data_5Y07 # _model_server_result.job_id os0Lb3Z8bThudyFF3neAsQ _model_server_result.datetime_utc '2024-10-19 21:22:53' _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 5y07 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 5Y07 # _exptl.entry_id 5Y07 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.87 _cell.angle_gamma 90 _cell.entry_id 5Y07 _cell.length_a 48.301 _cell.length_b 86.292 _cell.length_c 48.553 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y07 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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,D,E,F,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G N 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 O THR 117 A THR 117 1_555 D NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc2 A O ILE 120 A ILE 120 1_555 D NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 C O1 PRP . A PRP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc4 C O2 PRP . A PRP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc5 C O3 PRP . A PRP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc6 C O2B PRP . A PRP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc7 D NA NA . A NA 202 1_555 I O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc8 D NA NA . A NA 202 1_555 I O HOH . A HOH 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc9 E MG MG . A MG 203 1_555 I O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc10 E MG MG . A MG 203 1_555 I O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc11 B O THR 117 B THR 117 1_555 G NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc12 B O ILE 120 B ILE 120 1_555 G NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc13 F O1 PRP . B PRP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc14 F O2 PRP . B PRP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc15 F O3 PRP . B PRP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc16 F O3B PRP . B PRP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc17 G NA NA . B NA 202 1_555 J O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc18 G NA NA . B NA 202 1_555 J O HOH . B HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc19 G NA NA . B NA 202 1_555 J O HOH . B HOH 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc20 H MG MG . B MG 203 1_555 J O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc21 H MG MG . B MG 203 1_555 J O HOH . B HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5Y07 _atom_sites.fract_transf_matrix[1][1] 0.020704 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005884 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011589 _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] 0.021412 _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 C 2 PRP A 1 201 201 PRP PRP . D 3 NA A 1 202 202 NA NA . E 4 MG A 1 203 203 MG MG . F 2 PRP B 1 201 201 PRP PRP . G 3 NA B 1 202 202 NA NA . H 4 MG B 1 203 203 MG MG . I 5 HOH A 1 301 32 HOH HOH . I 5 HOH A 2 302 52 HOH HOH . I 5 HOH A 3 303 31 HOH HOH . I 5 HOH A 4 304 67 HOH HOH . I 5 HOH A 5 305 70 HOH HOH . I 5 HOH A 6 306 61 HOH HOH . I 5 HOH A 7 307 49 HOH HOH . I 5 HOH A 8 308 23 HOH HOH . I 5 HOH A 9 309 44 HOH HOH . I 5 HOH A 10 310 7 HOH HOH . I 5 HOH A 11 311 14 HOH HOH . I 5 HOH A 12 312 21 HOH HOH . I 5 HOH A 13 313 41 HOH HOH . I 5 HOH A 14 314 64 HOH HOH . I 5 HOH A 15 315 45 HOH HOH . I 5 HOH A 16 316 54 HOH HOH . I 5 HOH A 17 317 39 HOH HOH . I 5 HOH A 18 318 4 HOH HOH . I 5 HOH A 19 319 28 HOH HOH . I 5 HOH A 20 320 62 HOH HOH . I 5 HOH A 21 321 5 HOH HOH . I 5 HOH A 22 322 33 HOH HOH . I 5 HOH A 23 323 15 HOH HOH . I 5 HOH A 24 324 38 HOH HOH . I 5 HOH A 25 325 36 HOH HOH . I 5 HOH A 26 326 19 HOH HOH . I 5 HOH A 27 327 26 HOH HOH . I 5 HOH A 28 328 29 HOH HOH . I 5 HOH A 29 329 71 HOH HOH . I 5 HOH A 30 330 65 HOH HOH . I 5 HOH A 31 331 57 HOH HOH . I 5 HOH A 32 332 10 HOH HOH . I 5 HOH A 33 333 11 HOH HOH . I 5 HOH A 34 334 34 HOH HOH . I 5 HOH A 35 335 50 HOH HOH . I 5 HOH A 36 336 48 HOH HOH . J 5 HOH B 1 301 60 HOH HOH . J 5 HOH B 2 302 20 HOH HOH . J 5 HOH B 3 303 24 HOH HOH . J 5 HOH B 4 304 1 HOH HOH . J 5 HOH B 5 305 53 HOH HOH . J 5 HOH B 6 306 59 HOH HOH . J 5 HOH B 7 307 25 HOH HOH . J 5 HOH B 8 308 35 HOH HOH . J 5 HOH B 9 309 37 HOH HOH . J 5 HOH B 10 310 6 HOH HOH . J 5 HOH B 11 311 51 HOH HOH . J 5 HOH B 12 312 42 HOH HOH . J 5 HOH B 13 313 16 HOH HOH . J 5 HOH B 14 314 9 HOH HOH . J 5 HOH B 15 315 30 HOH HOH . J 5 HOH B 16 316 63 HOH HOH . J 5 HOH B 17 317 12 HOH HOH . J 5 HOH B 18 318 8 HOH HOH . J 5 HOH B 19 319 27 HOH HOH . J 5 HOH B 20 320 40 HOH HOH . J 5 HOH B 21 321 56 HOH HOH . J 5 HOH B 22 322 46 HOH HOH . J 5 HOH B 23 323 68 HOH HOH . J 5 HOH B 24 324 43 HOH HOH . J 5 HOH B 25 325 17 HOH HOH . J 5 HOH B 26 326 55 HOH HOH . J 5 HOH B 27 327 69 HOH HOH . J 5 HOH B 28 328 3 HOH HOH . J 5 HOH B 29 329 22 HOH HOH . J 5 HOH B 30 330 18 HOH HOH . J 5 HOH B 31 331 13 HOH HOH . J 5 HOH B 32 332 66 HOH HOH . J 5 HOH B 33 333 58 HOH HOH . J 5 HOH B 34 334 2 HOH HOH . J 5 HOH B 35 335 47 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _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 3 _atom_site.Cartn_x -2.633 _atom_site.Cartn_y -28.922 _atom_site.Cartn_z 12.364 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 32.18 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 202 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #