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- PDB-5syn: Cocrystal structure of the human acyl protein thioesterase 2 with... -

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Basic information

Entry
Database: PDB / ID: 5syn
TitleCocrystal structure of the human acyl protein thioesterase 2 with an isoform-selective inhibitor, ML349
ComponentsAcyl-protein thioesterase 2
Keywordshydrolase/hydrolase inhibitor / hydrolase / inhibitor / thioesterase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


prostaglandin catabolic process / protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / L1CAM interactions / acylglycerol catabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / Golgi stack / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase activity ...prostaglandin catabolic process / protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / L1CAM interactions / acylglycerol catabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / Golgi stack / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase activity / axon guidance / fatty acid metabolic process / cadherin binding / extracellular exosome / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-71T / Acyl-protein thioesterase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsStuckey, J.A. / Labby, K.J. / Meagher, J.L. / Won, S.J. / Martin, B.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R00 CA151460 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2 GM114848 United States
CitationJournal: ACS Chem. Biol. / Year: 2016
Title: Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2).
Authors: Won, S.J. / Davda, D. / Labby, K.J. / Hwang, S.Y. / Pricer, R. / Majmudar, J.D. / Armacost, K.A. / Rodriguez, L.A. / Rodriguez, C.L. / Chong, F.S. / Torossian, K.A. / Palakurthi, J. / Hur, E. ...Authors: Won, S.J. / Davda, D. / Labby, K.J. / Hwang, S.Y. / Pricer, R. / Majmudar, J.D. / Armacost, K.A. / Rodriguez, L.A. / Rodriguez, C.L. / Chong, F.S. / Torossian, K.A. / Palakurthi, J. / Hur, E.S. / Meagher, J.L. / Brooks, C.L. / Stuckey, J.A. / Martin, B.R.
History
DepositionAug 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-protein thioesterase 2
B: Acyl-protein thioesterase 2
C: Acyl-protein thioesterase 2
D: Acyl-protein thioesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,25014
Polymers99,0604
Non-polymers2,19110
Water5,585310
1
A: Acyl-protein thioesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2823
Polymers24,7651
Non-polymers5172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acyl-protein thioesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4686
Polymers24,7651
Non-polymers7035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Acyl-protein thioesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2823
Polymers24,7651
Non-polymers5172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Acyl-protein thioesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2202
Polymers24,7651
Non-polymers4551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.210, 79.790, 138.610
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Acyl-protein thioesterase 2 / APT-2 / Lysophospholipase II / LysoPLA II


Mass: 24764.959 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPLA2, APT2 / Production host: Escherichia coli (E. coli)
References: UniProt: O95372, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-71T / 2-[4-(4-methoxyphenyl)piperazine-1-carbonyl]-5lambda~6~-thieno[3,2-c][1]benzothiopyran-5,5(4H)-dione


Mass: 454.562 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H22N2O4S2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 mM sodium citrate pH 5.5, 20-24% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.64→55.81 Å / Num. obs: 97049 / % possible obs: 93.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.1

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Processing

Software
NameClassification
Cootmodel building
BUSTERrefinement
SCALAdata scaling
BALBESphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB:1FJ2 Chain A

1fj2


Resolution: 1.64→55.81 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25 --
Rwork0.22 --
obs-97049 93.2 %
Displacement parametersBiso mean: 22.553 Å2
Refinement stepCycle: LAST / Resolution: 1.64→55.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6547 0 148 310 7005

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