data_6IJ9 # _model_server_result.job_id jyWDYcyZAw8BTbN55nmGsg _model_server_result.datetime_utc '2024-11-15 02:22:08' _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 6ij9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":900}' # _entry.id 6IJ9 # _exptl.entry_id 6IJ9 _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 108.9 _cell.angle_gamma 90 _cell.entry_id 6IJ9 _cell.length_a 92.979 _cell.length_b 84.141 _cell.length_c 129.146 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IJ9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 F N N ? 2 G N N ? 2 H N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 75 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 75 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 75 _struct_conn.ptnr2_auth_asym_id D _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 75 _struct_conn.ptnr2_symmetry 1_555 _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 2.093 _struct_conn.pdbx_value_order ? # _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 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 6IJ9 _atom_sites.fract_transf_matrix[1][1] 0.010755 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003683 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011885 _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] 0.008184 _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 1 900 900 UDP UDP . F 2 UDP B 1 900 900 UDP UDP . G 2 UDP C 1 900 900 UDP UDP . H 2 UDP D 1 900 900 UDP UDP . I 3 HOH A 1 1001 27 HOH HOH . I 3 HOH A 2 1002 47 HOH HOH . I 3 HOH A 3 1003 7 HOH HOH . I 3 HOH A 4 1004 13 HOH HOH . I 3 HOH A 5 1005 41 HOH HOH . I 3 HOH A 6 1006 61 HOH HOH . I 3 HOH A 7 1007 54 HOH HOH . I 3 HOH A 8 1008 37 HOH HOH . I 3 HOH A 9 1009 57 HOH HOH . I 3 HOH A 10 1010 38 HOH HOH . I 3 HOH A 11 1011 42 HOH HOH . I 3 HOH A 12 1012 40 HOH HOH . I 3 HOH A 13 1013 36 HOH HOH . I 3 HOH A 14 1014 2 HOH HOH . J 3 HOH B 1 1001 55 HOH HOH . J 3 HOH B 2 1002 19 HOH HOH . J 3 HOH B 3 1003 33 HOH HOH . J 3 HOH B 4 1004 29 HOH HOH . J 3 HOH B 5 1005 34 HOH HOH . J 3 HOH B 6 1006 52 HOH HOH . J 3 HOH B 7 1007 43 HOH HOH . J 3 HOH B 8 1008 51 HOH HOH . J 3 HOH B 9 1009 21 HOH HOH . J 3 HOH B 10 1010 53 HOH HOH . J 3 HOH B 11 1011 30 HOH HOH . J 3 HOH B 12 1012 12 HOH HOH . J 3 HOH B 13 1013 5 HOH HOH . J 3 HOH B 14 1014 8 HOH HOH . J 3 HOH B 15 1015 11 HOH HOH . J 3 HOH B 16 1016 48 HOH HOH . J 3 HOH B 17 1017 17 HOH HOH . J 3 HOH B 18 1018 45 HOH HOH . K 3 HOH C 1 1001 46 HOH HOH . K 3 HOH C 2 1002 24 HOH HOH . K 3 HOH C 3 1003 10 HOH HOH . K 3 HOH C 4 1004 35 HOH HOH . K 3 HOH C 5 1005 15 HOH HOH . K 3 HOH C 6 1006 25 HOH HOH . K 3 HOH C 7 1007 1 HOH HOH . K 3 HOH C 8 1008 4 HOH HOH . K 3 HOH C 9 1009 26 HOH HOH . K 3 HOH C 10 1010 3 HOH HOH . K 3 HOH C 11 1011 6 HOH HOH . K 3 HOH C 12 1012 56 HOH HOH . K 3 HOH C 13 1013 60 HOH HOH . K 3 HOH C 14 1014 50 HOH HOH . L 3 HOH D 1 1001 9 HOH HOH . L 3 HOH D 2 1002 28 HOH HOH . L 3 HOH D 3 1003 44 HOH HOH . L 3 HOH D 4 1004 16 HOH HOH . L 3 HOH D 5 1005 18 HOH HOH . L 3 HOH D 6 1006 59 HOH HOH . L 3 HOH D 7 1007 49 HOH HOH . L 3 HOH D 8 1008 32 HOH HOH . L 3 HOH D 9 1009 58 HOH HOH . L 3 HOH D 10 1010 31 HOH HOH . L 3 HOH D 11 1011 39 HOH HOH . L 3 HOH D 12 1012 20 HOH HOH . L 3 HOH D 13 1013 22 HOH HOH . L 3 HOH D 14 1014 23 HOH HOH . L 3 HOH D 15 1015 14 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 UDP . . . E 2 -1.278 62.9 57.576 1 35.32 ? N1 UDP 900 A 1 HETATM 2 C C2 UDP . . . E 2 -1.467 64.063 58.315 1 37.01 ? C2 UDP 900 A 1 HETATM 3 N N3 UDP . . . E 2 -1.513 63.877 59.675 1 41.17 ? N3 UDP 900 A 1 HETATM 4 C C4 UDP . . . E 2 -1.397 62.684 60.355 1 41.51 ? C4 UDP 900 A 1 HETATM 5 C C5 UDP . . . E 2 -1.208 61.539 59.522 1 38.99 ? C5 UDP 900 A 1 HETATM 6 C C6 UDP . . . E 2 -1.163 61.676 58.192 1 35.41 ? C6 UDP 900 A 1 HETATM 7 O O2 UDP . . . E 2 -1.582 65.176 57.81 1 36.59 ? O2 UDP 900 A 1 HETATM 8 O O4 UDP . . . E 2 -1.466 62.673 61.594 1 43.39 ? O4 UDP 900 A 1 HETATM 9 C C1' UDP . . . E 2 -1.205 62.994 56.109 1 30.78 ? C1' UDP 900 A 1 HETATM 10 C C2' UDP . . . E 2 0.231 63.032 55.555 1 23.97 ? C2' UDP 900 A 1 HETATM 11 O O2' UDP . . . E 2 0.735 64.357 55.416 1 18.96 ? O2' UDP 900 A 1 HETATM 12 C C3' UDP . . . E 2 0.062 62.362 54.186 1 25.08 ? C3' UDP 900 A 1 HETATM 13 C C4' UDP . . . E 2 -1.024 61.323 54.462 1 25.98 ? C4' UDP 900 A 1 HETATM 14 O O4' UDP . . . E 2 -1.81 61.834 55.576 1 27.79 ? O4' UDP 900 A 1 HETATM 15 O O3' UDP . . . E 2 -0.342 63.24 53.134 1 18.14 ? O3' UDP 900 A 1 HETATM 16 C C5' UDP . . . E 2 -0.507 59.94 54.783 1 21.9 ? C5' UDP 900 A 1 HETATM 17 O O5' UDP . . . E 2 -0.399 59.182 53.565 1 26.57 ? O5' UDP 900 A 1 HETATM 18 P PA UDP . . . E 2 0.963 58.568 53.109 1 23.48 ? PA UDP 900 A 1 HETATM 19 O O1A UDP . . . E 2 0.945 58.418 51.622 1 27.54 ? O1A UDP 900 A 1 HETATM 20 O O2A UDP . . . E 2 2.124 59.353 53.702 1 29 ? O2A UDP 900 A 1 HETATM 21 O O3A UDP . . . E 2 1.002 57.135 53.808 1 32.31 ? O3A UDP 900 A 1 HETATM 22 P PB UDP . . . E 2 -0.203 56.112 53.904 1 33.01 ? PB UDP 900 A 1 HETATM 23 O O1B UDP . . . E 2 -0.907 55.915 52.54 1 36.92 ? O1B UDP 900 A 1 HETATM 24 O O2B UDP . . . E 2 0.47 54.808 54.41 1 34.92 ? O2B UDP 900 A 1 HETATM 25 O O3B UDP . . . E 2 -1.044 56.691 55.043 1 33.39 ? O3B UDP 900 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 25 #