data_5YVT # _model_server_result.job_id rX9gUJ7JYA3kFWUnUxfZDA _model_server_result.datetime_utc '2024-12-03 06:12:59' _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 5yvt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5YVT # _exptl.entry_id 5YVT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 24.305 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM 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 5YVT _cell.length_a 118.027 _cell.length_b 118.027 _cell.length_c 142.109 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YVT _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 _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 3 _struct_asym.id C _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 OD1 ASP 230 A ASP 230 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc2 A OD2 ASP 234 A ASP 234 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc3 C MG MG . A MG 401 1_555 F O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc4 C MG MG . A MG 401 1_555 F O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc5 C MG MG . A MG 401 1_555 B OD2 ASP 215 B ASP 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc6 C MG MG . A MG 401 1_555 G O HOH . B HOH 569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5YVT _atom_sites.fract_transf_matrix[1][1] 0.008473 _atom_sites.fract_transf_matrix[1][2] 0.004892 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009783 _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] 0.007037 _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 3 MG A 1 401 1 MG MG . D 4 NAI A 1 402 1 NAI NAI . E 4 NAI B 1 401 1 NAI NAI . F 5 HOH A 1 501 12 HOH HOH . F 5 HOH A 2 502 47 HOH HOH . F 5 HOH A 3 503 77 HOH HOH . F 5 HOH A 4 504 94 HOH HOH . F 5 HOH A 5 505 7 HOH HOH . F 5 HOH A 6 506 26 HOH HOH . F 5 HOH A 7 507 92 HOH HOH . F 5 HOH A 8 508 49 HOH HOH . F 5 HOH A 9 509 73 HOH HOH . F 5 HOH A 10 510 55 HOH HOH . F 5 HOH A 11 511 70 HOH HOH . F 5 HOH A 12 512 39 HOH HOH . F 5 HOH A 13 513 16 HOH HOH . F 5 HOH A 14 514 67 HOH HOH . F 5 HOH A 15 515 91 HOH HOH . F 5 HOH A 16 516 65 HOH HOH . F 5 HOH A 17 517 80 HOH HOH . G 5 HOH B 1 501 17 HOH HOH . G 5 HOH B 2 502 45 HOH HOH . G 5 HOH B 3 503 75 HOH HOH . G 5 HOH B 4 504 27 HOH HOH . G 5 HOH B 5 505 35 HOH HOH . G 5 HOH B 6 506 19 HOH HOH . G 5 HOH B 7 507 43 HOH HOH . G 5 HOH B 8 508 66 HOH HOH . G 5 HOH B 9 509 30 HOH HOH . G 5 HOH B 10 510 52 HOH HOH . G 5 HOH B 11 511 38 HOH HOH . G 5 HOH B 12 512 5 HOH HOH . G 5 HOH B 13 513 22 HOH HOH . G 5 HOH B 14 514 79 HOH HOH . G 5 HOH B 15 515 2 HOH HOH . G 5 HOH B 16 516 29 HOH HOH . G 5 HOH B 17 517 53 HOH HOH . G 5 HOH B 18 518 6 HOH HOH . G 5 HOH B 19 519 90 HOH HOH . G 5 HOH B 20 520 57 HOH HOH . G 5 HOH B 21 521 15 HOH HOH . G 5 HOH B 22 522 9 HOH HOH . G 5 HOH B 23 523 50 HOH HOH . G 5 HOH B 24 524 11 HOH HOH . G 5 HOH B 25 525 25 HOH HOH . G 5 HOH B 26 526 87 HOH HOH . G 5 HOH B 27 527 34 HOH HOH . G 5 HOH B 28 528 24 HOH HOH . G 5 HOH B 29 529 48 HOH HOH . G 5 HOH B 30 530 3 HOH HOH . G 5 HOH B 31 531 23 HOH HOH . G 5 HOH B 32 532 41 HOH HOH . G 5 HOH B 33 533 72 HOH HOH . G 5 HOH B 34 534 20 HOH HOH . G 5 HOH B 35 535 32 HOH HOH . G 5 HOH B 36 536 18 HOH HOH . G 5 HOH B 37 537 60 HOH HOH . G 5 HOH B 38 538 33 HOH HOH . G 5 HOH B 39 539 28 HOH HOH . G 5 HOH B 40 540 21 HOH HOH . G 5 HOH B 41 541 8 HOH HOH . G 5 HOH B 42 542 31 HOH HOH . G 5 HOH B 43 543 83 HOH HOH . G 5 HOH B 44 544 68 HOH HOH . G 5 HOH B 45 545 54 HOH HOH . G 5 HOH B 46 546 76 HOH HOH . G 5 HOH B 47 547 59 HOH HOH . G 5 HOH B 48 548 64 HOH HOH . G 5 HOH B 49 549 4 HOH HOH . G 5 HOH B 50 550 40 HOH HOH . G 5 HOH B 51 551 74 HOH HOH . G 5 HOH B 52 552 37 HOH HOH . G 5 HOH B 53 553 86 HOH HOH . G 5 HOH B 54 554 69 HOH HOH . G 5 HOH B 55 555 93 HOH HOH . G 5 HOH B 56 556 84 HOH HOH . G 5 HOH B 57 557 46 HOH HOH . G 5 HOH B 58 558 13 HOH HOH . G 5 HOH B 59 559 51 HOH HOH . G 5 HOH B 60 560 88 HOH HOH . G 5 HOH B 61 561 56 HOH HOH . G 5 HOH B 62 562 44 HOH HOH . G 5 HOH B 63 563 61 HOH HOH . G 5 HOH B 64 564 42 HOH HOH . G 5 HOH B 65 565 81 HOH HOH . G 5 HOH B 66 566 78 HOH HOH . G 5 HOH B 67 567 1 HOH HOH . G 5 HOH B 68 568 10 HOH HOH . G 5 HOH B 69 569 36 HOH HOH . G 5 HOH B 70 570 58 HOH HOH . G 5 HOH B 71 571 82 HOH HOH . G 5 HOH B 72 572 89 HOH HOH . G 5 HOH B 73 573 62 HOH HOH . G 5 HOH B 74 574 14 HOH HOH . G 5 HOH B 75 575 71 HOH HOH . G 5 HOH B 76 576 85 HOH HOH . G 5 HOH B 77 577 63 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id C _atom_site.label_entity_id 3 _atom_site.Cartn_x 41.893 _atom_site.Cartn_y -21.685 _atom_site.Cartn_z 27.151 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 52.58 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 401 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 109 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #