data_4YOQ # _model_server_result.job_id bTc6svNMrShvAWAwuvOsxQ _model_server_result.datetime_utc '2024-12-21 13:46:01' _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 4yoq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 4YOQ # _exptl.entry_id 4YOQ _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 4YOQ _cell.length_a 37.697 _cell.length_b 84.594 _cell.length_c 142.457 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YOQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 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 covale ? covale1 B O3' DC 5 B DC 5 1_555 B P 8OG 6 B 8OG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? covale ? covale2 B O3' 8OG 6 B 8OG 6 1_555 B P DT 7 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? metalc ? metalc1 A O SER 121 A SER 118 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc2 A O LEU 123 A LEU 120 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc3 A O VAL 126 A VAL 123 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc4 A SG CYS 201 A CYS 198 1_555 D FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc5 A SG CYS 208 A CYS 205 1_555 D FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc6 A SG CYS 211 A CYS 208 1_555 D FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc7 A SG CYS 217 A CYS 214 1_555 D FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc8 E NA NA . A NA 402 1_555 C OP1 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc9 E NA NA . A NA 402 1_555 I O HOH . C HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? hydrog WATSON-CRICK hydrog1 B N1 DA 2 B DA 2 1_555 C N3 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 2 B DA 2 1_555 C O4 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 3 B DG 3 1_555 C N3 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 3 B DG 3 1_555 C O2 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 3 B DG 3 1_555 C N4 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 4 B DA 4 1_555 C N3 DT 9 C DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 4 B DA 4 1_555 C O4 DT 9 C DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 5 B DC 5 1_555 C N1 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 5 B DC 5 1_555 C O6 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 5 B DC 5 1_555 C N2 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog11 B N3 DT 7 B DT 7 1_555 C N1 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog12 B O2 DT 7 B DT 7 1_555 C N6 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 8 B DG 8 1_555 C N3 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 8 B DG 8 1_555 C O2 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 8 B DG 8 1_555 C N4 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 9 B DG 9 1_555 C N3 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 9 B DG 9 1_555 C O2 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 9 B DG 9 1_555 C N4 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DA 10 B DA 10 1_555 C N3 DT 3 C DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N6 DA 10 B DA 10 1_555 C O4 DT 3 C DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog21 B O2 DC 11 B DC 11 1_555 C N2 DG 2 C DG 13 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 4YOQ _atom_sites.fract_transf_matrix[1][1] 0.026527 _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] 0.011821 _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] 0.00702 _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 SF4 A 1 401 400 SF4 SF4 . E 5 NA A 1 402 1 NA NA . F 6 GOL C 1 101 1 GOL GOL . G 7 HOH A 1 501 130 HOH HOH . G 7 HOH A 2 502 38 HOH HOH . G 7 HOH A 3 503 17 HOH HOH . G 7 HOH A 4 504 82 HOH HOH . G 7 HOH A 5 505 136 HOH HOH . G 7 HOH A 6 506 106 HOH HOH . G 7 HOH A 7 507 92 HOH HOH . G 7 HOH A 8 508 32 HOH HOH . G 7 HOH A 9 509 6 HOH HOH . G 7 HOH A 10 510 71 HOH HOH . G 7 HOH A 11 511 8 HOH HOH . G 7 HOH A 12 512 121 HOH HOH . G 7 HOH A 13 513 54 HOH HOH . G 7 HOH A 14 514 24 HOH HOH . G 7 HOH A 15 515 67 HOH HOH . G 7 HOH A 16 516 10 HOH HOH . G 7 HOH A 17 517 50 HOH HOH . G 7 HOH A 18 518 88 HOH HOH . G 7 HOH A 19 519 1 HOH HOH . G 7 HOH A 20 520 7 HOH HOH . G 7 HOH A 21 521 124 HOH HOH . G 7 HOH A 22 522 126 HOH HOH . G 7 HOH A 23 523 75 HOH HOH . G 7 HOH A 24 524 40 HOH HOH . G 7 HOH A 25 525 62 HOH HOH . G 7 HOH A 26 526 70 HOH HOH . G 7 HOH A 27 527 102 HOH HOH . G 7 HOH A 28 528 49 HOH HOH . G 7 HOH A 29 529 13 HOH HOH . G 7 HOH A 30 530 58 HOH HOH . G 7 HOH A 31 531 29 HOH HOH . G 7 HOH A 32 532 51 HOH HOH . G 7 HOH A 33 533 18 HOH HOH . G 7 HOH A 34 534 78 HOH HOH . G 7 HOH A 35 535 56 HOH HOH . G 7 HOH A 36 536 12 HOH HOH . G 7 HOH A 37 537 30 HOH HOH . G 7 HOH A 38 538 47 HOH HOH . G 7 HOH A 39 539 37 HOH HOH . G 7 HOH A 40 540 4 HOH HOH . G 7 HOH A 41 541 63 HOH HOH . G 7 HOH A 42 542 122 HOH HOH . G 7 HOH A 43 543 73 HOH HOH . G 7 HOH A 44 544 131 HOH HOH . G 7 HOH A 45 545 61 HOH HOH . G 7 HOH A 46 546 132 HOH HOH . G 7 HOH A 47 547 57 HOH HOH . G 7 HOH A 48 548 85 HOH HOH . G 7 HOH A 49 549 89 HOH HOH . G 7 HOH A 50 550 44 HOH HOH . G 7 HOH A 51 551 3 HOH HOH . G 7 HOH A 52 552 15 HOH HOH . G 7 HOH A 53 553 16 HOH HOH . G 7 HOH A 54 554 35 HOH HOH . G 7 HOH A 55 555 80 HOH HOH . G 7 HOH A 56 556 42 HOH HOH . G 7 HOH A 57 557 66 HOH HOH . G 7 HOH A 58 558 25 HOH HOH . G 7 HOH A 59 559 27 HOH HOH . G 7 HOH A 60 560 72 HOH HOH . G 7 HOH A 61 561 53 HOH HOH . G 7 HOH A 62 562 64 HOH HOH . G 7 HOH A 63 563 5 HOH HOH . G 7 HOH A 64 564 86 HOH HOH . G 7 HOH A 65 565 33 HOH HOH . G 7 HOH A 66 566 59 HOH HOH . G 7 HOH A 67 567 14 HOH HOH . G 7 HOH A 68 568 46 HOH HOH . G 7 HOH A 69 569 68 HOH HOH . G 7 HOH A 70 570 120 HOH HOH . G 7 HOH A 71 571 90 HOH HOH . G 7 HOH A 72 572 93 HOH HOH . G 7 HOH A 73 573 109 HOH HOH . G 7 HOH A 74 574 98 HOH HOH . G 7 HOH A 75 575 116 HOH HOH . G 7 HOH A 76 576 20 HOH HOH . G 7 HOH A 77 577 135 HOH HOH . G 7 HOH A 78 578 60 HOH HOH . G 7 HOH A 79 579 95 HOH HOH . G 7 HOH A 80 580 108 HOH HOH . G 7 HOH A 81 581 96 HOH HOH . G 7 HOH A 82 582 114 HOH HOH . G 7 HOH A 83 583 139 HOH HOH . G 7 HOH A 84 584 117 HOH HOH . G 7 HOH A 85 585 110 HOH HOH . G 7 HOH A 86 586 52 HOH HOH . G 7 HOH A 87 587 99 HOH HOH . G 7 HOH A 88 588 43 HOH HOH . G 7 HOH A 89 589 105 HOH HOH . G 7 HOH A 90 590 91 HOH HOH . G 7 HOH A 91 591 140 HOH HOH . G 7 HOH A 92 592 83 HOH HOH . G 7 HOH A 93 593 103 HOH HOH . G 7 HOH A 94 594 115 HOH HOH . G 7 HOH A 95 595 76 HOH HOH . G 7 HOH A 96 596 45 HOH HOH . G 7 HOH A 97 597 128 HOH HOH . G 7 HOH A 98 598 84 HOH HOH . G 7 HOH A 99 599 111 HOH HOH . H 7 HOH B 1 101 48 HOH HOH . H 7 HOH B 2 102 34 HOH HOH . H 7 HOH B 3 103 138 HOH HOH . H 7 HOH B 4 104 11 HOH HOH . H 7 HOH B 5 105 119 HOH HOH . H 7 HOH B 6 106 26 HOH HOH . H 7 HOH B 7 107 21 HOH HOH . H 7 HOH B 8 108 118 HOH HOH . H 7 HOH B 9 109 129 HOH HOH . H 7 HOH B 10 110 74 HOH HOH . H 7 HOH B 11 111 2 HOH HOH . H 7 HOH B 12 112 22 HOH HOH . H 7 HOH B 13 113 123 HOH HOH . I 7 HOH C 1 201 101 HOH HOH . I 7 HOH C 2 202 127 HOH HOH . I 7 HOH C 3 203 104 HOH HOH . I 7 HOH C 4 204 19 HOH HOH . I 7 HOH C 5 205 100 HOH HOH . I 7 HOH C 6 206 41 HOH HOH . I 7 HOH C 7 207 9 HOH HOH . I 7 HOH C 8 208 55 HOH HOH . I 7 HOH C 9 209 87 HOH HOH . I 7 HOH C 10 210 28 HOH HOH . I 7 HOH C 11 211 94 HOH HOH . I 7 HOH C 12 212 79 HOH HOH . I 7 HOH C 13 213 31 HOH HOH . I 7 HOH C 14 214 137 HOH HOH . I 7 HOH C 15 215 69 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 5 _atom_site.Cartn_x 25.684 _atom_site.Cartn_y 96.137 _atom_site.Cartn_z 5.477 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 44.62 _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 76 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 1 #