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- PDB-4pnc: E. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH INHIBITOR 7-MET... -

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Basic information

Entry
Database: PDB / ID: 4pnc
TitleE. COLI METHIONINE AMINOPEPTIDASE IN COMPLEX WITH INHIBITOR 7-METHOXY-2-METHYLEN-3,4-DIHYDRONAPHTHALEN-1(2H)-ONE
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHYDROLASE / HYDROLASE(ALPHA-AMINOACYLPEPTIDE) / METAL COMPLEX / METHIONINE AMINOPEPTIDASE / COVALENT INHIBITOR / 1-TETRALONE
Function / homology
Function and homology information


: / methionyl aminopeptidase / metalloaminopeptidase activity / metal ion binding
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-7NP / : / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.54 Å
AuthorsScheidig, A.J. / Altmeyer, M. / Klein, C.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Deutsche Krebshilfe Germany
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Beta-aminoketones as prodrugs for selective irreversible inhibitors of type-1 methionine aminopeptidases.
Authors: Altmeyer, M. / Amtmann, E. / Heyl, C. / Marschner, A. / Scheidig, A.J. / Klein, C.D.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Sep 27, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist
Revision 1.5Nov 20, 2019Group: Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total ..._refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7326
Polymers29,3421
Non-polymers3905
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.010, 66.820, 48.450
Angle α, β, γ (deg.)90.00, 111.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase / Methionyl aminopeptidase / MetAP / Peptidase M


Mass: 29341.775 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: map, BN17_45901, BU34_07510, ECs0170, LF82_1274 / Plasmid: PET28B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C3TPN7, methionyl aminopeptidase
#2: Chemical ChemComp-7NP / (2S)-7-methoxy-2-methyl-3,4-dihydronaphthalen-1(2H)-one / Bound form of 7-METHOXY-2-(PIPERIDIN-1-YLMETHYL)-3,4-DIHYDRONAPHTHALEN-1(2H)-ONE HYDROCHLORDIDE


Mass: 190.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14O2
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: PEG 4000, COBALT CHLORIDE, HEPES, METHIONINE, SODIUM CHLORIDE, POTASSIUM CHLORIDE, PH 7.1
PH range: 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 12, 2008 / Details: MONTEL MIRRORS
RadiationMonochromator: Montel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. obs: 61073 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 17.883 Å2 / Rsym value: 0.025 / Net I/σ(I): 31.09
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 3.01 % / Mean I/σ(I) obs: 10.67 / Rsym value: 0.113 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MAR345dtbdata collection
XDSdata scaling
XSCALEdata scaling
Cootmodel building
HKL2Mapmodel building
SHELXCDphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.54→19.69 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.023 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16533 1566 5 %RANDOM
Rwork0.13205 ---
obs0.13373 29747 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.864 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.41 Å2
2--0.78 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.54→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 18 475 2525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192259
X-RAY DIFFRACTIONr_bond_other_d0.0020.022205
X-RAY DIFFRACTIONr_angle_refined_deg2.2721.9763078
X-RAY DIFFRACTIONr_angle_other_deg0.96335121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65624.4998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56515423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4281514
X-RAY DIFFRACTIONr_chiral_restr0.1290.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022566
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02478
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_it1.30.9271119
X-RAY DIFFRACTIONr_mcbond_other1.210.9231118
X-RAY DIFFRACTIONr_mcangle_it1.9551.3841415
X-RAY DIFFRACTIONr_mcangle_other1.9831.3881416
X-RAY DIFFRACTIONr_scbond_it2.5111.2411140
X-RAY DIFFRACTIONr_scbond_other2.511.2421141
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.811.7421652
X-RAY DIFFRACTIONr_long_range_B_refined6.78210.9993153
X-RAY DIFFRACTIONr_long_range_B_other6.349.3442830
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.545→1.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 97 -
Rwork0.155 1854 -
obs--78.23 %

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