data_8YG2 # _entry.id 8YG2 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 8YG2 pdb_00008yg2 10.2210/pdb8yg2/pdb WWPDB D_1300045581 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2024-05-08 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8YG2 _pdbx_database_status.recvd_initial_deposition_date 2024-02-26 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email ysohma@wakayama-med.ac.jp _pdbx_contact_author.name_first Youhei _pdbx_contact_author.name_last Sohma _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-1154-3903 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Sawazaki, T.' 1 0000-0001-5650-998X 'Sasaki, D.' 2 0000-0002-2224-1900 'Sohma, Y.' 3 0000-0002-1154-3903 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_id_ASTM PNASA6 _citation.journal_id_CSD 0040 _citation.journal_id_ISSN 1091-6490 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 121 _citation.language ? _citation.page_first e2314704121 _citation.page_last e2314704121 _citation.title 'Catalysis driven by an amyloid-substrate complex.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1073/pnas.2314704121 _citation.pdbx_database_id_PubMed 38691589 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sawazaki, T.' 1 0000-0001-5650-998X primary 'Sasaki, D.' 2 0000-0002-2224-1900 primary 'Sohma, Y.' 3 0000-0002-1154-3903 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'Amyloidogenic peptide from Islet Amyloid Polypeptide' 715.862 1 ? ? ? ? 2 non-polymer syn 'FORMIC ACID' 46.025 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(PIV)NFGAIL(NH2)' _entity_poly.pdbx_seq_one_letter_code_can XNFGAILX _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'FORMIC ACID' _pdbx_entity_nonpoly.comp_id FMT # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 PIV n 1 2 ASN n 1 3 PHE n 1 4 GLY n 1 5 ALA n 1 6 ILE n 1 7 LEU n 1 8 NH2 n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 8 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 FMT non-polymer . 'FORMIC ACID' ? 'C H2 O2' 46.025 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PIV 'L-peptide linking' . 'PIVALIC ACID' ? 'C5 H10 O2' 102.132 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 PIV 1 0 0 PIV PIV A . n A 1 2 ASN 2 1 1 ASN ASN A . n A 1 3 PHE 3 2 2 PHE PHE A . n A 1 4 GLY 4 3 3 GLY GLY A . n A 1 5 ALA 5 4 4 ALA ALA A . n A 1 6 ILE 6 5 5 ILE ILE A . n A 1 7 LEU 7 6 6 LEU LEU A . n A 1 8 NH2 8 7 7 NH2 NH2 A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id FMT _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 101 _pdbx_nonpoly_scheme.pdb_mon_id FMT _pdbx_nonpoly_scheme.auth_mon_id FMT _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0267 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? DIALS ? ? ? 2.2.10 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? DIALS ? ? ? 2.2.10 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? 2.8.3 4 ? 'model building' ? ? ? ? ? ? ? ? ? ? ? Coot ? ? ? 0.9.6 5 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 88.60 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 8YG2 _cell.details ? _cell.formula_units_Z ? _cell.length_a 4.864 _cell.length_a_esd ? _cell.length_b 20.466 _cell.length_b_esd ? _cell.length_c 20.855 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 2 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8YG2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8YG2 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.54 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 15.15 _exptl_crystal.description Needle _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method EVAPORATION _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'Formic acid' _exptl_crystal_grow.pdbx_pH_range 2.0-3.0 _exptl_crystal_grow.temp 298 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 4M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2022-10-21 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.040 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-1A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.040 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-1A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 8YG2 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.250 _reflns.d_resolution_low 20.470 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 1063 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 91.9 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 2.000 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 59.1100 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.08400 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 1.25 _reflns_shell.d_res_low 1.27 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 55 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 2.00 _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all 94.8 _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.15500 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _refine.aniso_B[1][1] -0.11500 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.18900 _refine.aniso_B[2][2] -0.01100 _refine.aniso_B[2][3] 0.00000 _refine.aniso_B[3][3] 0.13500 _refine.B_iso_max ? _refine.B_iso_mean 5.94 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.963 _refine.correlation_coeff_Fo_to_Fc_free 0.951 _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8YG2 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.25 _refine.ls_d_res_low 20.47 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 1054 _refine.ls_number_reflns_R_free 63 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 91.1 _refine.ls_percent_reflns_R_free 5.977 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free 0.201 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.174 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'MASK BULK SOLVENT' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.070 _refine.pdbx_overall_ESU_R_Free 0.069 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B 0.881 _refine.overall_SU_ML 0.035 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 1.25 _refine_hist.d_res_low 20.47 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 54 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 51 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.009 0.014 67 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.003 0.018 75 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.733 1.920 82 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 1.045 2.001 157 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? 3.777 5.000 6 ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? 44.446 26.667 3 ? r_dihedral_angle_2_deg ? ? 'X-RAY DIFFRACTION' ? 14.912 15.000 5 ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_4_deg ? ? 'X-RAY DIFFRACTION' ? 0.043 0.200 6 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.005 0.020 81 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.002 0.020 30 ? r_gen_planes_other ? ? 'X-RAY DIFFRACTION' ? 0.014 0.200 3 ? r_nbd_refined ? ? 'X-RAY DIFFRACTION' ? 0.203 0.200 37 ? r_nbd_other ? ? 'X-RAY DIFFRACTION' ? 0.187 0.200 22 ? r_nbtor_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_other ? ? 'X-RAY DIFFRACTION' ? 0.030 0.200 1 ? r_xyhbond_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? 0.230 0.543 23 ? r_mcbond_it ? ? 'X-RAY DIFFRACTION' ? 0.231 0.650 24 ? r_mcbond_other ? ? 'X-RAY DIFFRACTION' ? 0.376 0.817 26 ? r_mcangle_it ? ? 'X-RAY DIFFRACTION' ? 0.380 0.825 27 ? r_mcangle_other ? ? 'X-RAY DIFFRACTION' ? 0.206 0.674 44 ? r_scbond_it ? ? 'X-RAY DIFFRACTION' ? 0.205 0.563 43 ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? 0.220 0.885 52 ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? 0.219 0.956 53 ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_long_range_B_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.25 _refine_ls_shell.d_res_low 1.28 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 1 _refine_ls_shell.number_reflns_R_work 74 _refine_ls_shell.percent_reflns_obs 94.94 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.2430 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_R_complete ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? _refine_ls_shell.R_factor_R_free 0.2630 # _struct.entry_id 8YG2 _struct.title 'Crystal structure of amyloidogenic peptide Piv-NFGAIL-NH2 from Islet Amyloid Polypeptide' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8YG2 _struct_keywords.text 'Amyloid, CASL, Protein fibril' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8YG2 _struct_ref.pdbx_db_accession 8YG2 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8YG2 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 8YG2 _struct_ref_seq.db_align_beg 0 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 7 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 0 _struct_ref_seq.pdbx_auth_seq_align_end 7 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 180 ? 1 MORE 0 ? 1 'SSA (A^2)' 1180 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A PIV 1 C A ? ? 1_555 A ASN 2 N A ? A PIV 0 A ASN 1 1_555 ? ? ? ? ? ? ? 1.348 ? ? covale2 covale both ? A PIV 1 C B ? ? 1_555 A ASN 2 N B ? A PIV 0 A ASN 1 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale3 covale both ? A LEU 7 C ? ? ? 1_555 A NH2 8 N ? ? A LEU 6 A NH2 7 1_555 ? ? ? ? ? ? ? 1.331 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 N A ASN 1 ? A CA A ASN 1 ? A 1.309 1.459 -0.150 0.020 N 2 1 N A ASN 1 ? B CA A ASN 1 ? B 1.279 1.459 -0.180 0.020 N # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 N _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 ASN _pdbx_validate_rmsd_angle.auth_seq_id_1 1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 B _pdbx_validate_rmsd_angle.auth_atom_id_2 CA _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 ASN _pdbx_validate_rmsd_angle.auth_seq_id_2 1 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 B _pdbx_validate_rmsd_angle.auth_atom_id_3 CB _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 ASN _pdbx_validate_rmsd_angle.auth_seq_id_3 1 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 B _pdbx_validate_rmsd_angle.angle_value 122.62 _pdbx_validate_rmsd_angle.angle_target_value 110.60 _pdbx_validate_rmsd_angle.angle_deviation 12.02 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.80 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_entry_details.entry_id 8YG2 _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.has_protein_modification ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ASN N N N N 14 ASN CA C N S 15 ASN C C N N 16 ASN O O N N 17 ASN CB C N N 18 ASN CG C N N 19 ASN OD1 O N N 20 ASN ND2 N N N 21 ASN OXT O N N 22 ASN H H N N 23 ASN H2 H N N 24 ASN HA H N N 25 ASN HB2 H N N 26 ASN HB3 H N N 27 ASN HD21 H N N 28 ASN HD22 H N N 29 ASN HXT H N N 30 FMT C C N N 31 FMT O1 O N N 32 FMT O2 O N N 33 FMT H H N N 34 FMT HO2 H N N 35 GLY N N N N 36 GLY CA C N N 37 GLY C C N N 38 GLY O O N N 39 GLY OXT O N N 40 GLY H H N N 41 GLY H2 H N N 42 GLY HA2 H N N 43 GLY HA3 H N N 44 GLY HXT H N N 45 ILE N N N N 46 ILE CA C N S 47 ILE C C N N 48 ILE O O N N 49 ILE CB C N S 50 ILE CG1 C N N 51 ILE CG2 C N N 52 ILE CD1 C N N 53 ILE OXT O N N 54 ILE H H N N 55 ILE H2 H N N 56 ILE HA H N N 57 ILE HB H N N 58 ILE HG12 H N N 59 ILE HG13 H N N 60 ILE HG21 H N N 61 ILE HG22 H N N 62 ILE HG23 H N N 63 ILE HD11 H N N 64 ILE HD12 H N N 65 ILE HD13 H N N 66 ILE HXT H N N 67 LEU N N N N 68 LEU CA C N S 69 LEU C C N N 70 LEU O O N N 71 LEU CB C N N 72 LEU CG C N N 73 LEU CD1 C N N 74 LEU CD2 C N N 75 LEU OXT O N N 76 LEU H H N N 77 LEU H2 H N N 78 LEU HA H N N 79 LEU HB2 H N N 80 LEU HB3 H N N 81 LEU HG H N N 82 LEU HD11 H N N 83 LEU HD12 H N N 84 LEU HD13 H N N 85 LEU HD21 H N N 86 LEU HD22 H N N 87 LEU HD23 H N N 88 LEU HXT H N N 89 NH2 N N N N 90 NH2 HN1 H N N 91 NH2 HN2 H N N 92 PHE N N N N 93 PHE CA C N S 94 PHE C C N N 95 PHE O O N N 96 PHE CB C N N 97 PHE CG C Y N 98 PHE CD1 C Y N 99 PHE CD2 C Y N 100 PHE CE1 C Y N 101 PHE CE2 C Y N 102 PHE CZ C Y N 103 PHE OXT O N N 104 PHE H H N N 105 PHE H2 H N N 106 PHE HA H N N 107 PHE HB2 H N N 108 PHE HB3 H N N 109 PHE HD1 H N N 110 PHE HD2 H N N 111 PHE HE1 H N N 112 PHE HE2 H N N 113 PHE HZ H N N 114 PHE HXT H N N 115 PIV CT C N N 116 PIV C1 C N N 117 PIV C2 C N N 118 PIV C3 C N N 119 PIV C C N N 120 PIV O1 O N N 121 PIV O2 O N N 122 PIV H11 H N N 123 PIV H12 H N N 124 PIV H13 H N N 125 PIV H21 H N N 126 PIV H22 H N N 127 PIV H23 H N N 128 PIV H31 H N N 129 PIV H32 H N N 130 PIV H33 H N N 131 PIV HO2 H N N 132 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ASN N CA sing N N 13 ASN N H sing N N 14 ASN N H2 sing N N 15 ASN CA C sing N N 16 ASN CA CB sing N N 17 ASN CA HA sing N N 18 ASN C O doub N N 19 ASN C OXT sing N N 20 ASN CB CG sing N N 21 ASN CB HB2 sing N N 22 ASN CB HB3 sing N N 23 ASN CG OD1 doub N N 24 ASN CG ND2 sing N N 25 ASN ND2 HD21 sing N N 26 ASN ND2 HD22 sing N N 27 ASN OXT HXT sing N N 28 FMT C O1 doub N N 29 FMT C O2 sing N N 30 FMT C H sing N N 31 FMT O2 HO2 sing N N 32 GLY N CA sing N N 33 GLY N H sing N N 34 GLY N H2 sing N N 35 GLY CA C sing N N 36 GLY CA HA2 sing N N 37 GLY CA HA3 sing N N 38 GLY C O doub N N 39 GLY C OXT sing N N 40 GLY OXT HXT sing N N 41 ILE N CA sing N N 42 ILE N H sing N N 43 ILE N H2 sing N N 44 ILE CA C sing N N 45 ILE CA CB sing N N 46 ILE CA HA sing N N 47 ILE C O doub N N 48 ILE C OXT sing N N 49 ILE CB CG1 sing N N 50 ILE CB CG2 sing N N 51 ILE CB HB sing N N 52 ILE CG1 CD1 sing N N 53 ILE CG1 HG12 sing N N 54 ILE CG1 HG13 sing N N 55 ILE CG2 HG21 sing N N 56 ILE CG2 HG22 sing N N 57 ILE CG2 HG23 sing N N 58 ILE CD1 HD11 sing N N 59 ILE CD1 HD12 sing N N 60 ILE CD1 HD13 sing N N 61 ILE OXT HXT sing N N 62 LEU N CA sing N N 63 LEU N H sing N N 64 LEU N H2 sing N N 65 LEU CA C sing N N 66 LEU CA CB sing N N 67 LEU CA HA sing N N 68 LEU C O doub N N 69 LEU C OXT sing N N 70 LEU CB CG sing N N 71 LEU CB HB2 sing N N 72 LEU CB HB3 sing N N 73 LEU CG CD1 sing N N 74 LEU CG CD2 sing N N 75 LEU CG HG sing N N 76 LEU CD1 HD11 sing N N 77 LEU CD1 HD12 sing N N 78 LEU CD1 HD13 sing N N 79 LEU CD2 HD21 sing N N 80 LEU CD2 HD22 sing N N 81 LEU CD2 HD23 sing N N 82 LEU OXT HXT sing N N 83 NH2 N HN1 sing N N 84 NH2 N HN2 sing N N 85 PHE N CA sing N N 86 PHE N H sing N N 87 PHE N H2 sing N N 88 PHE CA C sing N N 89 PHE CA CB sing N N 90 PHE CA HA sing N N 91 PHE C O doub N N 92 PHE C OXT sing N N 93 PHE CB CG sing N N 94 PHE CB HB2 sing N N 95 PHE CB HB3 sing N N 96 PHE CG CD1 doub Y N 97 PHE CG CD2 sing Y N 98 PHE CD1 CE1 sing Y N 99 PHE CD1 HD1 sing N N 100 PHE CD2 CE2 doub Y N 101 PHE CD2 HD2 sing N N 102 PHE CE1 CZ doub Y N 103 PHE CE1 HE1 sing N N 104 PHE CE2 CZ sing Y N 105 PHE CE2 HE2 sing N N 106 PHE CZ HZ sing N N 107 PHE OXT HXT sing N N 108 PIV CT C1 sing N N 109 PIV CT C2 sing N N 110 PIV CT C3 sing N N 111 PIV CT C sing N N 112 PIV C1 H11 sing N N 113 PIV C1 H12 sing N N 114 PIV C1 H13 sing N N 115 PIV C2 H21 sing N N 116 PIV C2 H22 sing N N 117 PIV C2 H23 sing N N 118 PIV C3 H31 sing N N 119 PIV C3 H32 sing N N 120 PIV C3 H33 sing N N 121 PIV C O1 doub N N 122 PIV C O2 sing N N 123 PIV O2 HO2 sing N N 124 # _pdbx_audit_support.funding_organization 'Japan Society for the Promotion of Science (JSPS)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3DGJ _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 8YG2 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.205592 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] -0.005028 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.048862 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.047964 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.pdbx_scat_Z _atom_type.pdbx_N_electrons _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b4 C 6 6 2.310 20.844 1.020 10.208 1.589 0.569 0.865 51.651 H 1 1 0.493 10.511 0.323 26.126 0.140 3.142 0.041 57.800 N 7 7 12.222 0.006 3.135 9.893 2.014 28.997 1.167 0.583 O 8 8 3.049 13.277 2.287 5.701 1.546 0.324 0.867 32.909 # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num _atom_site.calc_flag HETATM 1 C CT A PIV A 1 1 ? -1.817 -11.745 4.357 0.70 6.02 0 0 PIV A CT 1 ? HETATM 2 C CT B PIV A 1 1 ? -1.798 -12.032 5.428 0.30 4.43 0 0 PIV A CT 1 ? HETATM 3 C C1 A PIV A 1 1 ? -0.789 -12.716 3.814 0.70 6.03 0 0 PIV A C1 1 ? HETATM 4 C C1 B PIV A 1 1 ? -2.096 -12.107 3.929 0.30 4.42 0 0 PIV A C1 1 ? HETATM 5 C C2 A PIV A 1 1 ? -2.413 -12.389 5.598 0.70 6.02 0 0 PIV A C2 1 ? HETATM 6 C C2 B PIV A 1 1 ? -0.792 -13.129 5.781 0.30 4.39 0 0 PIV A C2 1 ? HETATM 7 C C3 A PIV A 1 1 ? -2.829 -11.569 3.228 0.70 6.00 0 0 PIV A C3 1 ? HETATM 8 C C3 B PIV A 1 1 ? -3.090 -12.199 6.225 0.30 4.44 0 0 PIV A C3 1 ? HETATM 9 C C A PIV A 1 1 ? -1.224 -10.401 4.786 0.70 5.94 0 0 PIV A C 1 ? HETATM 10 C C B PIV A 1 1 ? -1.201 -10.679 5.751 0.30 4.49 0 0 PIV A C 1 ? HETATM 11 O O1 A PIV A 1 1 ? -0.060 -10.112 4.546 0.70 6.05 0 0 PIV A O1 1 ? HETATM 12 O O1 B PIV A 1 1 ? -0.014 -10.603 6.046 0.30 4.46 0 0 PIV A O1 1 ? ATOM 13 N N A ASN A 1 2 ? -1.962 -9.494 5.456 0.70 5.62 0 1 ASN A N 1 ? ATOM 14 N N B ASN A 1 2 ? -1.974 -9.584 5.710 0.30 4.62 0 1 ASN A N 1 ? ATOM 15 C CA A ASN A 1 2 ? -1.556 -8.294 5.787 0.70 4.82 0 1 ASN A CA 1 ? ATOM 16 C CA B ASN A 1 2 ? -1.723 -8.334 5.814 0.30 4.98 0 1 ASN A CA 1 ? ATOM 17 C C A ASN A 1 2 ? -1.968 -7.852 7.197 0.70 4.89 0 1 ASN A C 1 ? ATOM 18 C C B ASN A 1 2 ? -2.007 -7.920 7.262 0.30 5.02 0 1 ASN A C 1 ? ATOM 19 O O A ASN A 1 2 ? -3.172 -7.809 7.480 0.70 5.00 0 1 ASN A O 1 ? ATOM 20 O O B ASN A 1 2 ? -3.184 -7.990 7.660 0.30 5.06 0 1 ASN A O 1 ? ATOM 21 C CB A ASN A 1 2 ? -1.977 -7.183 4.817 0.70 4.53 0 1 ASN A CB 1 ? ATOM 22 C CB B ASN A 1 2 ? -2.302 -7.291 4.849 0.30 5.09 0 1 ASN A CB 1 ? ATOM 23 C CG A ASN A 1 2 ? -1.462 -5.822 5.231 0.70 4.30 0 1 ASN A CG 1 ? ATOM 24 C CG B ASN A 1 2 ? -3.775 -7.003 5.072 0.30 5.14 0 1 ASN A CG 1 ? ATOM 25 O OD1 A ASN A 1 2 ? -0.256 -5.611 5.322 0.70 3.98 0 1 ASN A OD1 1 ? ATOM 26 O OD1 B ASN A 1 2 ? -4.597 -7.917 5.137 0.30 5.27 0 1 ASN A OD1 1 ? ATOM 27 N ND2 A ASN A 1 2 ? -2.366 -4.882 5.437 0.70 4.21 0 1 ASN A ND2 1 ? ATOM 28 N ND2 B ASN A 1 2 ? -4.125 -5.729 5.167 0.30 5.15 0 1 ASN A ND2 1 ? ATOM 29 N N . PHE A 1 3 ? -0.978 -7.520 8.018 1.00 4.96 0 2 PHE A N 1 ? ATOM 30 C CA . PHE A 1 3 ? -1.135 -7.032 9.410 1.00 5.12 0 2 PHE A CA 1 ? ATOM 31 C C . PHE A 1 3 ? -0.569 -5.618 9.535 1.00 5.19 0 2 PHE A C 1 ? ATOM 32 O O . PHE A 1 3 ? -0.759 -4.998 10.583 1.00 5.78 0 2 PHE A O 1 ? ATOM 33 C CB . PHE A 1 3 ? -0.435 -7.999 10.359 1.00 5.05 0 2 PHE A CB 1 ? ATOM 34 C CG . PHE A 1 3 ? -1.061 -9.369 10.354 1.00 5.06 0 2 PHE A CG 1 ? ATOM 35 C CD1 . PHE A 1 3 ? -2.159 -9.642 11.153 1.00 5.07 0 2 PHE A CD1 1 ? ATOM 36 C CD2 . PHE A 1 3 ? -0.584 -10.369 9.520 1.00 4.94 0 2 PHE A CD2 1 ? ATOM 37 C CE1 . PHE A 1 3 ? -2.739 -10.899 11.151 1.00 5.11 0 2 PHE A CE1 1 ? ATOM 38 C CE2 . PHE A 1 3 ? -1.168 -11.626 9.521 1.00 5.01 0 2 PHE A CE2 1 ? ATOM 39 C CZ . PHE A 1 3 ? -2.253 -11.884 10.324 1.00 5.02 0 2 PHE A CZ 1 ? ATOM 40 N N . GLY A 1 4 ? 0.066 -5.118 8.475 1.00 5.11 0 3 GLY A N 1 ? ATOM 41 C CA . GLY A 1 4 ? 0.762 -3.824 8.454 1.00 5.02 0 3 GLY A CA 1 ? ATOM 42 C C . GLY A 1 4 ? 0.083 -2.848 7.507 1.00 5.11 0 3 GLY A C 1 ? ATOM 43 O O . GLY A 1 4 ? -1.145 -2.946 7.292 1.00 4.75 0 3 GLY A O 1 ? ATOM 44 N N . ALA A 1 5 ? 0.866 -1.922 6.970 1.00 5.34 0 4 ALA A N 1 ? ATOM 45 C CA . ALA A 1 5 ? 0.396 -0.889 6.026 1.00 5.56 0 4 ALA A CA 1 ? ATOM 46 C C . ALA A 1 5 ? 0.998 -1.162 4.645 1.00 5.64 0 4 ALA A C 1 ? ATOM 47 O O . ALA A 1 5 ? 2.231 -1.327 4.543 1.00 5.63 0 4 ALA A O 1 ? ATOM 48 C CB . ALA A 1 5 ? 0.760 0.475 6.550 1.00 5.58 0 4 ALA A CB 1 ? ATOM 49 N N . ILE A 1 6 ? 0.148 -1.225 3.619 1.00 5.88 0 5 ILE A N 1 ? ATOM 50 C CA . ILE A 1 6 ? 0.588 -1.352 2.202 1.00 6.16 0 5 ILE A CA 1 ? ATOM 51 C C . ILE A 1 6 ? 0.042 -0.142 1.446 1.00 6.26 0 5 ILE A C 1 ? ATOM 52 O O . ILE A 1 6 ? -1.204 0.027 1.381 1.00 6.13 0 5 ILE A O 1 ? ATOM 53 C CB . ILE A 1 6 ? 0.157 -2.696 1.584 1.00 6.25 0 5 ILE A CB 1 ? ATOM 54 C CG1 . ILE A 1 6 ? 0.761 -3.869 2.360 1.00 6.30 0 5 ILE A CG1 1 ? ATOM 55 C CG2 . ILE A 1 6 ? 0.529 -2.753 0.112 1.00 6.22 0 5 ILE A CG2 1 ? ATOM 56 C CD1 . ILE A 1 6 ? 0.288 -5.233 1.897 1.00 6.36 0 5 ILE A CD1 1 ? ATOM 57 N N . LEU A 1 7 ? 0.960 0.705 0.975 1.00 6.61 0 6 LEU A N 1 ? ATOM 58 C CA . LEU A 1 7 ? 0.663 1.983 0.268 1.00 7.12 0 6 LEU A CA 1 ? ATOM 59 C C . LEU A 1 7 ? 0.822 1.732 -1.176 1.00 7.70 0 6 LEU A C 1 ? ATOM 60 O O . LEU A 1 7 ? 2.008 1.685 -1.561 1.00 7.97 0 6 LEU A O 1 ? ATOM 61 C CB . LEU A 1 7 ? 1.486 3.109 0.899 1.00 7.26 0 6 LEU A CB 1 ? ATOM 62 C CG . LEU A 1 7 ? 0.799 3.887 2.020 1.00 7.52 0 6 LEU A CG 1 ? ATOM 63 C CD1 . LEU A 1 7 ? 0.376 2.990 3.176 1.00 7.48 0 6 LEU A CD1 1 ? ATOM 64 C CD2 . LEU A 1 7 ? 1.717 4.986 2.516 1.00 7.49 0 6 LEU A CD2 1 ? HETATM 65 N N . NH2 A 1 8 ? -0.197 1.444 -1.983 1.00 7.97 0 7 NH2 A N 1 ? HETATM 66 C C . FMT B 2 . ? -3.082 -6.190 12.659 1.00 31.19 0 101 FMT A C 1 ? HETATM 67 O O1 . FMT B 2 . ? -3.001 -6.505 13.828 1.00 31.43 0 101 FMT A O1 1 ? HETATM 68 O O2 . FMT B 2 . ? -2.935 -4.986 12.197 1.00 31.09 0 101 FMT A O2 1 ? #