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- PDB-4coh: Crystal structure of Trypanosoma cruzi CYP51 bound to the sulfona... -

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Basic information

Entry
Database: PDB / ID: 4coh
TitleCrystal structure of Trypanosoma cruzi CYP51 bound to the sulfonamide derivative of the 4-aminopyridyl-based inhibitor
ComponentsSTEROL 14-ALPHA DEMETHYLASE
KeywordsTRANSFERASE / CYP51 / STEROL 14-DEMETHYLASE / STEROL BIOSYNTHESIS / CHAGAS DISEASE
Function / homology
Function and homology information


sterol 14-demethylase activity / sterol biosynthetic process / sterol 14alpha-demethylase / iron ion binding / heme binding / membrane
Similarity search - Function
: / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-T9H / Sterol 14-alpha demethylase / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsVieira, D.F. / Choi, J.Y. / Roush, W.R. / Podust, L.M.
CitationJournal: Chembiochem / Year: 2014
Title: Expanding the Binding Envelope of Cyp51 Inhibitors Targeting Trypanosoma Cruzi with 4-Aminopyridyl-Based Sulfonamide Derivatives
Authors: Vieira, D.F. / Choi, J.Y. / Roush, W.R. / Podust, L.M.
History
DepositionJan 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Jun 4, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: STEROL 14-ALPHA DEMETHYLASE
B: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6996
Polymers107,2002
Non-polymers2,4984
Water12,178676
1
A: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8493
Polymers53,6001
Non-polymers1,2492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8493
Polymers53,6001
Non-polymers1,2492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.218, 96.392, 137.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein STEROL 14-ALPHA DEMETHYLASE / TC14DM / CYTOCHROME P450 51 / LANOSTEROL 14-ALPHA DEMETHYLASE / STEROL 14-DEMETHYLASE / CYP51


Mass: 53600.125 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Plasmid: PCW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q5I4E1, UniProt: Q7Z1V1*PLUS, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-T9H / 2-fluoranyl-N-[(2R)-3-(1H-indol-3-yl)-1-oxidanylidene-1-(pyridin-4-ylamino)propan-2-yl]-4-(4-thiophen-2-ylsulfonylpiperazin-1-yl)benzamide


Mass: 632.728 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H29FN6O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 28 RESIDUES AT THE N-TERMINUS ARE REPLACED WITH THE MAKKTSSKGKL SEQUENCE, 6XHIS TAG ...FIRST 28 RESIDUES AT THE N-TERMINUS ARE REPLACED WITH THE MAKKTSSKGKL SEQUENCE, 6XHIS TAG ENGINEERED AT THE C- TERMINUS

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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: 49.3 % / Description: NONE
Crystal growpH: 7 / Details: 0.05 M AMMONIUM CITRATE, PH 7.0; 14% PEG 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 22, 2012 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.08→137.36 Å / Num. obs: 60841 / % possible obs: 95.6 % / Observed criterion σ(I): 1.5 / Redundancy: 7.2 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.2
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.8 / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WX2

2wx2


Resolution: 2.08→137.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.784 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24295 3024 5 %RANDOM
Rwork0.17415 ---
obs0.17751 57134 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.071 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2---1.41 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.08→137.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7035 0 174 676 7885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0122.02310203
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51623.086324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.597151275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8391560
X-RAY DIFFRACTIONr_chiral_restr0.130.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215730
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_it1.0771.54471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92327249
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.43933035
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2244.52954
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 188 -
Rwork0.247 2936 -
obs--67.4 %

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