data_5KAY
#
_model_server_result.job_id            QO73qNQKKOxdBuZwiTExaA 
_model_server_result.datetime_utc      '2025-08-31 18:05:11' 
_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          5kay 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    5KAY 
#
_exptl.entry_id    5KAY 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         87.27 
_cell.angle_beta          83.09 
_cell.angle_gamma         79.46 
_cell.entry_id            5KAY 
_cell.length_a            41.714 
_cell.length_b            41.496 
_cell.length_c            61.506 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KAY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 1 
A,B,C,D,E,F,G,H 3 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 D N N 
? 3 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
disulf ? disulf1 A SG CYS 125 A CYS 135 1_555 A SG CYS 127 A CYS 137 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.134 ? 
disulf ? disulf2 A SG CYS 125 A CYS 135 1_555 A SG CYS 127 A CYS 137 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.143 ? 
disulf ? disulf3 B SG CYS 125 B CYS 135 1_555 B SG CYS 127 B CYS 137 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc1 A OE1 GLN 104 A GLN 114 1_555 F NA NA . B NA 302 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc2 A OE1 GLU 112 A GLU 122 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc3 A NE2 HIS 115 A HIS 125 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? 
metalc ? metalc4 A OE2 GLU 186 A GLU 196 1_555 D NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc5 A OE1 GLU 190 A GLU 200 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc6 C ZN ZN . A ZN 301 1_555 G O HOH . A HOH 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc7 D NA NA . A NA 302 1_555 B OE2 GLU 186 B GLU 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc8 G O HOH . A HOH 445 1_655 F NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc9 B O SER 22 B SER 32 1_555 F NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc10 B OG SER 22 B SER 32 1_555 F NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? 
metalc ? metalc11 B OG1 THR 26 B THR 36 1_555 F NA NA . B NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc12 B OE1 GLU 112 B GLU 122 1_555 E ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc13 B NE2 HIS 115 B HIS 125 1_555 E ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc14 B OE2 GLU 190 B GLU 200 1_555 E ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? 
metalc ? metalc15 E ZN ZN . B ZN 301 1_555 H O HOH . B HOH 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc16 F NA NA . B NA 302 1_555 H O HOH . B HOH 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
#
_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                     5KAY 
_atom_sites.fract_transf_matrix[1][1]    0.023973 
_atom_sites.fract_transf_matrix[1][2]    -0.004462 
_atom_sites.fract_transf_matrix[1][3]    -0.002788 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.024513 
_atom_sites.fract_transf_matrix[2][3]    -0.000643 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.016383 
_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 ZN A 1 301 1 ZN ZN . 
D 3 NA A 1 302 2 NA NA . 
E 2 ZN B 1 301 2 ZN ZN . 
F 3 NA B 1 302 1 NA NA . 
G 4 HOH A 1 401 88 HOH HOH . 
G 4 HOH A 2 402 108 HOH HOH . 
G 4 HOH A 3 403 78 HOH HOH . 
G 4 HOH A 4 404 36 HOH HOH . 
G 4 HOH A 5 405 160 HOH HOH . 
G 4 HOH A 6 406 151 HOH HOH . 
G 4 HOH A 7 407 138 HOH HOH . 
G 4 HOH A 8 408 70 HOH HOH . 
G 4 HOH A 9 409 42 HOH HOH . 
G 4 HOH A 10 410 55 HOH HOH . 
G 4 HOH A 11 411 137 HOH HOH . 
G 4 HOH A 12 412 13 HOH HOH . 
G 4 HOH A 13 413 3 HOH HOH . 
G 4 HOH A 14 414 63 HOH HOH . 
G 4 HOH A 15 415 98 HOH HOH . 
G 4 HOH A 16 416 49 HOH HOH . 
G 4 HOH A 17 417 58 HOH HOH . 
G 4 HOH A 18 418 15 HOH HOH . 
G 4 HOH A 19 419 61 HOH HOH . 
G 4 HOH A 20 420 38 HOH HOH . 
G 4 HOH A 21 421 90 HOH HOH . 
G 4 HOH A 22 422 146 HOH HOH . 
G 4 HOH A 23 423 35 HOH HOH . 
G 4 HOH A 24 424 115 HOH HOH . 
G 4 HOH A 25 425 50 HOH HOH . 
G 4 HOH A 26 426 128 HOH HOH . 
G 4 HOH A 27 427 1 HOH HOH . 
G 4 HOH A 28 428 51 HOH HOH . 
G 4 HOH A 29 429 39 HOH HOH . 
G 4 HOH A 30 430 2 HOH HOH . 
G 4 HOH A 31 431 54 HOH HOH . 
G 4 HOH A 32 432 25 HOH HOH . 
G 4 HOH A 33 433 101 HOH HOH . 
G 4 HOH A 34 434 68 HOH HOH . 
G 4 HOH A 35 435 172 HOH HOH . 
G 4 HOH A 36 436 76 HOH HOH . 
G 4 HOH A 37 437 62 HOH HOH . 
G 4 HOH A 38 438 71 HOH HOH . 
G 4 HOH A 39 439 24 HOH HOH . 
G 4 HOH A 40 440 9 HOH HOH . 
G 4 HOH A 41 441 181 HOH HOH . 
G 4 HOH A 42 442 20 HOH HOH . 
G 4 HOH A 43 443 162 HOH HOH . 
G 4 HOH A 44 444 119 HOH HOH . 
G 4 HOH A 45 445 31 HOH HOH . 
G 4 HOH A 46 446 59 HOH HOH . 
G 4 HOH A 47 447 77 HOH HOH . 
G 4 HOH A 48 448 89 HOH HOH . 
G 4 HOH A 49 449 105 HOH HOH . 
G 4 HOH A 50 450 40 HOH HOH . 
G 4 HOH A 51 451 127 HOH HOH . 
G 4 HOH A 52 452 34 HOH HOH . 
G 4 HOH A 53 453 17 HOH HOH . 
G 4 HOH A 54 454 72 HOH HOH . 
G 4 HOH A 55 455 139 HOH HOH . 
G 4 HOH A 56 456 125 HOH HOH . 
G 4 HOH A 57 457 159 HOH HOH . 
G 4 HOH A 58 458 48 HOH HOH . 
G 4 HOH A 59 459 60 HOH HOH . 
G 4 HOH A 60 460 136 HOH HOH . 
G 4 HOH A 61 461 30 HOH HOH . 
G 4 HOH A 62 462 52 HOH HOH . 
G 4 HOH A 63 463 131 HOH HOH . 
G 4 HOH A 64 464 85 HOH HOH . 
G 4 HOH A 65 465 116 HOH HOH . 
G 4 HOH A 66 466 165 HOH HOH . 
G 4 HOH A 67 467 167 HOH HOH . 
G 4 HOH A 68 468 170 HOH HOH . 
G 4 HOH A 69 469 153 HOH HOH . 
G 4 HOH A 70 470 182 HOH HOH . 
G 4 HOH A 71 471 184 HOH HOH . 
G 4 HOH A 72 472 110 HOH HOH . 
G 4 HOH A 73 473 186 HOH HOH . 
G 4 HOH A 74 474 37 HOH HOH . 
G 4 HOH A 75 475 149 HOH HOH . 
G 4 HOH A 76 476 166 HOH HOH . 
G 4 HOH A 77 477 65 HOH HOH . 
G 4 HOH A 78 478 179 HOH HOH . 
H 4 HOH B 1 401 188 HOH HOH . 
H 4 HOH B 2 402 91 HOH HOH . 
H 4 HOH B 3 403 47 HOH HOH . 
H 4 HOH B 4 404 93 HOH HOH . 
H 4 HOH B 5 405 124 HOH HOH . 
H 4 HOH B 6 406 123 HOH HOH . 
H 4 HOH B 7 407 107 HOH HOH . 
H 4 HOH B 8 408 67 HOH HOH . 
H 4 HOH B 9 409 43 HOH HOH . 
H 4 HOH B 10 410 147 HOH HOH . 
H 4 HOH B 11 411 95 HOH HOH . 
H 4 HOH B 12 412 79 HOH HOH . 
H 4 HOH B 13 413 164 HOH HOH . 
H 4 HOH B 14 414 178 HOH HOH . 
H 4 HOH B 15 415 26 HOH HOH . 
H 4 HOH B 16 416 111 HOH HOH . 
H 4 HOH B 17 417 126 HOH HOH . 
H 4 HOH B 18 418 92 HOH HOH . 
H 4 HOH B 19 419 102 HOH HOH . 
H 4 HOH B 20 420 143 HOH HOH . 
H 4 HOH B 21 421 28 HOH HOH . 
H 4 HOH B 22 422 87 HOH HOH . 
H 4 HOH B 23 423 27 HOH HOH . 
H 4 HOH B 24 424 100 HOH HOH . 
H 4 HOH B 25 425 144 HOH HOH . 
H 4 HOH B 26 426 175 HOH HOH . 
H 4 HOH B 27 427 45 HOH HOH . 
H 4 HOH B 28 428 180 HOH HOH . 
H 4 HOH B 29 429 120 HOH HOH . 
H 4 HOH B 30 430 69 HOH HOH . 
H 4 HOH B 31 431 140 HOH HOH . 
H 4 HOH B 32 432 8 HOH HOH . 
H 4 HOH B 33 433 66 HOH HOH . 
H 4 HOH B 34 434 53 HOH HOH . 
H 4 HOH B 35 435 104 HOH HOH . 
H 4 HOH B 36 436 183 HOH HOH . 
H 4 HOH B 37 437 112 HOH HOH . 
H 4 HOH B 38 438 14 HOH HOH . 
H 4 HOH B 39 439 44 HOH HOH . 
H 4 HOH B 40 440 142 HOH HOH . 
H 4 HOH B 41 441 74 HOH HOH . 
H 4 HOH B 42 442 46 HOH HOH . 
H 4 HOH B 43 443 84 HOH HOH . 
H 4 HOH B 44 444 23 HOH HOH . 
H 4 HOH B 45 445 97 HOH HOH . 
H 4 HOH B 46 446 122 HOH HOH . 
H 4 HOH B 47 447 141 HOH HOH . 
H 4 HOH B 48 448 75 HOH HOH . 
H 4 HOH B 49 449 56 HOH HOH . 
H 4 HOH B 50 450 129 HOH HOH . 
H 4 HOH B 51 451 18 HOH HOH . 
H 4 HOH B 52 452 7 HOH HOH . 
H 4 HOH B 53 453 4 HOH HOH . 
H 4 HOH B 54 454 41 HOH HOH . 
H 4 HOH B 55 455 113 HOH HOH . 
H 4 HOH B 56 456 117 HOH HOH . 
H 4 HOH B 57 457 86 HOH HOH . 
H 4 HOH B 58 458 33 HOH HOH . 
H 4 HOH B 59 459 29 HOH HOH . 
H 4 HOH B 60 460 94 HOH HOH . 
H 4 HOH B 61 461 171 HOH HOH . 
H 4 HOH B 62 462 19 HOH HOH . 
H 4 HOH B 63 463 12 HOH HOH . 
H 4 HOH B 64 464 121 HOH HOH . 
H 4 HOH B 65 465 177 HOH HOH . 
H 4 HOH B 66 466 114 HOH HOH . 
H 4 HOH B 67 467 81 HOH HOH . 
H 4 HOH B 68 468 148 HOH HOH . 
H 4 HOH B 69 469 103 HOH HOH . 
H 4 HOH B 70 470 64 HOH HOH . 
H 4 HOH B 71 471 32 HOH HOH . 
H 4 HOH B 72 472 163 HOH HOH . 
H 4 HOH B 73 473 118 HOH HOH . 
H 4 HOH B 74 474 10 HOH HOH . 
H 4 HOH B 75 475 16 HOH HOH . 
H 4 HOH B 76 476 169 HOH HOH . 
H 4 HOH B 77 477 158 HOH HOH . 
H 4 HOH B 78 478 154 HOH HOH . 
H 4 HOH B 79 479 11 HOH HOH . 
H 4 HOH B 80 480 185 HOH HOH . 
H 4 HOH B 81 481 133 HOH HOH . 
H 4 HOH B 82 482 174 HOH HOH . 
H 4 HOH B 83 483 73 HOH HOH . 
H 4 HOH B 84 484 132 HOH HOH . 
H 4 HOH B 85 485 22 HOH HOH . 
H 4 HOH B 86 486 187 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         F 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               37.738 
_atom_site.Cartn_y               -1.833 
_atom_site.Cartn_z               45.165 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        25.75 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           302 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           190 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           506 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#