data_4D5M # _entry.id 4D5M # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.322 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4D5M PDBE EBI-62121 WWPDB D_1290062121 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4D5M _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2014-11-05 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Legrand, P.' 1 'Le Du, M.-H.' 2 'Valery, C.' 3 'Deville-Foillard, S.' 4 'Paternostre, M.' 5 'Artzner, F.' 6 # _citation.id primary _citation.title 'Atomic View of the Histidine Environment Stabilizing Higher- Ph Conformations of Ph-Dependent Proteins.' _citation.journal_abbrev Nat.Commun. _citation.journal_volume 6 _citation.page_first 7771 _citation.page_last ? _citation.year 2015 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 2041-1723 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 26190377 _citation.pdbx_database_id_DOI 10.1038/NCOMMS8771 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Valery, C.' 1 ? primary 'Deville-Foillard, S.' 2 ? primary 'Lefebvre, C.' 3 ? primary 'Taberner, N.' 4 ? primary 'Legrand, P.' 5 ? primary 'Meneau, F.' 6 ? primary 'Meriadec, C.' 7 ? primary 'Delvaux, C.' 8 ? primary 'Bizien, T.' 9 ? primary 'Kasotakis, E.' 10 ? primary 'Lopez-Iglesias, C.' 11 ? primary 'Gall, A.' 12 ? primary 'Bressanelli, S.' 13 ? primary 'Le Du, M.-H.' 14 ? primary 'Paternostre, M.' 15 ? primary 'Artzner, F.' 16 ? # _cell.entry_id 4D5M _cell.length_a 84.900 _cell.length_b 27.470 _cell.length_c 13.150 _cell.angle_alpha 90.00 _cell.angle_beta 98.83 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D5M _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # 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 TRIPTORELIN 1312.458 4 ? ? ? ;TRIPTORELIN IS A MEDICINE AVAILABLE IN A NUMBER OF COUNTRIES WORLDWIDE. IT IS AN ANALOGOUS OF THE GONADOTROPIN-RELEASING HORMONE. 5-OXO-D-PROLYL-L-HISTIDYL-L-TRYPTOPHANYL-L-SERYL-L-TYROSYL-D-TRYPTOPHANYL-L-LEUCYL-L-ARGINYL-L-PROLYL-L-GLYCINAMIDE. ; 2 non-polymer syn 'PHOSPHATE ION' 94.971 3 ? ? ? ? 3 water nat water 18.015 45 ? ? ? ? # _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 '(PCA)HWSY(DTR)LRPG(NH2)' _entity_poly.pdbx_seq_one_letter_code_can QHWSYWLRPGX _entity_poly.pdbx_strand_id A,B,C,D _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 PCA n 1 2 HIS n 1 3 TRP n 1 4 SER n 1 5 TYR n 1 6 DTR n 1 7 LEU n 1 8 ARG n 1 9 PRO n 1 10 GLY n 1 11 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _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 'TRIPTORELIN IS A MEDICINE AVAILABLE IN A NUMBER OF COUNTRIES WORLDWIDE.' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4D5M _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession 4D5M _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4D5M A 1 ? 11 ? 4D5M 1 ? 11 ? 1 11 2 1 4D5M B 1 ? 11 ? 4D5M 1 ? 11 ? 1 11 3 1 4D5M C 1 ? 11 ? 4D5M 1 ? 11 ? 1 11 4 1 4D5M D 1 ? 11 ? 4D5M 1 ? 11 ? 1 11 # 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 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 DTR 'D-peptide linking' . D-TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 PCA 'L-peptide linking' n 'PYROGLUTAMIC ACID' ? 'C5 H7 N O3' 129.114 PO4 non-polymer . 'PHOSPHATE ION' ? 'O4 P -3' 94.971 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # _exptl.entry_id 4D5M _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.42 _exptl_crystal.density_percent_sol 14 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.2 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '300 MM POTASSIUM PHOSPHATE BUFFER, PH 6.2 MIXED WITH 80 MG/ML TRIPTORELIN IN WATER.' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2011-07-06 _diffrn_detector.details 'KB MIRRORS' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'CHANNEL-CUT MONOCHROMATOR SI 111' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.78471 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SOLEIL BEAMLINE PROXIMA 1' _diffrn_source.pdbx_synchrotron_site SOLEIL _diffrn_source.pdbx_synchrotron_beamline 'PROXIMA 1' _diffrn_source.pdbx_wavelength 0.78471 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4D5M _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 41.95 _reflns.d_resolution_high 0.85 _reflns.number_obs 24802 _reflns.number_all ? _reflns.percent_possible_obs 98.6 _reflns.pdbx_Rmerge_I_obs 0.07 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 25.60 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 26.6 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 0.85 _reflns_shell.d_res_low 0.87 _reflns_shell.percent_possible_all 88.0 _reflns_shell.Rmerge_I_obs 0.20 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.40 _reflns_shell.pdbx_redundancy 6.3 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4D5M _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 24802 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 41.95 _refine.ls_d_res_high 0.85 _refine.ls_percent_reflns_obs 98.63 _refine.ls_R_factor_obs 0.08038 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.08001 _refine.ls_R_factor_R_free 0.08739 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 1306 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.991 _refine.correlation_coeff_Fo_to_Fc_free 0.996 _refine.B_iso_mean 1.746 _refine.aniso_B[1][1] -0.02 _refine.aniso_B[2][2] 0.00 _refine.aniso_B[3][3] 0.00 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.08 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _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_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY' _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct 'DIRECT METHODS' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.011 _refine.pdbx_overall_ESU_R_Free 0.011 _refine.overall_SU_ML 0.006 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 0.195 _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 380 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 45 _refine_hist.number_atoms_total 440 _refine_hist.d_res_high 0.85 _refine_hist.d_res_low 41.95 # 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 r_bond_refined_d 0.015 0.019 ? 472 'X-RAY DIFFRACTION' ? r_bond_other_d 0.009 0.020 ? 379 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.647 1.809 ? 637 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.875 2.978 ? 826 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 7.556 5.000 ? 38 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 41.492 18.182 ? 22 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 10.810 15.000 ? 42 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 15.600 15.000 ? 4 'X-RAY DIFFRACTION' ? r_chiral_restr 0.088 0.200 ? 45 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.018 0.021 ? 532 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 156 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? 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' ? r_mcbond_it 0.410 0.124 ? 184 'X-RAY DIFFRACTION' ? r_mcbond_other 0.404 0.125 ? 182 'X-RAY DIFFRACTION' ? r_mcangle_it 0.500 0.188 ? 208 'X-RAY DIFFRACTION' ? r_mcangle_other 0.499 0.187 ? 209 'X-RAY DIFFRACTION' ? r_scbond_it 0.509 0.161 ? 288 'X-RAY DIFFRACTION' ? r_scbond_other 0.508 0.161 ? 289 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other 0.697 0.238 ? 430 'X-RAY DIFFRACTION' ? r_long_range_B_refined 1.227 1.634 ? 685 'X-RAY DIFFRACTION' ? r_long_range_B_other 1.092 1.472 ? 658 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 5.515 3.000 ? 851 'X-RAY DIFFRACTION' ? r_sphericity_free 5.404 5.000 ? 6 'X-RAY DIFFRACTION' ? r_sphericity_bonded 2.528 5.000 ? 868 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 0.850 _refine_ls_shell.d_res_low 0.872 _refine_ls_shell.number_reflns_R_work 1658 _refine_ls_shell.R_factor_R_work 0.174 _refine_ls_shell.percent_reflns_obs 88.04 _refine_ls_shell.R_factor_R_free 0.162 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 87 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _struct_ncs_oper.id _struct_ncs_oper.code _struct_ncs_oper.details _struct_ncs_oper.matrix[1][1] _struct_ncs_oper.matrix[1][2] _struct_ncs_oper.matrix[1][3] _struct_ncs_oper.matrix[2][1] _struct_ncs_oper.matrix[2][2] _struct_ncs_oper.matrix[2][3] _struct_ncs_oper.matrix[3][1] _struct_ncs_oper.matrix[3][2] _struct_ncs_oper.matrix[3][3] _struct_ncs_oper.vector[1] _struct_ncs_oper.vector[2] _struct_ncs_oper.vector[3] 1 given ? 1.000000 0.009000 0.005000 -0.009000 1.000000 -0.002000 -0.005000 0.002000 1.000000 -0.05770 -13.72572 0.00171 2 given ? -1.000000 -0.004000 0.016000 -0.004000 1.000000 0.016000 -0.016000 0.016000 -1.000000 17.07359 -7.05721 25.86929 3 given ? -1.000000 -0.011000 -0.009000 -0.011000 1.000000 -0.008000 0.009000 -0.008000 -1.000000 17.52489 -20.43805 26.04363 # _struct.entry_id 4D5M _struct.title 'Gonadotropin-releasing hormone agonist' _struct.pdbx_descriptor TRIPTORELIN _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4D5M _struct_keywords.pdbx_keywords HORMONE _struct_keywords.text 'HORMONE, GNRH, LHRH, D-TRP, DECAPEPTIDE' # 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 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 3 ? I N N 3 ? J N N 3 ? K N N 3 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 HIS A 2 ? DTR A 6 ? HIS A 2 DTR A 6 5 ? 5 HELX_P HELX_P2 2 HIS B 2 ? DTR B 6 ? HIS B 2 DTR B 6 5 ? 5 HELX_P HELX_P3 3 HIS C 2 ? DTR C 6 ? HIS C 2 DTR C 6 5 ? 5 HELX_P HELX_P4 4 HIS D 2 ? DTR D 6 ? HIS D 2 DTR D 6 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 covale1 covale both ? A PCA 1 C A ? ? 1_555 A HIS 2 N ? ? A PCA 1 A HIS 2 1_555 ? ? ? ? ? ? ? 1.413 ? covale2 covale both ? A PCA 1 C B ? ? 1_555 A HIS 2 N ? ? A PCA 1 A HIS 2 1_555 ? ? ? ? ? ? ? 1.381 ? covale3 covale both ? A TYR 5 C A ? ? 1_555 A DTR 6 N ? ? A TYR 5 A DTR 6 1_555 ? ? ? ? ? ? ? 1.339 ? covale4 covale both ? A TYR 5 C B ? ? 1_555 A DTR 6 N ? ? A TYR 5 A DTR 6 1_555 ? ? ? ? ? ? ? 1.342 ? covale5 covale both ? A DTR 6 C ? ? ? 1_555 A LEU 7 N ? ? A DTR 6 A LEU 7 1_555 ? ? ? ? ? ? ? 1.340 ? covale6 covale both ? A GLY 10 C A ? ? 1_555 A NH2 11 N A ? A GLY 10 A NH2 11 1_555 ? ? ? ? ? ? ? 1.305 ? covale7 covale both ? A GLY 10 C B ? ? 1_555 A NH2 11 N B ? A GLY 10 A NH2 11 1_555 ? ? ? ? ? ? ? 1.279 ? covale8 covale both ? B PCA 1 C B ? ? 1_555 B HIS 2 N ? ? B PCA 1 B HIS 2 1_555 ? ? ? ? ? ? ? 1.447 ? covale9 covale both ? B PCA 1 C A ? ? 1_555 B HIS 2 N ? ? B PCA 1 B HIS 2 1_555 ? ? ? ? ? ? ? 1.269 ? covale10 covale both ? B TYR 5 C A ? ? 1_555 B DTR 6 N ? ? B TYR 5 B DTR 6 1_555 ? ? ? ? ? ? ? 1.326 ? covale11 covale both ? B TYR 5 C B ? ? 1_555 B DTR 6 N ? ? B TYR 5 B DTR 6 1_555 ? ? ? ? ? ? ? 1.337 ? covale12 covale both ? B DTR 6 C ? ? ? 1_555 B LEU 7 N ? ? B DTR 6 B LEU 7 1_555 ? ? ? ? ? ? ? 1.334 ? covale13 covale both ? B GLY 10 C B ? ? 1_555 B NH2 11 N B ? B GLY 10 B NH2 11 1_555 ? ? ? ? ? ? ? 1.305 ? covale14 covale both ? B GLY 10 C A ? ? 1_555 B NH2 11 N A ? B GLY 10 B NH2 11 1_555 ? ? ? ? ? ? ? 1.301 ? covale15 covale both ? C PCA 1 C ? ? ? 1_555 C HIS 2 N ? ? C PCA 1 C HIS 2 1_555 ? ? ? ? ? ? ? 1.346 ? covale16 covale both ? C TYR 5 C ? ? ? 1_555 C DTR 6 N ? ? C TYR 5 C DTR 6 1_555 ? ? ? ? ? ? ? 1.333 ? covale17 covale both ? C DTR 6 C ? ? ? 1_555 C LEU 7 N ? ? C DTR 6 C LEU 7 1_555 ? ? ? ? ? ? ? 1.334 ? covale18 covale both ? C GLY 10 C ? ? ? 1_555 C NH2 11 N ? ? C GLY 10 C NH2 11 1_555 ? ? ? ? ? ? ? 1.322 ? covale19 covale both ? D PCA 1 C ? ? ? 1_555 D HIS 2 N ? ? D PCA 1 D HIS 2 1_555 ? ? ? ? ? ? ? 1.341 ? covale20 covale both ? D TYR 5 C ? ? ? 1_555 D DTR 6 N ? ? D TYR 5 D DTR 6 1_555 ? ? ? ? ? ? ? 1.332 ? covale21 covale both ? D DTR 6 C ? ? ? 1_555 D LEU 7 N ? ? D DTR 6 D LEU 7 1_555 ? ? ? ? ? ? ? 1.342 ? covale22 covale both ? D GLY 10 C ? ? ? 1_555 D NH2 11 N ? ? D GLY 10 D NH2 11 1_555 ? ? ? ? ? ? ? 1.337 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC5 Software ? ? ? ? 11 'BINDING SITE FOR RESIDUE PO4 C 1011' AC6 Software ? ? ? ? 11 'BINDING SITE FOR RESIDUE PO4 B 1011' AC7 Software ? ? ? ? 11 'BINDING SITE FOR RESIDUE PO4 A 1011' # 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 AC5 11 PCA C 1 ? PCA C 1 . ? 1_554 ? 2 AC5 11 HIS C 2 ? HIS C 2 . ? 4_547 ? 3 AC5 11 ARG C 8 ? ARG C 8 . ? 1_555 ? 4 AC5 11 HOH J . ? HOH C 2001 . ? 1_554 ? 5 AC5 11 HOH J . ? HOH C 2003 . ? 1_554 ? 6 AC5 11 HOH J . ? HOH C 2015 . ? 1_555 ? 7 AC5 11 PCA D 1 ? PCA D 1 . ? 4_557 ? 8 AC5 11 HIS D 2 ? HIS D 2 . ? 1_554 ? 9 AC5 11 ARG D 8 ? ARG D 8 . ? 4_556 ? 10 AC5 11 GLY D 10 ? GLY D 10 . ? 4_557 ? 11 AC5 11 HOH K . ? HOH D 2001 . ? 4_557 ? 12 AC6 11 HIS A 2 ? HIS A 2 . ? 2_546 ? 13 AC6 11 HIS A 2 ? HIS A 2 . ? 1_545 ? 14 AC6 11 PCA B 1 ? PCA B 1 . ? 1_555 ? 15 AC6 11 PCA B 1 ? PCA B 1 . ? 2_556 ? 16 AC6 11 ARG B 8 ? ARG B 8 . ? 2_557 ? 17 AC6 11 ARG B 8 ? ARG B 8 . ? 1_554 ? 18 AC6 11 GLY B 10 ? GLY B 10 . ? 2_556 ? 19 AC6 11 HOH I . ? HOH B 2001 . ? 1_555 ? 20 AC6 11 HOH I . ? HOH B 2001 . ? 2_556 ? 21 AC6 11 HOH I . ? HOH B 2003 . ? 1_555 ? 22 AC6 11 HOH I . ? HOH B 2003 . ? 2_556 ? 23 AC7 11 PCA A 1 ? PCA A 1 . ? 2_557 ? 24 AC7 11 PCA A 1 ? PCA A 1 . ? 1_556 ? 25 AC7 11 ARG A 8 ? ARG A 8 . ? 1_555 ? 26 AC7 11 GLY A 10 ? GLY A 10 . ? 2_557 ? 27 AC7 11 HOH H . ? HOH A 2001 . ? 2_557 ? 28 AC7 11 HOH H . ? HOH A 2001 . ? 1_556 ? 29 AC7 11 HOH H . ? HOH A 2003 . ? 1_556 ? 30 AC7 11 HOH H . ? HOH A 2003 . ? 2_557 ? 31 AC7 11 HOH H . ? HOH A 2015 . ? 1_555 ? 32 AC7 11 HIS B 2 ? HIS B 2 . ? 1_556 ? 33 AC7 11 HIS B 2 ? HIS B 2 . ? 2_557 ? # _database_PDB_matrix.entry_id 4D5M _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 4D5M _atom_sites.fract_transf_matrix[1][1] 0.011779 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.001830 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.036403 _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] 0.076958 _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 C H N O P # 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 PCA 1 1 1 PCA PCA A . n A 1 2 HIS 2 2 2 HIS HIS A . n A 1 3 TRP 3 3 3 TRP TRP A . n A 1 4 SER 4 4 4 SER SER A . n A 1 5 TYR 5 5 5 TYR TYR A . n A 1 6 DTR 6 6 6 DTR DTR A . n A 1 7 LEU 7 7 7 LEU LEU A . n A 1 8 ARG 8 8 8 ARG ARG A . n A 1 9 PRO 9 9 9 PRO PRO A . n A 1 10 GLY 10 10 10 GLY GLY A . n A 1 11 NH2 11 11 11 NH2 NH2 A . n B 1 1 PCA 1 1 1 PCA PCA B . n B 1 2 HIS 2 2 2 HIS HIS B . n B 1 3 TRP 3 3 3 TRP TRP B . n B 1 4 SER 4 4 4 SER SER B . n B 1 5 TYR 5 5 5 TYR TYR B . n B 1 6 DTR 6 6 6 DTR DTR B . n B 1 7 LEU 7 7 7 LEU LEU B . n B 1 8 ARG 8 8 8 ARG ARG B . n B 1 9 PRO 9 9 9 PRO PRO B . n B 1 10 GLY 10 10 10 GLY GLY B . n B 1 11 NH2 11 11 11 NH2 NH2 B . n C 1 1 PCA 1 1 1 PCA PCA C . n C 1 2 HIS 2 2 2 HIS HIS C . n C 1 3 TRP 3 3 3 TRP TRP C . n C 1 4 SER 4 4 4 SER SER C . n C 1 5 TYR 5 5 5 TYR TYR C . n C 1 6 DTR 6 6 6 DTR DTR C . n C 1 7 LEU 7 7 7 LEU LEU C . n C 1 8 ARG 8 8 8 ARG ARG C . n C 1 9 PRO 9 9 9 PRO PRO C . n C 1 10 GLY 10 10 10 GLY GLY C . n C 1 11 NH2 11 11 11 NH2 NH2 C . n D 1 1 PCA 1 1 1 PCA PCA D . n D 1 2 HIS 2 2 2 HIS HIS D . n D 1 3 TRP 3 3 3 TRP TRP D . n D 1 4 SER 4 4 4 SER SER D . n D 1 5 TYR 5 5 5 TYR TYR D . n D 1 6 DTR 6 6 6 DTR DTR D . n D 1 7 LEU 7 7 7 LEU LEU D . n D 1 8 ARG 8 8 8 ARG ARG D . n D 1 9 PRO 9 9 9 PRO PRO D . n D 1 10 GLY 10 10 10 GLY GLY D . n D 1 11 NH2 11 11 11 NH2 NH2 D . 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 E 2 PO4 1 1011 1011 PO4 PO4 A . F 2 PO4 1 1011 1011 PO4 PO4 B . G 2 PO4 1 1011 1011 PO4 PO4 C . H 3 HOH 1 2001 2001 HOH HOH A . H 3 HOH 2 2003 2003 HOH HOH A . H 3 HOH 3 2004 2004 HOH HOH A . H 3 HOH 4 2005 2005 HOH HOH A . H 3 HOH 5 2006 2006 HOH HOH A . H 3 HOH 6 2007 2007 HOH HOH A . H 3 HOH 7 2008 2008 HOH HOH A . H 3 HOH 8 2009 2009 HOH HOH A . H 3 HOH 9 2010 2010 HOH HOH A . H 3 HOH 10 2011 2011 HOH HOH A . H 3 HOH 11 2012 2012 HOH HOH A . H 3 HOH 12 2013 2013 HOH HOH A . H 3 HOH 13 2014 2014 HOH HOH A . H 3 HOH 14 2015 2015 HOH HOH A . H 3 HOH 15 2016 2016 HOH HOH A . H 3 HOH 16 2017 2017 HOH HOH A . I 3 HOH 1 2001 2001 HOH HOH B . I 3 HOH 2 2002 2002 HOH HOH B . I 3 HOH 3 2003 2003 HOH HOH B . I 3 HOH 4 2004 2004 HOH HOH B . I 3 HOH 5 2005 2005 HOH HOH B . I 3 HOH 6 2006 2006 HOH HOH B . I 3 HOH 7 2007 2007 HOH HOH B . I 3 HOH 8 2008 2008 HOH HOH B . I 3 HOH 9 2009 2009 HOH HOH B . I 3 HOH 10 2010 2010 HOH HOH B . J 3 HOH 1 2001 2001 HOH HOH C . J 3 HOH 2 2002 2002 HOH HOH C . J 3 HOH 3 2003 2003 HOH HOH C . J 3 HOH 4 2004 2004 HOH HOH C . J 3 HOH 5 2005 2005 HOH HOH C . J 3 HOH 6 2008 2008 HOH HOH C . J 3 HOH 7 2010 2010 HOH HOH C . J 3 HOH 8 2011 2011 HOH HOH C . J 3 HOH 9 2012 2012 HOH HOH C . J 3 HOH 10 2013 2013 HOH HOH C . J 3 HOH 11 2014 2014 HOH HOH C . J 3 HOH 12 2015 2015 HOH HOH C . J 3 HOH 13 2016 2016 HOH HOH C . K 3 HOH 1 2001 2001 HOH HOH D . K 3 HOH 2 2003 2003 HOH HOH D . K 3 HOH 3 2004 2004 HOH HOH D . K 3 HOH 4 2005 2005 HOH HOH D . K 3 HOH 5 2007 2007 HOH HOH D . K 3 HOH 6 2008 2008 HOH HOH D . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A PCA 1 A PCA 1 ? GLU 'PYROGLUTAMIC ACID' 2 B PCA 1 B PCA 1 ? GLU 'PYROGLUTAMIC ACID' 3 C PCA 1 C PCA 1 ? GLU 'PYROGLUTAMIC ACID' 4 D PCA 1 D PCA 1 ? GLU 'PYROGLUTAMIC ACID' # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA monomeric 1 2 author_and_software_defined_assembly PISA monomeric 1 3 author_and_software_defined_assembly PISA monomeric 1 4 author_and_software_defined_assembly PISA monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,E,H 2 1 B,F,I 3 1 C,G,J 4 1 D,K # _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_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A PO4 1011 ? E PO4 . 2 1 B PO4 1011 ? F PO4 . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2015-08-12 2 'Structure model' 2 0 2020-03-11 # _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_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Derived calculations' 2 2 'Structure model' Other 3 2 'Structure model' 'Polymer sequence' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' entity_poly 2 2 'Structure model' pdbx_database_status 3 2 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 2 2 'Structure model' '_pdbx_database_status.status_code_sf' 3 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.8.0073 ? 1 XDS 'data reduction' . ? 2 XSCALE 'data scaling' . ? 3 SHELXD phasing . ? 4 # _pdbx_entry_details.entry_id 4D5M _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'TRIPTORELIN IS RELATED TO GONADORELIN WITH THE G6W.' # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 HIS A 2 ? ? 177.88 132.10 2 1 HIS B 2 ? ? -174.60 132.84 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'PHOSPHATE ION' PO4 3 water HOH #