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- PDB-4oxk: Multiple binding modes of inhibitor PT155 to the Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 4oxk
TitleMultiple binding modes of inhibitor PT155 to the Mycobacterium tuberculosis enoyl-ACP reductase InhA within a tetramer
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
Keywordsoxidoreductase/oxidoreductase inhibitor / Bacterial fatty acid biosynthesis / conformational profile of enzyme-inhibitor complex / inhibition kinetics / substrate-binding loop refolding / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1S5 / 3,6,9,12,15-pentaoxaoctadecan-17-amine / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8429 Å
AuthorsLi, H.J. / Pan, P. / Lai, C.T. / Liu, N. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102864 United States
Department of Energy (DOE, United States) United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR012408 United States
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA.
Authors: Li, H.J. / Lai, C.T. / Pan, P. / Yu, W. / Liu, N. / Bommineni, G.R. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / refine_hist
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _refine_hist.d_res_high / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,37514
Polymers122,9054
Non-polymers4,47010
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19370 Å2
ΔGint-133 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.265, 97.443, 182.576
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
Enoyl-[acyl-carrier-protein] reductase [NADH] / NADH-dependent enoyl-ACP reductase


Mass: 30726.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1531,MTCY277.05,Rv1484,inhA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-1S5 / 5-(4-amino-2-methylphenoxy)-2-hexyl-4-hydroxy-1-methylpyridinium


Mass: 314.422 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26N2O2
#4: Chemical ChemComp-2NV / 3,6,9,12,15-pentaoxaoctadecan-17-amine / Jeffamine ED-2001


Mass: 279.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H29NO5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM HEPES pH 8.0, 32% Jeffamine ED-2001 pH 7.0 / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2009
RadiationMonochromator: Double silicon(111) crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8429→50 Å / Num. obs: 137078 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.11 / Χ2: 1.218 / Net I/av σ(I): 17.617 / Net I/σ(I): 10.8 / Num. measured all: 903180
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8429-1.885.10.56967630.8899.7
1.88-1.926.10.5368530.999100
1.92-1.956.30.48367381.086100
1.95-1.996.50.43767821.111100
1.99-2.046.60.36968261.18100
2.04-2.086.60.31967741.251100
2.08-2.146.60.28667781.291100
2.14-2.196.70.23368051.264100
2.19-2.266.70.20868351.342100
2.26-2.336.70.18967991.334100
2.33-2.416.70.16968291.324100
2.41-2.516.80.15768361.284100
2.51-2.636.80.14368221.323100
2.63-2.766.80.12768461.26100
2.76-2.946.90.11468761.264100
2.94-3.166.90.10868821.346100
3.16-3.486.90.169201.254100
3.48-3.996.80.09169291.23899.9
3.99-5.026.60.07370031.129100
5.02-506.70.05971821.05798.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.14data extraction
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X23

2x23


Resolution: 1.8429→47.074 Å / FOM work R set: 0.8987 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 6877 5.02 %
Rwork0.1581 130026 -
obs0.1591 136903 99.38 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.233 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 80.6 Å2 / Biso mean: 26.5 Å2 / Biso min: 11.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.6348 Å20 Å2-0 Å2
2--5.5727 Å2-0 Å2
3----7.2075 Å2
Refinement stepCycle: final / Resolution: 1.8429→47.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7775 0 278 490 8543
Biso mean--22.85 34.42 -
Num. residues----1066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078603
X-RAY DIFFRACTIONf_angle_d1.19211785
X-RAY DIFFRACTIONf_chiral_restr0.0781316
X-RAY DIFFRACTIONf_plane_restr0.0061502
X-RAY DIFFRACTIONf_dihedral_angle_d15.6483248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8429-1.86380.26071860.23473768395486
1.8638-1.88580.21282270.212242414468100
1.8858-1.90870.2532340.199943024536100
1.9087-1.93290.21432150.181143124527100
1.9329-1.95830.23312330.18443234556100
1.9583-1.98520.23042500.17542904540100
1.9852-2.01350.19592270.162943044531100
2.0135-2.04360.19492020.161343444546100
2.0436-2.07550.19672340.155443374571100
2.0755-2.10960.18662120.154242904502100
2.1096-2.14590.18591980.150443634561100
2.1459-2.18490.1822160.1543784594100
2.1849-2.2270.18182490.144742964545100
2.227-2.27240.17252360.140843174553100
2.2724-2.32180.17582400.152643244564100
2.3218-2.37580.18481930.150343654558100
2.3758-2.43530.17782610.151243214582100
2.4353-2.50110.17982250.157243504575100
2.5011-2.57470.19472410.163443284569100
2.5747-2.65780.19172350.159843494584100
2.6578-2.75280.18432170.16543734590100
2.7528-2.8630.17812070.167343884595100
2.863-2.99330.19362420.171443514593100
2.9933-3.1510.21292480.1843734621100
3.151-3.34840.18362270.171343874614100
3.3484-3.60690.18052300.162844034633100
3.6069-3.96970.14382550.143843964651100
3.9697-4.54370.15142320.130744414673100
4.5437-5.72290.13812340.138544964730100
5.7229-47.08950.16112710.16484516478797
Refinement TLS params.Method: refined / Origin x: -43.1041 Å / Origin y: 24.3927 Å / Origin z: -22.9452 Å
111213212223313233
T0.096 Å2-0.0005 Å2-0.0106 Å2-0.149 Å20.0045 Å2--0.116 Å2
L0.6544 °2-0.0155 °2-0.0477 °2-0.972 °2-0.0728 °2--0.6562 °2
S-0.0243 Å °0.0589 Å °0.0184 Å °0.0322 Å °0.0142 Å °0.016 Å °-0.0124 Å °0.0079 Å °0.0106 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 510
2X-RAY DIFFRACTION1allB3 - 517
3X-RAY DIFFRACTION1allC3 - 528
4X-RAY DIFFRACTION1allD3 - 534

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