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- PDB-6ohq: Structure of compound 4 bound human Phospholipase D2 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 6ohq
TitleStructure of compound 4 bound human Phospholipase D2 catalytic domain
ComponentsPhospholipase D2
Keywordshydrolase/hydrolase inhibitor / phosphodiesterase / HYDROLASE / HKD motif / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Synthesis of PG / phosphatidic acid biosynthetic process / Synthesis of PA / synaptic vesicle recycling / regulation of vesicle-mediated transport / phospholipase D / phospholipid catabolic process / G protein-coupled receptor internalization / phospholipase D activity / small GTPase-mediated signal transduction ...Synthesis of PG / phosphatidic acid biosynthetic process / Synthesis of PA / synaptic vesicle recycling / regulation of vesicle-mediated transport / phospholipase D / phospholipid catabolic process / G protein-coupled receptor internalization / phospholipase D activity / small GTPase-mediated signal transduction / Fc-gamma receptor signaling pathway involved in phagocytosis / RAC2 GTPase cycle / Role of phospholipids in phagocytosis / RAC1 GTPase cycle / cytoskeleton organization / phosphatidylinositol binding / brush border membrane / presynapse / cytoplasmic vesicle / endoplasmic reticulum 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 / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Chem-MKA / Phospholipase D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.694 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
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase D2
B: Phospholipase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,79228
Polymers145,6942
Non-polymers3,09826
Water3,621201
1
A: Phospholipase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,39614
Polymers72,8471
Non-polymers1,54913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phospholipase D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,39614
Polymers72,8471
Non-polymers1,54913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.227, 131.517, 106.414
Angle α, β, γ (deg.)90.000, 112.050, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phospholipase D2 / hPLD2 / Choline phosphatase 2 / PLD1C / Phosphatidylcholine-hydrolyzing phospholipase D2


Mass: 72846.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLD2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O14939, phospholipase D
#2: Chemical ChemComp-MKA / 4-fluoro-N-{(2S)-1-[4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propan-2-yl}benzamide


Mass: 396.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25FN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 20% PEG3350, 0.1M bis-tris pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 43049 / % possible obs: 98.2 % / Redundancy: 3.4 % / CC1/2: 0.99 / Net I/σ(I): 3.9
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 4306 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OHM

6ohm


Resolution: 2.694→49.315 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.56
RfactorNum. reflection% reflection
Rfree0.2587 1587 5.09 %
Rwork0.2064 --
obs0.2091 31179 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.43 Å2 / Biso mean: 48.1632 Å2 / Biso min: 15.55 Å2
Refinement stepCycle: final / Resolution: 2.694→49.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9313 0 178 201 9692
Biso mean--84.59 38.92 -
Num. residues----1157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6945-2.78140.32911690.3012249193
2.7-2.80.23991630.2013270597
2.7814-2.88080.32671380.2806267698
2.8808-2.99620.28961380.2571265797
2.9962-3.13250.27831390.2522743100
3.1325-3.29760.28331300.23232741100
3.2976-3.50420.26641400.21212729100
3.5042-3.77470.26461410.1897272199
3.7747-4.15430.24181560.1774268698
4.1543-4.75510.21751250.1639269897
4.7551-5.98920.24281480.1822745100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1516-0.74120.19283.70660.65773.31810.05880.0499-0.63740.07340.05990.12930.53520.2208-0.10370.49650.0290.04570.2513-0.01430.36130.84393.290512.0534
22.6286-0.59790.51413.24350.55641.7110.04060.2382-0.1724-0.42350.0413-0.02980.14290.0653-0.05890.5994-0.03280.07660.2629-0.00180.251723.48319.2023-10.9309
31.4703-0.3003-0.24040.5671-0.25731.10280.0391-0.00130.0207-0.36240.0091-0.0686-0.06780.0492-0.02370.5447-0.00220.07810.2192-0.00010.254121.919312.7929-4.3146
42.3505-0.58510.67152.0491-0.36041.50810.0250.44830.149-0.71630.0845-0.0167-0.081-0.0883-0.14640.59720.00330.10580.3246-0.01260.325523.218825.3479-11.4038
56.9722-1.3982.01190.76260.39692.7787-0.04280.0121-0.17950.0120.0079-0.06360.08090.02110.10080.6755-0.07110.1140.20640.0170.372619.3847-3.85280.6003
61.30570.2588-0.02691.34250.48110.5284-0.0651-0.23270.00580.0392-0.0075-0.0172-0.0893-0.08590.02560.47910.01010.0680.30340.01420.269421.876821.514217.51
70.98090.2367-0.34330.82370.5590.61970.0003-0.11070.0874-0.06430.15320.128-0.1231-0.0406-0.01850.41550.01860.04270.20760.00370.274626.989328.56112.6433
84.25651.38171.69051.92950.78491.97070.08580.0760.0214-0.07640.0065-0.2967-0.01170.3345-0.07820.36170.00890.10280.2302-0.02470.240739.009419.696313.9113
90.3391-0.0782-0.11722.1776-0.66331.43370.07110.03260.195-0.01310.00220.1427-0.1822-0.1191-0.06930.60430.01230.10770.3249-0.01430.426323.291441.2417.9535
101.92390.80580.64931.00520.36722.57440.3854-0.5898-0.20110.4256-0.2705-0.10580.2694-0.28990.0170.5884-0.10460.02950.44020.07430.3445-1.3877-19.738456.9491
111.37290.4294-0.05971.59670.36951.91220.0851-0.2701-0.04020.2465-0.1381-0.14050.0044-0.02680.01650.3674-0.01310.06080.2370.01570.29743.1562-10.828444.3677
121.99540.43620.77462.96420.44771.4389-0.1282-0.17050.4198-0.04-0.03730.0348-0.3478-0.0870.14930.47430.07230.09470.31770.01840.2669-1.99812.215936.4699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 315 through 340 )A315 - 340
2X-RAY DIFFRACTION2chain 'A' and (resid 341 through 421 )A341 - 421
3X-RAY DIFFRACTION3chain 'A' and (resid 422 through 476 )A422 - 476
4X-RAY DIFFRACTION4chain 'A' and (resid 498 through 549 )A498 - 549
5X-RAY DIFFRACTION5chain 'A' and (resid 550 through 599 )A550 - 599
6X-RAY DIFFRACTION6chain 'A' and (resid 600 through 716 )A600 - 716
7X-RAY DIFFRACTION7chain 'A' and (resid 717 through 779 )A717 - 779
8X-RAY DIFFRACTION8chain 'A' and (resid 780 through 839 )A780 - 839
9X-RAY DIFFRACTION9chain 'A' and (resid 840 through 933 )A840 - 933
10X-RAY DIFFRACTION10chain 'B' and (resid 315 through 421 )B315 - 421
11X-RAY DIFFRACTION11chain 'B' and (resid 422 through 779 )B422 - 779
12X-RAY DIFFRACTION12chain 'B' and (resid 780 through 933 )B780 - 933

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