data_5DYN
#
_model_server_result.job_id            IaFATwCWxuLeVteMVmIoGA 
_model_server_result.datetime_utc      '2025-03-04 08:25:21' 
_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          5dyn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":404}' 
#
_entry.id    5DYN 
#
_exptl.entry_id    5DYN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SODIUM ION' 
_entity.pdbx_number_of_molecules    8 
_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            5DYN 
_cell.length_a            124.32 
_cell.length_b            48.9 
_cell.length_c            60.88 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DYN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_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,G,H,I,J,K,L,M 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D N N 
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J 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 OE1 GLN 25 A GLN 42 1_555 C NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
metalc ? metalc2 A OE1 GLN 25 A GLN 42 1_555 D NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? 
metalc ? metalc3 A OD1 ASP 35 A ASP 52 1_555 E NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? 
metalc ? metalc4 A OE1 GLU 38 A GLU 55 1_555 E NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc5 A OE2 GLU 38 A GLU 55 1_555 E NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? 
metalc ? metalc6 A OD2 ASP 58 A ASP 75 1_555 C NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? 
metalc ? metalc7 A OD1 ASP 58 A ASP 75 1_555 D NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc8 A O ASP 59 A ASP 76 1_555 D NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? 
metalc ? metalc9 A O SER 61 A SER 78 1_555 D NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? 
metalc ? metalc10 A OE1 GLU 86 A GLU 103 1_555 D NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.162 ? 
metalc ? metalc11 A OE2 GLU 86 A GLU 103 1_555 D NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? 
metalc ? metalc12 A O GLN 87 A GLN 104 1_555 C NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc13 C NA NA . A NA 401 1_555 B OD1 ASP 5 B ASP 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? 
metalc ? metalc14 C NA NA . A NA 401 1_555 B OD2 ASP 5 B ASP 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc15 E NA NA . A NA 403 1_555 L O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc16 E NA NA . A NA 403 1_555 B O PRO 61 B PRO 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc17 E NA NA . A NA 403 1_555 B O ALA 63 B ALA 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? 
metalc ? metalc18 B O PHE 34 B PHE 181 1_555 J NA NA . B NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? 
metalc ? metalc19 B O PRO 55 B PRO 202 1_555 J NA NA . B NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? 
metalc ? metalc20 B O TYR 90 B TYR 237 1_555 F NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? 
metalc ? metalc21 B O TRP 105 B TRP 252 1_555 F NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? 
metalc ? metalc22 B OE1 GLU 118 B GLU 265 1_555 H NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.927 ? 
metalc ? metalc23 B OD1 ASN 121 B ASN 268 1_555 H NA NA . B NA 403 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.548 ? 
metalc ? metalc24 B O GLY 144 B GLY 291 1_555 I NA NA . B NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? 
metalc ? metalc25 B O ALA 180 B ALA 327 1_555 H NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? 
metalc ? metalc26 B OD1 ASP 207 B ASP 354 1_555 I NA NA . B NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? 
metalc ? metalc27 B OG SER 212 B SER 359 1_555 J NA NA . B NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc28 B OG1 THR 213 B THR 360 1_555 G NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc29 B OH TYR 227 B TYR 374 1_555 G NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? 
#
_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                     5DYN 
_atom_sites.fract_transf_matrix[1][1]    0.008044 
_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]    0.02045 
_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]    0.016426 
_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 NA A 1 401 1 NA NA . 
D 3 NA A 1 402 5 NA NA . 
E 3 NA A 1 403 7 NA NA . 
F 3 NA B 1 401 2 NA NA . 
G 3 NA B 1 402 3 NA NA . 
H 3 NA B 1 403 4 NA NA . 
I 3 NA B 1 404 6 NA NA . 
J 3 NA B 1 405 8 NA NA . 
K 4 CL B 1 406 1 CL CL . 
L 5 HOH A 1 501 44 HOH HOH . 
L 5 HOH A 2 502 26 HOH HOH . 
L 5 HOH A 3 503 24 HOH HOH . 
L 5 HOH A 4 504 40 HOH HOH . 
L 5 HOH A 5 505 14 HOH HOH . 
L 5 HOH A 6 506 32 HOH HOH . 
L 5 HOH A 7 507 28 HOH HOH . 
L 5 HOH A 8 508 4 HOH HOH . 
L 5 HOH A 9 509 50 HOH HOH . 
L 5 HOH A 10 510 5 HOH HOH . 
L 5 HOH A 11 511 12 HOH HOH . 
L 5 HOH A 12 512 42 HOH HOH . 
L 5 HOH A 13 513 45 HOH HOH . 
L 5 HOH A 14 514 48 HOH HOH . 
M 5 HOH B 1 501 25 HOH HOH . 
M 5 HOH B 2 502 8 HOH HOH . 
M 5 HOH B 3 503 37 HOH HOH . 
M 5 HOH B 4 504 23 HOH HOH . 
M 5 HOH B 5 505 2 HOH HOH . 
M 5 HOH B 6 506 9 HOH HOH . 
M 5 HOH B 7 507 16 HOH HOH . 
M 5 HOH B 8 508 47 HOH HOH . 
M 5 HOH B 9 509 20 HOH HOH . 
M 5 HOH B 10 510 11 HOH HOH . 
M 5 HOH B 11 511 41 HOH HOH . 
M 5 HOH B 12 512 39 HOH HOH . 
M 5 HOH B 13 513 17 HOH HOH . 
M 5 HOH B 14 514 27 HOH HOH . 
M 5 HOH B 15 515 6 HOH HOH . 
M 5 HOH B 16 516 3 HOH HOH . 
M 5 HOH B 17 517 46 HOH HOH . 
M 5 HOH B 18 518 1 HOH HOH . 
M 5 HOH B 19 519 43 HOH HOH . 
M 5 HOH B 20 520 13 HOH HOH . 
M 5 HOH B 21 521 10 HOH HOH . 
M 5 HOH B 22 522 15 HOH HOH . 
M 5 HOH B 23 523 21 HOH HOH . 
M 5 HOH B 24 524 38 HOH HOH . 
M 5 HOH B 25 525 34 HOH HOH . 
M 5 HOH B 26 526 36 HOH HOH . 
M 5 HOH B 27 527 33 HOH HOH . 
M 5 HOH B 28 528 35 HOH HOH . 
M 5 HOH B 29 529 7 HOH HOH . 
M 5 HOH B 30 530 49 HOH HOH . 
M 5 HOH B 31 531 18 HOH HOH . 
M 5 HOH B 32 532 19 HOH HOH . 
M 5 HOH B 33 533 29 HOH HOH . 
M 5 HOH B 34 534 22 HOH HOH . 
M 5 HOH B 35 535 31 HOH HOH . 
M 5 HOH B 36 536 30 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         I 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               -11.927 
_atom_site.Cartn_y               9.805 
_atom_site.Cartn_z               -17.998 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        36.93 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           404 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#