data_5I1T # _model_server_result.job_id x9HcekqjGzQaQllMcCNPgA _model_server_result.datetime_utc '2025-02-05 12:03:56' _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 5i1t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 5I1T # _exptl.entry_id 5I1T _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 120 _cell.entry_id 5I1T _cell.length_a 98.082 _cell.length_b 98.082 _cell.length_c 108.327 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5I1T _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 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,G,H _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 # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 NAG NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG S 4 CTO 2 n B NAG 2 B 2 NAG S 4 CTO 2 n B NAG 3 B 3 NAG S 4 CTO 2 n C NAG 1 C 1 NAG S 5 CTO 2 n C NAG 2 C 2 NAG S 5 CTO 2 n C NAG 3 C 3 NAG S 5 CTO # 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 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 sing covale ? covale2 B O4 NAG . B NAG 2 1_555 B C1 NAG . B NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 sing covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 sing covale ? covale4 C O4 NAG . C NAG 2 1_555 C C1 NAG . C NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 sing metalc ? metalc1 A NE2 HIS 110 A HIS 134 1_555 D ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc2 A SG CYS 116 A CYS 140 1_555 D ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc3 A ND1 HIS 121 A HIS 145 1_555 D ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc4 A SG CYS 122 A CYS 146 1_555 D ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc5 A O LYS 155 A LYS 179 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc6 A O LYS 237 A LYS 261 1_555 E NA NA . A NA 402 4_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc7 A OD2 ASP 328 A ASP 352 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc8 A O TYR 330 A TYR 354 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc9 E NA NA . A NA 402 1_555 H O HOH . A HOH 572 4_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? # _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 5I1T _atom_sites.fract_transf_matrix[1][1] 0.010196 _atom_sites.fract_transf_matrix[1][2] 0.005886 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011773 _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] 0.009231 _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 3 ZN A 1 401 1 ZN ZN . E 4 NA A 1 402 2 NA NA . F 5 CL A 1 403 3 CL CL . G 6 GOL A 1 406 6 GOL GOL . H 7 HOH A 1 501 60 HOH HOH . H 7 HOH A 2 502 140 HOH HOH . H 7 HOH A 3 503 77 HOH HOH . H 7 HOH A 4 504 78 HOH HOH . H 7 HOH A 5 505 133 HOH HOH . H 7 HOH A 6 506 81 HOH HOH . H 7 HOH A 7 507 36 HOH HOH . H 7 HOH A 8 508 14 HOH HOH . H 7 HOH A 9 509 25 HOH HOH . H 7 HOH A 10 510 148 HOH HOH . H 7 HOH A 11 511 155 HOH HOH . H 7 HOH A 12 512 92 HOH HOH . H 7 HOH A 13 513 31 HOH HOH . H 7 HOH A 14 514 8 HOH HOH . H 7 HOH A 15 515 52 HOH HOH . H 7 HOH A 16 516 111 HOH HOH . H 7 HOH A 17 517 27 HOH HOH . H 7 HOH A 18 518 29 HOH HOH . H 7 HOH A 19 519 129 HOH HOH . H 7 HOH A 20 520 153 HOH HOH . H 7 HOH A 21 521 21 HOH HOH . H 7 HOH A 22 522 13 HOH HOH . H 7 HOH A 23 523 11 HOH HOH . H 7 HOH A 24 524 115 HOH HOH . H 7 HOH A 25 525 76 HOH HOH . H 7 HOH A 26 526 96 HOH HOH . H 7 HOH A 27 527 9 HOH HOH . H 7 HOH A 28 528 82 HOH HOH . H 7 HOH A 29 529 91 HOH HOH . H 7 HOH A 30 530 135 HOH HOH . H 7 HOH A 31 531 46 HOH HOH . H 7 HOH A 32 532 39 HOH HOH . H 7 HOH A 33 533 30 HOH HOH . H 7 HOH A 34 534 139 HOH HOH . H 7 HOH A 35 535 94 HOH HOH . H 7 HOH A 36 536 43 HOH HOH . H 7 HOH A 37 537 71 HOH HOH . H 7 HOH A 38 538 75 HOH HOH . H 7 HOH A 39 539 156 HOH HOH . H 7 HOH A 40 540 68 HOH HOH . H 7 HOH A 41 541 101 HOH HOH . H 7 HOH A 42 542 154 HOH HOH . H 7 HOH A 43 543 18 HOH HOH . H 7 HOH A 44 544 15 HOH HOH . H 7 HOH A 45 545 99 HOH HOH . H 7 HOH A 46 546 47 HOH HOH . H 7 HOH A 47 547 16 HOH HOH . H 7 HOH A 48 548 114 HOH HOH . H 7 HOH A 49 549 37 HOH HOH . H 7 HOH A 50 550 40 HOH HOH . H 7 HOH A 51 551 35 HOH HOH . H 7 HOH A 52 552 138 HOH HOH . H 7 HOH A 53 553 125 HOH HOH . H 7 HOH A 54 554 122 HOH HOH . H 7 HOH A 55 555 24 HOH HOH . H 7 HOH A 56 556 80 HOH HOH . H 7 HOH A 57 557 53 HOH HOH . H 7 HOH A 58 558 59 HOH HOH . H 7 HOH A 59 559 62 HOH HOH . H 7 HOH A 60 560 10 HOH HOH . H 7 HOH A 61 561 58 HOH HOH . H 7 HOH A 62 562 124 HOH HOH . H 7 HOH A 63 563 44 HOH HOH . H 7 HOH A 64 564 55 HOH HOH . H 7 HOH A 65 565 63 HOH HOH . H 7 HOH A 66 566 65 HOH HOH . H 7 HOH A 67 567 98 HOH HOH . H 7 HOH A 68 568 48 HOH HOH . H 7 HOH A 69 569 119 HOH HOH . H 7 HOH A 70 570 84 HOH HOH . H 7 HOH A 71 571 86 HOH HOH . H 7 HOH A 72 572 26 HOH HOH . H 7 HOH A 73 573 22 HOH HOH . H 7 HOH A 74 574 23 HOH HOH . H 7 HOH A 75 575 45 HOH HOH . H 7 HOH A 76 576 146 HOH HOH . H 7 HOH A 77 577 107 HOH HOH . H 7 HOH A 78 578 97 HOH HOH . H 7 HOH A 79 579 143 HOH HOH . H 7 HOH A 80 580 120 HOH HOH . H 7 HOH A 81 581 87 HOH HOH . H 7 HOH A 82 582 131 HOH HOH . H 7 HOH A 83 583 54 HOH HOH . H 7 HOH A 84 584 50 HOH HOH . H 7 HOH A 85 585 57 HOH HOH . H 7 HOH A 86 586 117 HOH HOH . H 7 HOH A 87 587 89 HOH HOH . H 7 HOH A 88 588 136 HOH HOH . H 7 HOH A 89 589 93 HOH HOH . H 7 HOH A 90 590 123 HOH HOH . H 7 HOH A 91 591 56 HOH HOH . H 7 HOH A 92 592 33 HOH HOH . H 7 HOH A 93 593 28 HOH HOH . H 7 HOH A 94 594 49 HOH HOH . H 7 HOH A 95 595 19 HOH HOH . H 7 HOH A 96 596 41 HOH HOH . H 7 HOH A 97 597 12 HOH HOH . H 7 HOH A 98 598 141 HOH HOH . H 7 HOH A 99 599 105 HOH HOH . H 7 HOH A 100 600 20 HOH HOH . H 7 HOH A 101 601 67 HOH HOH . H 7 HOH A 102 602 112 HOH HOH . H 7 HOH A 103 603 118 HOH HOH . H 7 HOH A 104 604 149 HOH HOH . H 7 HOH A 105 605 38 HOH HOH . H 7 HOH A 106 606 127 HOH HOH . H 7 HOH A 107 607 32 HOH HOH . H 7 HOH A 108 608 73 HOH HOH . H 7 HOH A 109 609 100 HOH HOH . H 7 HOH A 110 610 104 HOH HOH . H 7 HOH A 111 611 85 HOH HOH . H 7 HOH A 112 612 90 HOH HOH . H 7 HOH A 113 613 137 HOH HOH . H 7 HOH A 114 614 72 HOH HOH . H 7 HOH A 115 615 150 HOH HOH . H 7 HOH A 116 616 64 HOH HOH . H 7 HOH A 117 617 34 HOH HOH . H 7 HOH A 118 618 95 HOH HOH . H 7 HOH A 119 619 42 HOH HOH . H 7 HOH A 120 620 151 HOH HOH . H 7 HOH A 121 621 83 HOH HOH . H 7 HOH A 122 622 51 HOH HOH . H 7 HOH A 123 623 121 HOH HOH . H 7 HOH A 124 624 79 HOH HOH . H 7 HOH A 125 625 130 HOH HOH . H 7 HOH A 126 626 103 HOH HOH . H 7 HOH A 127 627 17 HOH HOH . H 7 HOH A 128 628 110 HOH HOH . H 7 HOH A 129 629 152 HOH HOH . H 7 HOH A 130 630 134 HOH HOH . H 7 HOH A 131 631 69 HOH HOH . H 7 HOH A 132 632 126 HOH HOH . H 7 HOH A 133 633 74 HOH HOH . H 7 HOH A 134 634 116 HOH HOH . H 7 HOH A 135 635 70 HOH HOH . H 7 HOH A 136 636 128 HOH HOH . H 7 HOH A 137 637 132 HOH HOH . H 7 HOH A 138 638 145 HOH HOH . H 7 HOH A 139 639 88 HOH HOH . H 7 HOH A 140 640 109 HOH HOH . H 7 HOH A 141 641 66 HOH HOH . H 7 HOH A 142 642 102 HOH HOH . H 7 HOH A 143 643 147 HOH HOH . H 7 HOH A 144 644 108 HOH HOH . H 7 HOH A 145 645 106 HOH HOH . H 7 HOH A 146 646 113 HOH HOH . H 7 HOH A 147 647 61 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 -63.653 _atom_site.Cartn_y -9.269 _atom_site.Cartn_z 11.975 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 56.91 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 402 _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 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #