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- PDB-6ohr: Structure of compound 5 bound human Phospholipase D1 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 6ohr
TitleStructure of compound 5 bound human Phospholipase D1 catalytic domain
ComponentsPhospholipase D1, chimeric constuct
Keywordshydrolase/hydrolase inhibitor / phosphodiesterase / HYDROLASE / HKD motif / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Synthesis of PG / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / cholinergic synapse / regulation of vesicle-mediated transport / cellular response to nutrient / phospholipase D / phospholipid catabolic process / regulation of synaptic vesicle cycle ...Synthesis of PG / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / cholinergic synapse / regulation of vesicle-mediated transport / cellular response to nutrient / phospholipase D / phospholipid catabolic process / regulation of synaptic vesicle cycle / phospholipase D activity / small GTPase-mediated signal transduction / CDC42 GTPase cycle / tertiary granule membrane / RHOG GTPase cycle / endocytic vesicle / RHOA GTPase cycle / Role of phospholipids in phagocytosis / specific granule membrane / RAC1 GTPase cycle / phosphatidylinositol binding / positive regulation of translation / chemotaxis / late endosome membrane / cytoplasmic vesicle / Ras protein signal transduction / endosome / apical plasma membrane / Golgi membrane / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Phospholipase D, eukaryotic type / Phospholipase D family / Phospholipase D Active site motif / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Phospholipase D, eukaryotic type / Phospholipase D family / Phospholipase D Active site motif / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / PH domain / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Chem-MKG / Phospholipase D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMetrick, C.M. / Chodaparambil, J.V.
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Human PLD structures enable drug design and characterization of isoenzyme selectivity.
Authors: Metrick, C.M. / Peterson, E.A. / Santoro, J.C. / Enyedy, I.J. / Murugan, P. / Chen, T. / Michelsen, K. / Cullivan, M. / Spilker, K.A. / Kumar, P.R. / May-Dracka, T.L. / Chodaparambil, J.V.
History
DepositionApr 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase D1, chimeric constuct
B: Phospholipase D1, chimeric constuct
C: Phospholipase D1, chimeric constuct
D: Phospholipase D1, chimeric constuct
E: Phospholipase D1, chimeric constuct
F: Phospholipase D1, chimeric constuct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,58812
Polymers443,9276
Non-polymers2,6616
Water00
1
A: Phospholipase D1, chimeric constuct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4312
Polymers73,9881
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phospholipase D1, chimeric constuct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4312
Polymers73,9881
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phospholipase D1, chimeric constuct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4312
Polymers73,9881
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phospholipase D1, chimeric constuct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4312
Polymers73,9881
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Phospholipase D1, chimeric constuct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4312
Polymers73,9881
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Phospholipase D1, chimeric constuct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4312
Polymers73,9881
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.039, 155.106, 273.560
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
Phospholipase D1, chimeric constuct / hPLD1 / Choline phosphatase 1 / Phosphatidylcholine-hydrolyzing phospholipase D1


Mass: 73987.852 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLD1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13393, phospholipase D
#2: Chemical
ChemComp-MKG / 4-fluoro-N-{(2S)-1-[(5R)-5-(3-fluorophenyl)-2-oxo-1-oxa-3,9-diazaspiro[5.5]undecan-9-yl]propan-2-yl}benzamide


Mass: 443.486 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H27F2N3O3 / Feature type: SUBJECT OF INVESTIGATION

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1M Tris-HCl pH 8.8, 2.81M sodium acetate pH 7.6, 0.04-0.05M glycine pH 9.5, 0.3-0.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 66130 / % possible obs: 99.8 % / Redundancy: 31.1 % / CC1/2: 0.99 / Net I/σ(I): 4.1
Reflection shellResolution: 3.2→4 Å / Num. unique obs: 6614

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OHM

6ohm


Resolution: 3.2→48.362 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.97
RfactorNum. reflection% reflection
Rfree0.2472 6614 10 %
Rwork0.2212 --
obs0.2238 66130 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→48.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25680 0 192 0 25872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326521
X-RAY DIFFRACTIONf_angle_d0.59436140
X-RAY DIFFRACTIONf_dihedral_angle_d6.07315471
X-RAY DIFFRACTIONf_chiral_restr0.0463982
X-RAY DIFFRACTIONf_plane_restr0.0044677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.23640.31582170.31721952X-RAY DIFFRACTION99
3.2364-3.27450.30472140.30451924X-RAY DIFFRACTION100
3.2745-3.31440.29892210.29591988X-RAY DIFFRACTION100
3.3144-3.35630.30842160.27961946X-RAY DIFFRACTION100
3.3563-3.40050.29562150.2731939X-RAY DIFFRACTION100
3.4005-3.44710.27452240.26712012X-RAY DIFFRACTION100
3.4471-3.49630.27242100.26281894X-RAY DIFFRACTION100
3.4963-3.54850.27962200.25691977X-RAY DIFFRACTION100
3.5485-3.60390.2512210.24051982X-RAY DIFFRACTION100
3.6039-3.6630.22922150.23541937X-RAY DIFFRACTION100
3.663-3.72610.26722220.22542000X-RAY DIFFRACTION100
3.7261-3.79380.24282150.21181935X-RAY DIFFRACTION100
3.7938-3.86680.23672210.22131991X-RAY DIFFRACTION100
3.8668-3.94570.21632160.21151944X-RAY DIFFRACTION100
3.9457-4.03140.24392210.20771984X-RAY DIFFRACTION100
4.0314-4.12520.22892170.20811952X-RAY DIFFRACTION100
4.1252-4.22830.21772200.19481977X-RAY DIFFRACTION100
4.2283-4.34250.22822190.2021967X-RAY DIFFRACTION100
4.3425-4.47020.19682200.19371983X-RAY DIFFRACTION100
4.4702-4.61440.19952210.18391985X-RAY DIFFRACTION100
4.6144-4.77920.2092190.18161981X-RAY DIFFRACTION100
4.7792-4.97030.21572220.18361986X-RAY DIFFRACTION100
4.9703-5.19630.25932220.20231999X-RAY DIFFRACTION100
5.1963-5.46990.22882220.2091999X-RAY DIFFRACTION100
5.4699-5.81210.25672220.21542007X-RAY DIFFRACTION100
5.8121-6.260.232220.22192004X-RAY DIFFRACTION100
6.26-6.88830.28092230.22962005X-RAY DIFFRACTION100
6.8883-7.88140.26062270.21412042X-RAY DIFFRACTION100
7.8814-9.91560.22822280.18782054X-RAY DIFFRACTION100
9.9156-48.36780.28842420.24842170X-RAY DIFFRACTION100

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