data_4G06 # _model_server_result.job_id T10hlGiuRXo9WmgFz6RNiA _model_server_result.datetime_utc '2024-11-15 11:49:00' _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 4g06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":102}' # _entry.id 4G06 # _exptl.entry_id 4G06 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 90 _cell.angle_gamma 90 _cell.entry_id 4G06 _cell.length_a 62.722 _cell.length_b 62.722 _cell.length_c 73.441 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4G06 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 D 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 covale ? covale1 A C LYS 57 A LYS 57 1_555 A N MSE 58 A MSE 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 58 A MSE 58 1_555 A N GLY 59 A GLY 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C THR 71 A THR 71 1_555 A N MSE 72 A MSE 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale4 A C MSE 72 A MSE 72 1_555 A N VAL 73 A VAL 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 B C LYS 57 B LYS 57 1_555 B N MSE 58 B MSE 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 B C MSE 58 B MSE 58 1_555 B N GLY 59 B GLY 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 B C THR 71 B THR 71 1_555 B N MSE 72 B MSE 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 B C MSE 72 B MSE 72 1_555 B N VAL 73 B VAL 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id DT _chem_comp.mon_nstd_flag y _chem_comp.name "THYMIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _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 OP3 P DT sing 70 n n OP3 HOP3 DT sing 71 n n P OP1 DT doub 72 n n P OP2 DT sing 73 n n P O5' DT sing 74 n n OP2 HOP2 DT sing 75 n n O5' C5' DT sing 76 n n C5' C4' DT sing 77 n n C5' H5' DT sing 78 n n C5' "H5''" DT sing 79 n n C4' O4' DT sing 80 n n C4' C3' DT sing 81 n n C4' H4' DT sing 82 n n O4' C1' DT sing 83 n n C3' O3' DT sing 84 n n C3' C2' DT sing 85 n n C3' H3' DT sing 86 n n O3' HO3' DT sing 87 n n C2' C1' DT sing 88 n n C2' H2' DT sing 89 n n C2' "H2''" DT sing 90 n n C1' N1 DT sing 91 n n C1' H1' DT sing 92 n n N1 C2 DT sing 93 n n N1 C6 DT sing 94 n n C2 O2 DT doub 95 n n C2 N3 DT sing 96 n n N3 C4 DT sing 97 n n N3 H3 DT sing 98 n n C4 O4 DT doub 99 n n C4 C5 DT sing 100 n n C5 C7 DT sing 101 n n C5 C6 DT doub 102 n n C7 H71 DT sing 103 n n C7 H72 DT sing 104 n n C7 H73 DT sing 105 n n C6 H6 DT sing 106 n n # _atom_sites.entry_id 4G06 _atom_sites.fract_transf_matrix[1][1] 0.015943 _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] 0.015943 _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] 0.013616 _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 DT A 1 101 6 DT DT . D 2 DT A 1 102 7 DT DT . E 3 PEG B 1 101 1 PEG PEG . F 4 HOH A 1 201 1 HOH HOH . G 4 HOH B 1 201 2 HOH HOH . G 4 HOH B 2 202 3 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 P P DT . . . D 2 -0.816 27.381 -8.209 1 34.38 ? P DT 102 A 1 HETATM 2 O OP1 DT . . . D 2 -1.975 26.586 -7.752 1 31.07 ? OP1 DT 102 A 1 HETATM 3 O OP2 DT . . . D 2 -1.061 28.793 -8.57 1 38.6 ? OP2 DT 102 A 1 HETATM 4 O O5' DT . . . D 2 0.335 27.283 -7.086 1 35.76 ? O5' DT 102 A 1 HETATM 5 C C5' DT . . . D 2 -0.044 27.599 -5.731 1 39.12 ? C5' DT 102 A 1 HETATM 6 C C4' DT . . . D 2 1.003 27.225 -4.692 1 36.76 ? C4' DT 102 A 1 HETATM 7 O O4' DT . . . D 2 2.259 27.064 -5.374 1 34.16 ? O4' DT 102 A 1 HETATM 8 C C3' DT . . . D 2 1.268 28.238 -3.574 1 34.05 ? C3' DT 102 A 1 HETATM 9 O O3' DT . . . D 2 1.564 27.569 -2.354 1 25.62 ? O3' DT 102 A 1 HETATM 10 C C2' DT . . . D 2 2.462 29.05 -4.09 1 38.79 ? C2' DT 102 A 1 HETATM 11 C C1' DT . . . D 2 3.103 28.177 -5.174 1 35.76 ? C1' DT 102 A 1 HETATM 12 N N1 DT . . . D 2 3.384 28.805 -6.533 1 40.18 ? N1 DT 102 A 1 HETATM 13 C C2 DT . . . D 2 3.36 27.998 -7.652 1 41.68 ? C2 DT 102 A 1 HETATM 14 O O2 DT . . . D 2 3.119 26.808 -7.659 1 40.26 ? O2 DT 102 A 1 HETATM 15 N N3 DT . . . D 2 3.64 28.633 -8.832 1 53.47 ? N3 DT 102 A 1 HETATM 16 C C4 DT . . . D 2 3.93 29.964 -9.062 1 57.42 ? C4 DT 102 A 1 HETATM 17 O O4 DT . . . D 2 4.16 30.446 -10.18 1 58.14 ? O4 DT 102 A 1 HETATM 18 C C5 DT . . . D 2 3.94 30.755 -7.871 1 52.87 ? C5 DT 102 A 1 HETATM 19 C C7 DT . . . D 2 4.234 32.203 -8.081 1 56.8 ? C7 DT 102 A 1 HETATM 20 C C6 DT . . . D 2 3.677 30.16 -6.681 1 49.36 ? C6 DT 102 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #