data_3QTB # _model_server_result.job_id 82Y1QhX7UYAAcUuQksOUog _model_server_result.datetime_utc '2025-03-06 07:18:16' _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 3qtb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":135}' # _entry.id 3QTB # _exptl.entry_id 3QTB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 116.82 _cell.angle_gamma 90 _cell.entry_id 3QTB _cell.length_a 109.607 _cell.length_b 42.655 _cell.length_c 61.289 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QTB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 covale ? covale1 A C MSE 22 A MSE 1 1_555 A N ILE 23 A ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 A C TYR 24 A TYR 3 1_555 A N MSE 25 A MSE 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C MSE 25 A MSE 4 1_555 A N PRO 26 A PRO 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale4 B C TYR 24 B TYR 3 1_555 B N MSE 25 B MSE 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale5 B C MSE 25 B MSE 4 1_555 B N PRO 26 B PRO 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? # _chem_comp.formula 'C10 H14 N5 O6 P' _chem_comp.formula_weight 331.222 _chem_comp.id D5M _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 O5' C5' D5M sing 89 n n O5' P D5M sing 90 n n C5' C4' D5M sing 91 n n C5' "H5'1" D5M sing 92 n n C5' "H5'2" D5M sing 93 n n C4' O4' D5M sing 94 n n C4' C3' D5M sing 95 n n C4' H4' D5M sing 96 n n O4' C1' D5M sing 97 n n C3' O3' D5M sing 98 n n C3' C2' D5M sing 99 n n C3' H1 D5M sing 100 n n O3' H3' D5M sing 101 n n C2' C1' D5M sing 102 n n C2' "H2'1" D5M sing 103 n n C2' "H2'2" D5M sing 104 n n C1' N9 D5M sing 105 n n C1' H1' D5M sing 106 n n N9 C8 D5M sing 107 n y N9 C4 D5M sing 108 n y C8 N7 D5M doub 109 n y C8 H8 D5M sing 110 n n N7 C5 D5M sing 111 n y C5 C6 D5M sing 112 n y C5 C4 D5M doub 113 n y C6 N6 D5M sing 114 n n C6 N1 D5M doub 115 n y N6 HN61 D5M sing 116 n n N6 HN62 D5M sing 117 n n N1 C2 D5M sing 118 n y C2 N3 D5M doub 119 n y C2 H2 D5M sing 120 n n N3 C4 D5M sing 121 n y P O1P D5M doub 122 n n P O3P D5M sing 123 n n P O2P D5M sing 124 n n O3P H3P D5M sing 125 n n O2P H2P D5M sing 126 n n # _atom_sites.entry_id 3QTB _atom_sites.fract_transf_matrix[1][1] 0.009124 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004612 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023444 _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] 0.018282 _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 D5M A 1 135 1 D5M D5M . D 3 ACT B 1 135 1 ACT ACT . E 3 ACT B 1 136 1 ACT ACT . F 3 ACT B 1 137 1 ACT ACT . G 4 HOH A 1 136 1 HOH HOH . G 4 HOH A 2 137 2 HOH HOH . G 4 HOH A 3 138 3 HOH HOH . G 4 HOH A 4 139 4 HOH HOH . G 4 HOH A 5 140 6 HOH HOH . G 4 HOH A 6 141 7 HOH HOH . G 4 HOH A 7 142 9 HOH HOH . G 4 HOH A 8 143 10 HOH HOH . G 4 HOH A 9 144 11 HOH HOH . G 4 HOH A 10 145 12 HOH HOH . G 4 HOH A 11 146 14 HOH HOH . G 4 HOH A 12 147 16 HOH HOH . G 4 HOH A 13 148 17 HOH HOH . G 4 HOH A 14 149 18 HOH HOH . G 4 HOH A 15 150 19 HOH HOH . G 4 HOH A 16 151 20 HOH HOH . G 4 HOH A 17 152 21 HOH HOH . G 4 HOH A 18 153 22 HOH HOH . G 4 HOH A 19 154 23 HOH HOH . G 4 HOH A 20 155 24 HOH HOH . G 4 HOH A 21 156 34 HOH HOH . G 4 HOH A 22 157 36 HOH HOH . G 4 HOH A 23 158 37 HOH HOH . G 4 HOH A 24 159 38 HOH HOH . G 4 HOH A 25 160 39 HOH HOH . G 4 HOH A 26 161 40 HOH HOH . G 4 HOH A 27 162 41 HOH HOH . G 4 HOH A 28 163 42 HOH HOH . G 4 HOH A 29 164 48 HOH HOH . G 4 HOH A 30 165 49 HOH HOH . H 4 HOH B 1 138 5 HOH HOH . H 4 HOH B 2 139 8 HOH HOH . H 4 HOH B 3 140 13 HOH HOH . H 4 HOH B 4 141 15 HOH HOH . H 4 HOH B 5 142 25 HOH HOH . H 4 HOH B 6 143 26 HOH HOH . H 4 HOH B 7 144 27 HOH HOH . H 4 HOH B 8 145 28 HOH HOH . H 4 HOH B 9 146 29 HOH HOH . H 4 HOH B 10 147 30 HOH HOH . H 4 HOH B 11 148 31 HOH HOH . H 4 HOH B 12 149 32 HOH HOH . H 4 HOH B 13 150 33 HOH HOH . H 4 HOH B 14 151 35 HOH HOH . H 4 HOH B 15 152 43 HOH HOH . H 4 HOH B 16 153 44 HOH HOH . H 4 HOH B 17 154 45 HOH HOH . H 4 HOH B 18 155 46 HOH HOH . H 4 HOH B 19 156 47 HOH HOH . H 4 HOH B 20 157 50 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 O O5' D5M . . . C 2 19.354 15.168 -8.715 1 79.49 ? O5' D5M 135 A 1 HETATM 2 C C5' D5M . . . C 2 19.553 16.576 -8.596 1 68.92 ? C5' D5M 135 A 1 HETATM 3 C C4' D5M . . . C 2 18.232 17.359 -8.605 1 67.14 ? C4' D5M 135 A 1 HETATM 4 O O4' D5M . . . C 2 17.218 16.564 -9.225 1 65.82 ? O4' D5M 135 A 1 HETATM 5 C C3' D5M . . . C 2 17.712 17.766 -7.222 1 58.32 ? C3' D5M 135 A 1 HETATM 6 O O3' D5M . . . C 2 17.132 19.09 -7.19 1 49.06 ? O3' D5M 135 A 1 HETATM 7 C C2' D5M . . . C 2 16.64 16.742 -6.945 1 57.51 ? C2' D5M 135 A 1 HETATM 8 C C1' D5M . . . C 2 16.112 16.425 -8.341 1 58.72 ? C1' D5M 135 A 1 HETATM 9 N N9 D5M . . . C 2 15.554 15.058 -8.432 1 64.9 ? N9 D5M 135 A 1 HETATM 10 C C8 D5M . . . C 2 16.223 13.884 -8.347 1 67.24 ? C8 D5M 135 A 1 HETATM 11 N N7 D5M . . . C 2 15.37 12.829 -8.471 1 64.41 ? N7 D5M 135 A 1 HETATM 12 C C5 D5M . . . C 2 14.126 13.324 -8.64 1 67.9 ? C5 D5M 135 A 1 HETATM 13 C C6 D5M . . . C 2 12.75 12.78 -8.835 1 64.87 ? C6 D5M 135 A 1 HETATM 14 N N6 D5M . . . C 2 12.506 11.448 -8.873 1 63.07 ? N6 D5M 135 A 1 HETATM 15 N N1 D5M . . . C 2 11.738 13.673 -8.976 1 63.38 ? N1 D5M 135 A 1 HETATM 16 C C2 D5M . . . C 2 11.949 15.011 -8.934 1 62.88 ? C2 D5M 135 A 1 HETATM 17 N N3 D5M . . . C 2 13.159 15.571 -8.764 1 64.72 ? N3 D5M 135 A 1 HETATM 18 C C4 D5M . . . C 2 14.264 14.797 -8.617 1 68.41 ? C4 D5M 135 A 1 HETATM 19 P P D5M . . . C 2 20.612 14.168 -8.88 1 88.01 ? P D5M 135 A 1 HETATM 20 O O1P D5M . . . C 2 21.551 14.553 -7.76 1 101.44 ? O1P D5M 135 A 1 HETATM 21 O O3P D5M . . . C 2 20.043 12.768 -8.774 1 84.54 ? O3P D5M 135 A 1 HETATM 22 O O2P D5M . . . C 2 21.153 14.532 -10.241 1 84.29 ? O2P D5M 135 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #