data_3LFM # _model_server_result.job_id YDJqn9fCMTP6VmvFAQh0Qw _model_server_result.datetime_utc '2024-11-23 20:04:48' _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 3lfm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":506}' # _entry.id 3LFM # _exptl.entry_id 3LFM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 256.255 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-methylthymidine _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 3LFM _cell.length_a 142.86 _cell.length_b 142.86 _cell.length_c 83.8 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LFM _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _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 NE2 HIS 221 A HIS 231 1_555 D FE FE2 . A FE2 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc2 A OD1 ASP 223 A ASP 233 1_555 D FE FE2 . A FE2 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc3 A NE2 HIS 297 A HIS 307 1_555 D FE FE2 . A FE2 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc4 D FE FE2 . A FE2 507 1_555 C O2' OGA . A OGA 1550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc5 D FE FE2 . A FE2 507 1_555 C O2 OGA . A OGA 1550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? # _chem_comp.formula 'C11 H16 N2 O5' _chem_comp.formula_weight 256.255 _chem_comp.id 3DT _chem_comp.mon_nstd_flag . _chem_comp.name 3-methylthymidine _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 3DT sing 1 n n N1 C6 3DT sing 2 n n N1 C1' 3DT sing 3 n n C2 O2 3DT doub 4 n n C2 N3 3DT sing 5 n n N3 C4 3DT sing 6 n n N3 CN 3DT sing 7 n n C4 O4 3DT doub 8 n n C4 C5 3DT sing 9 n n C5 C6 3DT doub 10 n n C5 C7 3DT sing 11 n n C1' C2' 3DT sing 12 n n C1' O4' 3DT sing 13 n n C2' C3' 3DT sing 14 n n C3' O3' 3DT sing 15 n n C3' C4' 3DT sing 16 n n C4' O4' 3DT sing 17 n n C4' C5' 3DT sing 18 n n C5' O5' 3DT sing 19 n n C6 H6 3DT sing 20 n n C7 H7 3DT sing 21 n n C7 H7A 3DT sing 22 n n C7 H7B 3DT sing 23 n n CN HN 3DT sing 24 n n CN HNA 3DT sing 25 n n CN HNB 3DT sing 26 n n C1' H1' 3DT sing 27 n n C2' H2' 3DT sing 28 n n C2' "H2'A" 3DT sing 29 n n C3' H3' 3DT sing 30 n n O3' HO3' 3DT sing 31 n n C4' H4' 3DT sing 32 n n C5' H5' 3DT sing 33 n n C5' "H5'A" 3DT sing 34 n n O5' HO5' 3DT sing 35 n n # _atom_sites.entry_id 3LFM _atom_sites.fract_transf_matrix[1][1] 0.007 _atom_sites.fract_transf_matrix[1][2] 0.004041 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008083 _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] 0.011933 _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 3DT A 1 506 503 3DT DT . C 3 OGA A 1 1550 1550 OGA OGA . D 4 FE2 A 1 507 300 FE2 FE2 . # 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 3DT . . . B 2 29.108 -6.783 -28.872 1 101.96 ? N1 3DT 506 A 1 HETATM 2 C C2 3DT . . . B 2 28.562 -7.304 -27.696 1 101.44 ? C2 3DT 506 A 1 HETATM 3 O O2 3DT . . . B 2 29.168 -8.166 -27.06 1 100.78 ? O2 3DT 506 A 1 HETATM 4 N N3 3DT . . . B 2 27.299 -6.87 -27.269 1 101.21 ? N3 3DT 506 A 1 HETATM 5 C C4 3DT . . . B 2 26.591 -5.928 -28.024 1 100.49 ? C4 3DT 506 A 1 HETATM 6 O O4 3DT . . . B 2 25.481 -5.553 -27.648 1 98.06 ? O4 3DT 506 A 1 HETATM 7 C C5 3DT . . . B 2 27.139 -5.417 -29.197 1 100.21 ? C5 3DT 506 A 1 HETATM 8 C C6 3DT . . . B 2 28.394 -5.841 -29.62 1 100.82 ? C6 3DT 506 A 1 HETATM 9 C C7 3DT . . . B 2 26.367 -4.394 -30.03 1 98.76 ? C7 3DT 506 A 1 HETATM 10 C CN 3DT . . . B 2 26.719 -7.394 -26.012 1 100.56 ? CN 3DT 506 A 1 HETATM 11 C C1' 3DT . . . B 2 30.449 -7.219 -29.331 1 103.05 ? C1' 3DT 506 A 1 HETATM 12 C C2' 3DT . . . B 2 30.388 -8.224 -30.476 1 104.38 ? C2' 3DT 506 A 1 HETATM 13 C C3' 3DT . . . B 2 31.877 -8.208 -30.811 1 104.87 ? C3' 3DT 506 A 1 HETATM 14 O O3' 3DT . . . B 2 32.604 -8.894 -29.787 1 106.06 ? O3' 3DT 506 A 1 HETATM 15 C C4' 3DT . . . B 2 32.17 -6.708 -30.789 1 105.24 ? C4' 3DT 506 A 1 HETATM 16 O O4' 3DT . . . B 2 31.208 -6.131 -29.884 1 103.98 ? O4' 3DT 506 A 1 HETATM 17 C C5' 3DT . . . B 2 31.936 -6.097 -32.174 1 105.09 ? C5' 3DT 506 A 1 HETATM 18 O O5' 3DT . . . B 2 30.63 -6.432 -32.645 1 105.49 ? O5' 3DT 506 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 18 #