data_5V07 # _model_server_result.job_id t28vGXTJc0Sr1NqnsXvrgw _model_server_result.datetime_utc '2025-01-18 09:42:32' _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 5v07 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":403}' # _entry.id 5V07 # _exptl.entry_id 5V07 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM 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 90 _cell.entry_id 5V07 _cell.length_a 73.837 _cell.length_b 73.837 _cell.length_c 179.067 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V07 _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 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,I,J,K _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 5 _struct_asym.id F _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 SG CYS 80 Z CYS 80 1_555 E MN MN . Z MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc2 A OD2 ASP 152 Z ASP 152 1_555 D MN MN . Z MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc3 A OD1 ASP 152 Z ASP 152 1_555 G MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc4 A OD2 ASP 171 Z ASP 171 1_555 D MN MN . Z MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc5 A O SER 222 Z SER 222 1_555 F NA NA . Z NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc6 A OG SER 229 Z SER 229 1_555 F NA NA . Z NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc7 A O ILE 233 Z ILE 233 1_555 F NA NA . Z NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc8 D MN MN . Z MN 401 1_555 I O HOH . Z HOH 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc9 D MN MN . Z MN 401 1_555 I O HOH . Z HOH 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc10 D MN MN . Z MN 401 1_555 I O HOH . Z HOH 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc11 D MN MN . Z MN 401 1_555 C OP1 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc12 F NA NA . Z NA 403 1_555 B OP2 DT 4 A DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc13 F NA NA . Z NA 403 1_555 J O HOH . A HOH 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc14 I O HOH . Z HOH 505 1_555 G MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc15 I O HOH . Z HOH 510 1_555 H MN MN . B MN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc16 I O HOH . Z HOH 534 1_555 G MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc17 I O HOH . Z HOH 539 1_555 G MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc18 I O HOH . Z HOH 601 1_555 H MN MN . B MN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc19 C O3' DT 1 B DT 1 1_555 G MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc20 C OP1 DT 1 B DT 1 1_555 H MN MN . B MN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc21 C OP1 DC 2 B DC 2 1_555 G MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc22 H MN MN . B MN 102 1_555 K O HOH . B HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc23 H MN MN . B MN 102 1_555 K O HOH . B HOH 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc24 H MN MN . B MN 102 1_555 K O HOH . B HOH 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? hydrog WATSON-CRICK hydrog1 B N3 DC 1 A DC 1 1_555 C N1 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 1 A DC 1 1_555 C O6 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 1 A DC 1 1_555 C N2 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 2 A DG 2 1_555 C N3 DC 9 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 2 A DG 2 1_555 C O2 DC 9 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 2 A DG 2 1_555 C N4 DC 9 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DC 3 A DC 3 1_555 C N1 DG 8 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N4 DC 3 A DC 3 1_555 C O6 DG 8 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O2 DC 3 A DC 3 1_555 C N2 DG 8 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DT 4 A DT 4 1_555 C N1 DA 7 B DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O4 DT 4 A DT 4 1_555 C N6 DA 7 B DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 5 A DA 5 1_555 C N3 DT 6 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N6 DA 5 A DA 5 1_555 C O4 DT 6 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DG 6 A DG 6 1_555 C N3 DC 5 B DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N2 DG 6 A DG 6 1_555 C O2 DC 5 B DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O6 DG 6 A DG 6 1_555 C N4 DC 5 B DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DT 7 A DT 7 1_555 C N1 DA 4 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O4 DT 7 A DT 7 1_555 C N6 DA 4 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DC 8 A DC 8 1_555 C N1 DG 3 B DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N4 DC 8 A DC 8 1_555 C O6 DG 3 B DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O2 DC 8 A DC 8 1_555 C N2 DG 3 B DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DG 9 A DG 9 1_555 C N3 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 DG 9 A DG 9 1_555 C O2 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 DG 9 A DG 9 1_555 C N4 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N1 DA 10 A DA 10 1_555 C N3 DT 1 B DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N6 DA 10 A DA 10 1_555 C O4 DT 1 B DT 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 5V07 _atom_sites.fract_transf_matrix[1][1] 0.013543 _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] 0.013543 _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] 0.005585 _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 Z 1 401 1 MN MN . E 4 MN Z 1 402 3 MN MN . F 5 NA Z 1 403 1 NA NA . G 4 MN B 1 101 1 MN MN . H 4 MN B 1 102 2 MN MN . I 6 HOH Z 1 501 97 HOH HOH . I 6 HOH Z 2 502 82 HOH HOH . I 6 HOH Z 3 503 49 HOH HOH . I 6 HOH Z 4 504 29 HOH HOH . I 6 HOH Z 5 505 30 HOH HOH . I 6 HOH Z 6 506 43 HOH HOH . I 6 HOH Z 7 507 95 HOH HOH . I 6 HOH Z 8 508 118 HOH HOH . I 6 HOH Z 9 509 106 HOH HOH . I 6 HOH Z 10 510 31 HOH HOH . I 6 HOH Z 11 511 91 HOH HOH . I 6 HOH Z 12 512 13 HOH HOH . I 6 HOH Z 13 513 39 HOH HOH . I 6 HOH Z 14 514 110 HOH HOH . I 6 HOH Z 15 515 102 HOH HOH . I 6 HOH Z 16 516 55 HOH HOH . I 6 HOH Z 17 517 44 HOH HOH . I 6 HOH Z 18 518 100 HOH HOH . I 6 HOH Z 19 519 20 HOH HOH . I 6 HOH Z 20 520 83 HOH HOH . I 6 HOH Z 21 521 24 HOH HOH . I 6 HOH Z 22 522 79 HOH HOH . I 6 HOH Z 23 523 123 HOH HOH . I 6 HOH Z 24 524 1 HOH HOH . I 6 HOH Z 25 525 9 HOH HOH . I 6 HOH Z 26 526 10 HOH HOH . I 6 HOH Z 27 527 17 HOH HOH . I 6 HOH Z 28 528 5 HOH HOH . I 6 HOH Z 29 529 112 HOH HOH . I 6 HOH Z 30 530 122 HOH HOH . I 6 HOH Z 31 531 33 HOH HOH . I 6 HOH Z 32 532 120 HOH HOH . I 6 HOH Z 33 533 51 HOH HOH . I 6 HOH Z 34 534 3 HOH HOH . I 6 HOH Z 35 535 81 HOH HOH . I 6 HOH Z 36 536 28 HOH HOH . I 6 HOH Z 37 537 26 HOH HOH . I 6 HOH Z 38 538 125 HOH HOH . I 6 HOH Z 39 539 4 HOH HOH . I 6 HOH Z 40 540 12 HOH HOH . I 6 HOH Z 41 541 70 HOH HOH . I 6 HOH Z 42 542 99 HOH HOH . I 6 HOH Z 43 543 77 HOH HOH . I 6 HOH Z 44 544 38 HOH HOH . I 6 HOH Z 45 545 116 HOH HOH . I 6 HOH Z 46 546 109 HOH HOH . I 6 HOH Z 47 547 65 HOH HOH . I 6 HOH Z 48 548 46 HOH HOH . I 6 HOH Z 49 549 107 HOH HOH . I 6 HOH Z 50 550 42 HOH HOH . I 6 HOH Z 51 551 48 HOH HOH . I 6 HOH Z 52 552 114 HOH HOH . I 6 HOH Z 53 553 75 HOH HOH . I 6 HOH Z 54 554 108 HOH HOH . I 6 HOH Z 55 555 111 HOH HOH . I 6 HOH Z 56 556 8 HOH HOH . I 6 HOH Z 57 557 60 HOH HOH . I 6 HOH Z 58 558 57 HOH HOH . I 6 HOH Z 59 559 117 HOH HOH . I 6 HOH Z 60 560 76 HOH HOH . I 6 HOH Z 61 561 98 HOH HOH . I 6 HOH Z 62 562 113 HOH HOH . I 6 HOH Z 63 563 11 HOH HOH . I 6 HOH Z 64 564 96 HOH HOH . I 6 HOH Z 65 565 16 HOH HOH . I 6 HOH Z 66 566 52 HOH HOH . I 6 HOH Z 67 567 35 HOH HOH . I 6 HOH Z 68 568 129 HOH HOH . I 6 HOH Z 69 569 23 HOH HOH . I 6 HOH Z 70 570 61 HOH HOH . I 6 HOH Z 71 571 21 HOH HOH . I 6 HOH Z 72 572 94 HOH HOH . I 6 HOH Z 73 573 59 HOH HOH . I 6 HOH Z 74 574 105 HOH HOH . I 6 HOH Z 75 575 85 HOH HOH . I 6 HOH Z 76 576 104 HOH HOH . I 6 HOH Z 77 577 14 HOH HOH . I 6 HOH Z 78 578 90 HOH HOH . I 6 HOH Z 79 579 47 HOH HOH . I 6 HOH Z 80 580 27 HOH HOH . I 6 HOH Z 81 581 74 HOH HOH . I 6 HOH Z 82 582 41 HOH HOH . I 6 HOH Z 83 583 131 HOH HOH . I 6 HOH Z 84 584 132 HOH HOH . I 6 HOH Z 85 585 2 HOH HOH . I 6 HOH Z 86 586 58 HOH HOH . I 6 HOH Z 87 587 124 HOH HOH . I 6 HOH Z 88 588 54 HOH HOH . I 6 HOH Z 89 589 62 HOH HOH . I 6 HOH Z 90 590 127 HOH HOH . I 6 HOH Z 91 591 50 HOH HOH . I 6 HOH Z 92 592 63 HOH HOH . I 6 HOH Z 93 593 115 HOH HOH . I 6 HOH Z 94 594 36 HOH HOH . I 6 HOH Z 95 595 6 HOH HOH . I 6 HOH Z 96 596 103 HOH HOH . I 6 HOH Z 97 597 119 HOH HOH . I 6 HOH Z 98 598 128 HOH HOH . I 6 HOH Z 99 599 126 HOH HOH . I 6 HOH Z 100 600 92 HOH HOH . I 6 HOH Z 101 601 32 HOH HOH . I 6 HOH Z 102 602 121 HOH HOH . J 6 HOH A 1 101 72 HOH HOH . J 6 HOH A 2 102 130 HOH HOH . J 6 HOH A 3 103 87 HOH HOH . J 6 HOH A 4 104 73 HOH HOH . J 6 HOH A 5 105 37 HOH HOH . J 6 HOH A 6 106 88 HOH HOH . J 6 HOH A 7 107 67 HOH HOH . J 6 HOH A 8 108 84 HOH HOH . J 6 HOH A 9 109 45 HOH HOH . J 6 HOH A 10 110 53 HOH HOH . J 6 HOH A 11 111 15 HOH HOH . J 6 HOH A 12 112 64 HOH HOH . J 6 HOH A 13 113 89 HOH HOH . J 6 HOH A 14 114 25 HOH HOH . J 6 HOH A 15 115 40 HOH HOH . J 6 HOH A 16 116 71 HOH HOH . J 6 HOH A 17 117 69 HOH HOH . K 6 HOH B 1 201 22 HOH HOH . K 6 HOH B 2 202 86 HOH HOH . K 6 HOH B 3 203 68 HOH HOH . K 6 HOH B 4 204 93 HOH HOH . K 6 HOH B 5 205 7 HOH HOH . K 6 HOH B 6 206 34 HOH HOH . K 6 HOH B 7 207 80 HOH HOH . K 6 HOH B 8 208 101 HOH HOH . K 6 HOH B 9 209 78 HOH HOH . K 6 HOH B 10 210 56 HOH HOH . K 6 HOH B 11 211 66 HOH HOH . K 6 HOH B 12 212 18 HOH HOH . K 6 HOH B 13 213 19 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 19.425 _atom_site.Cartn_y 12.097 _atom_site.Cartn_z -12.331 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 46.14 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 403 _atom_site.auth_asym_id Z _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 1 #