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- PDB-5ae3: Ether Lipid-Generating Enzyme AGPS in complex with antimycin A -

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Basic information

Entry
Database: PDB / ID: 5ae3
TitleEther Lipid-Generating Enzyme AGPS in complex with antimycin A
ComponentsALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
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
Chem-AWB / FLAVIN-ADENINE DINUCLEOTIDE / Alkyldihydroxyacetonephosphate synthase, peroxisomal
Similarity search - Component
Biological speciesCAVIA PORCELLUS (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 9, 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)297,38015
Polymers291,7554
Non-polymers5,62511
Water10,611589
1
C: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
D: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,6427
Polymers145,8772
Non-polymers2,7645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-75 kcal/mol
Surface area38160 Å2
MethodPISA
2
A: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
B: ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,7388
Polymers145,8772
Non-polymers2,8606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-84.8 kcal/mol
Surface area37410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.159, 98.850, 107.722
Angle α, β, γ (deg.)90.80, 90.50, 94.79
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.978507, 0.200969, -0.046206), (0.201107, -0.979568, -0.001707), (-0.045605, -0.007622, -0.998931)-6.76225, 91.73347, 109.31046
3given(0.98796, 0.024883, 0.152694), (0.134807, 0.345793, -0.928576), (-0.075907, 0.937981, 0.338276)13.00418, 12.46668, -37.97738
4given(0.996277, 0.055574, -0.065905), (0.080769, -0.334447, 0.938947), (0.030139, -0.940774, -0.337691)9.63939, 81.84209, 146.49431

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Components

#1: Protein
ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL / ALKYL-DHAP SYNTHASE / ALKYLGLYCERONE-PHOSPHATE SYNTHASE / ALKYL-DHAP SYNTHASE / ALKYLGLYCERONE- ...ALKYL-DHAP SYNTHASE / ALKYLGLYCERONE-PHOSPHATE SYNTHASE / ALKYL-DHAP SYNTHASE / ALKYLGLYCERONE-PHOSPHATE SYNTHASE / ALKYL-DIHYDRO XYACETONEPHOSPHATE 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-AWB / [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate


Mass: 548.625 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H40N2O9
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.22 Å3/Da / Density % sol: 44.69 % / Description: NONE
Crystal growpH: 7.5 / Details: PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23 / Wavelength: 1.00005
DetectorDate: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.18→34.67 Å / Num. obs: 123594 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.9 / % possible all: 93.1

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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: 2.18→107.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.058 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1333 1.1 %RANDOM
Rwork0.19139 ---
obs0.19209 122248 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20.25 Å2-0.19 Å2
2---0.8 Å2-1.37 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.18→107.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17118 0 383 589 18090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01917928
X-RAY DIFFRACTIONr_bond_other_d0.0030.0216788
X-RAY DIFFRACTIONr_angle_refined_deg1.791.97624295
X-RAY DIFFRACTIONr_angle_other_deg1.045338626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9652171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00523.966822
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.018152990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.29815113
X-RAY DIFFRACTIONr_chiral_restr0.10.22625
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120219
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024212
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_it2.8783.5628699
X-RAY DIFFRACTIONr_mcbond_other2.8783.5628700
X-RAY DIFFRACTIONr_mcangle_it4.1595.33210856
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4913.9869229
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 87 -
Rwork0.276 8885 -
obs--92.76 %

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