data_5DB9 # _model_server_result.job_id HBKzg-Gb49bwU6cY0OqR3w _model_server_result.datetime_utc '2024-11-04 23:47:03' _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 5db9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":101}' # _entry.id 5DB9 # _exptl.entry_id 5DB9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _entity.src_method man _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 105.63 _cell.angle_gamma 90 _cell.entry_id 5DB9 _cell.length_a 54.201 _cell.length_b 79.278 _cell.length_c 54.72 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DB9 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 ? 5 E N N ? 5 F 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 covale ? covale1 C O3' DT 3 P DT 3 1_555 C P FMG 4 P FMG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? covale ? covale2 C O3' FMG 4 P FMG 4 1_555 C P DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? metalc ? metalc1 A O VAL 65 A VAL 65 1_555 F NA NA . D NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.118 ? metalc ? metalc2 A O THR 101 A THR 101 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc3 A O VAL 103 A VAL 103 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc4 A O ILE 106 A ILE 106 1_555 E NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc5 E NA NA . A NA 401 1_555 G O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.087 ? metalc ? metalc6 E NA NA . A NA 401 1_555 C OP1 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc7 E NA NA . A NA 401 1_555 I O HOH . P HOH 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc8 D OP1 DC 3 D DC 3 1_555 F NA NA . D NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.181 ? metalc ? metalc9 D OP2 DC 3 D DC 3 1_555 F NA NA . D NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? hydrog WATSON-CRICK hydrog1 B N3 DC 1 T DC 1 1_555 D N1 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 1 T DC 1 1_555 D O6 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 1 T DC 1 1_555 D N2 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DC 2 T DC 2 1_555 D N1 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N4 DC 2 T DC 2 1_555 D O6 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O2 DC 2 T DC 2 1_555 D N2 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 DG 3 T DG 3 1_555 D N3 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N2 DG 3 T DG 3 1_555 D O2 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O6 DG 3 T DG 3 1_555 D N4 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 4 T DA 4 1_555 D N3 DT 2 D DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 4 T DA 4 1_555 D O4 DT 2 D DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DC 5 T DC 5 1_555 D N1 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N4 DC 5 T DC 5 1_555 D O6 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O2 DC 5 T DC 5 1_555 D N2 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog15 B N3 DT 7 T DT 7 1_555 C N1 DA 10 P DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 8 T DC 8 1_555 C N1 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 8 T DC 8 1_555 C O6 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 8 T DC 8 1_555 C N2 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DG 9 T DG 9 1_555 C N3 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N2 DG 9 T DG 9 1_555 C O2 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O6 DG 9 T DG 9 1_555 C N4 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N3 DC 10 T DC 10 1_555 C N1 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N4 DC 10 T DC 10 1_555 C O6 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O2 DC 10 T DC 10 1_555 C N2 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N1 DA 11 T DA 11 1_555 C N3 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N6 DA 11 T DA 11 1_555 C O4 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N3 DT 12 T DT 12 1_555 C N1 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O4 DT 12 T DT 12 1_555 C N6 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-FMG MISPAIR' hydrog29 B O6 DG 13 T DG 13 1_555 C N1 FMG 4 P FMG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N1 DA 14 T DA 14 1_555 C N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N6 DA 14 T DA 14 1_555 C O4 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B N1 DG 15 T DG 15 1_555 C N3 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N2 DG 15 T DG 15 1_555 C O2 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B O6 DG 15 T DG 15 1_555 C N4 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N3 DC 16 T DC 16 1_555 C N1 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B N4 DC 16 T DC 16 1_555 C O6 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 B O2 DC 16 T DC 16 1_555 C N2 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 5DB9 _atom_sites.fract_transf_matrix[1][1] 0.01845 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005161 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012614 _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] 0.018976 _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 E 5 NA A 1 401 341 NA NA . F 5 NA D 1 101 342 NA NA . G 6 HOH A 1 501 73 HOH HOH . G 6 HOH A 2 502 59 HOH HOH . G 6 HOH A 3 503 48 HOH HOH . G 6 HOH A 4 504 79 HOH HOH . G 6 HOH A 5 505 94 HOH HOH . G 6 HOH A 6 506 56 HOH HOH . G 6 HOH A 7 507 22 HOH HOH . G 6 HOH A 8 508 2 HOH HOH . G 6 HOH A 9 509 15 HOH HOH . G 6 HOH A 10 510 46 HOH HOH . G 6 HOH A 11 511 96 HOH HOH . G 6 HOH A 12 512 34 HOH HOH . G 6 HOH A 13 513 93 HOH HOH . G 6 HOH A 14 514 11 HOH HOH . G 6 HOH A 15 515 58 HOH HOH . G 6 HOH A 16 516 26 HOH HOH . G 6 HOH A 17 517 95 HOH HOH . G 6 HOH A 18 518 37 HOH HOH . G 6 HOH A 19 519 33 HOH HOH . G 6 HOH A 20 520 82 HOH HOH . G 6 HOH A 21 521 50 HOH HOH . G 6 HOH A 22 522 69 HOH HOH . G 6 HOH A 23 523 89 HOH HOH . G 6 HOH A 24 524 51 HOH HOH . G 6 HOH A 25 525 38 HOH HOH . G 6 HOH A 26 526 61 HOH HOH . G 6 HOH A 27 527 67 HOH HOH . G 6 HOH A 28 528 43 HOH HOH . G 6 HOH A 29 529 4 HOH HOH . G 6 HOH A 30 530 65 HOH HOH . G 6 HOH A 31 531 55 HOH HOH . G 6 HOH A 32 532 6 HOH HOH . G 6 HOH A 33 533 13 HOH HOH . G 6 HOH A 34 534 54 HOH HOH . G 6 HOH A 35 535 23 HOH HOH . G 6 HOH A 36 536 32 HOH HOH . G 6 HOH A 37 537 60 HOH HOH . G 6 HOH A 38 538 62 HOH HOH . G 6 HOH A 39 539 29 HOH HOH . G 6 HOH A 40 540 85 HOH HOH . G 6 HOH A 41 541 3 HOH HOH . G 6 HOH A 42 542 20 HOH HOH . G 6 HOH A 43 543 44 HOH HOH . G 6 HOH A 44 544 74 HOH HOH . G 6 HOH A 45 545 17 HOH HOH . G 6 HOH A 46 546 14 HOH HOH . G 6 HOH A 47 547 57 HOH HOH . G 6 HOH A 48 548 63 HOH HOH . G 6 HOH A 49 549 90 HOH HOH . G 6 HOH A 50 550 71 HOH HOH . G 6 HOH A 51 551 45 HOH HOH . G 6 HOH A 52 552 9 HOH HOH . G 6 HOH A 53 553 19 HOH HOH . G 6 HOH A 54 554 53 HOH HOH . G 6 HOH A 55 555 16 HOH HOH . G 6 HOH A 56 556 64 HOH HOH . G 6 HOH A 57 557 21 HOH HOH . G 6 HOH A 58 558 27 HOH HOH . G 6 HOH A 59 559 91 HOH HOH . G 6 HOH A 60 560 49 HOH HOH . G 6 HOH A 61 561 36 HOH HOH . G 6 HOH A 62 562 75 HOH HOH . G 6 HOH A 63 563 78 HOH HOH . H 6 HOH T 1 101 5 HOH HOH . H 6 HOH T 2 102 8 HOH HOH . H 6 HOH T 3 103 81 HOH HOH . H 6 HOH T 4 104 35 HOH HOH . H 6 HOH T 5 105 84 HOH HOH . H 6 HOH T 6 106 86 HOH HOH . H 6 HOH T 7 107 42 HOH HOH . H 6 HOH T 8 108 80 HOH HOH . I 6 HOH P 1 101 10 HOH HOH . I 6 HOH P 2 102 7 HOH HOH . I 6 HOH P 3 103 28 HOH HOH . I 6 HOH P 4 104 97 HOH HOH . J 6 HOH D 1 201 72 HOH HOH . J 6 HOH D 2 202 24 HOH HOH . J 6 HOH D 3 203 12 HOH HOH . J 6 HOH D 4 204 40 HOH HOH . J 6 HOH D 5 205 66 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 F _atom_site.label_entity_id 5 _atom_site.Cartn_x 32.681 _atom_site.Cartn_y -9.892 _atom_site.Cartn_z -4.249 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 31.11 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 101 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #