data_1P4Y
#
_model_server_result.job_id            P-nKoZsR-SUYaB7UodCJqA 
_model_server_result.datetime_utc      '2025-03-03 00:10:03' 
_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          1p4y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":36}' 
#
_entry.id    1P4Y 
#
_exptl.entry_id    1P4Y 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SODIUM ION' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          110.01 
_cell.angle_gamma         90 
_cell.entry_id            1P4Y 
_cell.length_a            66.513 
_cell.length_b            24.179 
_cell.length_c            37.004 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1P4Y 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -12.662182 0 34.770176 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N 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 O5' DC 1 A DC 1 1_555 D NA NA . A NA 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc2 A N3 DG 10 A DG 10 1_555 E NA NA . A NA 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? 
metalc ? metalc3 C NA NA . A NA 21 1_555 G O HOH . A HOH 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.81 ? 
metalc ? metalc4 C NA NA . A NA 21 1_555 G O HOH . A HOH 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? 
metalc ? metalc5 C NA NA . A NA 21 1_555 G O HOH . A HOH 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? 
metalc ? metalc6 C NA NA . A NA 21 1_555 G O HOH . A HOH 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? 
metalc ? metalc7 D NA NA . A NA 36 1_555 G O HOH . A HOH 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? 
metalc ? metalc8 E NA NA . A NA 49 1_555 G O HOH . A HOH 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? 
metalc ? metalc9 B O4' DG 9 B DG 19 1_555 F NA NA . B NA 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? 
metalc ? metalc10 F NA NA . B NA 55 1_555 H O HOH . B HOH 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? 
hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 10 B DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 10 B DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 10 B DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N3 DC 2 A DC 2 1_555 B N1 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N4 DC 2 A DC 2 1_555 B O6 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O2 DC 2 A DC 2 1_555 B N2 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N1 DG 3 A DG 3 1_555 B N3 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N2 DG 3 A DG 3 1_555 B O2 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O6 DG 3 A DG 3 1_555 B N4 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 7 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 7 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 7 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N3 DC 5 A DC 5 1_555 B N1 DG 6 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N4 DC 5 A DC 5 1_555 B O6 DG 6 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A O2 DC 5 A DC 5 1_555 B N2 DG 6 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N1 DG 6 A DG 6 1_555 B N3 DC 5 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N2 DG 6 A DG 6 1_555 B O2 DC 5 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A O6 DG 6 A DG 6 1_555 B N4 DC 5 B DC 15 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                     1P4Y 
_atom_sites.fract_transf_matrix[1][1]    0.015035 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005475 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.041358 
_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]    0.02876 
_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 2 NA A 1 21 21 NA N . 
D 2 NA A 1 36 36 NA N . 
E 2 NA A 1 49 49 NA N . 
F 2 NA B 1 55 55 NA N . 
G 3 HOH A 1 22 22 HOH W . 
G 3 HOH A 2 24 24 HOH W . 
G 3 HOH A 3 25 25 HOH W . 
G 3 HOH A 4 26 26 HOH W . 
G 3 HOH A 5 27 27 HOH W . 
G 3 HOH A 6 32 32 HOH W . 
G 3 HOH A 7 33 33 HOH W . 
G 3 HOH A 8 34 34 HOH W . 
G 3 HOH A 9 37 37 HOH W . 
G 3 HOH A 10 38 38 HOH W . 
G 3 HOH A 11 39 39 HOH W . 
G 3 HOH A 12 41 41 HOH W . 
G 3 HOH A 13 43 43 HOH W . 
G 3 HOH A 14 46 46 HOH W . 
G 3 HOH A 15 47 47 HOH W . 
G 3 HOH A 16 48 48 HOH W . 
G 3 HOH A 17 51 51 HOH W . 
G 3 HOH A 18 54 54 HOH W . 
G 3 HOH A 19 56 56 HOH W . 
G 3 HOH A 20 58 58 HOH W . 
G 3 HOH A 21 59 59 HOH W . 
G 3 HOH A 22 62 62 HOH W . 
G 3 HOH A 23 67 67 HOH W . 
G 3 HOH A 24 70 70 HOH W . 
G 3 HOH A 25 71 71 HOH W . 
G 3 HOH A 26 72 72 HOH W . 
G 3 HOH A 27 78 78 HOH W . 
G 3 HOH A 28 80 80 HOH W . 
G 3 HOH A 29 81 81 HOH W . 
G 3 HOH A 30 82 82 HOH W . 
G 3 HOH A 31 84 84 HOH W . 
G 3 HOH A 32 85 85 HOH W . 
G 3 HOH A 33 86 86 HOH W . 
G 3 HOH A 34 87 87 HOH W . 
G 3 HOH A 35 88 88 HOH W . 
G 3 HOH A 36 90 90 HOH W . 
G 3 HOH A 37 95 95 HOH W . 
G 3 HOH A 38 97 97 HOH W . 
G 3 HOH A 39 98 98 HOH W . 
G 3 HOH A 40 101 101 HOH W . 
G 3 HOH A 41 103 103 HOH W . 
G 3 HOH A 42 105 105 HOH W . 
G 3 HOH A 43 107 107 HOH W . 
G 3 HOH A 44 109 109 HOH W . 
G 3 HOH A 45 110 110 HOH W . 
G 3 HOH A 46 115 115 HOH W . 
G 3 HOH A 47 116 116 HOH W . 
G 3 HOH A 48 119 119 HOH W . 
G 3 HOH A 49 120 120 HOH W . 
G 3 HOH A 50 121 121 HOH W . 
G 3 HOH A 51 122 122 HOH W . 
G 3 HOH A 52 123 123 HOH W . 
G 3 HOH A 53 125 125 HOH W . 
G 3 HOH A 54 127 127 HOH W . 
G 3 HOH A 55 130 130 HOH W . 
G 3 HOH A 56 131 131 HOH W . 
G 3 HOH A 57 132 132 HOH W . 
H 3 HOH B 1 23 23 HOH W . 
H 3 HOH B 2 28 28 HOH W . 
H 3 HOH B 3 29 29 HOH W . 
H 3 HOH B 4 30 30 HOH W . 
H 3 HOH B 5 31 31 HOH W . 
H 3 HOH B 6 35 35 HOH W . 
H 3 HOH B 7 40 40 HOH W . 
H 3 HOH B 8 42 42 HOH W . 
H 3 HOH B 9 44 44 HOH W . 
H 3 HOH B 10 45 45 HOH W . 
H 3 HOH B 11 50 50 HOH W . 
H 3 HOH B 12 52 52 HOH W . 
H 3 HOH B 13 53 53 HOH W . 
H 3 HOH B 14 57 57 HOH W . 
H 3 HOH B 15 60 60 HOH W . 
H 3 HOH B 16 61 61 HOH W . 
H 3 HOH B 17 63 63 HOH W . 
H 3 HOH B 18 64 64 HOH W . 
H 3 HOH B 19 65 65 HOH W . 
H 3 HOH B 20 66 66 HOH W . 
H 3 HOH B 21 68 68 HOH W . 
H 3 HOH B 22 69 69 HOH W . 
H 3 HOH B 23 73 73 HOH W . 
H 3 HOH B 24 74 74 HOH W . 
H 3 HOH B 25 75 75 HOH W . 
H 3 HOH B 26 76 76 HOH W . 
H 3 HOH B 27 77 77 HOH W . 
H 3 HOH B 28 79 79 HOH W . 
H 3 HOH B 29 83 83 HOH W . 
H 3 HOH B 30 89 89 HOH W . 
H 3 HOH B 31 91 91 HOH W . 
H 3 HOH B 32 92 92 HOH W . 
H 3 HOH B 33 93 93 HOH W . 
H 3 HOH B 34 94 94 HOH W . 
H 3 HOH B 35 96 96 HOH W . 
H 3 HOH B 36 99 99 HOH W . 
H 3 HOH B 37 100 100 HOH W . 
H 3 HOH B 38 102 102 HOH W . 
H 3 HOH B 39 104 104 HOH W . 
H 3 HOH B 40 106 106 HOH W . 
H 3 HOH B 41 108 108 HOH W . 
H 3 HOH B 42 111 111 HOH W . 
H 3 HOH B 43 112 112 HOH W . 
H 3 HOH B 44 113 113 HOH W . 
H 3 HOH B 45 114 114 HOH W . 
H 3 HOH B 46 117 117 HOH W . 
H 3 HOH B 47 118 118 HOH W . 
H 3 HOH B 48 124 124 HOH W . 
H 3 HOH B 49 126 126 HOH W . 
H 3 HOH B 50 128 128 HOH W . 
H 3 HOH B 51 129 129 HOH W . 
#
_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       2 
_atom_site.Cartn_x               -24.328 
_atom_site.Cartn_y               -1.078 
_atom_site.Cartn_z               32.517 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        9.82 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           36 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#