data_5MQJ # _model_server_result.job_id yLFsK7k0CY2lYu9SDAhy5Q _model_server_result.datetime_utc '2024-11-13 06:24:33' _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 5mqj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5MQJ # _exptl.entry_id 5MQJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 5MQJ _cell.length_a 92.695 _cell.length_b 92.695 _cell.length_c 338.083 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MQJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J 1 1 C,D,K,L,M,N,O,P 2 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 E N N ? 2 H N N ? 2 K N N ? 2 N 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 F OP1 UMP . A UMP 302 1_555 G MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc2 B OE1 GLU 74 B GLU 53 1_555 J MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? metalc ? metalc3 B OE2 GLU 148 B GLU 127 1_555 J MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc4 I OP2 UMP . B UMP 302 1_555 J MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc5 C OE2 GLU 148 C GLU 127 1_555 M MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? metalc ? metalc6 L OP2 UMP . C UMP 302 1_555 M MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc7 N O1B UDP . D UDP 301 1_555 P MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc8 O OP2 UMP . D UMP 302 1_555 P MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 C2 UDP sing 356 n n N1 C6 UDP sing 357 n n N1 C1' UDP sing 358 n n C2 N3 UDP sing 359 n n C2 O2 UDP doub 360 n n N3 C4 UDP sing 361 n n N3 HN3 UDP sing 362 n n C4 C5 UDP sing 363 n n C4 O4 UDP doub 364 n n C5 C6 UDP doub 365 n n C5 H5 UDP sing 366 n n C6 H6 UDP sing 367 n n C1' C2' UDP sing 368 n n C1' O4' UDP sing 369 n n C1' H1' UDP sing 370 n n C2' O2' UDP sing 371 n n C2' C3' UDP sing 372 n n C2' H2' UDP sing 373 n n O2' HO2' UDP sing 374 n n C3' C4' UDP sing 375 n n C3' O3' UDP sing 376 n n C3' H3' UDP sing 377 n n C4' O4' UDP sing 378 n n C4' C5' UDP sing 379 n n C4' H4' UDP sing 380 n n O3' HO3' UDP sing 381 n n C5' O5' UDP sing 382 n n C5' "H5'1" UDP sing 383 n n C5' "H5'2" UDP sing 384 n n O5' PA UDP sing 385 n n PA O1A UDP doub 386 n n PA O2A UDP sing 387 n n PA O3A UDP sing 388 n n O2A HOA2 UDP sing 389 n n O3A PB UDP sing 390 n n PB O1B UDP doub 391 n n PB O2B UDP sing 392 n n PB O3B UDP sing 393 n n O2B HOB2 UDP sing 394 n n O3B HOB3 UDP sing 395 n n # _atom_sites.entry_id 5MQJ _atom_sites.fract_transf_matrix[1][1] 0.010788 _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] 0.010788 _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] 0.002958 _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 E 2 UDP A 1 301 500 UDP UDP . F 3 UMP A 1 302 510 UMP DU . G 4 MG A 1 303 520 MG MG . H 2 UDP B 1 301 500 UDP UDP . I 3 UMP B 1 302 510 UMP DU . J 4 MG B 1 303 520 MG MG . K 2 UDP C 1 301 500 UDP UDP . L 3 UMP C 1 302 510 UMP DU . M 4 MG C 1 303 520 MG MG . N 2 UDP D 1 301 500 UDP UDP . O 3 UMP D 1 302 510 UMP DU . P 4 MG D 1 303 520 MG MG . # 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 UDP . . . E 2 -59.003 58.544 366.621 1 144.06 ? N1 UDP 301 A 1 HETATM 2 C C2 UDP . . . E 2 -58.056 59.555 366.621 1 151.92 ? C2 UDP 301 A 1 HETATM 3 N N3 UDP . . . E 2 -57.012 59.376 367.503 1 152.62 ? N3 UDP 301 A 1 HETATM 4 C C4 UDP . . . E 2 -56.822 58.312 368.365 1 148.61 ? C4 UDP 301 A 1 HETATM 5 C C5 UDP . . . E 2 -57.829 57.29 368.289 1 144.53 ? C5 UDP 301 A 1 HETATM 6 C C6 UDP . . . E 2 -58.867 57.433 367.44 1 142.62 ? C6 UDP 301 A 1 HETATM 7 O O2 UDP . . . E 2 -58.115 60.532 365.887 1 157.63 ? O2 UDP 301 A 1 HETATM 8 O O4 UDP . . . E 2 -55.857 58.32 369.142 1 148.95 ? O4 UDP 301 A 1 HETATM 9 C C1' UDP . . . E 2 -60.184 58.702 365.74 1 138.26 ? C1' UDP 301 A 1 HETATM 10 C C2' UDP . . . E 2 -60.291 57.666 364.624 1 137.78 ? C2' UDP 301 A 1 HETATM 11 O O2' UDP . . . E 2 -59.53 58.052 363.489 1 144.99 ? O2' UDP 301 A 1 HETATM 12 C C3' UDP . . . E 2 -61.796 57.681 364.344 1 134.07 ? C3' UDP 301 A 1 HETATM 13 C C4' UDP . . . E 2 -62.398 57.94 365.726 1 129.01 ? C4' UDP 301 A 1 HETATM 14 O O4' UDP . . . E 2 -61.356 58.557 366.516 1 131.71 ? O4' UDP 301 A 1 HETATM 15 O O3' UDP . . . E 2 -62.204 58.66 363.391 1 137.93 ? O3' UDP 301 A 1 HETATM 16 C C5' UDP . . . E 2 -62.943 56.726 366.443 1 122.97 ? C5' UDP 301 A 1 HETATM 17 O O5' UDP . . . E 2 -61.972 55.655 366.458 1 121.05 ? O5' UDP 301 A 1 HETATM 18 P PA UDP . . . E 2 -62.332 54.121 366.246 1 117.08 ? PA UDP 301 A 1 HETATM 19 O O1A UDP . . . E 2 -63.277 53.831 365.144 1 117.67 ? O1A UDP 301 A 1 HETATM 20 O O2A UDP . . . E 2 -61.079 53.27 366.101 1 115.16 ? O2A UDP 301 A 1 HETATM 21 O O3A UDP . . . E 2 -63.026 53.684 367.605 1 117.66 ? O3A UDP 301 A 1 HETATM 22 P PB UDP . . . E 2 -63.902 52.391 367.891 1 119.67 ? PB UDP 301 A 1 HETATM 23 O O1B UDP . . . E 2 -63.333 51.285 367.021 1 121.73 ? O1B UDP 301 A 1 HETATM 24 O O2B UDP . . . E 2 -65.284 52.664 367.545 1 120.63 ? O2B UDP 301 A 1 HETATM 25 O O3B UDP . . . E 2 -63.666 52.111 369.373 1 118.78 ? O3B UDP 301 A 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #