data_6UG2 # _entry.id 6UG2 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.336 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 6UG2 WWPDB D_1000244557 # _pdbx_database_related.db_name PDB _pdbx_database_related.details 'same molecule in a different crystal form' _pdbx_database_related.db_id 6UFU _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6UG2 _pdbx_database_status.recvd_initial_deposition_date 2019-09-25 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Mulligan, V.K.' 1 0000-0001-6038-8922 'Kang, C.S.' 2 0000-0003-0959-0783 'Antselovich, I.' 3 0000-0002-2208-9937 'Sawaya, M.R.' 4 0000-0003-0874-9043 'Yeates, T.O.' 5 0000-0001-5709-9839 'Baker, D.' 6 0000-0001-7896-6217 # _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 'Protein Sci.' _citation.journal_id_ASTM PRCIEI _citation.journal_id_CSD 0795 _citation.journal_id_ISSN 1469-896X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 29 _citation.language ? _citation.page_first 2433 _citation.page_last 2445 _citation.title 'Computational design of mixed chirality peptide macrocycles with internal symmetry.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/pro.3974 _citation.pdbx_database_id_PubMed 33058266 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mulligan, V.K.' 1 0000-0001-6038-8922 primary 'Kang, C.S.' 2 0000-0003-0959-0783 primary 'Sawaya, M.R.' 3 ? primary 'Rettie, S.' 4 ? primary 'Li, X.' 5 ? primary 'Antselovich, I.' 6 ? primary 'Craven, T.W.' 7 ? primary 'Watkins, A.M.' 8 ? primary 'Labonte, J.W.' 9 ? primary 'DiMaio, F.' 10 ? primary 'Yeates, T.O.' 11 0000-0001-5709-9839 primary 'Baker, D.' 12 ? # _cell.entry_id 6UG2 _cell.length_a 9.810 _cell.length_b 17.050 _cell.length_c 20.590 _cell.angle_alpha 105.16 _cell.angle_beta 92.17 _cell.angle_gamma 105.93 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UG2 _symmetry.space_group_name_H-M 'P -1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 2 # 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 'C2-1, Zappy, crystal form 2' 1021.079 1 ? ? ? ;Residue 1 is partially racemized. Both DSN and SER are present at this position. The racemization was an undesired side product of the peptide synthesis. ; 2 non-polymer syn 'CALCIUM ION' 40.078 1 ? ? ? ? 3 water nat water 18.015 15 ? ? ? ? # _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 '(DSN)(DGL)(AIB)SL(DSN)(DGL)(AIB)SL' _entity_poly.pdbx_seq_one_letter_code_can SEASLSEASL _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DSN y 1 1 SER y 1 2 DGL n 1 3 AIB n 1 4 SER n 1 5 LEU n 1 6 DSN n 1 7 DGL n 1 8 AIB n 1 9 SER n 1 10 LEU 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 10 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6UG2 _struct_ref.pdbx_db_accession 6UG2 _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 6UG2 _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 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6UG2 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # 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 AIB 'L-peptide linking' n 'ALPHA-AMINOISOBUTYRIC ACID' ? 'C4 H9 N O2' 103.120 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 DGL 'D-peptide linking' . 'D-GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 DSN 'D-peptide linking' . D-SERINE ? 'C3 H7 N O3' 105.093 HOH non-polymer . WATER ? 'H2 O' 18.015 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 # _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 6UG2 _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 1.55 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 20.86 _exptl_crystal.description 'needle, 200 microns long and less than 5 microns thick' _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_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.2 M calcium chloride, 0.1 M HEPES, pH 7.5, 28% (w/v) PEG 400' _exptl_crystal_grow.pdbx_pH_range ? # _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 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-02-14 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Si (111)' _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 0.97918 _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 'APS BEAMLINE 24-ID-E' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97918 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 24-ID-E _diffrn_source.pdbx_synchrotron_site APS # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 6UG2 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 19.734 _reflns.d_resolution_high 1.100 _reflns.number_obs 4357 _reflns.number_all ? _reflns.percent_possible_obs 87.4 _reflns.pdbx_Rmerge_I_obs 0.25000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 4.0800 _reflns.B_iso_Wilson_estimate 11.43 _reflns.pdbx_redundancy 4.753 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.10 _reflns_shell.d_res_low 1.13 _reflns_shell.percent_possible_all 66.9 _reflns_shell.Rmerge_I_obs 0.89800 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.140 _reflns_shell.pdbx_redundancy 4.06 _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 240 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_Rrim_I_all ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 6UG2 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 4353 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.360 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.73 _refine.ls_d_res_high 1.10 _refine.ls_percent_reflns_obs 87.5 _refine.ls_R_factor_obs 0.154 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.151 _refine.ls_R_factor_R_free 0.182 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.990 _refine.ls_number_reflns_R_free 435 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 11.18 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.077 _refine.pdbx_overall_phase_error 17.010 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 76 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 15 _refine_hist.number_atoms_total 92 _refine_hist.d_res_high 1.10 _refine_hist.d_res_low 19.73 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.017 ? ? 101 'X-RAY DIFFRACTION' ? f_angle_d 3.495 ? ? 144 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 28.557 ? ? 40 'X-RAY DIFFRACTION' ? f_chiral_restr 1.587 ? ? 18 'X-RAY DIFFRACTION' ? f_plane_restr 0.023 ? ? 16 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 1.1000 1.2600 1149 0.2650 77.00 0.3120 . . 127 . . . . 'X-RAY DIFFRACTION' . 1.2600 1.5900 1355 0.1894 90.00 0.2237 . . 150 . . . . 'X-RAY DIFFRACTION' . 1.5900 19.7300 1414 0.1167 95.00 0.1452 . . 158 . . . . # _struct.entry_id 6UG2 _struct.title 'C2 symmetric peptide design number 1, Zappy, crystal form 2' _struct.pdbx_descriptor 'C2-1, Zappy, crystal form 1' _struct.pdbx_model_details 'S2 symmetric cyclic peptide' _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6UG2 _struct_keywords.text 'cyclic peptide, 2-fold symmetric, L and D-amino acids, DE NOVO PROTEIN' _struct_keywords.pdbx_keywords 'DE NOVO PROTEIN' # 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 ? C N N 3 ? # 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 DSN 1 C A ? ? 1_555 A DGL 2 N ? ? A DSN 1 A DGL 2 1_555 ? ? ? ? ? ? ? 1.311 ? ? covale2 covale both ? A SER 1 C B ? ? 1_555 A DGL 2 N ? ? A SER 1 A DGL 2 1_555 ? ? ? ? ? ? ? 1.364 ? ? covale3 covale both ? A SER 1 C C ? ? 1_555 A DGL 2 N ? ? A SER 1 A DGL 2 1_555 ? ? ? ? ? ? ? 1.380 ? ? covale4 covale both ? A DSN 1 N A ? ? 1_555 A LEU 10 C ? ? A DSN 1 A LEU 10 1_555 ? ? ? ? ? ? ? 1.296 ? ? covale5 covale both ? A SER 1 N B ? ? 1_555 A LEU 10 C ? ? A SER 1 A LEU 10 1_555 ? ? ? ? ? ? ? 1.318 sing ? covale6 covale both ? A SER 1 N C ? ? 1_555 A LEU 10 C ? ? A SER 1 A LEU 10 1_555 ? ? ? ? ? ? ? 1.348 sing ? covale7 covale both ? A DGL 2 C ? ? ? 1_555 A AIB 3 N ? ? A DGL 2 A AIB 3 1_555 ? ? ? ? ? ? ? 1.363 ? ? covale8 covale both ? A AIB 3 C ? ? ? 1_555 A SER 4 N ? ? A AIB 3 A SER 4 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale9 covale both ? A LEU 5 C ? ? ? 1_555 A DSN 6 N ? ? A LEU 5 A DSN 6 1_555 ? ? ? ? ? ? ? 1.259 ? ? covale10 covale both ? A DSN 6 C ? ? ? 1_555 A DGL 7 N ? ? A DSN 6 A DGL 7 1_555 ? ? ? ? ? ? ? 1.303 ? ? covale11 covale both ? A DGL 7 C ? ? ? 1_555 A AIB 8 N ? ? A DGL 7 A AIB 8 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale12 covale both ? A AIB 8 C ? ? ? 1_555 A SER 9 N ? ? A AIB 8 A SER 9 1_555 ? ? ? ? ? ? ? 1.328 ? ? metalc1 metalc ? ? A DGL 2 OE1 ? ? ? 1_555 B CA . CA ? ? A DGL 2 A CA 101 1_555 ? ? ? ? ? ? ? 2.633 ? ? metalc2 metalc ? ? A DGL 2 OE2 ? ? ? 1_555 B CA . CA ? ? A DGL 2 A CA 101 1_555 ? ? ? ? ? ? ? 2.485 ? ? metalc3 metalc ? ? A DGL 2 O ? ? ? 1_555 B CA . CA ? ? A DGL 2 A CA 101 1_455 ? ? ? ? ? ? ? 2.438 ? ? metalc4 metalc ? ? A DGL 2 OE1 ? ? ? 1_555 B CA . CA ? ? A DGL 2 A CA 101 2_676 ? ? ? ? ? ? ? 2.340 ? ? metalc5 metalc ? ? A DGL 7 OE1 ? ? ? 1_555 B CA . CA ? ? A DGL 7 A CA 101 2_566 ? ? ? ? ? ? ? 2.450 ? ? metalc6 metalc ? ? A DGL 7 OE2 ? ? ? 1_555 B CA . CA ? ? A DGL 7 A CA 101 2_566 ? ? ? ? ? ? ? 2.507 ? ? metalc7 metalc ? ? B CA . CA ? ? ? 1_555 C HOH . O ? ? A CA 101 A HOH 204 1_555 ? ? ? ? ? ? ? 2.393 ? ? metalc8 metalc ? ? B CA . CA ? ? ? 1_555 C HOH . O ? ? A CA 101 A HOH 207 1_555 ? ? ? ? ? ? ? 2.421 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id CA _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'binding site for residue CA A 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 DGL A 2 ? DGL A 2 . ? 1_555 ? 2 AC1 4 DGL A 2 ? DGL A 2 . ? 1_655 ? 3 AC1 4 HOH C . ? HOH A 204 . ? 1_555 ? 4 AC1 4 HOH C . ? HOH A 207 . ? 1_555 ? # _atom_sites.entry_id 6UG2 _atom_sites.fract_transf_matrix[1][1] 0.101937 _atom_sites.fract_transf_matrix[1][2] 0.029099 _atom_sites.fract_transf_matrix[1][3] 0.012621 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.060994 _atom_sites.fract_transf_matrix[2][3] 0.018001 _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] 0.050675 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? CA ? ? 8.75937 8.41257 2.76798 ? 9.64476 0.47514 97.39057 ? 0.0 ;3-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? H ? ? 0.51345 0.48472 ? ? 24.73122 6.32584 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # 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 DSN 1 1 1 DSN DSN A . y A 1 1 SER 1 1 1 SER SER A . y A 1 2 DGL 2 2 2 DGL DGL A . n A 1 3 AIB 3 3 3 AIB AIB A . n A 1 4 SER 4 4 4 SER SER A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 DSN 6 6 6 DSN DSN A . n A 1 7 DGL 7 7 7 DGL DGL A . n A 1 8 AIB 8 8 8 AIB AIB A . n A 1 9 SER 9 9 9 SER SER A . n A 1 10 LEU 10 10 10 LEU LEU A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CA 1 101 101 CA CA A . C 3 HOH 1 201 201 HOH HOH A . C 3 HOH 2 202 202 HOH HOH A . C 3 HOH 3 203 203 HOH HOH A . C 3 HOH 4 204 204 HOH HOH A . C 3 HOH 5 205 205 HOH HOH A . C 3 HOH 6 206 206 HOH HOH A . C 3 HOH 7 207 207 HOH HOH A . C 3 HOH 8 208 208 HOH HOH A . C 3 HOH 9 209 209 HOH HOH A . C 3 HOH 10 210 210 HOH HOH A . C 3 HOH 11 211 211 HOH HOH A . C 3 HOH 12 212 212 HOH HOH A . C 3 HOH 13 213 213 HOH HOH A . C 3 HOH 14 214 214 HOH HOH A . C 3 HOH 15 215 215 HOH HOH A . # _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 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _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_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE2 ? A DGL 2 ? A DGL 2 ? 1_555 51.2 ? 2 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? A DGL 2 ? A DGL 2 ? 1_555 43.2 ? 3 OE2 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? A DGL 2 ? A DGL 2 ? 1_555 16.6 ? 4 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 0.0 ? 5 OE2 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 51.2 ? 6 O ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 43.2 ? 7 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE1 ? A DGL 7 ? A DGL 7 ? 1_555 91.5 ? 8 OE2 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE1 ? A DGL 7 ? A DGL 7 ? 1_555 41.3 ? 9 O ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE1 ? A DGL 7 ? A DGL 7 ? 1_555 54.9 ? 10 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE1 ? A DGL 7 ? A DGL 7 ? 1_555 91.5 ? 11 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE2 ? A DGL 7 ? A DGL 7 ? 1_555 100.1 ? 12 OE2 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE2 ? A DGL 7 ? A DGL 7 ? 1_555 49.6 ? 13 O ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE2 ? A DGL 7 ? A DGL 7 ? 1_555 62.3 ? 14 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE2 ? A DGL 7 ? A DGL 7 ? 1_555 100.1 ? 15 OE1 ? A DGL 7 ? A DGL 7 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 OE2 ? A DGL 7 ? A DGL 7 ? 1_555 8.8 ? 16 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 204 ? 1_555 123.6 ? 17 OE2 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 204 ? 1_555 72.4 ? 18 O ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 204 ? 1_555 82.9 ? 19 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 204 ? 1_555 123.6 ? 20 OE1 ? A DGL 7 ? A DGL 7 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 204 ? 1_555 32.8 ? 21 OE2 ? A DGL 7 ? A DGL 7 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 204 ? 1_555 24.0 ? 22 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 207 ? 1_555 72.1 ? 23 OE2 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 207 ? 1_555 79.8 ? 24 O ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 207 ? 1_555 64.4 ? 25 OE1 ? A DGL 2 ? A DGL 2 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 207 ? 1_555 72.1 ? 26 OE1 ? A DGL 7 ? A DGL 7 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 207 ? 1_555 101.0 ? 27 OE2 ? A DGL 7 ? A DGL 7 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 207 ? 1_555 102.1 ? 28 O ? C HOH . ? A HOH 204 ? 1_555 CA ? B CA . ? A CA 101 ? 1_555 O ? C HOH . ? A HOH 207 ? 1_555 103.0 ? # _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 2020-12-02 # _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 ? # 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 ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? V1.16-3549 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? 20180808 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? 20180808 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.25 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXD ? ? ? . 5 # _pdbx_entry_details.entry_id 6UG2 _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ;Residue 1 is partially racemized. Both DSN and SER are present at this position. The racemization was an undesired side product of the peptide synthesis. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 O A DSN 1 ? A C A DSN 1 ? A N A DGL 2 ? ? 110.49 122.70 -12.21 1.60 Y 2 1 O A SER 1 ? B C A SER 1 ? B N A DGL 2 ? ? 133.45 122.70 10.75 1.60 Y # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 DSN _pdbx_validate_peptide_omega.auth_asym_id_1 A _pdbx_validate_peptide_omega.auth_seq_id_1 1 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 A _pdbx_validate_peptide_omega.auth_comp_id_2 DGL _pdbx_validate_peptide_omega.auth_asym_id_2 A _pdbx_validate_peptide_omega.auth_seq_id_2 2 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega -149.93 # _pdbx_validate_main_chain_plane.id 1 _pdbx_validate_main_chain_plane.PDB_model_num 1 _pdbx_validate_main_chain_plane.auth_comp_id SER _pdbx_validate_main_chain_plane.auth_asym_id A _pdbx_validate_main_chain_plane.auth_seq_id 1 _pdbx_validate_main_chain_plane.PDB_ins_code ? _pdbx_validate_main_chain_plane.label_alt_id C _pdbx_validate_main_chain_plane.improper_torsion_angle 12.13 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Department of Energy (DOE, United States)' 'United States' DE-FC02-02ER63421 1 'Department of Energy (DOE, United States)' 'United States' DE-AC02-06CH11357 2 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 water HOH # _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 ? # _space_group.name_H-M_alt 'P -1' _space_group.name_Hall '-P 1' _space_group.IT_number 2 _space_group.crystal_system triclinic _space_group.id 1 # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -x,-y,-z #