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- PDB-4bbz: Structure of human butyrylcholinesterase inhibited by CBDP (2-min... -

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Basic information

Entry
Database: PDB / ID: 4bbz
TitleStructure of human butyrylcholinesterase inhibited by CBDP (2-min soak): Cresyl-phosphoserine adduct
ComponentsCHOLINESTERASE
KeywordsHYDROLASE / ACETYLCHOLINESTERASE / NERVE TRANSMISSION / INHIBITION / ALPHA-BETA HYDROLASE
Function / homology
Function and homology information


cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / acetylcholinesterase activity / choline metabolic process / hydrolase activity, acting on ester bonds / Aspirin ADME / nuclear envelope lumen / Synthesis of PC / Synthesis, secretion, and deacylation of Ghrelin / catalytic activity / response to glucocorticoid / xenobiotic metabolic process / learning / amyloid-beta binding / blood microparticle / negative regulation of cell population proliferation / endoplasmic reticulum lumen / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2-methylphenyl) dihydrogen phosphate / Cholinesterase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCarletti, E. / Colletier, J.-P. / Schopfer, L.M. / Santoni, G. / Masson, P. / Lockridge, O. / Nachon, F. / Weik, M.
CitationJournal: Chem.Res.Toxicol. / Year: 2013
Title: Inhibition Pathways of the Potent Organophosphate Cbdp with Cholinesterases Revealed by X-Ray Crystallographic Snapshots and Mass Spectrometry
Authors: Carletti, E. / Colletier, J.-P. / Schopfer, L.M. / Santoni, G. / Masson, P. / Lockridge, O. / Nachon, F. / Weik, M.
History
DepositionSep 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: CHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,57521
Polymers59,6991
Non-polymers2,87620
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.680, 154.680, 126.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CHOLINESTERASE / / ACYLCHOLINE ACYLHYDROLASE / BUTYRYLCHOLINE ESTERASE / CHOLINE ESTERASE II / PSEUDOCHOLINESTERASE


Mass: 59699.480 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 29-557 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CRESYL-PHOSPHATE ADDUCT ON S198 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGS / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P06276, cholinesterase

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Sugars , 3 types, 6 molecules

#2: Polysaccharide beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 153 molecules

#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-4OJ / (2-methylphenyl) dihydrogen phosphate / o-cresyl-phosphate


Mass: 188.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9O4P
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.18 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 2.1 M AMMONIUM SULFATE, 0.1 M MES BUFFER PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.7→54.7 Å / Num. obs: 21049 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 29
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.2 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P0I

1p0i


Resolution: 2.7→54.688 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1053 5 %
Rwork0.1663 --
obs0.1693 21049 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→54.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 186 139 4527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084534
X-RAY DIFFRACTIONf_angle_d1.2696176
X-RAY DIFFRACTIONf_dihedral_angle_d19.8831681
X-RAY DIFFRACTIONf_chiral_restr0.088674
X-RAY DIFFRACTIONf_plane_restr0.004775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.8230.27521300.20152470X-RAY DIFFRACTION99
2.823-2.97180.27151310.19832477X-RAY DIFFRACTION99
2.9718-3.1580.29141310.18532495X-RAY DIFFRACTION99
3.158-3.40180.23291300.17682464X-RAY DIFFRACTION99
3.4018-3.7440.20211300.15452475X-RAY DIFFRACTION98
3.744-4.28560.21861310.1432503X-RAY DIFFRACTION98
4.2856-5.39870.19481330.14542510X-RAY DIFFRACTION98
5.3987-54.69880.22121370.18152602X-RAY DIFFRACTION96
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)
11.71110.44090.14821.61310.41772.5274-0.05360.3157-0.2752-0.40940.1311-0.0890.15280.03620.04920.2526-0.0817-0.03970.1341-0.12930.1826-14.7815-32.1307-35.3739
21.24290.01250.46892.1013-0.27862.26520-0.4443-0.16780.16720.13140.07080.1157-0.32620.07460.1418-0.0458-0.07520.1915-0.07540.1819-19.4174-31.9835-10.8545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:316)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 317:529)

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