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- PDB-5jwc: Structure of NDH2 from plasmodium falciparum in complex with RYL-552 -

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Basic information

Entry
Database: PDB / ID: 5jwc
TitleStructure of NDH2 from plasmodium falciparum in complex with RYL-552
ComponentsNADH dehydrogenase, putative
KeywordsMEMBRANE PROTEIN / PfNDH2 / NDH2 / plasmodium falciparum / malaria / Inhibitor
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / quinone reductase (NADPH) activity / NADH dehydrogenase (quinone) (non-electrogenic) activity / oxidoreductase activity / nucleotide binding / mitochondrion / metal ion binding
Similarity search - Function
: / PfNDH2 helical insertion domain / : / NDH2 C-terminal domain / Alternative NADH dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-4W0 / FLAVIN-ADENINE DINUCLEOTIDE / NADH:ubiquinone reductase (non-electrogenic)
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsYu, Y.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria
Authors: Yang, Y. / Yu, Y. / Li, X. / Li, J. / Wu, Y. / Yu, J. / Ge, J. / Huang, Z. / Jiang, L. / Rao, Y. / Yang, M.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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

Downloads & links

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Assembly

Deposited unit
A: NADH dehydrogenase, putative
H: NADH dehydrogenase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,18922
Polymers120,5982
Non-polymers5,59020
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-113 kcal/mol
Surface area43170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.603, 192.603, 92.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 2 molecules AH

#1: Protein NADH dehydrogenase, putative


Mass: 60299.215 Da / Num. of mol.: 2 / Fragment: UNP residues 25-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFI0735c / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8I302, NADH dehydrogenase

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Non-polymers , 5 types, 468 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#5: Chemical
ChemComp-4W0 / 5-fluoro-3-methyl-2-{4-[4-(trifluoromethoxy)benzyl]phenyl}quinolin-4(1H)-one


Mass: 427.391 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H17F4NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: protein (10mg/ml) reservoir solution (2.7M sodium acetate trihydrate, pH screen kit from Hampoton Research at 4.8 or 10.0 )

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 105189 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.24 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.462 / Net I/av σ(I): 20.872 / Net I/σ(I): 12.4 / Num. measured all: 558294
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.05-2.125.40.7391100
2.12-2.215.40.5241100
2.21-2.315.40.3861100
2.31-2.435.40.2931100
2.43-2.585.40.2181100
2.58-2.785.40.1461100
2.78-3.065.40.0991100
3.06-3.515.30.0711100
3.51-4.424.80.062199.9
4.42-5050.047198.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6G

4g6g


Resolution: 2.051→30.453 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.9
RfactorNum. reflection% reflection
Rfree0.2205 5245 4.99 %
Rwork0.1871 --
obs0.1888 105154 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.27 Å2 / Biso mean: 40.38 Å2 / Biso min: 20.66 Å2
Refinement stepCycle: final / Resolution: 2.051→30.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8094 0 380 448 8922
Biso mean--44.47 43.65 -
Num. residues----990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098702
X-RAY DIFFRACTIONf_angle_d1.27111801
X-RAY DIFFRACTIONf_chiral_restr0.0571256
X-RAY DIFFRACTIONf_plane_restr0.0051429
X-RAY DIFFRACTIONf_dihedral_angle_d16.2953285
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 (%)
2.0508-2.07410.28711620.259132963458100
2.0741-2.09850.28841690.252533563525100
2.0985-2.1240.28241720.24832613433100
2.124-2.15090.28071620.244333843546100
2.1509-2.17920.26421900.233732913481100
2.1792-2.20910.26121800.23433093489100
2.2091-2.24060.24331520.22633423494100
2.2406-2.27410.23291920.213833083500100
2.2741-2.30960.28641550.221133473502100
2.3096-2.34740.28821610.224433323493100
2.3474-2.38790.2911920.220633233515100
2.3879-2.43130.28841630.220833303493100
2.4313-2.4780.28431840.221833263510100
2.478-2.52860.25721790.215832993478100
2.5286-2.58350.27821630.212533103473100
2.5835-2.64360.2442060.210233123518100
2.6436-2.70970.20791670.203233523519100
2.7097-2.78290.26111800.216333093489100
2.7829-2.86470.27941400.212933583498100
2.8647-2.95710.26241800.217933503530100
2.9571-3.06270.22241620.206533623524100
3.0627-3.18520.23141710.209333263497100
3.1852-3.330.21491840.191433223506100
3.33-3.50530.21161850.173533473532100
3.5053-3.72460.21491730.169933103483100
3.7246-4.01160.18392000.154433503550100
4.0116-4.41420.16861730.145633323505100
4.4142-5.05040.17031700.150433763546100
5.0504-6.35350.2191940.177133563550100
6.3535-30.45660.18991840.16163333351797

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