data_3NGU # _model_server_result.job_id OaUhUIH49HbfSwLzxnbqnw _model_server_result.datetime_utc '2024-12-27 01:35:58' _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 3ngu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":152}' # _entry.id 3NGU # _exptl.entry_id 3NGU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 3NGU _cell.length_a 123.213 _cell.length_b 123.213 _cell.length_c 137.983 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NGU _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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 # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3NGU _atom_sites.fract_transf_matrix[1][1] 0.008116 _atom_sites.fract_transf_matrix[1][2] 0.004686 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009372 _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] 0.007247 _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 ADP A 1 152 1 ADP ADP . D 2 ADP B 1 152 2 ADP ADP . E 3 HOH A 1 153 1 HOH HOH . E 3 HOH A 2 154 2 HOH HOH . E 3 HOH A 3 155 3 HOH HOH . E 3 HOH A 4 156 4 HOH HOH . E 3 HOH A 5 157 5 HOH HOH . E 3 HOH A 6 158 8 HOH HOH . E 3 HOH A 7 159 9 HOH HOH . E 3 HOH A 8 160 10 HOH HOH . E 3 HOH A 9 161 11 HOH HOH . E 3 HOH A 10 162 12 HOH HOH . E 3 HOH A 11 163 13 HOH HOH . E 3 HOH A 12 164 15 HOH HOH . E 3 HOH A 13 165 16 HOH HOH . E 3 HOH A 14 166 17 HOH HOH . E 3 HOH A 15 167 18 HOH HOH . E 3 HOH A 16 168 20 HOH HOH . E 3 HOH A 17 169 24 HOH HOH . E 3 HOH A 18 170 27 HOH HOH . E 3 HOH A 19 171 33 HOH HOH . E 3 HOH A 20 172 34 HOH HOH . E 3 HOH A 21 173 38 HOH HOH . E 3 HOH A 22 174 43 HOH HOH . E 3 HOH A 23 175 46 HOH HOH . E 3 HOH A 24 176 91 HOH HOH . E 3 HOH A 25 177 93 HOH HOH . F 3 HOH B 1 153 6 HOH HOH . F 3 HOH B 2 154 28 HOH HOH . F 3 HOH B 3 155 29 HOH HOH . F 3 HOH B 4 156 30 HOH HOH . F 3 HOH B 5 157 31 HOH HOH . F 3 HOH B 6 158 47 HOH HOH . F 3 HOH B 7 159 49 HOH HOH . F 3 HOH B 8 160 61 HOH HOH . F 3 HOH B 9 161 64 HOH HOH . F 3 HOH B 10 162 68 HOH HOH . F 3 HOH B 11 163 69 HOH HOH . F 3 HOH B 12 164 72 HOH HOH . F 3 HOH B 13 165 73 HOH HOH . F 3 HOH B 14 166 95 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 PB ADP . . . C 2 -15.885 -9.192 -5.732 1 55.23 ? PB ADP 152 A 1 HETATM 2 O O1B ADP . . . C 2 -15.36 -10.501 -5.102 1 62.84 ? O1B ADP 152 A 1 HETATM 3 O O2B ADP . . . C 2 -14.733 -8.178 -5.855 1 57.35 ? O2B ADP 152 A 1 HETATM 4 O O3B ADP . . . C 2 -16.509 -9.208 -7.143 1 60.21 ? O3B ADP 152 A 1 HETATM 5 P PA ADP . . . C 2 -18.254 -9.345 -3.975 1 59.66 ? PA ADP 152 A 1 HETATM 6 O O1A ADP . . . C 2 -18.171 -8.877 -2.443 1 56.53 ? O1A ADP 152 A 1 HETATM 7 O O2A ADP . . . C 2 -18.156 -10.843 -4.204 1 65.13 ? O2A ADP 152 A 1 HETATM 8 O O3A ADP . . . C 2 -16.947 -8.583 -4.693 1 60.27 ? O3A ADP 152 A 1 HETATM 9 O O5' ADP . . . C 2 -19.45 -8.602 -4.818 1 53.85 ? O5' ADP 152 A 1 HETATM 10 C C5' ADP . . . C 2 -19.808 -9.218 -6.118 1 55.14 ? C5' ADP 152 A 1 HETATM 11 C C4' ADP . . . C 2 -20.352 -8.163 -7.09 1 54.11 ? C4' ADP 152 A 1 HETATM 12 O O4' ADP . . . C 2 -21.479 -7.524 -6.456 1 57.48 ? O4' ADP 152 A 1 HETATM 13 C C3' ADP . . . C 2 -19.526 -6.868 -7.209 1 57.86 ? C3' ADP 152 A 1 HETATM 14 O O3' ADP . . . C 2 -18.455 -7.219 -8.005 1 52.64 ? O3' ADP 152 A 1 HETATM 15 C C2' ADP . . . C 2 -20.522 -5.844 -7.755 1 59.36 ? C2' ADP 152 A 1 HETATM 16 O O2' ADP . . . C 2 -20.833 -6.078 -9.155 1 62.17 ? O2' ADP 152 A 1 HETATM 17 C C1' ADP . . . C 2 -21.758 -6.248 -6.888 1 55.24 ? C1' ADP 152 A 1 HETATM 18 N N9 ADP . . . C 2 -21.691 -5.495 -5.642 1 56.85 ? N9 ADP 152 A 1 HETATM 19 C C8 ADP . . . C 2 -20.867 -5.703 -4.562 1 60.94 ? C8 ADP 152 A 1 HETATM 20 N N7 ADP . . . C 2 -20.956 -4.702 -3.613 1 58.93 ? N7 ADP 152 A 1 HETATM 21 C C5 ADP . . . C 2 -21.915 -3.83 -4.098 1 64.9 ? C5 ADP 152 A 1 HETATM 22 C C6 ADP . . . C 2 -22.579 -2.571 -3.653 1 69.16 ? C6 ADP 152 A 1 HETATM 23 N N6 ADP . . . C 2 -22.281 -1.96 -2.454 1 73.45 ? N6 ADP 152 A 1 HETATM 24 N N1 ADP . . . C 2 -23.471 -2.053 -4.56 1 70.28 ? N1 ADP 152 A 1 HETATM 25 C C2 ADP . . . C 2 -23.843 -2.583 -5.744 1 58.5 ? C2 ADP 152 A 1 HETATM 26 N N3 ADP . . . C 2 -23.284 -3.689 -6.181 1 57.16 ? N3 ADP 152 A 1 HETATM 27 C C4 ADP . . . C 2 -22.351 -4.332 -5.452 1 58.91 ? C4 ADP 152 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #