data_8YDW
#
_model_server_result.job_id            uI3HUvcOI0jFtKU-Lz-gbw 
_model_server_result.datetime_utc      '2025-08-28 14:44:08' 
_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          8ydw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    8YDW 
#
_exptl.entry_id    8YDW 
_exptl.method      'X-RAY DIFFRACTION' 
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_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            8YDW 
_cell.length_a            74.76 
_cell.length_b            74.76 
_cell.length_c            100.07 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YDW 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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                             D 
_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 B SG CYS 4 B CYS 336 1_555 B SG CYS 29 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 B SG CYS 47 B CYS 379 1_555 B SG CYS 100 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
disulf ? disulf3 B SG CYS 59 B CYS 391 1_555 B SG CYS 193 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
disulf ? disulf4 B SG CYS 148 B CYS 480 1_555 B SG CYS 156 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc1 B O ASN 73 B ASN 405 1_555 D NA NA . B NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc2 B OG SER 76 B SER 408 1_555 D NA NA . B NA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? 
#
_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                     8YDW 
_atom_sites.fract_transf_matrix[1][1]    0.013376 
_atom_sites.fract_transf_matrix[1][2]    0.007723 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015445 
_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]    0.009993 
_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
C 3 GOL B 1 601 102 GOL GOL . 
D 4 NA B 1 602 1 NA NA . 
E 5 HOH A 1 101 15 HOH HOH . 
E 5 HOH A 2 102 100 HOH HOH . 
E 5 HOH A 3 103 62 HOH HOH . 
E 5 HOH A 4 104 5 HOH HOH . 
E 5 HOH A 5 105 43 HOH HOH . 
E 5 HOH A 6 106 27 HOH HOH . 
E 5 HOH A 7 107 199 HOH HOH . 
E 5 HOH A 8 108 35 HOH HOH . 
E 5 HOH A 9 109 39 HOH HOH . 
E 5 HOH A 10 110 41 HOH HOH . 
E 5 HOH A 11 111 200 HOH HOH . 
F 5 HOH B 1 701 31 HOH HOH . 
F 5 HOH B 2 702 170 HOH HOH . 
F 5 HOH B 3 703 12 HOH HOH . 
F 5 HOH B 4 704 104 HOH HOH . 
F 5 HOH B 5 705 36 HOH HOH . 
F 5 HOH B 6 706 29 HOH HOH . 
F 5 HOH B 7 707 92 HOH HOH . 
F 5 HOH B 8 708 11 HOH HOH . 
F 5 HOH B 9 709 3 HOH HOH . 
F 5 HOH B 10 710 83 HOH HOH . 
F 5 HOH B 11 711 16 HOH HOH . 
F 5 HOH B 12 712 26 HOH HOH . 
F 5 HOH B 13 713 9 HOH HOH . 
F 5 HOH B 14 714 21 HOH HOH . 
F 5 HOH B 15 715 8 HOH HOH . 
F 5 HOH B 16 716 32 HOH HOH . 
F 5 HOH B 17 717 105 HOH HOH . 
F 5 HOH B 18 718 13 HOH HOH . 
F 5 HOH B 19 719 23 HOH HOH . 
F 5 HOH B 20 720 17 HOH HOH . 
F 5 HOH B 21 721 6 HOH HOH . 
F 5 HOH B 22 722 10 HOH HOH . 
F 5 HOH B 23 723 202 HOH HOH . 
F 5 HOH B 24 724 24 HOH HOH . 
F 5 HOH B 25 725 2 HOH HOH . 
F 5 HOH B 26 726 77 HOH HOH . 
F 5 HOH B 27 727 88 HOH HOH . 
F 5 HOH B 28 728 4 HOH HOH . 
F 5 HOH B 29 729 166 HOH HOH . 
F 5 HOH B 30 730 7 HOH HOH . 
F 5 HOH B 31 731 20 HOH HOH . 
F 5 HOH B 32 732 73 HOH HOH . 
F 5 HOH B 33 733 22 HOH HOH . 
F 5 HOH B 34 734 130 HOH HOH . 
F 5 HOH B 35 735 19 HOH HOH . 
F 5 HOH B 36 736 81 HOH HOH . 
F 5 HOH B 37 737 95 HOH HOH . 
F 5 HOH B 38 738 80 HOH HOH . 
F 5 HOH B 39 739 55 HOH HOH . 
F 5 HOH B 40 740 190 HOH HOH . 
F 5 HOH B 41 741 67 HOH HOH . 
F 5 HOH B 42 742 94 HOH HOH . 
F 5 HOH B 43 743 33 HOH HOH . 
F 5 HOH B 44 744 54 HOH HOH . 
F 5 HOH B 45 745 169 HOH HOH . 
F 5 HOH B 46 746 99 HOH HOH . 
F 5 HOH B 47 747 203 HOH HOH . 
F 5 HOH B 48 748 70 HOH HOH . 
F 5 HOH B 49 749 56 HOH HOH . 
F 5 HOH B 50 750 52 HOH HOH . 
F 5 HOH B 51 751 51 HOH HOH . 
F 5 HOH B 52 752 204 HOH HOH . 
F 5 HOH B 53 753 48 HOH HOH . 
F 5 HOH B 54 754 173 HOH HOH . 
F 5 HOH B 55 755 188 HOH HOH . 
F 5 HOH B 56 756 101 HOH HOH . 
F 5 HOH B 57 757 103 HOH HOH . 
F 5 HOH B 58 758 205 HOH HOH . 
F 5 HOH B 59 759 86 HOH HOH . 
F 5 HOH B 60 760 68 HOH HOH . 
F 5 HOH B 61 761 82 HOH HOH . 
F 5 HOH B 62 762 129 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         D 
_atom_site.label_entity_id       4 
_atom_site.Cartn_x               -39.166 
_atom_site.Cartn_y               -3.35 
_atom_site.Cartn_z               2.641 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        65.31 
_atom_site.pdbx_formal_charge    0 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           602 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           224 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           1 
#