data_4YPH
#
_model_server_result.job_id            6b7n-2RlsZz3rhk1pgjBeg 
_model_server_result.datetime_utc      '2024-12-21 12:24:32' 
_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          4yph 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":402}' 
#
_entry.id    4YPH 
#
_exptl.entry_id    4YPH 
_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            4YPH 
_cell.length_a            37.636 
_cell.length_b            83.757 
_cell.length_c            142.735 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YPH 
_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 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? 
covale ? covale2 B O3' 8OG 6 B 8OG 6 1_555 B P DT 7 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? 
metalc ? metalc1 A O SER 121 A SER 118 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc2 A O LEU 123 A LEU 120 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? 
metalc ? metalc3 A O VAL 126 A VAL 123 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? 
metalc ? metalc4 A SG CYS 201 A CYS 198 1_555 D FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc5 A SG CYS 208 A CYS 205 1_555 D FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc6 A SG CYS 211 A CYS 208 1_555 D FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc7 A SG CYS 217 A CYS 214 1_555 D FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? 
metalc ? metalc8 E NA NA . A NA 402 1_555 F O HOH . A HOH 540 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? 
metalc ? metalc9 E NA NA . A NA 402 1_555 C OP1 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? 
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                     4YPH 
_atom_sites.fract_transf_matrix[1][1]    0.02657 
_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]    0.011939 
_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]    0.007006 
_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 HOH A 1 501 22 HOH HOH . 
F 6 HOH A 2 502 45 HOH HOH . 
F 6 HOH A 3 503 47 HOH HOH . 
F 6 HOH A 4 504 10 HOH HOH . 
F 6 HOH A 5 505 55 HOH HOH . 
F 6 HOH A 6 506 8 HOH HOH . 
F 6 HOH A 7 507 48 HOH HOH . 
F 6 HOH A 8 508 39 HOH HOH . 
F 6 HOH A 9 509 25 HOH HOH . 
F 6 HOH A 10 510 34 HOH HOH . 
F 6 HOH A 11 511 16 HOH HOH . 
F 6 HOH A 12 512 7 HOH HOH . 
F 6 HOH A 13 513 24 HOH HOH . 
F 6 HOH A 14 514 4 HOH HOH . 
F 6 HOH A 15 515 15 HOH HOH . 
F 6 HOH A 16 516 12 HOH HOH . 
F 6 HOH A 17 517 9 HOH HOH . 
F 6 HOH A 18 518 28 HOH HOH . 
F 6 HOH A 19 519 13 HOH HOH . 
F 6 HOH A 20 520 21 HOH HOH . 
F 6 HOH A 21 521 11 HOH HOH . 
F 6 HOH A 22 522 33 HOH HOH . 
F 6 HOH A 23 523 23 HOH HOH . 
F 6 HOH A 24 524 51 HOH HOH . 
F 6 HOH A 25 525 20 HOH HOH . 
F 6 HOH A 26 526 17 HOH HOH . 
F 6 HOH A 27 527 6 HOH HOH . 
F 6 HOH A 28 528 57 HOH HOH . 
F 6 HOH A 29 529 44 HOH HOH . 
F 6 HOH A 30 530 46 HOH HOH . 
F 6 HOH A 31 531 49 HOH HOH . 
F 6 HOH A 32 532 65 HOH HOH . 
F 6 HOH A 33 533 3 HOH HOH . 
F 6 HOH A 34 534 30 HOH HOH . 
F 6 HOH A 35 535 36 HOH HOH . 
F 6 HOH A 36 536 60 HOH HOH . 
F 6 HOH A 37 537 29 HOH HOH . 
F 6 HOH A 38 538 52 HOH HOH . 
F 6 HOH A 39 539 61 HOH HOH . 
F 6 HOH A 40 540 26 HOH HOH . 
F 6 HOH A 41 541 62 HOH HOH . 
F 6 HOH A 42 542 31 HOH HOH . 
F 6 HOH A 43 543 18 HOH HOH . 
G 6 HOH B 1 101 32 HOH HOH . 
G 6 HOH B 2 102 38 HOH HOH . 
G 6 HOH B 3 103 27 HOH HOH . 
G 6 HOH B 4 104 35 HOH HOH . 
G 6 HOH B 5 105 37 HOH HOH . 
G 6 HOH B 6 106 5 HOH HOH . 
H 6 HOH C 1 101 14 HOH HOH . 
H 6 HOH C 2 102 67 HOH HOH . 
H 6 HOH C 3 103 19 HOH HOH . 
H 6 HOH C 4 104 66 HOH HOH . 
H 6 HOH C 5 105 41 HOH HOH . 
H 6 HOH C 6 106 64 HOH HOH . 
H 6 HOH C 7 107 40 HOH HOH . 
H 6 HOH C 8 108 63 HOH HOH . 
H 6 HOH C 9 109 56 HOH HOH . 
H 6 HOH C 10 110 54 HOH HOH . 
H 6 HOH C 11 111 43 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               -26.591 
_atom_site.Cartn_y               11.486 
_atom_site.Cartn_z               -5.528 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        64.59 
_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              17 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#