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- PDB-5adz: Ether Lipid-Generating Enzyme AGPS in complex with inhibitor 1a -

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Basic information

Entry
Database: PDB / ID: 5adz
TitleEther Lipid-Generating Enzyme AGPS in complex with inhibitor 1a
ComponentsALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMALAlkylglycerone phosphate synthase
KeywordsTRANSFERASE / ETHER PHOSPHOLIPID / CANCER / FLAVIN
Function / homology
Function and homology information


alkylglycerone-phosphate synthase / alkylglycerone-phosphate synthase activity / ether lipid biosynthetic process / peroxisomal membrane / FAD binding / peroxisome
Similarity search - Function
Double Stranded RNA Binding Domain - #650 / GMP Synthetase; Chain A, domain 3 - #330 / Alpha-Beta Plaits - #3450 / Alkyldihydroxyacetonephosphate synthase / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal ...Double Stranded RNA Binding Domain - #650 / GMP Synthetase; Chain A, domain 3 - #330 / Alpha-Beta Plaits - #3450 / Alkyldihydroxyacetonephosphate synthase / Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / GMP Synthetase; Chain A, domain 3 / Double Stranded RNA Binding Domain / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-KQS / Alkyldihydroxyacetonephosphate synthase, peroxisomal
Similarity search - Component
Biological speciesCAVIA PORCELLUS (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPiano, V. / Benjamin, D.I. / Valente, S. / Nenci, S. / Marrocco, B. / Mai, A. / Aliverti, A. / Nomura, D.K. / Mattevi, A.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Discovery of Inhibitors for the Ether Lipid-Generating Enzyme Agps as Anti-Cancer Agents.
Authors: Piano, V. / Benjamin, D.I. / Valente, S. / Nenci, S. / Marrocco, B. / Mai, A. / Aliverti, A. / Nomura, D.K. / Mattevi, A.
History
DepositionAug 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,20612
Polymers291,7554
Non-polymers4,4528
Water12,124673
1
A: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,1036
Polymers145,8772
Non-polymers2,2264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-48.3 kcal/mol
Surface area38860 Å2
MethodPISA
2
C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,1036
Polymers145,8772
Non-polymers2,2264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-46.8 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.060, 99.610, 107.970
Angle α, β, γ (deg.)90.57, 90.04, 94.76
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.986939, 0.139062, -0.08132), (0.03233, 0.323549, 0.945659), (0.157816, -0.935937, 0.314827)-17.8582, 31.94442, 24.29697
3given(0.997038, 0.073722, 0.021929), (0.044592, -0.321749, -0.945774), (-0.062669, 0.943951, -0.324083)-20.43661, 165.8324, -28.25166
4given(1), (1), (1)

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Components

#1: Protein
ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL / Alkylglycerone phosphate synthase / ALKYL-DHAP SYNTHASE / ALKYLGLYCERONE-PHOSPHATE SYNTHASE / ALKYL-DIHYDROXYACETONEPHOSPHATE SYNTHASE


Mass: 72938.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAVIA PORCELLUS (domestic guinea pig) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P97275, alkylglycerone-phosphate synthase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-KQS / (3S)-3-(2-fluorophenyl)-N-((2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)methyl)butanamide)


Mass: 327.353 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18FN3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.24 Å3/Da / Density % sol: 45.16 % / Description: NONE
Crystal growpH: 7.5 / Details: PEG 1500 20%, HEPES, PH 7.5, 100 MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→32 Å / Num. obs: 117589 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BBY

4bby


Resolution: 2.2→107.96 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.952 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25344 1260 1.1 %RANDOM
Rwork0.19514 ---
obs0.19575 115973 91.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.08 Å22.41 Å2-1.07 Å2
2--0.62 Å2-0.74 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→107.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17487 0 308 673 18468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01918229
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217089
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.97324700
X-RAY DIFFRACTIONr_angle_other_deg1.021339326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81552212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91823.945839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.754153072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.84715115
X-RAY DIFFRACTIONr_chiral_restr0.0940.22651
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120590
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024299
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_it2.3063.2118871
X-RAY DIFFRACTIONr_mcbond_other2.2993.2118868
X-RAY DIFFRACTIONr_mcangle_it3.4974.80611068
X-RAY DIFFRACTIONr_mcangle_other3.4974.80611068
X-RAY DIFFRACTIONr_scbond_it2.9113.6039358
X-RAY DIFFRACTIONr_scbond_other2.9123.6039354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6025.26113625
X-RAY DIFFRACTIONr_long_range_B_refined6.34126.20221691
X-RAY DIFFRACTIONr_long_range_B_other6.33726.18621571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 87 -
Rwork0.263 8540 -
obs--90.28 %

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