data_8Y2L # _model_server_result.job_id cEYN7XmPzUS1sHyGrN90JA _model_server_result.datetime_utc '2025-02-23 23:14:45' _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":"E","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 . . . E 3 62.786 51.785 -16.881 1 166.19 0 N1 UDP 602 A 1 HETATM 2 C C2 UDP . . . E 3 64.014 51.269 -16.501 1 160.92 0 C2 UDP 602 A 1 HETATM 3 N N3 UDP . . . E 3 64.366 51.517 -15.197 1 162.65 0 N3 UDP 602 A 1 HETATM 4 C C4 UDP . . . E 3 63.633 52.211 -14.253 1 164.71 0 C4 UDP 602 A 1 HETATM 5 C C5 UDP . . . E 3 62.373 52.711 -14.722 1 165.87 0 C5 UDP 602 A 1 HETATM 6 C C6 UDP . . . E 3 62.001 52.484 -15.992 1 166.49 0 C6 UDP 602 A 1 HETATM 7 O O2 UDP . . . E 3 64.738 50.64 -17.261 1 159.17 0 O2 UDP 602 A 1 HETATM 8 O O4 UDP . . . E 3 64.088 52.351 -13.118 1 164.37 0 O4 UDP 602 A 1 HETATM 9 C C1' UDP . . . E 3 62.35 51.548 -18.275 1 177.49 0 C1' UDP 602 A 1 HETATM 10 C C2' UDP . . . E 3 61.372 50.374 -18.399 1 186.85 0 C2' UDP 602 A 1 HETATM 11 O O2' UDP . . . E 3 61.771 49.535 -19.46 1 186.49 0 O2' UDP 602 A 1 HETATM 12 C C3' UDP . . . E 3 60.033 51.065 -18.69 1 193 0 C3' UDP 602 A 1 HETATM 13 C C4' UDP . . . E 3 60.476 52.336 -19.427 1 191.48 0 C4' UDP 602 A 1 HETATM 14 O O4' UDP . . . E 3 61.703 52.709 -18.755 1 183.77 0 O4' UDP 602 A 1 HETATM 15 O O3' UDP . . . E 3 59.193 50.26 -19.509 1 195.84 0 O3' UDP 602 A 1 HETATM 16 C C5' UDP . . . E 3 59.515 53.501 -19.413 1 194.09 0 C5' UDP 602 A 1 HETATM 17 O O5' UDP . . . E 3 58.303 53.134 -18.7 1 200.78 0 O5' UDP 602 A 1 HETATM 18 P PA UDP . . . E 3 57.409 54.271 -18.003 1 207.24 0 PA UDP 602 A 1 HETATM 19 O O1A UDP . . . E 3 55.959 53.935 -18.165 1 204.58 0 O1A UDP 602 A 1 HETATM 20 O O2A UDP . . . E 3 57.936 54.544 -16.633 1 199.91 0 O2A UDP 602 A 1 HETATM 21 O O3A UDP . . . E 3 57.714 55.538 -18.937 1 223.05 0 O3A UDP 602 A 1 HETATM 22 P PB UDP . . . E 3 56.776 56.289 -20.015 1 242.57 0 PB UDP 602 A 1 HETATM 23 O O1B UDP . . . E 3 57.504 56.195 -21.335 1 248.79 0 O1B UDP 602 A 1 HETATM 24 O O2B UDP . . . E 3 56.635 57.711 -19.525 1 243.28 0 O2B UDP 602 A 1 HETATM 25 O O3B UDP . . . E 3 55.463 55.534 -20.013 1 221.28 0 O3B UDP 602 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 59 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #