data_1SM8 # _model_server_result.job_id 60bONXp15OpMjGdT9ZqhUQ _model_server_result.datetime_utc '2024-11-24 19:25:56' _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 1sm8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1170}' # _entry.id 1SM8 # _exptl.entry_id 1SM8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 468.142 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-TRIPHOSPHATE" _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 1SM8 _cell.length_a 57.934 _cell.length_b 77.714 _cell.length_c 91.619 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SM8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,F,G,H,I,J,K,L,M _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 ? 4 G N N ? 4 J N N ? 4 K 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 D CR CR . A CR 2171 1_555 G O2G DUT . B DUT 2170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc2 F CR CR . B CR 3171 1_555 K O3G DUT . C DUT 3170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc3 J O2G DUT . C DUT 1170 1_555 I CR CR . C CR 1171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? # _chem_comp.formula 'C9 H15 N2 O14 P3' _chem_comp.formula_weight 468.142 _chem_comp.id DUT _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-TRIPHOSPHATE" _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 N1 C2 DUT sing 70 n n N1 C6 DUT sing 71 n n N1 C1' DUT sing 72 n n C2 N3 DUT sing 73 n n C2 O2 DUT doub 74 n n N3 C4 DUT sing 75 n n N3 HN3 DUT sing 76 n n C4 C5 DUT sing 77 n n C4 O4 DUT doub 78 n n C5 C6 DUT doub 79 n n C5 H5 DUT sing 80 n n C6 H6 DUT sing 81 n n C1' C2' DUT sing 82 n n C1' O4' DUT sing 83 n n C1' H1' DUT sing 84 n n C2' C3' DUT sing 85 n n C2' "H2'1" DUT sing 86 n n C2' "H2'2" DUT sing 87 n n C3' C4' DUT sing 88 n n C3' O3' DUT sing 89 n n C3' H3' DUT sing 90 n n C4' O4' DUT sing 91 n n C4' C5' DUT sing 92 n n C4' H4' DUT sing 93 n n O3' HO3' DUT sing 94 n n C5' O5' DUT sing 95 n n C5' "H5'1" DUT sing 96 n n C5' "H5'2" DUT sing 97 n n O5' PA DUT sing 98 n n PA O1A DUT doub 99 n n PA O2A DUT sing 100 n n PA O3A DUT sing 101 n n O2A HOA2 DUT sing 102 n n O3A PB DUT sing 103 n n PB O1B DUT doub 104 n n PB O2B DUT sing 105 n n PB O3B DUT sing 106 n n O2B HOB2 DUT sing 107 n n O3B PG DUT sing 108 n n PG O1G DUT doub 109 n n PG O2G DUT sing 110 n n PG O3G DUT sing 111 n n O2G HOG2 DUT sing 112 n n O3G HOG3 DUT sing 113 n n # _atom_sites.entry_id 1SM8 _atom_sites.fract_transf_matrix[1][1] 0.017261 _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] 0.012868 _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] 0.010915 _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 CR A 1 2171 151 CR CR3 . E 3 NO3 A 1 2172 1 NO3 NO3 . F 2 CR B 1 3171 151 CR CR3 . G 4 DUT B 1 2170 150 DUT DUT . H 5 TRS B 1 3172 2 TRS TRS . I 2 CR C 1 1171 151 CR CR3 . J 4 DUT C 1 1170 150 DUT DUT . K 4 DUT C 1 3170 150 DUT DUT . L 6 HOH A 1 2173 7 HOH HOH . L 6 HOH A 2 2174 8 HOH HOH . M 6 HOH C 1 3171 3 HOH HOH . M 6 HOH C 2 3172 4 HOH HOH . M 6 HOH C 3 3173 5 HOH HOH . M 6 HOH C 4 3174 6 HOH HOH . M 6 HOH C 5 3175 9 HOH HOH . M 6 HOH C 6 3176 10 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 DUT . . . J 4 20.128 -9.808 -7.91 1 57.85 ? N1 DUT 1170 C 1 HETATM 2 C C2 DUT . . . J 4 19.132 -10.513 -8.485 1 58.13 ? C2 DUT 1170 C 1 HETATM 3 N N3 DUT . . . J 4 17.906 -10.529 -7.841 1 57.52 ? N3 DUT 1170 C 1 HETATM 4 C C4 DUT . . . J 4 17.598 -9.87 -6.644 1 57.1 ? C4 DUT 1170 C 1 HETATM 5 C C5 DUT . . . J 4 18.652 -9.113 -6.013 1 57.29 ? C5 DUT 1170 C 1 HETATM 6 C C6 DUT . . . J 4 19.87 -9.07 -6.609 1 57.39 ? C6 DUT 1170 C 1 HETATM 7 O O2 DUT . . . J 4 19.301 -11.106 -9.504 1 59.31 ? O2 DUT 1170 C 1 HETATM 8 O O4 DUT . . . J 4 16.26 -10.006 -6.135 1 55.07 ? O4 DUT 1170 C 1 HETATM 9 C C1' DUT . . . J 4 21.555 -9.557 -8.302 1 58.9 ? C1' DUT 1170 C 1 HETATM 10 C C2' DUT . . . J 4 21.539 -8.373 -9.17 1 59.17 ? C2' DUT 1170 C 1 HETATM 11 C C3' DUT . . . J 4 22.418 -7.316 -8.544 1 60.38 ? C3' DUT 1170 C 1 HETATM 12 C C4' DUT . . . J 4 23.407 -8.094 -7.718 1 62.63 ? C4' DUT 1170 C 1 HETATM 13 O O4' DUT . . . J 4 22.711 -9.322 -7.425 1 61.61 ? O4' DUT 1170 C 1 HETATM 14 O O3' DUT . . . J 4 22.602 -5.908 -8.478 1 61.74 ? O3' DUT 1170 C 1 HETATM 15 C C5' DUT . . . J 4 23.76 -7.953 -6.213 1 66.63 ? C5' DUT 1170 C 1 HETATM 16 O O5' DUT . . . J 4 22.459 -7.668 -5.389 1 71.53 ? O5' DUT 1170 C 1 HETATM 17 P PA DUT . . . J 4 22.901 -7.19 -3.939 1 74.39 ? PA DUT 1170 C 1 HETATM 18 O O1A DUT . . . J 4 23.743 -5.933 -3.902 1 74.99 ? O1A DUT 1170 C 1 HETATM 19 O O2A DUT . . . J 4 21.636 -7.117 -3.137 1 74.07 ? O2A DUT 1170 C 1 HETATM 20 O O3A DUT . . . J 4 23.43 -8.399 -2.977 1 75.45 ? O3A DUT 1170 C 1 HETATM 21 P PB DUT . . . J 4 24.798 -8.406 -2.12 1 77.3 ? PB DUT 1170 C 1 HETATM 22 O O1B DUT . . . J 4 24.888 -7.097 -1.392 1 77.08 ? O1B DUT 1170 C 1 HETATM 23 O O2B DUT . . . J 4 24.68 -9.532 -1.186 1 78.48 ? O2B DUT 1170 C 1 HETATM 24 O O3B DUT . . . J 4 26.055 -8.605 -3.057 1 79.02 ? O3B DUT 1170 C 1 HETATM 25 P PG DUT . . . J 4 26.939 -7.91 -4.217 1 81.8 ? PG DUT 1170 C 1 HETATM 26 O O1G DUT . . . J 4 28.15 -8.092 -3.373 1 81.25 ? O1G DUT 1170 C 1 HETATM 27 O O2G DUT . . . J 4 26.614 -6.453 -4.298 1 82.11 ? O2G DUT 1170 C 1 HETATM 28 O O3G DUT . . . J 4 27.217 -8.522 -5.596 1 82.4 ? O3G DUT 1170 C 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #