data_5L58 # _model_server_result.job_id ahugBFxeu_W0cH_IjmMvPQ _model_server_result.datetime_utc '2024-11-22 00:16:26' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5l58 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 5L58 # _exptl.entry_id 5L58 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 513.692 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[(3~{R})-1-[6-cyclohexylsulfanyl-5-[[(1~{R},3~{S})-5-oxidanyl-2-adamantyl]carbamoyl]pyridin-2-yl]pyrrolidin-3-yl]ethanoic acid' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5L58 _cell.length_a 72.166 _cell.length_b 72.166 _cell.length_c 179.829 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L58 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_557 y,x,-z+2 0 1 0 1 0 0 0 0 -1 0 0 359.658 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NH2 _struct_conn.ptnr1_label_comp_id ARG _struct_conn.ptnr1_label_seq_id 314 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ARG _struct_conn.ptnr1_auth_seq_id 314 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id O3X _struct_conn.ptnr2_label_comp_id NDP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id NDP _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.297 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C28 H39 N3 O4 S' _chem_comp.formula_weight 513.692 _chem_comp.id 6MX _chem_comp.mon_nstd_flag . _chem_comp.name '2-[(3~{R})-1-[6-cyclohexylsulfanyl-5-[[(1~{R},3~{S})-5-oxidanyl-2-adamantyl]carbamoyl]pyridin-2-yl]pyrrolidin-3-yl]ethanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C27 C19 6MX sing 1 n n C27 C25 6MX sing 2 n n C19 C20 6MX sing 3 n n C19 C18 6MX sing 4 n n C20 C21 6MX sing 5 n n O3 C25 6MX sing 6 n n C25 C26 6MX sing 7 n n C25 C24 6MX sing 8 n n C26 C21 6MX sing 9 n n C18 N2 6MX sing 10 n n C18 C23 6MX sing 11 n n C21 C22 6MX sing 12 n n N2 C17 6MX sing 13 n n O2 C17 6MX doub 14 n n C12 C13 6MX sing 15 n n C12 C11 6MX sing 16 n n C24 C23 6MX sing 17 n n C13 C14 6MX sing 18 n n C17 C9 6MX sing 19 n n C23 C22 6MX sing 20 n n C9 C8 6MX doub 21 n y C9 C10 6MX sing 22 n y S C11 6MX sing 23 n n S C10 6MX sing 24 n n C11 C16 6MX sing 25 n n C8 C7 6MX sing 26 n y C10 N1 6MX doub 27 n y C7 C6 6MX doub 28 n y C14 C15 6MX sing 29 n n N1 C6 6MX sing 30 n y C6 N 6MX sing 31 n n C16 C15 6MX sing 32 n n N C5 6MX sing 33 n n N C4 6MX sing 34 n n C5 C2 6MX sing 35 n n C4 C3 6MX sing 36 n n C1 C2 6MX sing 37 n n C1 C 6MX sing 38 n n C2 C3 6MX sing 39 n n O C 6MX doub 40 n n C O1 6MX sing 41 n n N2 H1 6MX sing 42 n n C18 H2 6MX sing 43 n n C23 H3 6MX sing 44 n n C22 H4 6MX sing 45 n n C22 H5 6MX sing 46 n n C24 H6 6MX sing 47 n n C24 H7 6MX sing 48 n n O3 H8 6MX sing 49 n n C26 H9 6MX sing 50 n n C26 H10 6MX sing 51 n n C21 H11 6MX sing 52 n n C20 H12 6MX sing 53 n n C20 H13 6MX sing 54 n n C27 H14 6MX sing 55 n n C27 H15 6MX sing 56 n n C19 H16 6MX sing 57 n n C8 H17 6MX sing 58 n n C7 H18 6MX sing 59 n n C11 H19 6MX sing 60 n n C16 H20 6MX sing 61 n n C16 H21 6MX sing 62 n n C15 H22 6MX sing 63 n n C15 H23 6MX sing 64 n n C14 H24 6MX sing 65 n n C14 H25 6MX sing 66 n n C13 H26 6MX sing 67 n n C13 H27 6MX sing 68 n n C12 H28 6MX sing 69 n n C12 H29 6MX sing 70 n n C4 H30 6MX sing 71 n n C4 H31 6MX sing 72 n n C3 H32 6MX sing 73 n n C3 H33 6MX sing 74 n n C5 H34 6MX sing 75 n n C5 H35 6MX sing 76 n n C2 H36 6MX sing 77 n n C1 H37 6MX sing 78 n n C1 H38 6MX sing 79 n n O1 H39 6MX sing 80 n n # _atom_sites.entry_id 5L58 _atom_sites.fract_transf_matrix[1][1] 0.013857 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013857 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.005561 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code B 2 NDP A 1 501 501 NDP NDP . C 3 6MX A 1 502 1 6MX 04I . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _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_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O2 6MX . . . C 3 15.155 25.639 181.487 1 62.33 ? O2 6MX 502 A 1 HETATM 2 C C17 6MX . . . C 3 15.173 24.423 181.592 1 56.46 ? C17 6MX 502 A 1 HETATM 3 N N2 6MX . . . C 3 16.227 23.714 181.198 1 56.68 ? N2 6MX 502 A 1 HETATM 4 C C18 6MX . . . C 3 17.459 24.383 180.828 1 55.52 ? C18 6MX 502 A 1 HETATM 5 C C23 6MX . . . C 3 18.485 24.261 181.946 1 52.16 ? C23 6MX 502 A 1 HETATM 6 C C22 6MX . . . C 3 18.844 22.796 182.172 1 50.14 ? C22 6MX 502 A 1 HETATM 7 C C24 6MX . . . C 3 19.748 25.028 181.573 1 54.71 ? C24 6MX 502 A 1 HETATM 8 C C25 6MX . . . C 3 20.33 24.445 180.288 1 56.85 ? C25 6MX 502 A 1 HETATM 9 O O3 6MX . . . C 3 21.507 25.172 179.923 1 56.06 ? O3 6MX 502 A 1 HETATM 10 C C26 6MX . . . C 3 20.683 22.98 180.514 1 54.8 ? C26 6MX 502 A 1 HETATM 11 C C21 6MX . . . C 3 19.427 22.201 180.894 1 53.15 ? C21 6MX 502 A 1 HETATM 12 C C20 6MX . . . C 3 18.401 22.325 179.77 1 58.02 ? C20 6MX 502 A 1 HETATM 13 C C27 6MX . . . C 3 19.306 24.55 179.16 1 58.12 ? C27 6MX 502 A 1 HETATM 14 C C19 6MX . . . C 3 18.042 23.791 179.552 1 58.44 ? C19 6MX 502 A 1 HETATM 15 C C9 6MX . . . C 3 13.978 23.735 182.185 1 48.31 ? C9 6MX 502 A 1 HETATM 16 C C8 6MX . . . C 3 12.824 24.472 182.421 1 44.72 ? C8 6MX 502 A 1 HETATM 17 C C7 6MX . . . C 3 11.714 23.847 182.974 1 47.15 ? C7 6MX 502 A 1 HETATM 18 C C10 6MX . . . C 3 14.004 22.388 182.511 1 48.07 ? C10 6MX 502 A 1 HETATM 19 S S 6MX . . . C 3 15.379 21.433 182.252 1 53.84 ? S 6MX 502 A 1 HETATM 20 C C11 6MX . . . C 3 14.866 19.743 182.321 1 54.23 ? C11 6MX 502 A 1 HETATM 21 C C16 6MX . . . C 3 14.85 19.268 183.771 1 53.32 ? C16 6MX 502 A 1 HETATM 22 C C15 6MX . . . C 3 14.371 17.824 183.854 1 50.83 ? C15 6MX 502 A 1 HETATM 23 C C14 6MX . . . C 3 15.258 16.912 183.015 1 51.69 ? C14 6MX 502 A 1 HETATM 24 C C13 6MX . . . C 3 15.343 17.409 181.575 1 51.38 ? C13 6MX 502 A 1 HETATM 25 C C12 6MX . . . C 3 15.818 18.857 181.528 1 53.03 ? C12 6MX 502 A 1 HETATM 26 N N1 6MX . . . C 3 12.915 21.8 183.048 1 45.7 ? N1 6MX 502 A 1 HETATM 27 C C6 6MX . . . C 3 11.783 22.493 183.281 1 46.96 ? C6 6MX 502 A 1 HETATM 28 N N 6MX . . . C 3 10.688 21.828 183.841 1 46.66 ? N 6MX 502 A 1 HETATM 29 C C4 6MX . . . C 3 10.795 20.433 184.235 1 48.84 ? C4 6MX 502 A 1 HETATM 30 C C3 6MX . . . C 3 9.583 20.283 185.145 1 54.81 ? C3 6MX 502 A 1 HETATM 31 C C5 6MX . . . C 3 9.414 22.492 184.059 1 48.6 ? C5 6MX 502 A 1 HETATM 32 C C2 6MX . . . C 3 8.781 21.579 185.104 1 55.67 ? C2 6MX 502 A 1 HETATM 33 C C1 6MX . . . C 3 7.329 21.279 184.754 1 59.38 ? C1 6MX 502 A 1 HETATM 34 C C 6MX . . . C 3 6.739 20.407 185.836 1 60.11 ? C 6MX 502 A 1 HETATM 35 O O1 6MX . . . C 3 6.869 20.71 187.011 1 62.21 ? O1 6MX 502 A 1 HETATM 36 O O 6MX . . . C 3 6.068 19.302 185.526 1 58.92 ? O 6MX 502 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 36 #