data_4LVK # _model_server_result.job_id 5wdwOR7GGaKT0D0LUJZP_g _model_server_result.datetime_utc '2024-11-22 10:29:32' _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 4lvk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 4LVK # _exptl.entry_id 4LVK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _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 120 _cell.entry_id 4LVK _cell.length_a 112.743 _cell.length_b 112.743 _cell.length_c 91.66 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LVK _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_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 _struct_conn.pdbx_value_order metalc ? metalc1 A ND1 HIS 125 A HIS 126 1_555 D MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc2 A OE2 GLU 128 A GLU 129 1_555 D MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc3 A NE2 HIS 132 A HIS 133 1_555 D MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc4 A NE2 HIS 134 A HIS 135 1_555 D MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc5 D MN MN . A MN 201 1_555 C O3' DG 15 C DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? metalc ? metalc6 D MN MN . A MN 201 1_555 C OP1 DT 16 C DT 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc7 B OP2 DT 3 B DT 3 1_555 E NA NA . B NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? hydrog WATSON-CRICK hydrog1 B N1 DA 1 B DA 1 1_555 C N3 DT 7 C DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 1 B DA 1 1_555 C O4 DT 7 C DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DC 2 B DC 2 1_555 C N1 DG 6 C DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N4 DC 2 B DC 2 1_555 C O6 DG 6 C DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O2 DC 2 B DC 2 1_555 C N2 DG 6 C DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 3 B DT 3 1_555 C N1 DA 5 C DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 3 B DT 3 1_555 C N6 DA 5 C DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DT 4 B DT 4 1_555 C N1 DA 4 C DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O4 DT 4 B DT 4 1_555 C N6 DA 4 C DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DT 5 B DT 5 1_555 C N1 DA 3 C DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O4 DT 5 B DT 5 1_555 C N6 DA 3 C DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 6 B DA 6 1_555 C N3 DT 2 C DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N6 DA 6 B DA 6 1_555 C O4 DT 2 C DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DT 7 B DT 7 1_555 C N1 DA 1 C DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O4 DT 7 B DT 7 1_555 C N6 DA 1 C DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog16 C N3 DT 12 C DT 23 1_555 C O6 DG 15 C DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog17 C O2 DT 12 C DT 23 1_555 C N1 DG 15 C DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4LVK _atom_sites.fract_transf_matrix[1][1] 0.00887 _atom_sites.fract_transf_matrix[1][2] 0.005121 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010242 _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] 0.01091 _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 D 4 MN A 1 201 201 MN MN . E 5 NA B 1 101 1 NA NA . F 6 HOH A 1 301 1 HOH HOH . F 6 HOH A 2 302 3 HOH HOH . F 6 HOH A 3 303 6 HOH HOH . F 6 HOH A 4 304 7 HOH HOH . F 6 HOH A 5 305 8 HOH HOH . F 6 HOH A 6 306 10 HOH HOH . F 6 HOH A 7 307 11 HOH HOH . F 6 HOH A 8 308 12 HOH HOH . F 6 HOH A 9 309 18 HOH HOH . F 6 HOH A 10 310 19 HOH HOH . F 6 HOH A 11 311 21 HOH HOH . F 6 HOH A 12 312 22 HOH HOH . F 6 HOH A 13 313 24 HOH HOH . F 6 HOH A 14 314 27 HOH HOH . F 6 HOH A 15 315 29 HOH HOH . F 6 HOH A 16 316 30 HOH HOH . F 6 HOH A 17 317 32 HOH HOH . F 6 HOH A 18 318 34 HOH HOH . F 6 HOH A 19 319 36 HOH HOH . F 6 HOH A 20 320 40 HOH HOH . F 6 HOH A 21 321 43 HOH HOH . F 6 HOH A 22 322 44 HOH HOH . F 6 HOH A 23 323 48 HOH HOH . F 6 HOH A 24 324 49 HOH HOH . F 6 HOH A 25 325 50 HOH HOH . F 6 HOH A 26 326 52 HOH HOH . F 6 HOH A 27 327 57 HOH HOH . F 6 HOH A 28 328 70 HOH HOH . F 6 HOH A 29 329 72 HOH HOH . F 6 HOH A 30 330 76 HOH HOH . F 6 HOH A 31 331 88 HOH HOH . F 6 HOH A 32 332 89 HOH HOH . F 6 HOH A 33 333 92 HOH HOH . F 6 HOH A 34 334 102 HOH HOH . F 6 HOH A 35 335 107 HOH HOH . F 6 HOH A 36 336 109 HOH HOH . F 6 HOH A 37 337 111 HOH HOH . F 6 HOH A 38 338 113 HOH HOH . F 6 HOH A 39 339 115 HOH HOH . F 6 HOH A 40 340 117 HOH HOH . F 6 HOH A 41 341 119 HOH HOH . F 6 HOH A 42 342 120 HOH HOH . F 6 HOH A 43 343 121 HOH HOH . F 6 HOH A 44 344 123 HOH HOH . F 6 HOH A 45 345 125 HOH HOH . F 6 HOH A 46 346 130 HOH HOH . F 6 HOH A 47 347 132 HOH HOH . F 6 HOH A 48 348 133 HOH HOH . F 6 HOH A 49 349 135 HOH HOH . F 6 HOH A 50 350 143 HOH HOH . F 6 HOH A 51 351 145 HOH HOH . F 6 HOH A 52 352 152 HOH HOH . F 6 HOH A 53 353 157 HOH HOH . F 6 HOH A 54 354 159 HOH HOH . F 6 HOH A 55 355 160 HOH HOH . F 6 HOH A 56 356 161 HOH HOH . F 6 HOH A 57 357 162 HOH HOH . F 6 HOH A 58 358 167 HOH HOH . G 6 HOH B 1 201 46 HOH HOH . H 6 HOH C 1 101 4 HOH HOH . H 6 HOH C 2 102 9 HOH HOH . H 6 HOH C 3 103 13 HOH HOH . H 6 HOH C 4 104 41 HOH HOH . H 6 HOH C 5 105 55 HOH HOH . H 6 HOH C 6 106 56 HOH HOH . H 6 HOH C 7 107 86 HOH HOH . H 6 HOH C 8 108 146 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MN _atom_site.label_atom_id MN _atom_site.label_comp_id MN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 4 _atom_site.Cartn_x -9.147 _atom_site.Cartn_y 46.843 _atom_site.Cartn_z -9.736 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 40.15 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 201 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #