data_5YIE # _model_server_result.job_id vzzPcFCjWf2kYOiw_WjFHQ _model_server_result.datetime_utc '2024-11-24 08:21:06' _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 5yie # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 5YIE # _exptl.entry_id 5YIE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 4 _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 5YIE _cell.length_a 106.6 _cell.length_b 106.6 _cell.length_c 72.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YIE _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 E _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 disulf ? disulf1 A SG CYS 45 A CYS 49 1_555 A SG CYS 50 A CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 247 A CYS 251 1_555 A SG CYS 283 A CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc1 A OD1 ASP 32 A ASP 36 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? metalc ? metalc2 A OD2 ASP 212 A ASP 216 1_555 E NA NA . A NA 404 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc3 D O23 8VF . A 8VF 403 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc4 D O26 8VF . A 8VF 403 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? # _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 5YIE _atom_sites.fract_transf_matrix[1][1] 0.009381 _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] 0.009381 _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] 0.01385 _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 B 2 CPS A 1 401 1 CPS CPS . C 2 CPS A 1 402 2 CPS CPS . D 3 8VF A 1 403 1 8VF 742 . E 4 NA A 1 404 1 NA NA . F 5 HOH A 1 501 47 HOH HOH . F 5 HOH A 2 502 51 HOH HOH . F 5 HOH A 3 503 150 HOH HOH . F 5 HOH A 4 504 48 HOH HOH . F 5 HOH A 5 505 60 HOH HOH . F 5 HOH A 6 506 37 HOH HOH . F 5 HOH A 7 507 42 HOH HOH . F 5 HOH A 8 508 71 HOH HOH . F 5 HOH A 9 509 52 HOH HOH . F 5 HOH A 10 510 23 HOH HOH . F 5 HOH A 11 511 61 HOH HOH . F 5 HOH A 12 512 55 HOH HOH . F 5 HOH A 13 513 86 HOH HOH . F 5 HOH A 14 514 15 HOH HOH . F 5 HOH A 15 515 1 HOH HOH . F 5 HOH A 16 516 149 HOH HOH . F 5 HOH A 17 517 45 HOH HOH . F 5 HOH A 18 518 49 HOH HOH . F 5 HOH A 19 519 41 HOH HOH . F 5 HOH A 20 520 36 HOH HOH . F 5 HOH A 21 521 19 HOH HOH . F 5 HOH A 22 522 208 HOH HOH . F 5 HOH A 23 523 138 HOH HOH . F 5 HOH A 24 524 29 HOH HOH . F 5 HOH A 25 525 21 HOH HOH . F 5 HOH A 26 526 171 HOH HOH . F 5 HOH A 27 527 56 HOH HOH . F 5 HOH A 28 528 9 HOH HOH . F 5 HOH A 29 529 34 HOH HOH . F 5 HOH A 30 530 178 HOH HOH . F 5 HOH A 31 531 12 HOH HOH . F 5 HOH A 32 532 58 HOH HOH . F 5 HOH A 33 533 153 HOH HOH . F 5 HOH A 34 534 38 HOH HOH . F 5 HOH A 35 535 39 HOH HOH . F 5 HOH A 36 536 43 HOH HOH . F 5 HOH A 37 537 30 HOH HOH . F 5 HOH A 38 538 33 HOH HOH . F 5 HOH A 39 539 181 HOH HOH . F 5 HOH A 40 540 46 HOH HOH . F 5 HOH A 41 541 44 HOH HOH . F 5 HOH A 42 542 35 HOH HOH . F 5 HOH A 43 543 2 HOH HOH . F 5 HOH A 44 544 130 HOH HOH . F 5 HOH A 45 545 14 HOH HOH . F 5 HOH A 46 546 25 HOH HOH . F 5 HOH A 47 547 121 HOH HOH . F 5 HOH A 48 548 54 HOH HOH . F 5 HOH A 49 549 26 HOH HOH . F 5 HOH A 50 550 206 HOH HOH . F 5 HOH A 51 551 62 HOH HOH . F 5 HOH A 52 552 106 HOH HOH . F 5 HOH A 53 553 4 HOH HOH . F 5 HOH A 54 554 57 HOH HOH . F 5 HOH A 55 555 10 HOH HOH . F 5 HOH A 56 556 24 HOH HOH . F 5 HOH A 57 557 163 HOH HOH . F 5 HOH A 58 558 198 HOH HOH . F 5 HOH A 59 559 123 HOH HOH . F 5 HOH A 60 560 97 HOH HOH . F 5 HOH A 61 561 27 HOH HOH . F 5 HOH A 62 562 6 HOH HOH . F 5 HOH A 63 563 194 HOH HOH . F 5 HOH A 64 564 177 HOH HOH . F 5 HOH A 65 565 105 HOH HOH . F 5 HOH A 66 566 40 HOH HOH . F 5 HOH A 67 567 11 HOH HOH . F 5 HOH A 68 568 28 HOH HOH . F 5 HOH A 69 569 200 HOH HOH . F 5 HOH A 70 570 151 HOH HOH . F 5 HOH A 71 571 68 HOH HOH . F 5 HOH A 72 572 173 HOH HOH . F 5 HOH A 73 573 20 HOH HOH . F 5 HOH A 74 574 174 HOH HOH . F 5 HOH A 75 575 50 HOH HOH . F 5 HOH A 76 576 147 HOH HOH . F 5 HOH A 77 577 53 HOH HOH . F 5 HOH A 78 578 22 HOH HOH . F 5 HOH A 79 579 184 HOH HOH . F 5 HOH A 80 580 7 HOH HOH . F 5 HOH A 81 581 87 HOH HOH . F 5 HOH A 82 582 188 HOH HOH . F 5 HOH A 83 583 154 HOH HOH . F 5 HOH A 84 584 118 HOH HOH . F 5 HOH A 85 585 137 HOH HOH . F 5 HOH A 86 586 95 HOH HOH . F 5 HOH A 87 587 220 HOH HOH . F 5 HOH A 88 588 84 HOH HOH . F 5 HOH A 89 589 65 HOH HOH . F 5 HOH A 90 590 102 HOH HOH . F 5 HOH A 91 591 63 HOH HOH . F 5 HOH A 92 592 180 HOH HOH . F 5 HOH A 93 593 31 HOH HOH . F 5 HOH A 94 594 169 HOH HOH . F 5 HOH A 95 595 81 HOH HOH . F 5 HOH A 96 596 217 HOH HOH . F 5 HOH A 97 597 161 HOH HOH . F 5 HOH A 98 598 166 HOH HOH . F 5 HOH A 99 599 67 HOH HOH . F 5 HOH A 100 600 72 HOH HOH . F 5 HOH A 101 601 211 HOH HOH . F 5 HOH A 102 602 143 HOH HOH . F 5 HOH A 103 603 212 HOH HOH . F 5 HOH A 104 604 75 HOH HOH . F 5 HOH A 105 605 82 HOH HOH . F 5 HOH A 106 606 183 HOH HOH . F 5 HOH A 107 607 8 HOH HOH . F 5 HOH A 108 608 185 HOH HOH . F 5 HOH A 109 609 207 HOH HOH . F 5 HOH A 110 610 59 HOH HOH . F 5 HOH A 111 611 213 HOH HOH . F 5 HOH A 112 612 221 HOH HOH . F 5 HOH A 113 613 78 HOH HOH . F 5 HOH A 114 614 201 HOH HOH . F 5 HOH A 115 615 205 HOH HOH . F 5 HOH A 116 616 187 HOH HOH . F 5 HOH A 117 617 186 HOH HOH . F 5 HOH A 118 618 162 HOH HOH . F 5 HOH A 119 619 172 HOH HOH . F 5 HOH A 120 620 113 HOH HOH . F 5 HOH A 121 621 214 HOH HOH . F 5 HOH A 122 622 222 HOH HOH . F 5 HOH A 123 623 89 HOH HOH . F 5 HOH A 124 624 215 HOH HOH . F 5 HOH A 125 625 83 HOH HOH . F 5 HOH A 126 626 196 HOH HOH . F 5 HOH A 127 627 176 HOH HOH . F 5 HOH A 128 628 17 HOH HOH . F 5 HOH A 129 629 218 HOH HOH . F 5 HOH A 130 630 193 HOH HOH . F 5 HOH A 131 631 192 HOH HOH . F 5 HOH A 132 632 203 HOH HOH . F 5 HOH A 133 633 199 HOH HOH . F 5 HOH A 134 634 204 HOH HOH . F 5 HOH A 135 635 3 HOH HOH . F 5 HOH A 136 636 210 HOH HOH . F 5 HOH A 137 637 197 HOH HOH . F 5 HOH A 138 638 32 HOH HOH . F 5 HOH A 139 639 164 HOH HOH . F 5 HOH A 140 640 167 HOH HOH . F 5 HOH A 141 641 223 HOH HOH . F 5 HOH A 142 642 209 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 E _atom_site.label_entity_id 4 _atom_site.Cartn_x 15.325 _atom_site.Cartn_y -29.432 _atom_site.Cartn_z -24.429 _atom_site.occupancy 0.5 _atom_site.B_iso_or_equiv 46.53 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 404 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #