data_5XIW # _model_server_result.job_id ebeesRxLUzYf2EItT-K43g _model_server_result.datetime_utc '2024-11-16 21:58:24' _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 5xiw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":504}' # _entry.id 5XIW # _exptl.entry_id 5XIW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 399.437 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide _entity.pdbx_number_of_molecules 2 _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 5XIW _cell.length_a 105.491 _cell.length_b 159.148 _cell.length_c 181.702 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XIW _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 ? 11 N N N ? 11 T 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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.85 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.138 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc9 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc10 H MG MG . A MG 502 1_555 U O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc11 H MG MG . A MG 502 1_555 U O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc12 H MG MG . A MG 502 1_555 U O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc13 H MG MG . A MG 502 1_555 V O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc15 B OD2 ASP 177 B ASP 177 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc16 K O2A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc17 L MG MG . B MG 502 1_555 V O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? metalc ? metalc18 L MG MG . B MG 502 1_555 V O HOH . B HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc19 L MG MG . B MG 502 1_555 V O HOH . B HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? metalc ? metalc20 L MG MG . B MG 502 1_555 W O HOH . C HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc21 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? metalc ? metalc22 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc23 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc24 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc25 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc26 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.17 ? metalc ? metalc27 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc28 O O3G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc29 O O2B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc30 P MG MG . C MG 502 1_555 W O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc31 P MG MG . C MG 502 1_555 W O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc32 P MG MG . C MG 502 1_555 W O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc33 P MG MG . C MG 502 1_555 W O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc34 S MG MG . D MG 502 1_555 X O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc35 S MG MG . D MG 502 1_555 X O HOH . D HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? # _chem_comp.formula 'C22 H25 N O6' _chem_comp.formula_weight 399.437 _chem_comp.id LOC _chem_comp.mon_nstd_flag . _chem_comp.name N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms COLCHICINE # 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 O4 C12 LOC doub 302 n n C12 C13 LOC sing 303 n n C12 N1 LOC sing 304 n n N1 C11 LOC sing 305 n n C11 C14 LOC sing 306 n n C11 C10 LOC sing 307 n n C14 C15 LOC doub 308 n n C14 C21 LOC sing 309 n n C15 C16 LOC sing 310 n n C10 C9 LOC sing 311 n n C9 C8 LOC sing 312 n n C8 C7 LOC doub 313 n y C8 C22 LOC sing 314 n y C7 C5 LOC sing 315 n y C5 C3 LOC doub 316 n y C5 O3 LOC sing 317 n n C3 C1 LOC sing 318 n y C3 O2 LOC sing 319 n n C1 O1 LOC sing 320 n n C1 C22 LOC doub 321 n y O1 C2 LOC sing 322 n n O2 C4 LOC sing 323 n n O3 C6 LOC sing 324 n n C22 C21 LOC sing 325 n n C21 C20 LOC doub 326 n n C20 C19 LOC sing 327 n n C19 C17 LOC doub 328 n n C17 C16 LOC sing 329 n n C17 O6 LOC sing 330 n n C16 O5 LOC doub 331 n n O6 C18 LOC sing 332 n n C13 H13 LOC sing 333 n n C13 H13A LOC sing 334 n n C13 H13B LOC sing 335 n n N1 HN1 LOC sing 336 n n C11 H11 LOC sing 337 n n C15 H15 LOC sing 338 n n C10 H10 LOC sing 339 n n C10 H10A LOC sing 340 n n C9 H9 LOC sing 341 n n C9 H9A LOC sing 342 n n C7 H7 LOC sing 343 n n C2 H2 LOC sing 344 n n C2 H2A LOC sing 345 n n C2 H2B LOC sing 346 n n C4 H4 LOC sing 347 n n C4 H4A LOC sing 348 n n C4 H4B LOC sing 349 n n C6 H6 LOC sing 350 n n C6 H6A LOC sing 351 n n C6 H6B LOC sing 352 n n C20 H20 LOC sing 353 n n C19 H19 LOC sing 354 n n C18 H18 LOC sing 355 n n C18 H18A LOC sing 356 n n C18 H18B LOC sing 357 n n # _atom_sites.entry_id 5XIW _atom_sites.fract_transf_matrix[1][1] 0.009479 _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] 0.006283 _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] 0.005504 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GOL A 1 504 601 GOL GOL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 505 MES MES . N 11 LOC B 1 504 1 LOC LOC . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 504 CA CA . R 5 GTP D 1 501 501 GTP GTP . S 6 MG D 1 502 502 MG MG . T 11 LOC D 1 503 2 LOC LOC . U 12 HOH A 1 601 6 HOH HOH . U 12 HOH A 2 602 7 HOH HOH . U 12 HOH A 3 603 12 HOH HOH . U 12 HOH A 4 604 11 HOH HOH . U 12 HOH A 5 605 8 HOH HOH . U 12 HOH A 6 606 9 HOH HOH . U 12 HOH A 7 607 1 HOH HOH . V 12 HOH B 1 601 31 HOH HOH . V 12 HOH B 2 602 24 HOH HOH . V 12 HOH B 3 603 28 HOH HOH . V 12 HOH B 4 604 27 HOH HOH . V 12 HOH B 5 605 32 HOH HOH . V 12 HOH B 6 606 10 HOH HOH . V 12 HOH B 7 607 21 HOH HOH . V 12 HOH B 8 608 29 HOH HOH . V 12 HOH B 9 609 25 HOH HOH . V 12 HOH B 10 610 26 HOH HOH . W 12 HOH C 1 601 13 HOH HOH . W 12 HOH C 2 602 15 HOH HOH . W 12 HOH C 3 603 14 HOH HOH . W 12 HOH C 4 604 16 HOH HOH . W 12 HOH C 5 605 17 HOH HOH . W 12 HOH C 6 606 18 HOH HOH . W 12 HOH C 7 607 22 HOH HOH . W 12 HOH C 8 608 23 HOH HOH . W 12 HOH C 9 609 30 HOH HOH . X 12 HOH D 1 601 20 HOH HOH . X 12 HOH D 2 602 19 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 O4 LOC . . . N 11 -15.573 69.611 -45.845 1 65.56 ? O4 LOC 504 B 1 HETATM 2 C C12 LOC . . . N 11 -16.589 69.979 -46.265 1 63.61 ? C12 LOC 504 B 1 HETATM 3 C C13 LOC . . . N 11 -16.605 70.901 -47.461 1 62.66 ? C13 LOC 504 B 1 HETATM 4 N N1 LOC . . . N 11 -17.884 69.587 -45.659 1 62.75 ? N1 LOC 504 B 1 HETATM 5 C C11 LOC . . . N 11 -17.964 68.746 -44.563 1 61.2 ? C11 LOC 504 B 1 HETATM 6 C C14 LOC . . . N 11 -17.446 67.311 -44.908 1 62.89 ? C14 LOC 504 B 1 HETATM 7 C C15 LOC . . . N 11 -18.011 66.764 -46.173 1 62 ? C15 LOC 504 B 1 HETATM 8 C C10 LOC . . . N 11 -19.391 68.774 -43.986 1 60.77 ? C10 LOC 504 B 1 HETATM 9 C C9 LOC . . . N 11 -19.563 67.858 -42.729 1 60.87 ? C9 LOC 504 B 1 HETATM 10 C C8 LOC . . . N 11 -18.258 67.639 -41.916 1 58.79 ? C8 LOC 504 B 1 HETATM 11 C C7 LOC . . . N 11 -18.21 68.025 -40.487 1 58.42 ? C7 LOC 504 B 1 HETATM 12 C C5 LOC . . . N 11 -17.012 67.847 -39.745 1 57.96 ? C5 LOC 504 B 1 HETATM 13 C C3 LOC . . . N 11 -15.901 67.301 -40.36 1 57.24 ? C3 LOC 504 B 1 HETATM 14 C C1 LOC . . . N 11 -15.921 66.913 -41.769 1 58.25 ? C1 LOC 504 B 1 HETATM 15 O O1 LOC . . . N 11 -14.702 66.352 -42.336 1 60.95 ? O1 LOC 504 B 1 HETATM 16 C C2 LOC . . . N 11 -13.733 67.322 -42.743 1 61.99 ? C2 LOC 504 B 1 HETATM 17 O O2 LOC . . . N 11 -14.703 67.121 -39.589 1 55.2 ? O2 LOC 504 B 1 HETATM 18 C C4 LOC . . . N 11 -14.643 65.843 -38.927 1 55.78 ? C4 LOC 504 B 1 HETATM 19 O O3 LOC . . . N 11 -16.935 68.21 -38.352 1 58.23 ? O3 LOC 504 B 1 HETATM 20 C C6 LOC . . . N 11 -17.748 69.25 -37.952 1 58.83 ? C6 LOC 504 B 1 HETATM 21 C C22 LOC . . . N 11 -17.175 67.088 -42.515 1 58.79 ? C22 LOC 504 B 1 HETATM 22 C C21 LOC . . . N 11 -16.977 66.675 -43.883 1 61.07 ? C21 LOC 504 B 1 HETATM 23 C C20 LOC . . . N 11 -16.972 65.303 -43.729 1 59.93 ? C20 LOC 504 B 1 HETATM 24 C C19 LOC . . . N 11 -16.731 64.347 -44.699 1 62.5 ? C19 LOC 504 B 1 HETATM 25 C C17 LOC . . . N 11 -17.078 64.379 -46.086 1 62.8 ? C17 LOC 504 B 1 HETATM 26 C C16 LOC . . . N 11 -17.76 65.46 -46.815 1 63.33 ? C16 LOC 504 B 1 HETATM 27 O O5 LOC . . . N 11 -18.136 65.285 -47.986 1 65.92 ? O5 LOC 504 B 1 HETATM 28 O O6 LOC . . . N 11 -16.316 63.486 -46.92 1 61.05 ? O6 LOC 504 B 1 HETATM 29 C C18 LOC . . . N 11 -16.919 62.293 -47.191 1 60.61 ? C18 LOC 504 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 29 #