data_8Y2L # _model_server_result.job_id ZYd2R-nSBMNK-0PnyJGrvg _model_server_result.datetime_utc '2025-02-23 23:31:03' _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 8y2l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":602}' # _entry.id 8Y2L # _exptl.entry_id 8Y2L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 8Y2L _cell.length_a 155.166 _cell.length_b 268.755 _cell.length_c 194.862 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y2L _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 3 E N N ? 3 G N N ? 3 I 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 OD2 ASP 291 A ASP 288 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.747 ? metalc ? metalc2 A OE1 GLU 518 A GLU 515 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.743 ? metalc ? metalc3 A OG SER 521 A SER 518 1_555 D MN MN . A MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.761 ? metalc ? metalc4 D MN MN . A MN 601 1_555 E O1A UDP . A UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? metalc ? metalc5 D MN MN . A MN 601 1_555 E O3B UDP . A UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.745 ? metalc ? metalc6 B OD2 ASP 291 B ASP 288 1_555 F MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.729 ? metalc ? metalc7 B OE1 GLU 518 B GLU 515 1_555 F MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.762 ? metalc ? metalc8 B OG SER 521 B SER 518 1_555 F MN MN . B MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.78 ? metalc ? metalc9 F MN MN . B MN 601 1_555 G O1A UDP . B UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.756 ? metalc ? metalc10 F MN MN . B MN 601 1_555 G O3B UDP . B UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.751 ? metalc ? metalc11 C OD2 ASP 291 C ASP 288 1_555 H MN MN . C MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.748 ? metalc ? metalc12 C OE1 GLU 518 C GLU 515 1_555 H MN MN . C MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.748 ? metalc ? metalc13 C OG SER 521 C SER 518 1_555 H MN MN . C MN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? metalc ? metalc14 H MN MN . C MN 601 1_555 I O1A UDP . C UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? metalc ? metalc15 H MN MN . C MN 601 1_555 I O3B UDP . C UDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.747 ? # _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 8Y2L _atom_sites.fract_transf_matrix[1][1] 0.006445 _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] 0.003721 _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] 0.005132 _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 D 2 MN A 1 601 1 MN MN . E 3 UDP A 1 602 1 UDP UDP . F 2 MN B 1 601 2 MN MN . G 3 UDP B 1 602 2 UDP UDP . H 2 MN C 1 601 3 MN MN . I 3 UDP C 1 602 3 UDP UDP . J 4 HOH A 1 701 1 HOH HOH . J 4 HOH A 2 702 4 HOH HOH . J 4 HOH A 3 703 6 HOH HOH . J 4 HOH A 4 704 12 HOH HOH . J 4 HOH A 5 705 5 HOH HOH . K 4 HOH B 1 701 2 HOH HOH . K 4 HOH B 2 702 8 HOH HOH . K 4 HOH B 3 703 9 HOH HOH . K 4 HOH B 4 704 13 HOH HOH . L 4 HOH C 1 701 3 HOH HOH . L 4 HOH C 2 702 10 HOH HOH . L 4 HOH C 3 703 11 HOH HOH . L 4 HOH C 4 704 14 HOH HOH . L 4 HOH C 5 705 7 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 . . . I 3 52.222 121.293 48.011 1 159.62 0 N1 UDP 602 C 1 HETATM 2 C C2 UDP . . . I 3 51.2 120.438 48.39 1 154.95 0 C2 UDP 602 C 1 HETATM 3 N N3 UDP . . . I 3 51.259 120.01 49.693 1 155.61 0 N3 UDP 602 C 1 HETATM 4 C C4 UDP . . . I 3 52.213 120.34 50.637 1 157.14 0 C4 UDP 602 C 1 HETATM 5 C C5 UDP . . . I 3 53.236 121.229 50.169 1 157.91 0 C5 UDP 602 C 1 HETATM 6 C C6 UDP . . . I 3 53.206 121.664 48.899 1 159.22 0 C6 UDP 602 C 1 HETATM 7 O O2 UDP . . . I 3 50.308 120.083 47.631 1 155.54 0 O2 UDP 602 C 1 HETATM 8 O O4 UDP . . . I 3 52.13 119.871 51.772 1 157.96 0 O4 UDP 602 C 1 HETATM 9 C C1' UDP . . . I 3 52.217 121.787 46.615 1 171.01 0 C1' UDP 602 C 1 HETATM 10 C C2' UDP . . . I 3 51.647 123.204 46.483 1 178.12 0 C2' UDP 602 C 1 HETATM 11 O O2' UDP . . . I 3 50.737 123.25 45.403 1 176.24 0 O2' UDP 602 C 1 HETATM 12 C C3' UDP . . . I 3 52.9 124.054 46.232 1 184.4 0 C3' UDP 602 C 1 HETATM 13 C C4' UDP . . . I 3 53.819 123.072 45.493 1 185.53 0 C4' UDP 602 C 1 HETATM 14 O O4' UDP . . . I 3 53.546 121.802 46.136 1 177.46 0 O4' UDP 602 C 1 HETATM 15 O O3' UDP . . . I 3 52.601 125.195 45.436 1 184.66 0 O3' UDP 602 C 1 HETATM 16 C C5' UDP . . . I 3 55.305 123.349 45.529 1 190 0 C5' UDP 602 C 1 HETATM 17 O O5' UDP . . . I 3 55.594 124.444 46.444 1 200.12 0 O5' UDP 602 C 1 HETATM 18 P PA UDP . . . I 3 57.078 124.656 47.025 1 206.01 0 PA UDP 602 C 1 HETATM 19 O O1A UDP . . . I 3 57.51 126.074 46.808 1 200.66 0 O1A UDP 602 C 1 HETATM 20 O O2A UDP . . . I 3 57.155 124.088 48.404 1 198.83 0 O2A UDP 602 C 1 HETATM 21 O O3A UDP . . . I 3 57.953 123.741 46.041 1 216.42 0 O3A UDP 602 C 1 HETATM 22 P PB UDP . . . I 3 59.037 124.184 44.931 1 233.98 0 PB UDP 602 C 1 HETATM 23 O O1B UDP . . . I 3 58.502 123.686 43.61 1 238.74 0 O1B UDP 602 C 1 HETATM 24 O O2B UDP . . . I 3 60.334 123.519 45.324 1 236.16 0 O2B UDP 602 C 1 HETATM 25 O O3B UDP . . . I 3 59.103 125.698 45.007 1 213.9 0 O3B UDP 602 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #