data_1PY0
#
_model_server_result.job_id            5H526T7W-1e0Ds4ZPfGH-Q 
_model_server_result.datetime_utc      '2025-04-03 14:50:32' 
_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          1py0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":195}' 
#
_entry.id    1PY0 
#
_exptl.entry_id    1PY0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              511.613 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            7,10,13-TRI(CARBOXYMETHYL)-5,15-DIOXO-4,7,10,13,16-PENTAAZA-1,19-DITHIANONADECANE 
_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         120 
_cell.entry_id            1PY0 
_cell.length_a            42.7 
_cell.length_b            42.7 
_cell.length_c            116.9 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1PY0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 A SG CYS 53 A CYS 51 1_555 E S1 YMA . A YMA 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale2 A SG CYS 56 A CYS 54 1_555 E S2 YMA . A YMA 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? 
metalc ? metalc1 A ND1 HIS 42 A HIS 40 1_555 B ZN ZN . A ZN 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc2 A SG CYS 80 A CYS 78 1_555 B ZN ZN . A ZN 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc3 A ND1 HIS 83 A HIS 81 1_555 B ZN ZN . A ZN 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc4 A SD MET 88 A MET 86 1_555 B ZN ZN . A ZN 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? 
#
_chem_comp.formula           'C18 H33 N5 O8 S2' 
_chem_comp.formula_weight    511.613 
_chem_comp.id                YMA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              7,10,13-TRI(CARBOXYMETHYL)-5,15-DIOXO-4,7,10,13,16-PENTAAZA-1,19-DITHIANONADECANE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
O8 C2 YMA doub 352 n n 
C2 O7 YMA sing 353 n n 
C2 C1 YMA sing 354 n n 
O7 HO7 YMA sing 355 n n 
C1 N1 YMA sing 356 n n 
C1 H11 YMA sing 357 n n 
C1 H12 YMA sing 358 n n 
N1 C10 YMA sing 359 n n 
N1 C3 YMA sing 360 n n 
C10 C11 YMA sing 361 n n 
C10 H101 YMA sing 362 n n 
C10 H102 YMA sing 363 n n 
C11 N3 YMA sing 364 n n 
C11 H111 YMA sing 365 n n 
C11 H112 YMA sing 366 n n 
N3 C14 YMA sing 367 n n 
N3 C12 YMA sing 368 n n 
C14 C15 YMA sing 369 n n 
C14 H141 YMA sing 370 n n 
C14 H142 YMA sing 371 n n 
C15 N5 YMA sing 372 n n 
C15 O6 YMA doub 373 n n 
N5 C16 YMA sing 374 n n 
N5 HN5 YMA sing 375 n n 
C16 C18 YMA sing 376 n n 
C16 H161 YMA sing 377 n n 
C16 H162 YMA sing 378 n n 
C18 S2 YMA sing 379 n n 
C18 H181 YMA sing 380 n n 
C18 H182 YMA sing 381 n n 
S2 HS2 YMA sing 382 n n 
C12 C13 YMA sing 383 n n 
C12 H121 YMA sing 384 n n 
C12 H122 YMA sing 385 n n 
C13 O4 YMA sing 386 n n 
C13 O3 YMA doub 387 n n 
O4 HO4 YMA sing 388 n n 
C3 C4 YMA sing 389 n n 
C3 H31 YMA sing 390 n n 
C3 H32 YMA sing 391 n n 
C4 N2 YMA sing 392 n n 
C4 H41 YMA sing 393 n n 
C4 H42 YMA sing 394 n n 
N2 C5 YMA sing 395 n n 
N2 C7 YMA sing 396 n n 
C5 C6 YMA sing 397 n n 
C5 H51 YMA sing 398 n n 
C5 H52 YMA sing 399 n n 
C6 O2 YMA doub 400 n n 
C6 O1 YMA sing 401 n n 
O1 HO1 YMA sing 402 n n 
C7 C8 YMA sing 403 n n 
C7 H71 YMA sing 404 n n 
C7 H72 YMA sing 405 n n 
C8 O5 YMA doub 406 n n 
C8 N4 YMA sing 407 n n 
N4 C9 YMA sing 408 n n 
N4 HN4 YMA sing 409 n n 
C9 C17 YMA sing 410 n n 
C9 H91 YMA sing 411 n n 
C9 H92 YMA sing 412 n n 
C17 S1 YMA sing 413 n n 
C17 H171 YMA sing 414 n n 
C17 H172 YMA sing 415 n n 
S1 HS1 YMA sing 416 n n 
#
_atom_sites.entry_id                     1PY0 
_atom_sites.fract_transf_matrix[1][1]    0.023419 
_atom_sites.fract_transf_matrix[1][2]    0.013521 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.027042 
_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]    0.008554 
_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 ZN A 1 124 121 ZN ZN . 
C 3 Y1 A 1 125 122 Y1 Y . 
D 4 SO4 A 1 126 123 SO4 SO4 . 
E 5 YMA A 1 195 195 YMA YMA . 
F 6 HOH A 1 196 124 HOH HOH . 
F 6 HOH A 2 197 125 HOH HOH . 
F 6 HOH A 3 198 126 HOH HOH . 
F 6 HOH A 4 199 127 HOH HOH . 
F 6 HOH A 5 200 128 HOH HOH . 
F 6 HOH A 6 201 129 HOH HOH . 
F 6 HOH A 7 202 130 HOH HOH . 
F 6 HOH A 8 203 131 HOH HOH . 
F 6 HOH A 9 204 132 HOH HOH . 
F 6 HOH A 10 205 133 HOH HOH . 
F 6 HOH A 11 206 134 HOH HOH . 
F 6 HOH A 12 207 135 HOH HOH . 
F 6 HOH A 13 208 136 HOH HOH . 
F 6 HOH A 14 209 137 HOH HOH . 
F 6 HOH A 15 210 138 HOH HOH . 
F 6 HOH A 16 211 139 HOH HOH . 
F 6 HOH A 17 212 140 HOH HOH . 
F 6 HOH A 18 213 141 HOH HOH . 
F 6 HOH A 19 214 142 HOH HOH . 
F 6 HOH A 20 215 143 HOH HOH . 
F 6 HOH A 21 216 144 HOH HOH . 
F 6 HOH A 22 217 145 HOH HOH . 
F 6 HOH A 23 218 146 HOH HOH . 
F 6 HOH A 24 219 147 HOH HOH . 
F 6 HOH A 25 220 148 HOH HOH . 
F 6 HOH A 26 221 149 HOH HOH . 
F 6 HOH A 27 222 150 HOH HOH . 
F 6 HOH A 28 223 151 HOH HOH . 
F 6 HOH A 29 224 152 HOH HOH . 
F 6 HOH A 30 225 153 HOH HOH . 
F 6 HOH A 31 226 154 HOH HOH . 
F 6 HOH A 32 227 155 HOH HOH . 
F 6 HOH A 33 228 156 HOH HOH . 
F 6 HOH A 34 229 157 HOH HOH . 
F 6 HOH A 35 230 158 HOH HOH . 
F 6 HOH A 36 231 159 HOH HOH . 
F 6 HOH A 37 232 160 HOH HOH . 
F 6 HOH A 38 233 161 HOH HOH . 
F 6 HOH A 39 234 162 HOH HOH . 
F 6 HOH A 40 235 163 HOH HOH . 
F 6 HOH A 41 236 164 HOH HOH . 
F 6 HOH A 42 237 165 HOH HOH . 
F 6 HOH A 43 238 166 HOH HOH . 
F 6 HOH A 44 239 167 HOH HOH . 
F 6 HOH A 45 240 168 HOH HOH . 
F 6 HOH A 46 241 169 HOH HOH . 
F 6 HOH A 47 242 170 HOH HOH . 
F 6 HOH A 48 243 171 HOH HOH . 
F 6 HOH A 49 244 172 HOH HOH . 
F 6 HOH A 50 245 173 HOH HOH . 
F 6 HOH A 51 246 174 HOH HOH . 
F 6 HOH A 52 247 175 HOH HOH . 
F 6 HOH A 53 248 176 HOH HOH . 
F 6 HOH A 54 249 177 HOH HOH . 
F 6 HOH A 55 250 178 HOH HOH . 
F 6 HOH A 56 251 179 HOH HOH . 
F 6 HOH A 57 252 180 HOH HOH . 
F 6 HOH A 58 253 181 HOH HOH . 
F 6 HOH A 59 254 182 HOH HOH . 
F 6 HOH A 60 255 183 HOH HOH . 
F 6 HOH A 61 256 184 HOH HOH . 
F 6 HOH A 62 257 185 HOH HOH . 
F 6 HOH A 63 258 186 HOH HOH . 
F 6 HOH A 64 259 187 HOH HOH . 
F 6 HOH A 65 260 188 HOH HOH . 
F 6 HOH A 66 261 189 HOH HOH . 
F 6 HOH A 67 262 190 HOH HOH . 
F 6 HOH A 68 263 191 HOH HOH . 
F 6 HOH A 69 264 192 HOH HOH . 
F 6 HOH A 70 265 193 HOH HOH . 
F 6 HOH A 71 266 194 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 O O8 YMA . . . E 5 3.6 14.705 2.42 0.7 73.88 ? O8 YMA 195 A 1 
HETATM 2 C C2 YMA . . . E 5 3.227 13.51 3.027 0.7 74.32 ? C2 YMA 195 A 1 
HETATM 3 O O7 YMA . . . E 5 2.234 13.477 3.939 0.7 73.85 ? O7 YMA 195 A 1 
HETATM 4 C C1 YMA . . . E 5 3.918 12.189 2.679 0.7 74.62 ? C1 YMA 195 A 1 
HETATM 5 N N1 YMA . . . E 5 3.202 11.428 1.673 0.7 74.11 ? N1 YMA 195 A 1 
HETATM 6 C C10 YMA . . . E 5 3.53 11.539 0.229 0.7 72.79 ? C10 YMA 195 A 1 
HETATM 7 C C11 YMA . . . E 5 3.555 13.005 -0.271 0.7 70.69 ? C11 YMA 195 A 1 
HETATM 8 N N3 YMA . . . E 5 2.708 13.294 -1.453 0.7 69.14 ? N3 YMA 195 A 1 
HETATM 9 C C14 YMA . . . E 5 2.108 14.661 -1.586 0.7 65.7 ? C14 YMA 195 A 1 
HETATM 10 C C15 YMA . . . E 5 0.897 14.763 -2.131 0.7 61.54 ? C15 YMA 195 A 1 
HETATM 11 N N5 YMA . . . E 5 0.766 16.12 -2.221 0.7 56.08 ? N5 YMA 195 A 1 
HETATM 12 C C16 YMA . . . E 5 1.488 17.3 -1.521 0.7 48.22 ? C16 YMA 195 A 1 
HETATM 13 C C18 YMA . . . E 5 2.802 18.188 -1.061 0.7 42.13 ? C18 YMA 195 A 1 
HETATM 14 S S2 YMA . . . E 5 3.844 18.47 -2.524 0.7 32.41 ? S2 YMA 195 A 1 
HETATM 15 O O6 YMA . . . E 5 0.041 13.974 -2.369 0.7 62.62 ? O6 YMA 195 A 1 
HETATM 16 C C12 YMA . . . E 5 2.535 12.286 -2.527 0.7 70.51 ? C12 YMA 195 A 1 
HETATM 17 C C13 YMA . . . E 5 1.614 11.176 -2.153 0.7 71.95 ? C13 YMA 195 A 1 
HETATM 18 O O4 YMA . . . E 5 2.021 9.853 -2.244 0.7 73.38 ? O4 YMA 195 A 1 
HETATM 19 O O3 YMA . . . E 5 0.387 11.478 -1.713 0.7 72.31 ? O3 YMA 195 A 1 
HETATM 20 C C3 YMA . . . E 5 2.153 10.5 2.157 0.7 74.74 ? C3 YMA 195 A 1 
HETATM 21 C C4 YMA . . . E 5 1.005 10.281 1.142 0.7 75.01 ? C4 YMA 195 A 1 
HETATM 22 N N2 YMA . . . E 5 -0.197 10.323 1.661 0.7 74.4 ? N2 YMA 195 A 1 
HETATM 23 C C5 YMA . . . E 5 -0.518 10.508 3.194 0.7 75.29 ? C5 YMA 195 A 1 
HETATM 24 C C6 YMA . . . E 5 -1.287 11.733 3.561 0.7 75.85 ? C6 YMA 195 A 1 
HETATM 25 O O2 YMA . . . E 5 -2.633 11.635 3.88 0.7 76.28 ? O2 YMA 195 A 1 
HETATM 26 O O1 YMA . . . E 5 -0.663 12.923 3.562 0.7 75.85 ? O1 YMA 195 A 1 
HETATM 27 C C7 YMA . . . E 5 -1.471 10.088 0.824 0.7 72.86 ? C7 YMA 195 A 1 
HETATM 28 C C8 YMA . . . E 5 -2.175 11.565 0.577 0.7 71.43 ? C8 YMA 195 A 1 
HETATM 29 O O5 YMA . . . E 5 -1.335 12.677 -0.201 0.7 71.19 ? O5 YMA 195 A 1 
HETATM 30 N N4 YMA . . . E 5 -3.029 12.414 1.113 0.7 69.18 ? N4 YMA 195 A 1 
HETATM 31 C C9 YMA . . . E 5 -3.06 13.96 1.288 0.7 65.75 ? C9 YMA 195 A 1 
HETATM 32 C C17 YMA . . . E 5 -2.973 15.136 2.352 0.7 63.05 ? C17 YMA 195 A 1 
HETATM 33 S S1 YMA . . . E 5 -4.181 15.586 3.655 0.7 57.12 ? S1 YMA 195 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           33 
#