data_4PB2 # _model_server_result.job_id 4QxxVOdOj55IC9v9Qqissg _model_server_result.datetime_utc '2024-11-22 20:48:05' _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 4pb2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4PB2 # _exptl.entry_id 4PB2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 262.192 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-FLUOROURIDINE _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 4PB2 _cell.length_a 119.772 _cell.length_b 119.772 _cell.length_c 83.214 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PB2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 59.886 -103.725595 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 119.772 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 O ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc2 A OD1 ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc3 A O VAL 158 A VAL 152 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc4 A OG SER 189 A SER 183 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc5 A O ILE 190 A ILE 184 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc6 C NA NA . A NA 502 1_555 E O HOH . A HOH 658 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? # _chem_comp.formula 'C9 H11 F N2 O6' _chem_comp.formula_weight 262.192 _chem_comp.id 5UD _chem_comp.mon_nstd_flag . _chem_comp.name 5-FLUOROURIDINE _chem_comp.type non-polymer _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 F5 C5 5UD sing 1 n n C5 C4 5UD sing 2 n n C5 C6 5UD doub 3 n n C4 O4 5UD doub 4 n n C4 N3 5UD sing 5 n n N3 C2 5UD sing 6 n n N3 HN3 5UD sing 7 n n C2 O2 5UD doub 8 n n C2 N1 5UD sing 9 n n C6 N1 5UD sing 10 n n C6 H6 5UD sing 11 n n N1 C1' 5UD sing 12 n n C1' C2' 5UD sing 13 n n C1' O4' 5UD sing 14 n n C1' H1' 5UD sing 15 n n C2' O2' 5UD sing 16 n n C2' C3' 5UD sing 17 n n C2' H2' 5UD sing 18 n n O2' HO2' 5UD sing 19 n n C3' O3' 5UD sing 20 n n C3' C4' 5UD sing 21 n n C3' H3' 5UD sing 22 n n O3' HO3' 5UD sing 23 n n C4' O4' 5UD sing 24 n n C4' C5' 5UD sing 25 n n C4' H4' 5UD sing 26 n n C5' O5' 5UD sing 27 n n C5' "H5'1" 5UD sing 28 n n C5' "H5'2" 5UD sing 29 n n O5' HO5' 5UD sing 30 n n # _atom_sites.entry_id 4PB2 _atom_sites.fract_transf_matrix[1][1] 0.008349 _atom_sites.fract_transf_matrix[1][2] 0.00482 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009641 _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] 0.012017 _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 B 2 5UD A 1 501 1 5UD FU0 . C 3 NA A 1 502 1 NA NA . D 4 DMU A 1 503 503 DMU DMU . E 5 HOH A 1 601 93 HOH HOH . E 5 HOH A 2 602 2 HOH HOH . E 5 HOH A 3 603 110 HOH HOH . E 5 HOH A 4 604 15 HOH HOH . E 5 HOH A 5 605 82 HOH HOH . E 5 HOH A 6 606 89 HOH HOH . E 5 HOH A 7 607 95 HOH HOH . E 5 HOH A 8 608 5 HOH HOH . E 5 HOH A 9 609 18 HOH HOH . E 5 HOH A 10 610 4 HOH HOH . E 5 HOH A 11 611 126 HOH HOH . E 5 HOH A 12 612 12 HOH HOH . E 5 HOH A 13 613 100 HOH HOH . E 5 HOH A 14 614 1 HOH HOH . E 5 HOH A 15 615 3 HOH HOH . E 5 HOH A 16 616 6 HOH HOH . E 5 HOH A 17 617 7 HOH HOH . E 5 HOH A 18 618 8 HOH HOH . E 5 HOH A 19 619 9 HOH HOH . E 5 HOH A 20 620 10 HOH HOH . E 5 HOH A 21 621 14 HOH HOH . E 5 HOH A 22 622 22 HOH HOH . E 5 HOH A 23 623 23 HOH HOH . E 5 HOH A 24 624 24 HOH HOH . E 5 HOH A 25 625 25 HOH HOH . E 5 HOH A 26 626 26 HOH HOH . E 5 HOH A 27 627 27 HOH HOH . E 5 HOH A 28 628 31 HOH HOH . E 5 HOH A 29 629 33 HOH HOH . E 5 HOH A 30 630 35 HOH HOH . E 5 HOH A 31 631 42 HOH HOH . E 5 HOH A 32 632 45 HOH HOH . E 5 HOH A 33 633 46 HOH HOH . E 5 HOH A 34 634 47 HOH HOH . E 5 HOH A 35 635 49 HOH HOH . E 5 HOH A 36 636 54 HOH HOH . E 5 HOH A 37 637 56 HOH HOH . E 5 HOH A 38 638 59 HOH HOH . E 5 HOH A 39 639 61 HOH HOH . E 5 HOH A 40 640 62 HOH HOH . E 5 HOH A 41 641 65 HOH HOH . E 5 HOH A 42 642 66 HOH HOH . E 5 HOH A 43 643 69 HOH HOH . E 5 HOH A 44 644 72 HOH HOH . E 5 HOH A 45 645 73 HOH HOH . E 5 HOH A 46 646 75 HOH HOH . E 5 HOH A 47 647 78 HOH HOH . E 5 HOH A 48 648 79 HOH HOH . E 5 HOH A 49 649 84 HOH HOH . E 5 HOH A 50 650 87 HOH HOH . E 5 HOH A 51 651 88 HOH HOH . E 5 HOH A 52 652 90 HOH HOH . E 5 HOH A 53 653 92 HOH HOH . E 5 HOH A 54 654 111 HOH HOH . E 5 HOH A 55 655 114 HOH HOH . E 5 HOH A 56 656 120 HOH HOH . E 5 HOH A 57 657 137 HOH HOH . E 5 HOH A 58 658 144 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 F F5 5UD . . . B 2 49.312 -22.115 -5.402 1 37.8 ? F5 5UD 501 A 1 HETATM 2 C C5 5UD . . . B 2 49.784 -21.607 -6.518 1 41.75 ? C5 5UD 501 A 1 HETATM 3 C C4 5UD . . . B 2 49.178 -21.958 -7.773 1 38.85 ? C4 5UD 501 A 1 HETATM 4 O O4 5UD . . . B 2 48.222 -22.729 -7.805 1 48.07 ? O4 5UD 501 A 1 HETATM 5 N N3 5UD . . . B 2 49.685 -21.416 -8.937 1 41.85 ? N3 5UD 501 A 1 HETATM 6 C C2 5UD . . . B 2 50.751 -20.556 -8.881 1 42.14 ? C2 5UD 501 A 1 HETATM 7 O O2 5UD . . . B 2 51.2 -20.077 -9.907 1 39.42 ? O2 5UD 501 A 1 HETATM 8 C C6 5UD . . . B 2 50.826 -20.765 -6.495 1 40.81 ? C6 5UD 501 A 1 HETATM 9 N N1 5UD . . . B 2 51.311 -20.238 -7.678 1 40.88 ? N1 5UD 501 A 1 HETATM 10 C C1' 5UD . . . B 2 52.47 -19.3 -7.643 1 43.24 ? C1' 5UD 501 A 1 HETATM 11 C C2' 5UD . . . B 2 52.046 -17.839 -7.735 1 42.1 ? C2' 5UD 501 A 1 HETATM 12 O O2' 5UD . . . B 2 52.979 -17.133 -8.528 1 42.82 ? O2' 5UD 501 A 1 HETATM 13 C C3' 5UD . . . B 2 52.129 -17.358 -6.3 1 39.47 ? C3' 5UD 501 A 1 HETATM 14 O O3' 5UD . . . B 2 52.415 -15.966 -6.263 1 42.12 ? O3' 5UD 501 A 1 HETATM 15 C C4' 5UD . . . B 2 53.309 -18.161 -5.781 1 42.53 ? C4' 5UD 501 A 1 HETATM 16 O O4' 5UD . . . B 2 53.213 -19.451 -6.442 1 39.75 ? O4' 5UD 501 A 1 HETATM 17 C C5' 5UD . . . B 2 53.177 -18.362 -4.284 1 40.52 ? C5' 5UD 501 A 1 HETATM 18 O O5' 5UD . . . B 2 51.931 -18.851 -3.801 1 41.72 ? O5' 5UD 501 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 103 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 18 #