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- PDB-5idz: Structure of Human Enolase 2 in complex with (S)-(1-hydroxy-2-oxo... -

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Basic information

Entry
Database: PDB / ID: 5idz
TitleStructure of Human Enolase 2 in complex with (S)-(1-hydroxy-2-oxopiperidin-3-yl)phosphonate
ComponentsGamma-enolase
KeywordsLYASE/LYASE INHIBITOR / enolase gamma / glycolysis / neuron specific enolase / carbohydrate metabolism / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / gluconeogenesis / glycolytic process / perikaryon ...phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / gluconeogenesis / glycolytic process / perikaryon / magnesium ion binding / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6BM / TRIETHYLENE GLYCOL / Gamma-enolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.63 Å
AuthorsLeonard, P.G. / Muller, F.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP140612 United States
American Cancer Society365082 United States
CitationJournal: To Be Published
Title: Pomhex, a cell-permeable Enolase inhibitor for Collateral Lethality targeting of ENO1-deleted Glioblastoma
Authors: Lin, Y.H. / Satani, N. / Hammoudi, N. / Felini, F. / Leonard, P.G. / Maxwell, D. / Link, T. / Lee, G.R. / Bosajou, A. / Duoli, S. / Marszalek, J.R. / Sun, Y.T. / McMurray, J. / Mandal, P.J. ...Authors: Lin, Y.H. / Satani, N. / Hammoudi, N. / Felini, F. / Leonard, P.G. / Maxwell, D. / Link, T. / Lee, G.R. / Bosajou, A. / Duoli, S. / Marszalek, J.R. / Sun, Y.T. / McMurray, J. / Mandal, P.J. / DiFrancesco, M.E. / Czako, B. / Wang, A. / Bornmann, W. / DePinho, R.A. / Muller, F.L.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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: Gamma-enolase
B: Gamma-enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0388
Polymers96,2992
Non-polymers7396
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-15 kcal/mol
Surface area29330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.100, 108.740, 116.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gamma-enolase / 2-phospho-D-glycerate hydro-lyase / Enolase 2 / Neural enolase / Neuron-specific enolase / NSE


Mass: 48149.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENO2 / Plasmid: pJL-H6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 plysS / References: UniProt: P09104, phosphopyruvate hydratase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-6BM / [(3S)-1-hydroxy-2-oxopiperidin-3-yl]phosphonic acid


Mass: 195.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10NO5P
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM ammonium acetate, 100 mM Bis-Tris, 18-22% w/v PEG3350, 6.5, overnight crystal soak in reservoir solution supplemented with 4 mM compound

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2014
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.63→79.48 Å / Num. obs: 26400 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.036 / Rrim(I) all: 0.097 / Net I/σ(I): 15.6 / Num. measured all: 182044 / Scaling rejects: 44
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.63-2.756.60.339199.3
9.11-79.486.40.036199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.32 Å54.37 Å
Translation7.32 Å54.37 Å

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Processing

Software
NameVersionClassification
iMOSFLM7.1.1data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIX1.9-1662refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZCW

4zcw


Resolution: 2.63→54.37 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.28
RfactorNum. reflection% reflection
Rfree0.2181 1383 5.25 %
Rwork0.1621 --
obs0.165 26345 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.16 Å2 / Biso mean: 35.6921 Å2 / Biso min: 11.29 Å2
Refinement stepCycle: final / Resolution: 2.63→54.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6664 0 46 154 6864
Biso mean--38.56 31.15 -
Num. residues----870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046865
X-RAY DIFFRACTIONf_angle_d0.6929271
X-RAY DIFFRACTIONf_chiral_restr0.0251035
X-RAY DIFFRACTIONf_plane_restr0.0021218
X-RAY DIFFRACTIONf_dihedral_angle_d13.1092549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.63-2.7240.32481430.2122434257799
2.724-2.83310.27051540.201824222576100
2.8331-2.9620.26851370.184324722609100
2.962-3.11820.22121420.184824492591100
3.1182-3.31350.29381300.193924762606100
3.3135-3.56930.25631290.180924972626100
3.5693-3.92840.21411550.152224692624100
3.9284-4.49660.19351200.137525332653100
4.4966-5.66430.16191120.136725672679100
5.6643-54.38160.16241610.142326432804100

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