data_3SZ4 # _model_server_result.job_id ay5lFGieBIXCWtUwCrefQg _model_server_result.datetime_utc '2024-11-14 08:12:45' _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 3sz4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":218}' # _entry.id 3SZ4 # _exptl.entry_id 3SZ4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 3 _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 90 _cell.angle_gamma 120 _cell.entry_id 3SZ4 _cell.length_a 108.327 _cell.length_b 108.327 _cell.length_c 47.824 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SZ4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 54.1635 -93.813934 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 108.327 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _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 metalc ? metalc1 A OD2 ASP 102 A ASP 102 1_555 B MG MG . A MG 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc2 A OE2 GLU 112 A GLU 112 1_555 B MG MG . A MG 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc3 A O ILE 113 A ILE 113 1_555 B MG MG . A MG 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? # _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 83 n n O5' P D5M sing 84 n n C5' C4' D5M sing 85 n n C5' "H5'1" D5M sing 86 n n C5' "H5'2" D5M sing 87 n n C4' O4' D5M sing 88 n n C4' C3' D5M sing 89 n n C4' H4' D5M sing 90 n n O4' C1' D5M sing 91 n n C3' O3' D5M sing 92 n n C3' C2' D5M sing 93 n n C3' H1 D5M sing 94 n n O3' H3' D5M sing 95 n n C2' C1' D5M sing 96 n n C2' "H2'1" D5M sing 97 n n C2' "H2'2" D5M sing 98 n n C1' N9 D5M sing 99 n n C1' H1' D5M sing 100 n n N9 C8 D5M sing 101 n y N9 C4 D5M sing 102 n y C8 N7 D5M doub 103 n y C8 H8 D5M sing 104 n n N7 C5 D5M sing 105 n y C5 C6 D5M sing 106 n y C5 C4 D5M doub 107 n y C6 N6 D5M sing 108 n n C6 N1 D5M doub 109 n y N6 HN61 D5M sing 110 n n N6 HN62 D5M sing 111 n n N1 C2 D5M sing 112 n y C2 N3 D5M doub 113 n y C2 H2 D5M sing 114 n n N3 C4 D5M sing 115 n y P O1P D5M doub 116 n n P O3P D5M sing 117 n n P O2P D5M sing 118 n n O3P H3P D5M sing 119 n n O2P H2P D5M sing 120 n n # _atom_sites.entry_id 3SZ4 _atom_sites.fract_transf_matrix[1][1] 0.009231 _atom_sites.fract_transf_matrix[1][2] 0.00533 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010659 _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] 0.02091 _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 MG A 1 217 210 MG MG . C 3 D5M A 1 218 211 D5M D5M . D 4 HOH A 1 219 219 HOH HOH . D 4 HOH A 2 220 220 HOH HOH . D 4 HOH A 3 221 221 HOH HOH . D 4 HOH A 4 222 222 HOH HOH . D 4 HOH A 5 223 223 HOH HOH . D 4 HOH A 6 224 224 HOH HOH . D 4 HOH A 7 225 225 HOH HOH . D 4 HOH A 8 226 226 HOH HOH . D 4 HOH A 9 227 227 HOH HOH . D 4 HOH A 10 228 228 HOH HOH . D 4 HOH A 11 229 212 HOH HOH . D 4 HOH A 12 230 213 HOH HOH . D 4 HOH A 13 231 214 HOH HOH . D 4 HOH A 14 232 215 HOH HOH . D 4 HOH A 15 233 216 HOH HOH . D 4 HOH A 16 234 217 HOH HOH . D 4 HOH A 17 235 218 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 3 35.283 -16.643 9.578 0.7 58.49 ? O5' D5M 218 A 1 HETATM 2 C C5' D5M . . . C 3 36.158 -17.504 10.318 0.7 61.46 ? C5' D5M 218 A 1 HETATM 3 C C4' D5M . . . C 3 37.327 -16.636 10.77 0.7 64.04 ? C4' D5M 218 A 1 HETATM 4 O O4' D5M . . . C 3 37.853 -17.079 12.009 0.7 65.69 ? O4' D5M 218 A 1 HETATM 5 C C3' D5M . . . C 3 38.485 -16.656 9.791 0.7 64.8 ? C3' D5M 218 A 1 HETATM 6 O O3' D5M . . . C 3 38.993 -15.326 9.73 0.7 63.78 ? O3' D5M 218 A 1 HETATM 7 C C2' D5M . . . C 3 39.557 -17.539 10.371 0.7 65.58 ? C2' D5M 218 A 1 HETATM 8 C C1' D5M . . . C 3 39.131 -17.68 11.823 0.7 67.81 ? C1' D5M 218 A 1 HETATM 9 N N9 D5M . . . C 3 38.925 -19.093 12.18 0.7 70.54 ? N9 D5M 218 A 1 HETATM 10 C C8 D5M . . . C 3 38.564 -20.099 11.362 0.7 71.53 ? C8 D5M 218 A 1 HETATM 11 N N7 D5M . . . C 3 38.467 -21.237 12.09 0.7 72.01 ? N7 D5M 218 A 1 HETATM 12 C C5 D5M . . . C 3 38.763 -20.912 13.368 0.7 73.09 ? C5 D5M 218 A 1 HETATM 13 C C6 D5M . . . C 3 38.827 -21.64 14.547 0.7 73.74 ? C6 D5M 218 A 1 HETATM 14 N N6 D5M . . . C 3 38.549 -22.964 14.506 0.7 73.6 ? N6 D5M 218 A 1 HETATM 15 N N1 D5M . . . C 3 39.155 -21.01 15.713 0.7 74.44 ? N1 D5M 218 A 1 HETATM 16 C C2 D5M . . . C 3 39.424 -19.685 15.749 0.7 74.06 ? C2 D5M 218 A 1 HETATM 17 N N3 D5M . . . C 3 39.367 -18.959 14.615 0.7 74.03 ? N3 D5M 218 A 1 HETATM 18 C C4 D5M . . . C 3 39.042 -19.555 13.424 0.7 72.45 ? C4 D5M 218 A 1 HETATM 19 P P D5M . . . C 3 34.051 -17.144 8.651 0.7 55.5 ? P D5M 218 A 1 HETATM 20 O O1P D5M . . . C 3 34.694 -18.159 7.762 0.7 56.28 ? O1P D5M 218 A 1 HETATM 21 O O3P D5M . . . C 3 33.576 -15.947 7.878 0.7 53.59 ? O3P D5M 218 A 1 HETATM 22 O O2P D5M . . . C 3 33.09 -17.707 9.656 0.7 52.14 ? O2P D5M 218 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 22 #