data_5JDN
#
_model_server_result.job_id            -y2sX5lc2buOwBT6QJxDow 
_model_server_result.datetime_utc      '2024-11-15 03:39:40' 
_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          5jdn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    5JDN 
#
_exptl.entry_id    5JDN 
_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    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            5JDN 
_cell.length_a            49.67 
_cell.length_b            72.463 
_cell.length_c            96.428 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5JDN 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,N 
_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                      2 
_struct_asym.id                             B 
_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
metalc ? metalc1 A O ALA 47 A ALA 47 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? 
metalc ? metalc2 A OG1 THR 50 A THR 50 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? 
metalc ? metalc3 A O THR 50 A THR 50 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
metalc ? metalc4 A OG SER 51 A SER 51 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc5 A OE1 GLU 54 A GLU 54 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? 
metalc ? metalc6 A OE2 GLU 54 A GLU 54 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc7 A O ILE 118 A ILE 118 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc8 A OD1 ASP 121 A ASP 121 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? 
metalc ? metalc9 A O GLY 122 A GLY 122 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? 
metalc ? metalc10 A OD2 ASP 127 A ASP 127 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? 
metalc ? metalc11 A O THR 209 A THR 209 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? 
metalc ? metalc12 A OE2 GLU 213 A GLU 213 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc13 A OE1 GLU 213 A GLU 213 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc14 A OE2 GLU 213 A GLU 213 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? 
metalc ? metalc15 A OG SER 236 A SER 236 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? 
metalc ? metalc16 C SR SR . A SR 402 1_555 N O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? 
metalc ? metalc17 D SR SR . A SR 403 1_555 E O23 OLC . A OLC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? 
metalc ? metalc18 D SR SR . A SR 403 1_555 E O25 OLC . A OLC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? 
#
_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                     5JDN 
_atom_sites.fract_transf_matrix[1][1]    0.020133 
_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]    0.0138 
_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]    0.01037 
_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
B 2 NA A 1 401 1 NA NA . 
C 3 SR A 1 402 1 SR SR . 
D 3 SR A 1 403 2 SR SR . 
E 4 OLC A 1 404 1 OLC MON . 
F 4 OLC A 1 405 2 OLC MON . 
G 5 MYS A 1 406 1 MYS FAT . 
H 5 MYS A 1 407 2 MYS FAT . 
I 5 MYS A 1 408 3 MYS FAT . 
J 5 MYS A 1 409 4 MYS FAT . 
K 5 MYS A 1 410 5 MYS FAT . 
L 6 1PE A 1 411 1 1PE PEG . 
M 6 1PE A 1 412 2 1PE PEG . 
N 7 HOH A 1 501 8 HOH HOH . 
N 7 HOH A 2 502 12 HOH HOH . 
N 7 HOH A 3 503 9 HOH HOH . 
N 7 HOH A 4 504 25 HOH HOH . 
N 7 HOH A 5 505 13 HOH HOH . 
N 7 HOH A 6 506 1 HOH HOH . 
N 7 HOH A 7 507 7 HOH HOH . 
N 7 HOH A 8 508 4 HOH HOH . 
N 7 HOH A 9 509 2 HOH HOH . 
N 7 HOH A 10 510 26 HOH HOH . 
N 7 HOH A 11 511 11 HOH HOH . 
N 7 HOH A 12 512 27 HOH HOH . 
N 7 HOH A 13 513 5 HOH HOH . 
N 7 HOH A 14 514 15 HOH HOH . 
N 7 HOH A 15 515 19 HOH HOH . 
N 7 HOH A 16 516 28 HOH HOH . 
N 7 HOH A 17 517 6 HOH HOH . 
N 7 HOH A 18 518 14 HOH HOH . 
N 7 HOH A 19 519 17 HOH HOH . 
N 7 HOH A 20 520 30 HOH HOH . 
N 7 HOH A 21 521 18 HOH HOH . 
N 7 HOH A 22 522 10 HOH HOH . 
N 7 HOH A 23 523 23 HOH HOH . 
N 7 HOH A 24 524 3 HOH HOH . 
N 7 HOH A 25 525 24 HOH HOH . 
N 7 HOH A 26 526 16 HOH HOH . 
N 7 HOH A 27 527 21 HOH HOH . 
N 7 HOH A 28 528 20 HOH HOH . 
N 7 HOH A 29 529 32 HOH HOH . 
N 7 HOH A 30 530 22 HOH HOH . 
N 7 HOH A 31 531 31 HOH HOH . 
N 7 HOH A 32 532 29 HOH HOH . 
N 7 HOH A 33 533 33 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         B 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               6.771 
_atom_site.Cartn_y               18.218 
_atom_site.Cartn_z               20.129 
_atom_site.occupancy             0.71 
_atom_site.B_iso_or_equiv        36.6 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           401 
_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           22 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           1 
#