data_3P9Z # _model_server_result.job_id 7vZDqwfYUb2GMh4sh_LFgA _model_server_result.datetime_utc '2025-02-05 06:09:45' _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 3p9z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3P9Z # _exptl.entry_id 3P9Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 102.046 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MALONATE 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 3P9Z _cell.length_a 55.407 _cell.length_b 57.676 _cell.length_c 74.624 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3P9Z _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 _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 covale ? covale1 A C MSE 4 A MSE 1 1_555 A N ARG 5 A ARG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C LYS 63 A LYS 60 1_555 A N MSE 64 A MSE 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale3 A C MSE 64 A MSE 61 1_555 A N LEU 65 A LEU 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale4 A C PHE 90 A PHE 87 1_555 A N MSE 91 A MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C MSE 91 A MSE 88 1_555 A N GLY 92 A GLY 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? # _chem_comp.formula 'C3 H2 O4 -2' _chem_comp.formula_weight 102.046 _chem_comp.id MLI _chem_comp.mon_nstd_flag . _chem_comp.name 'MALONATE ION' _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 C1 C2 MLI sing 218 n n C1 C3 MLI sing 219 n n C1 H11 MLI sing 220 n n C1 H12 MLI sing 221 n n C2 O6 MLI doub 222 n n C2 O7 MLI sing 223 n n C3 O8 MLI doub 224 n n C3 O9 MLI sing 225 n n # _atom_sites.entry_id 3P9Z _atom_sites.fract_transf_matrix[1][1] 0.018048 _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] 0.017338 _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] 0.013401 _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 MLI A 1 301 301 MLI MLI . C 3 HOH A 1 227 227 HOH HOH . C 3 HOH A 2 228 228 HOH HOH . C 3 HOH A 3 229 229 HOH HOH . C 3 HOH A 4 230 230 HOH HOH . C 3 HOH A 5 231 231 HOH HOH . C 3 HOH A 6 232 232 HOH HOH . C 3 HOH A 7 233 233 HOH HOH . C 3 HOH A 8 234 234 HOH HOH . C 3 HOH A 9 235 235 HOH HOH . C 3 HOH A 10 236 236 HOH HOH . C 3 HOH A 11 237 237 HOH HOH . C 3 HOH A 12 238 238 HOH HOH . C 3 HOH A 13 239 239 HOH HOH . C 3 HOH A 14 240 240 HOH HOH . C 3 HOH A 15 241 241 HOH HOH . C 3 HOH A 16 242 242 HOH HOH . C 3 HOH A 17 243 243 HOH HOH . C 3 HOH A 18 244 244 HOH HOH . C 3 HOH A 19 245 245 HOH HOH . C 3 HOH A 20 246 246 HOH HOH . C 3 HOH A 21 247 247 HOH HOH . C 3 HOH A 22 248 248 HOH HOH . C 3 HOH A 23 249 249 HOH HOH . C 3 HOH A 24 250 250 HOH HOH . C 3 HOH A 25 251 251 HOH HOH . C 3 HOH A 26 252 252 HOH HOH . C 3 HOH A 27 253 253 HOH HOH . C 3 HOH A 28 254 254 HOH HOH . C 3 HOH A 29 255 255 HOH HOH . C 3 HOH A 30 256 256 HOH HOH . C 3 HOH A 31 257 257 HOH HOH . C 3 HOH A 32 258 258 HOH HOH . C 3 HOH A 33 259 259 HOH HOH . C 3 HOH A 34 260 260 HOH HOH . C 3 HOH A 35 261 261 HOH HOH . C 3 HOH A 36 262 262 HOH HOH . C 3 HOH A 37 263 263 HOH HOH . C 3 HOH A 38 264 264 HOH HOH . C 3 HOH A 39 265 265 HOH HOH . C 3 HOH A 40 266 266 HOH HOH . C 3 HOH A 41 267 267 HOH HOH . C 3 HOH A 42 268 268 HOH HOH . C 3 HOH A 43 269 269 HOH HOH . C 3 HOH A 44 270 270 HOH HOH . C 3 HOH A 45 271 271 HOH HOH . C 3 HOH A 46 272 272 HOH HOH . C 3 HOH A 47 273 273 HOH HOH . C 3 HOH A 48 274 274 HOH HOH . C 3 HOH A 49 275 275 HOH HOH . C 3 HOH A 50 276 276 HOH HOH . C 3 HOH A 51 277 277 HOH HOH . C 3 HOH A 52 278 278 HOH HOH . C 3 HOH A 53 279 279 HOH HOH . C 3 HOH A 54 280 280 HOH HOH . C 3 HOH A 55 281 281 HOH HOH . C 3 HOH A 56 282 282 HOH HOH . C 3 HOH A 57 283 283 HOH HOH . C 3 HOH A 58 284 284 HOH HOH . C 3 HOH A 59 285 285 HOH HOH . C 3 HOH A 60 286 286 HOH HOH . C 3 HOH A 61 287 287 HOH HOH . C 3 HOH A 62 288 288 HOH HOH . C 3 HOH A 63 289 289 HOH HOH . C 3 HOH A 64 290 290 HOH HOH . C 3 HOH A 65 291 291 HOH HOH . C 3 HOH A 66 292 292 HOH HOH . C 3 HOH A 67 293 293 HOH HOH . C 3 HOH A 68 294 294 HOH HOH . C 3 HOH A 69 295 295 HOH HOH . C 3 HOH A 70 296 296 HOH HOH . C 3 HOH A 71 297 297 HOH HOH . C 3 HOH A 72 298 298 HOH HOH . C 3 HOH A 73 299 299 HOH HOH . C 3 HOH A 74 300 300 HOH HOH . C 3 HOH A 75 302 302 HOH HOH . C 3 HOH A 76 303 303 HOH HOH . C 3 HOH A 77 304 304 HOH HOH . C 3 HOH A 78 305 305 HOH HOH . C 3 HOH A 79 306 306 HOH HOH . C 3 HOH A 80 307 307 HOH HOH . C 3 HOH A 81 308 308 HOH HOH . C 3 HOH A 82 309 309 HOH HOH . C 3 HOH A 83 310 310 HOH HOH . C 3 HOH A 84 311 311 HOH HOH . C 3 HOH A 85 312 312 HOH HOH . C 3 HOH A 86 313 313 HOH HOH . C 3 HOH A 87 314 314 HOH HOH . C 3 HOH A 88 315 315 HOH HOH . C 3 HOH A 89 316 316 HOH HOH . C 3 HOH A 90 317 317 HOH HOH . C 3 HOH A 91 318 318 HOH HOH . C 3 HOH A 92 319 319 HOH HOH . C 3 HOH A 93 320 320 HOH HOH . C 3 HOH A 94 321 321 HOH HOH . C 3 HOH A 95 322 322 HOH HOH . C 3 HOH A 96 323 323 HOH HOH . C 3 HOH A 97 324 324 HOH HOH . C 3 HOH A 98 325 325 HOH HOH . C 3 HOH A 99 326 326 HOH HOH . C 3 HOH A 100 327 327 HOH HOH . C 3 HOH A 101 328 328 HOH HOH . C 3 HOH A 102 329 329 HOH HOH . C 3 HOH A 103 330 330 HOH HOH . C 3 HOH A 104 331 331 HOH HOH . C 3 HOH A 105 332 332 HOH HOH . C 3 HOH A 106 333 333 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 C C1 MLI . . . B 2 7.734 4.523 19.875 1 40.81 ? C1 MLI 301 A 1 HETATM 2 C C2 MLI . . . B 2 7.096 3.245 19.366 1 40.94 ? C2 MLI 301 A 1 HETATM 3 C C3 MLI . . . B 2 9.134 4.665 19.311 1 43.51 ? C3 MLI 301 A 1 HETATM 4 O O6 MLI . . . B 2 6.121 3.329 18.584 1 38.79 ? O6 MLI 301 A 1 HETATM 5 O O7 MLI . . . B 2 7.561 2.144 19.748 1 40.32 ? O7 MLI 301 A 1 HETATM 6 O O8 MLI . . . B 2 9.999 5.243 20.001 1 44.17 ? O8 MLI 301 A 1 HETATM 7 O O9 MLI . . . B 2 9.393 4.213 18.177 1 43.28 ? O9 MLI 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 7 #