data_5FM0 # _model_server_result.job_id EbY6pGt1nZFZiypWdiXmeA _model_server_result.datetime_utc '2024-11-23 11:39:28' _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 5fm0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1256}' # _entry.id 5FM0 # _exptl.entry_id 5FM0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 489.374 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PIMELOYL-AMP _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 5FM0 _cell.length_a 50.61 _cell.length_b 78.36 _cell.length_c 166.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FM0 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,O,P _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 ? 2 C N N ? 2 J 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 SD MET 17 A MET 16 1_555 G PT PT . A PT 1260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc2 A SD MET 17 A MET 16 1_555 I PT PT . A PT 1262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc3 A OD1 ASP 196 A ASP 195 1_555 F MG MG . A MG 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc4 A OD1 ASP 197 A ASP 196 1_555 F MG MG . A MG 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc5 A SD MET 210 A MET 209 1_555 H PT PT . A PT 1261 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc6 C OAH WAQ . A WAQ 1256 1_555 E MG MG . A MG 1258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc7 C OAD WAQ . A WAQ 1256 1_555 F MG MG . A MG 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc8 D O21 PPV . A PPV 1257 1_555 E MG MG . A MG 1258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc9 D O12 PPV . A PPV 1257 1_555 E MG MG . A MG 1258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc10 D O31 PPV . A PPV 1257 1_555 F MG MG . A MG 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? metalc ? metalc11 D O32 PPV . A PPV 1257 1_555 F MG MG . A MG 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc12 E MG MG . A MG 1258 1_555 O O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc13 E MG MG . A MG 1258 1_555 O O HOH . A HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc14 F MG MG . A MG 1259 1_555 O O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc15 B SD MET 17 B MET 16 1_555 L PT PT . B PT 1259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc16 B SD MET 17 B MET 16 1_555 N PT PT . B PT 1261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc17 B SD MET 210 B MET 209 1_555 M PT PT . B PT 1260 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.655 ? # _chem_comp.formula 'C17 H24 N5 O10 P' _chem_comp.formula_weight 489.374 _chem_comp.id WAQ _chem_comp.mon_nstd_flag . _chem_comp.name PIMELOYL-AMP _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 N1 C6 WAQ doub 388 n y N1 C2 WAQ sing 389 n y C2 N3 WAQ doub 390 n y C2 H2 WAQ sing 391 n n N3 C4 WAQ sing 392 n y C5 C4 WAQ doub 393 n y C4 N9 WAQ sing 394 n y C6 C5 WAQ sing 395 n y C5 N7 WAQ sing 396 n y N6 C6 WAQ sing 397 n n N6 HN6 WAQ sing 398 n n N6 HN6A WAQ sing 399 n n N7 C8 WAQ doub 400 n y C8 N9 WAQ sing 401 n y C8 H8 WAQ sing 402 n n N9 C1' WAQ sing 403 n n C2' C1' WAQ sing 404 n n C1' O4' WAQ sing 405 n n C1' H1' WAQ sing 406 n n C2' O2' WAQ sing 407 n n C2' C3' WAQ sing 408 n n C2' H2' WAQ sing 409 n n O2' HO2' WAQ sing 410 n n C3' O3' WAQ sing 411 n n C3' C4' WAQ sing 412 n n C3' H3' WAQ sing 413 n n O3' HO3' WAQ sing 414 n n O4' C4' WAQ sing 415 n n C4' C5' WAQ sing 416 n n C4' H4' WAQ sing 417 n n O5' C5' WAQ sing 418 n n C5' H5' WAQ sing 419 n n C5' "H5'A" WAQ sing 420 n n O5' PBG WAQ sing 421 n n CAW OAB WAQ sing 422 n n OAB HOAB WAQ sing 423 n n OAC CAX WAQ doub 424 n n OAD PBG WAQ doub 425 n n OAE CAW WAQ doub 426 n n PBG OAH WAQ sing 427 n n OAH HOAH WAQ sing 428 n n CAM CAK WAQ sing 429 n n CAK CAL WAQ sing 430 n n CAK HAK WAQ sing 431 n n CAK HAKA WAQ sing 432 n n CAN CAL WAQ sing 433 n n CAL HAL WAQ sing 434 n n CAL HALA WAQ sing 435 n n CAO CAM WAQ sing 436 n n CAM HAM WAQ sing 437 n n CAM HAMA WAQ sing 438 n n CAN CAW WAQ sing 439 n n CAN HAN WAQ sing 440 n n CAN HANA WAQ sing 441 n n CAX CAO WAQ sing 442 n n CAO HAO WAQ sing 443 n n CAO HAOA WAQ sing 444 n n PBG OAU WAQ sing 445 n n OAU CAX WAQ sing 446 n n # _atom_sites.entry_id 5FM0 _atom_sites.fract_transf_matrix[1][1] 0.019759 _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] 0.012762 _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] 0.005999 _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 WAQ A 1 1256 1256 WAQ WAQ . D 3 PPV A 1 1257 1257 PPV PPV . E 4 MG A 1 1258 1258 MG MG . F 4 MG A 1 1259 1259 MG MG . G 5 PT A 1 1260 1260 PT PT . H 5 PT A 1 1261 1261 PT PT . I 5 PT A 1 1262 1262 PT PT . J 2 WAQ B 1 1257 1257 WAQ WAQ . K 3 PPV B 1 1258 1258 PPV PPV . L 5 PT B 1 1259 1259 PT PT . M 5 PT B 1 1260 1260 PT PT . N 5 PT B 1 1261 1261 PT PT . O 6 HOH A 1 2001 2001 HOH HOH . O 6 HOH A 2 2002 2002 HOH HOH . O 6 HOH A 3 2003 2003 HOH HOH . O 6 HOH A 4 2004 2004 HOH HOH . O 6 HOH A 5 2005 2005 HOH HOH . O 6 HOH A 6 2006 2006 HOH HOH . O 6 HOH A 7 2007 2007 HOH HOH . O 6 HOH A 8 2008 2008 HOH HOH . O 6 HOH A 9 2009 2009 HOH HOH . O 6 HOH A 10 2010 2010 HOH HOH . P 6 HOH B 1 2001 2001 HOH HOH . P 6 HOH B 2 2002 2002 HOH HOH . P 6 HOH B 3 2003 2003 HOH HOH . P 6 HOH B 4 2004 2004 HOH HOH . P 6 HOH B 5 2005 2005 HOH HOH . P 6 HOH B 6 2006 2006 HOH HOH . P 6 HOH B 7 2007 2007 HOH HOH . P 6 HOH B 8 2008 2008 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 N N1 WAQ . . . C 2 10.858 -26.702 -23.033 1 42.36 ? N1 WAQ 1256 A 1 HETATM 2 C C2 WAQ . . . C 2 11.664 -26.424 -24.139 1 47.83 ? C2 WAQ 1256 A 1 HETATM 3 N N3 WAQ . . . C 2 11.782 -27.363 -25.144 1 45.45 ? N3 WAQ 1256 A 1 HETATM 4 C C4 WAQ . . . C 2 11.111 -28.527 -25.046 1 49.68 ? C4 WAQ 1256 A 1 HETATM 5 C C5 WAQ . . . C 2 10.328 -28.776 -23.992 1 45.94 ? C5 WAQ 1256 A 1 HETATM 6 C C6 WAQ . . . C 2 10.214 -27.868 -23.002 1 40.81 ? C6 WAQ 1256 A 1 HETATM 7 N N6 WAQ . . . C 2 9.42 -28.159 -21.977 1 32.95 ? N6 WAQ 1256 A 1 HETATM 8 N N7 WAQ . . . C 2 9.792 -29.992 -24.169 1 49.17 ? N7 WAQ 1256 A 1 HETATM 9 C C8 WAQ . . . C 2 10.246 -30.47 -25.322 1 51.09 ? C8 WAQ 1256 A 1 HETATM 10 N N9 WAQ . . . C 2 11.064 -29.576 -25.868 1 44.3 ? N9 WAQ 1256 A 1 HETATM 11 C C1' WAQ . . . C 2 11.822 -29.661 -27.142 1 40.21 ? C1' WAQ 1256 A 1 HETATM 12 C C2' WAQ . . . C 2 12.965 -30.69 -27.011 1 42.92 ? C2' WAQ 1256 A 1 HETATM 13 O O2' WAQ . . . C 2 14.114 -30.371 -27.803 1 37.19 ? O2' WAQ 1256 A 1 HETATM 14 C C3' WAQ . . . C 2 12.343 -31.922 -27.614 1 48.87 ? C3' WAQ 1256 A 1 HETATM 15 O O3' WAQ . . . C 2 13.34 -32.85 -28.113 1 47.12 ? O3' WAQ 1256 A 1 HETATM 16 C C4' WAQ . . . C 2 11.502 -31.358 -28.766 1 44.82 ? C4' WAQ 1256 A 1 HETATM 17 O O4' WAQ . . . C 2 10.938 -30.131 -28.211 1 45.78 ? O4' WAQ 1256 A 1 HETATM 18 C C5' WAQ . . . C 2 10.5 -32.448 -29.008 1 40.98 ? C5' WAQ 1256 A 1 HETATM 19 O O5' WAQ . . . C 2 9.567 -32.294 -28.036 1 41.87 ? O5' WAQ 1256 A 1 HETATM 20 O OAB WAQ . . . C 2 -0.344 -30.622 -32.285 1 65.14 ? OAB WAQ 1256 A 1 HETATM 21 O OAC WAQ . . . C 2 5.648 -34.213 -29.279 1 57.71 ? OAC WAQ 1256 A 1 HETATM 22 O OAD WAQ . . . C 2 8.855 -34.685 -28.784 1 51.82 ? OAD WAQ 1256 A 1 HETATM 23 O OAE WAQ . . . C 2 -0.289 -32.804 -32.718 1 58.1 ? OAE WAQ 1256 A 1 HETATM 24 O OAH WAQ . . . C 2 7.875 -33.731 -26.558 1 44.12 ? OAH WAQ 1256 A 1 HETATM 25 C CAK WAQ . . . C 2 3.897 -31.506 -32.09 1 56.77 ? CAK WAQ 1256 A 1 HETATM 26 C CAL WAQ . . . C 2 2.443 -30.926 -32.149 1 52.79 ? CAL WAQ 1256 A 1 HETATM 27 C CAM WAQ . . . C 2 4.219 -32.21 -30.771 1 45.45 ? CAM WAQ 1256 A 1 HETATM 28 C CAN WAQ . . . C 2 1.483 -31.872 -31.454 1 51.41 ? CAN WAQ 1256 A 1 HETATM 29 C CAO WAQ . . . C 2 5.705 -32.052 -30.473 1 56.13 ? CAO WAQ 1256 A 1 HETATM 30 O OAU WAQ . . . C 2 7.208 -32.609 -28.68 1 66.33 ? OAU WAQ 1256 A 1 HETATM 31 C CAW WAQ . . . C 2 0.184 -31.756 -32.216 1 56.05 ? CAW WAQ 1256 A 1 HETATM 32 C CAX WAQ . . . C 2 6.18 -33.094 -29.424 1 61.34 ? CAX WAQ 1256 A 1 HETATM 33 P PBG WAQ . . . C 2 8.417 -33.452 -27.882 1 45.47 ? PBG WAQ 1256 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 33 #