data_5H3A # _model_server_result.job_id p9LwJ8sukc9-GBSpZ_Ljtg _model_server_result.datetime_utc '2024-10-11 02:16:07' _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 5h3a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 5H3A # _exptl.entry_id 5H3A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _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 116.24 _cell.angle_gamma 90 _cell.entry_id 5H3A _cell.length_a 63.41 _cell.length_b 79.539 _cell.length_c 67.283 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5H3A _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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 ? 3 D N N ? 3 F 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 414 n n N1 C6 UMP sing 415 n n N1 C1' UMP sing 416 n n C2 N3 UMP sing 417 n n C2 O2 UMP doub 418 n n N3 C4 UMP sing 419 n n N3 HN3 UMP sing 420 n n C4 C5 UMP sing 421 n n C4 O4 UMP doub 422 n n C5 C6 UMP doub 423 n n C5 H5 UMP sing 424 n n C6 H6 UMP sing 425 n n C1' C2' UMP sing 426 n n C1' O4' UMP sing 427 n n C1' H1' UMP sing 428 n n C2' C3' UMP sing 429 n n C2' H2' UMP sing 430 n n C2' "H2''" UMP sing 431 n n C3' C4' UMP sing 432 n n C3' O3' UMP sing 433 n n C3' H3' UMP sing 434 n n C4' O4' UMP sing 435 n n C4' C5' UMP sing 436 n n C4' H4' UMP sing 437 n n O3' HO3' UMP sing 438 n n C5' O5' UMP sing 439 n n C5' H5' UMP sing 440 n n C5' "H5''" UMP sing 441 n n O5' P UMP sing 442 n n P OP1 UMP doub 443 n n P OP2 UMP sing 444 n n P OP3 UMP sing 445 n n OP2 HOP2 UMP sing 446 n n OP3 HOP3 UMP sing 447 n n # _atom_sites.entry_id 5H3A _atom_sites.fract_transf_matrix[1][1] 0.01577 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007775 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012572 _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] 0.016571 _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 D16 A 1 401 414 D16 D16 . D 3 UMP A 1 402 314 UMP UMP . E 2 D16 B 1 401 415 D16 D16 . F 3 UMP B 1 402 315 UMP UMP . G 4 HOH A 1 501 4 HOH HOH . G 4 HOH A 2 502 20 HOH HOH . G 4 HOH A 3 503 9 HOH HOH . G 4 HOH A 4 504 8 HOH HOH . G 4 HOH A 5 505 33 HOH HOH . G 4 HOH A 6 506 3 HOH HOH . G 4 HOH A 7 507 43 HOH HOH . G 4 HOH A 8 508 12 HOH HOH . G 4 HOH A 9 509 30 HOH HOH . G 4 HOH A 10 510 19 HOH HOH . G 4 HOH A 11 511 17 HOH HOH . G 4 HOH A 12 512 11 HOH HOH . G 4 HOH A 13 513 18 HOH HOH . G 4 HOH A 14 514 6 HOH HOH . G 4 HOH A 15 515 45 HOH HOH . G 4 HOH A 16 516 47 HOH HOH . G 4 HOH A 17 517 46 HOH HOH . G 4 HOH A 18 518 2 HOH HOH . G 4 HOH A 19 519 25 HOH HOH . H 4 HOH B 1 501 10 HOH HOH . H 4 HOH B 2 502 21 HOH HOH . H 4 HOH B 3 503 32 HOH HOH . H 4 HOH B 4 504 39 HOH HOH . H 4 HOH B 5 505 42 HOH HOH . H 4 HOH B 6 506 41 HOH HOH . H 4 HOH B 7 507 1 HOH HOH . H 4 HOH B 8 508 29 HOH HOH . H 4 HOH B 9 509 5 HOH HOH . H 4 HOH B 10 510 24 HOH HOH . H 4 HOH B 11 511 38 HOH HOH . H 4 HOH B 12 512 37 HOH HOH . H 4 HOH B 13 513 22 HOH HOH . H 4 HOH B 14 514 15 HOH HOH . H 4 HOH B 15 515 7 HOH HOH . H 4 HOH B 16 516 13 HOH HOH . H 4 HOH B 17 517 28 HOH HOH . H 4 HOH B 18 518 44 HOH HOH . H 4 HOH B 19 519 23 HOH HOH . H 4 HOH B 20 520 40 HOH HOH . H 4 HOH B 21 521 14 HOH HOH . H 4 HOH B 22 522 27 HOH HOH . H 4 HOH B 23 523 16 HOH HOH . H 4 HOH B 24 524 31 HOH HOH . H 4 HOH B 25 525 36 HOH HOH . H 4 HOH B 26 526 26 HOH HOH . H 4 HOH B 27 527 34 HOH HOH . H 4 HOH B 28 528 35 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 . . . F 3 46.382 8.604 74.376 1 52.17 ? N1 UMP 402 B 1 HETATM 2 C C2 UMP . . . F 3 47.195 7.49 74.512 1 51.33 ? C2 UMP 402 B 1 HETATM 3 N N3 UMP . . . F 3 46.676 6.317 74.797 1 52.28 ? N3 UMP 402 B 1 HETATM 4 C C4 UMP . . . F 3 45.385 6.162 74.97 1 52.13 ? C4 UMP 402 B 1 HETATM 5 C C5 UMP . . . F 3 44.552 7.235 74.833 1 55.17 ? C5 UMP 402 B 1 HETATM 6 C C6 UMP . . . F 3 45.084 8.46 74.536 1 54.49 ? C6 UMP 402 B 1 HETATM 7 O O2 UMP . . . F 3 48.405 7.58 74.379 1 49.76 ? O2 UMP 402 B 1 HETATM 8 O O4 UMP . . . F 3 44.914 5.067 75.234 1 52.18 ? O4 UMP 402 B 1 HETATM 9 C C1' UMP . . . F 3 46.964 9.911 74.097 1 57.72 ? C1' UMP 402 B 1 HETATM 10 C C2' UMP . . . F 3 47.561 10.041 72.726 1 51.61 ? C2' UMP 402 B 1 HETATM 11 C C3' UMP . . . F 3 47.353 11.49 72.432 1 51.85 ? C3' UMP 402 B 1 HETATM 12 C C4' UMP . . . F 3 46.091 11.843 73.146 1 57.2 ? C4' UMP 402 B 1 HETATM 13 O O3' UMP . . . F 3 48.416 12.193 73.03 1 53.05 ? O3' UMP 402 B 1 HETATM 14 O O4' UMP . . . F 3 46.037 10.968 74.244 1 53.77 ? O4' UMP 402 B 1 HETATM 15 C C5' UMP . . . F 3 44.901 11.595 72.251 1 49.63 ? C5' UMP 402 B 1 HETATM 16 O O5' UMP . . . F 3 44.779 12.666 71.342 1 59.61 ? O5' UMP 402 B 1 HETATM 17 P P UMP . . . F 3 44.532 12.486 69.808 1 49.64 ? P UMP 402 B 1 HETATM 18 O OP1 UMP . . . F 3 45.713 11.806 69.33 1 47.38 -1 OP1 UMP 402 B 1 HETATM 19 O OP2 UMP . . . F 3 44.383 13.843 69.342 1 56.69 ? OP2 UMP 402 B 1 HETATM 20 O OP3 UMP . . . F 3 43.289 11.749 69.758 1 50.55 ? OP3 UMP 402 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #