Å
111213212223313233
T0.2193 Å20.0982 Å20.0061 Å2-0.3464 Å20.0054 Å2--0.4585 Å2
L1.7166 °2-0.2835 °20.0168 °2-4.1181 °2-3.714 °2--9.1308 °2
S0.0084 Å °0.0339 Å °0.2198 Å °-0.3441 Å °-0.3143 Å °-0.5197 Å °0.3369 Å °0.7221 Å °0.0855 Å °
Refinement TLS groupSelection details: all

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