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- PDB-3qv8: Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in... -

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Basic information

Entry
Database: PDB / ID: 3qv8
TitleCrystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with benzothiazole-2,5-disulfonic acid.
ComponentsPyruvate kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PYRUVATE KINASE / GLYCOLYSIS / TIM Barrel / Sugar kinase / ADP/ATP binding / cytosol / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / magnesium ion binding / ATP binding
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 1,3-benzothiazole-2,5-disulfonic acid / Pyruvate kinase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMorgan, H.P. / Auld, D.S. / McNae, I.W. / Nowicki, M.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site.
Authors: Morgan, H.P. / McNae, I.W. / Nowicki, M.W. / Zhong, W. / Michels, P.A. / Auld, D.S. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Aug 17, 2011Group: Structure summary
Revision 1.4Sep 21, 2011Group: Database references
Revision 1.5Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
D: Pyruvate kinase
A: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9068
Polymers108,9362
Non-polymers9716
Water3,801211
1
D: Pyruvate kinase
A: Pyruvate kinase
hetero molecules

D: Pyruvate kinase
A: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,81316
Polymers217,8724
Non-polymers1,94112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area14140 Å2
ΔGint-132 kcal/mol
Surface area66060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.554, 131.282, 167.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Pyruvate kinase / PK


Mass: 54467.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Strain: BEL46 / Gene: PKY / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q27686, pyruvate kinase
#2: Chemical ChemComp-S62 / 1,3-benzothiazole-2,5-disulfonic acid


Mass: 295.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO6S3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 7-16% PEG 8,000, 20 mM TEA buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10-25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→44.41 Å / Num. all: 360184 / Num. obs: 49123 / % possible obs: 100 % / Observed criterion σ(F): 2.45 / Observed criterion σ(I): 2.45 / Redundancy: 7.3 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.102 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value
2.45-2.587.50.5634.170890.605
7.75-44.416.80.05138.416670.055

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Processing

Software
NameVersionClassification
DNAdata collection
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PKL

1pkl


Resolution: 2.45→44.41 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.583 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26576 2485 5.1 %RANDOM
Rwork0.23448 ---
obs0.23608 46606 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.196 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2--3.92 Å20 Å2
3----2.79 Å2
Refinement stepCycle: LAST / Resolution: 2.45→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6748 0 54 211 7013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226928
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9629394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6725891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00424.77304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33151198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7231543
X-RAY DIFFRACTIONr_chiral_restr0.0790.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215168
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5361.54415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01927134
X-RAY DIFFRACTIONr_scbond_it1.40132513
X-RAY DIFFRACTIONr_scangle_it2.4484.52256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 175 -
Rwork0.323 3409 -
obs--99.92 %

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