data_1MQ2 # _model_server_result.job_id E8EKd9ESJFlcMh2dAHXgeA _model_server_result.datetime_utc '2025-03-05 02:21:14' _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 1mq2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":338}' # _entry.id 1MQ2 # _exptl.entry_id 1MQ2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 5 _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 106.1 _cell.angle_gamma 90 _cell.entry_id 1MQ2 _cell.length_a 55.2 _cell.length_b 81 _cell.length_c 55.6 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MQ2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 5 _struct_asym.id E _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 O3' DC 5 T DC 5 1_555 A P 8OG 6 T 8OG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? covale ? covale2 A O3' 8OG 6 T 8OG 6 1_555 A P DT 7 T DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale3 B O3' DG 9 P DG 9 1_555 B P 2DA 10 P 2DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? metalc ? metalc1 B OP1 DG 9 P DG 9 1_555 F NA NA . A NA 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc2 C OP1 DC 3 D DC 3 1_555 G NA NA . A NA 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc3 H O HOH . D HOH 346 1_555 G NA NA . A NA 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc4 D O LYS 60 A LYS 60 1_555 G NA NA . A NA 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc5 D O LEU 62 A LEU 62 1_555 G NA NA . A NA 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc6 D O VAL 65 A VAL 65 1_555 G NA NA . A NA 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc7 D O THR 101 A THR 101 1_555 F NA NA . A NA 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc8 D O VAL 103 A VAL 103 1_555 F NA NA . A NA 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc9 D O ILE 106 A ILE 106 1_555 F NA NA . A NA 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc10 F NA NA . A NA 341 1_555 I O HOH . A HOH 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc11 F NA NA . A NA 341 1_555 I O HOH . A HOH 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc12 G NA NA . A NA 342 1_555 I O HOH . A HOH 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 T DC 1 1_555 C N1 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 T DC 1 1_555 C O6 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 T DC 1 1_555 C N2 DG 5 D DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DC 2 T DC 2 1_555 C N1 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 DC 2 T DC 2 1_555 C O6 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 DC 2 T DC 2 1_555 C N2 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DG 3 T DG 3 1_555 C N3 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 DG 3 T DG 3 1_555 C O2 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 DG 3 T DG 3 1_555 C N4 DC 3 D DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DA 4 T DA 4 1_555 C N3 DT 2 D DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 DA 4 T DA 4 1_555 C O4 DT 2 D DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DC 5 T DC 5 1_555 C N1 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 DC 5 T DC 5 1_555 C O6 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 DC 5 T DC 5 1_555 C N2 DG 1 D DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DT 7 T DT 7 1_555 B N1 2DA 10 P 2DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O4 DT 7 T DT 7 1_555 B N6 2DA 10 P 2DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 DC 8 T DC 8 1_555 B N1 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N4 DC 8 T DC 8 1_555 B O6 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O2 DC 8 T DC 8 1_555 B N2 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 DG 9 T DG 9 1_555 B N3 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 DG 9 T DG 9 1_555 B O2 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 DG 9 T DG 9 1_555 B N4 DC 8 P DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N3 DC 10 T DC 10 1_555 B N1 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N4 DC 10 T DC 10 1_555 B O6 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A O2 DC 10 T DC 10 1_555 B N2 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog26 A N1 DA 11 T DA 11 1_555 B N3 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 DT 12 T DT 12 1_555 B N1 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O4 DT 12 T DT 12 1_555 B N6 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N3 DC 13 T DC 13 1_555 B N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N4 DC 13 T DC 13 1_555 B O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A O2 DC 13 T DC 13 1_555 B N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N1 DA 14 T DA 14 1_555 B N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N6 DA 14 T DA 14 1_555 B O4 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N1 DG 15 T DG 15 1_555 B N3 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N2 DG 15 T DG 15 1_555 B O2 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A O6 DG 15 T DG 15 1_555 B N4 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A N3 DC 16 T DC 16 1_555 B N1 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 A N4 DC 16 T DC 16 1_555 B O6 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 A O2 DC 16 T DC 16 1_555 B N2 DG 1 P DG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 160 n n O5' P D5M sing 161 n n C5' C4' D5M sing 162 n n C5' "H5'1" D5M sing 163 n n C5' "H5'2" D5M sing 164 n n C4' O4' D5M sing 165 n n C4' C3' D5M sing 166 n n C4' H4' D5M sing 167 n n O4' C1' D5M sing 168 n n C3' O3' D5M sing 169 n n C3' C2' D5M sing 170 n n C3' H1 D5M sing 171 n n O3' H3' D5M sing 172 n n C2' C1' D5M sing 173 n n C2' "H2'1" D5M sing 174 n n C2' "H2'2" D5M sing 175 n n C1' N9 D5M sing 176 n n C1' H1' D5M sing 177 n n N9 C8 D5M sing 178 n y N9 C4 D5M sing 179 n y C8 N7 D5M doub 180 n y C8 H8 D5M sing 181 n n N7 C5 D5M sing 182 n y C5 C6 D5M sing 183 n y C5 C4 D5M doub 184 n y C6 N6 D5M sing 185 n n C6 N1 D5M doub 186 n y N6 HN61 D5M sing 187 n n N6 HN62 D5M sing 188 n n N1 C2 D5M sing 189 n y C2 N3 D5M doub 190 n y C2 H2 D5M sing 191 n n N3 C4 D5M sing 192 n y P O1P D5M doub 193 n n P O3P D5M sing 194 n n P O2P D5M sing 195 n n O3P H3P D5M sing 196 n n O2P H2P D5M sing 197 n n # _atom_sites.entry_id 1MQ2 _atom_sites.fract_transf_matrix[1][1] 0.018116 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005229 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012346 _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] 0.01872 _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 E 5 D5M T 1 338 338 D5M A . F 6 NA A 1 341 341 NA NA . G 6 NA A 1 342 342 NA NA . H 7 HOH D 1 346 346 HOH HOH . I 7 HOH A 1 344 344 HOH HOH . I 7 HOH A 2 345 345 HOH HOH . I 7 HOH A 3 347 347 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 . . . E 5 11.458 3.385 9.861 0.5 54.09 ? O5' D5M 338 T 1 HETATM 2 C C5' D5M . . . E 5 12.536 4.2 9.404 0.5 54.02 ? C5' D5M 338 T 1 HETATM 3 C C4' D5M . . . E 5 12.124 4.967 8.169 0.5 53.96 ? C4' D5M 338 T 1 HETATM 4 O O4' D5M . . . E 5 13.14 5.949 7.854 0.5 53.85 ? O4' D5M 338 T 1 HETATM 5 C C3' D5M . . . E 5 11.949 4.106 6.914 0.5 53.95 ? C3' D5M 338 T 1 HETATM 6 O O3' D5M . . . E 5 10.718 4.426 6.258 0.5 53.65 ? O3' D5M 338 T 1 HETATM 7 C C2' D5M . . . E 5 13.136 4.479 6.041 0.5 53.79 ? C2' D5M 338 T 1 HETATM 8 C C1' D5M . . . E 5 13.434 5.903 6.47 0.5 53.66 ? C1' D5M 338 T 1 HETATM 9 N N9 D5M . . . E 5 14.831 6.302 6.294 0.5 53.34 ? N9 D5M 338 T 1 HETATM 10 C C8 D5M . . . E 5 15.932 5.829 6.966 0.5 53.08 ? C8 D5M 338 T 1 HETATM 11 N N7 D5M . . . E 5 17.06 6.374 6.581 0.5 52.92 ? N7 D5M 338 T 1 HETATM 12 C C5 D5M . . . E 5 16.679 7.267 5.59 0.5 53.03 ? C5 D5M 338 T 1 HETATM 13 C C6 D5M . . . E 5 17.412 8.156 4.782 0.5 52.98 ? C6 D5M 338 T 1 HETATM 14 N N6 D5M . . . E 5 18.739 8.293 4.846 0.5 52.83 ? N6 D5M 338 T 1 HETATM 15 N N1 D5M . . . E 5 16.727 8.907 3.892 0.5 52.86 ? N1 D5M 338 T 1 HETATM 16 C C2 D5M . . . E 5 15.397 8.768 3.827 0.5 52.76 ? C2 D5M 338 T 1 HETATM 17 N N3 D5M . . . E 5 14.597 7.969 4.53 0.5 53 ? N3 D5M 338 T 1 HETATM 18 C C4 D5M . . . E 5 15.308 7.236 5.404 0.5 53.09 ? C4 D5M 338 T 1 HETATM 19 P P D5M . . . E 5 11.281 3.052 11.41 0.5 54.46 ? P D5M 338 T 1 HETATM 20 O O1P D5M . . . E 5 12.599 2.602 11.927 0.5 54.47 ? O1P D5M 338 T 1 HETATM 21 O O3P D5M . . . E 5 10.97 4.335 12.092 0.5 54.38 ? O3P D5M 338 T 1 HETATM 22 O O2P D5M . . . E 5 10.099 2.163 11.551 0.5 54.11 ? O2P D5M 338 T 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #