data_6Y08 # _model_server_result.job_id FLservoit6LakVsO3jS20Q _model_server_result.datetime_utc '2024-11-25 02:48:16' _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 6y08 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 6Y08 # _exptl.entry_id 6Y08 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 96.15 _cell.angle_gamma 90 _cell.entry_id 6Y08 _cell.length_a 160.545 _cell.length_b 88.057 _cell.length_c 68.262 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y08 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 E N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 387 n n N1 C6 UMP sing 388 n n N1 C1' UMP sing 389 n n C2 N3 UMP sing 390 n n C2 O2 UMP doub 391 n n N3 C4 UMP sing 392 n n N3 HN3 UMP sing 393 n n C4 C5 UMP sing 394 n n C4 O4 UMP doub 395 n n C5 C6 UMP doub 396 n n C5 H5 UMP sing 397 n n C6 H6 UMP sing 398 n n C1' C2' UMP sing 399 n n C1' O4' UMP sing 400 n n C1' H1' UMP sing 401 n n C2' C3' UMP sing 402 n n C2' H2' UMP sing 403 n n C2' "H2''" UMP sing 404 n n C3' C4' UMP sing 405 n n C3' O3' UMP sing 406 n n C3' H3' UMP sing 407 n n C4' O4' UMP sing 408 n n C4' C5' UMP sing 409 n n C4' H4' UMP sing 410 n n O3' HO3' UMP sing 411 n n C5' O5' UMP sing 412 n n C5' H5' UMP sing 413 n n C5' "H5''" UMP sing 414 n n O5' P UMP sing 415 n n P OP1 UMP doub 416 n n P OP2 UMP sing 417 n n P OP3 UMP sing 418 n n OP2 HOP2 UMP sing 419 n n OP3 HOP3 UMP sing 420 n n # _atom_sites.entry_id 6Y08 _atom_sites.fract_transf_matrix[1][1] 0.006229 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000671 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011356 _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] 0.014734 _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 UMP A 1 501 501 UMP UMP . D 3 08D A 1 502 502 08D 08D . E 2 UMP B 1 501 501 UMP UMP . F 3 08D B 1 502 502 08D 08D . G 4 HOH A 1 601 8 HOH HOH . G 4 HOH A 2 602 22 HOH HOH . G 4 HOH A 3 603 64 HOH HOH . G 4 HOH A 4 604 26 HOH HOH . G 4 HOH A 5 605 43 HOH HOH . G 4 HOH A 6 606 52 HOH HOH . G 4 HOH A 7 607 1 HOH HOH . G 4 HOH A 8 608 75 HOH HOH . G 4 HOH A 9 609 19 HOH HOH . G 4 HOH A 10 610 167 HOH HOH . G 4 HOH A 11 611 11 HOH HOH . G 4 HOH A 12 612 24 HOH HOH . G 4 HOH A 13 613 53 HOH HOH . G 4 HOH A 14 614 39 HOH HOH . G 4 HOH A 15 615 209 HOH HOH . G 4 HOH A 16 616 50 HOH HOH . G 4 HOH A 17 617 9 HOH HOH . G 4 HOH A 18 618 21 HOH HOH . G 4 HOH A 19 619 54 HOH HOH . G 4 HOH A 20 620 73 HOH HOH . G 4 HOH A 21 621 215 HOH HOH . G 4 HOH A 22 622 66 HOH HOH . G 4 HOH A 23 623 35 HOH HOH . G 4 HOH A 24 624 4 HOH HOH . G 4 HOH A 25 625 58 HOH HOH . G 4 HOH A 26 626 208 HOH HOH . G 4 HOH A 27 627 197 HOH HOH . G 4 HOH A 28 628 33 HOH HOH . G 4 HOH A 29 629 99 HOH HOH . G 4 HOH A 30 630 27 HOH HOH . G 4 HOH A 31 631 102 HOH HOH . G 4 HOH A 32 632 15 HOH HOH . G 4 HOH A 33 633 76 HOH HOH . G 4 HOH A 34 634 59 HOH HOH . G 4 HOH A 35 635 37 HOH HOH . G 4 HOH A 36 636 93 HOH HOH . H 4 HOH B 1 601 38 HOH HOH . H 4 HOH B 2 602 200 HOH HOH . H 4 HOH B 3 603 17 HOH HOH . H 4 HOH B 4 604 3 HOH HOH . H 4 HOH B 5 605 74 HOH HOH . H 4 HOH B 6 606 51 HOH HOH . H 4 HOH B 7 607 211 HOH HOH . H 4 HOH B 8 608 195 HOH HOH . H 4 HOH B 9 609 42 HOH HOH . H 4 HOH B 10 610 20 HOH HOH . H 4 HOH B 11 611 13 HOH HOH . H 4 HOH B 12 612 194 HOH HOH . H 4 HOH B 13 613 16 HOH HOH . H 4 HOH B 14 614 23 HOH HOH . H 4 HOH B 15 615 82 HOH HOH . H 4 HOH B 16 616 88 HOH HOH . H 4 HOH B 17 617 14 HOH HOH . H 4 HOH B 18 618 61 HOH HOH . H 4 HOH B 19 619 31 HOH HOH . H 4 HOH B 20 620 30 HOH HOH . H 4 HOH B 21 621 47 HOH HOH . H 4 HOH B 22 622 41 HOH HOH . H 4 HOH B 23 623 69 HOH HOH . H 4 HOH B 24 624 29 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 UMP . . . C 2 21.908 -20.377 0.401 1 43.38 ? N1 UMP 501 A 1 HETATM 2 C C2 UMP . . . C 2 22.575 -21.501 0.92 1 41.55 ? C2 UMP 501 A 1 HETATM 3 N N3 UMP . . . C 2 22.079 -22.787 0.721 1 38.61 ? N3 UMP 501 A 1 HETATM 4 C C4 UMP . . . C 2 20.897 -22.935 -0.031 1 42.24 ? C4 UMP 501 A 1 HETATM 5 C C5 UMP . . . C 2 20.197 -21.787 -0.554 1 43.97 ? C5 UMP 501 A 1 HETATM 6 C C6 UMP . . . C 2 20.708 -20.5 -0.336 1 43.13 ? C6 UMP 501 A 1 HETATM 7 O O2 UMP . . . C 2 23.629 -21.362 1.599 1 37.62 ? O2 UMP 501 A 1 HETATM 8 O O4 UMP . . . C 2 20.513 -24.115 -0.17 1 42.48 ? O4 UMP 501 A 1 HETATM 9 C C1' UMP . . . C 2 22.477 -19.046 0.664 1 37.58 ? C1' UMP 501 A 1 HETATM 10 C C2' UMP . . . C 2 23.756 -18.733 -0.121 1 35.71 ? C2' UMP 501 A 1 HETATM 11 C C3' UMP . . . C 2 23.629 -17.235 -0.295 1 37.74 ? C3' UMP 501 A 1 HETATM 12 C C4' UMP . . . C 2 22.142 -17.02 -0.503 1 36.28 ? C4' UMP 501 A 1 HETATM 13 O O3' UMP . . . C 2 23.973 -16.572 0.931 1 39.47 ? O3' UMP 501 A 1 HETATM 14 O O4' UMP . . . C 2 21.557 -18.053 0.312 1 35.95 ? O4' UMP 501 A 1 HETATM 15 C C5' UMP . . . C 2 21.755 -17.263 -1.988 1 33.89 ? C5' UMP 501 A 1 HETATM 16 O O5' UMP . . . C 2 21.987 -16.147 -2.817 1 37.61 ? O5' UMP 501 A 1 HETATM 17 P P UMP . . . C 2 22.947 -16.218 -4.13 1 39.35 ? P UMP 501 A 1 HETATM 18 O OP1 UMP . . . C 2 22.193 -16.652 -5.419 1 42.31 -1 OP1 UMP 501 A 1 HETATM 19 O OP2 UMP . . . C 2 23.554 -14.853 -4.542 1 40.24 -1 OP2 UMP 501 A 1 HETATM 20 O OP3 UMP . . . C 2 24.114 -17.161 -4.021 1 39.02 ? OP3 UMP 501 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #