data_3PFI # _model_server_result.job_id vd4rGrkB5eWoX-j5_nUdGg _model_server_result.datetime_utc '2024-10-19 12:24:35' _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 3pfi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":336}' # _entry.id 3PFI # _exptl.entry_id 3PFI _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 3PFI _cell.length_a 111.482 _cell.length_b 111.482 _cell.length_c 355.089 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PFI _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 1 A,B,C,D,E,F 2 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 # 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 GLU 78 A GLU 75 1_555 A N MSE 79 A MSE 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C MSE 79 A MSE 76 1_555 A N SER 80 A SER 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C PRO 89 A PRO 86 1_555 A N MSE 90 A MSE 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 90 A MSE 87 1_555 A N ILE 91 A ILE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C ALA 129 A ALA 126 1_555 A N MSE 130 A MSE 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C MSE 130 A MSE 127 1_555 A N GLU 131 A GLU 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C GLY 165 A GLY 162 1_555 A N MSE 166 A MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 A C MSE 166 A MSE 163 1_555 A N LEU 167 A LEU 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale9 A C GLY 176 A GLY 173 1_555 A N MSE 177 A MSE 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale10 A C MSE 177 A MSE 174 1_555 A N GLN 178 A GLN 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 A C ALA 263 A ALA 260 1_555 A N MSE 264 A MSE 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale12 A C MSE 264 A MSE 261 1_555 A N ASP 265 A ASP 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 B C GLU 78 B GLU 75 1_555 B N MSE 79 B MSE 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 B C MSE 79 B MSE 76 1_555 B N SER 80 B SER 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 B C PRO 89 B PRO 86 1_555 B N MSE 90 B MSE 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale16 B C MSE 90 B MSE 87 1_555 B N ILE 91 B ILE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale17 B C ALA 129 B ALA 126 1_555 B N MSE 130 B MSE 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale18 B C MSE 130 B MSE 127 1_555 B N GLU 131 B GLU 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale19 B C GLY 165 B GLY 162 1_555 B N MSE 166 B MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale20 B C MSE 166 B MSE 163 1_555 B N LEU 167 B LEU 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale21 B C GLY 176 B GLY 173 1_555 B N MSE 177 B MSE 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale22 B C MSE 177 B MSE 174 1_555 B N GLN 178 B GLN 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale23 B C ALA 263 B ALA 260 1_555 B N MSE 264 B MSE 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale24 B C MSE 264 B MSE 261 1_555 B N ASP 265 B ASP 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? # _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 ? # _atom_sites.entry_id 3PFI _atom_sites.fract_transf_matrix[1][1] 0.00897 _atom_sites.fract_transf_matrix[1][2] 0.005179 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010358 _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] 0.002816 _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 1 336 1 ADP ADP . D 2 ADP B 1 336 2 ADP ADP . E 3 HOH A 1 337 4 HOH HOH . E 3 HOH A 2 338 5 HOH HOH . E 3 HOH A 3 339 7 HOH HOH . E 3 HOH A 4 340 8 HOH HOH . E 3 HOH A 5 341 9 HOH HOH . E 3 HOH A 6 342 10 HOH HOH . E 3 HOH A 7 343 11 HOH HOH . E 3 HOH A 8 344 12 HOH HOH . E 3 HOH A 9 345 14 HOH HOH . E 3 HOH A 10 346 18 HOH HOH . E 3 HOH A 11 347 20 HOH HOH . E 3 HOH A 12 348 21 HOH HOH . E 3 HOH A 13 349 25 HOH HOH . E 3 HOH A 14 350 26 HOH HOH . E 3 HOH A 15 351 27 HOH HOH . E 3 HOH A 16 352 29 HOH HOH . E 3 HOH A 17 353 30 HOH HOH . E 3 HOH A 18 354 31 HOH HOH . E 3 HOH A 19 355 32 HOH HOH . E 3 HOH A 20 356 33 HOH HOH . F 3 HOH B 1 337 3 HOH HOH . F 3 HOH B 2 338 6 HOH HOH . F 3 HOH B 3 339 13 HOH HOH . F 3 HOH B 4 340 15 HOH HOH . F 3 HOH B 5 341 16 HOH HOH . F 3 HOH B 6 342 17 HOH HOH . F 3 HOH B 7 343 19 HOH HOH . F 3 HOH B 8 344 22 HOH HOH . F 3 HOH B 9 345 23 HOH HOH . F 3 HOH B 10 346 24 HOH HOH . F 3 HOH B 11 347 28 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 . . . D 2 9.787 30.779 152.029 1 50.64 ? PB ADP 336 B 1 HETATM 2 O O1B ADP . . . D 2 8.887 31.136 150.869 1 50.01 ? O1B ADP 336 B 1 HETATM 3 O O2B ADP . . . D 2 9.122 30.855 153.384 1 51.22 ? O2B ADP 336 B 1 HETATM 4 O O3B ADP . . . D 2 10.616 29.542 151.785 1 52.16 ? O3B ADP 336 B 1 HETATM 5 P PA ADP . . . D 2 11.183 32.703 153.484 1 52.65 ? PA ADP 336 B 1 HETATM 6 O O1A ADP . . . D 2 10.083 33.704 153.748 1 59.47 ? O1A ADP 336 B 1 HETATM 7 O O2A ADP . . . D 2 11.504 31.628 154.489 1 60.1 ? O2A ADP 336 B 1 HETATM 8 O O3A ADP . . . D 2 10.868 31.965 152.087 1 49.07 ? O3A ADP 336 B 1 HETATM 9 O O5' ADP . . . D 2 12.531 33.528 153.191 1 50.04 ? O5' ADP 336 B 1 HETATM 10 C C5' ADP . . . D 2 13.408 33.059 152.168 1 52.64 ? C5' ADP 336 B 1 HETATM 11 C C4' ADP . . . D 2 14.733 33.799 152.198 1 48.69 ? C4' ADP 336 B 1 HETATM 12 O O4' ADP . . . D 2 14.757 34.716 151.105 1 49.94 ? O4' ADP 336 B 1 HETATM 13 C C3' ADP . . . D 2 14.926 34.608 153.471 1 48.08 ? C3' ADP 336 B 1 HETATM 14 O O3' ADP . . . D 2 16.279 34.536 153.918 1 45.1 ? O3' ADP 336 B 1 HETATM 15 C C2' ADP . . . D 2 14.626 36.037 153.089 1 50.77 ? C2' ADP 336 B 1 HETATM 16 O O2' ADP . . . D 2 15.563 36.928 153.693 1 56.79 ? O2' ADP 336 B 1 HETATM 17 C C1' ADP . . . D 2 14.769 36.069 151.58 1 50.02 ? C1' ADP 336 B 1 HETATM 18 N N9 ADP . . . D 2 13.671 36.857 150.98 1 44.63 ? N9 ADP 336 B 1 HETATM 19 C C8 ADP . . . D 2 12.467 36.394 150.618 1 43.86 ? C8 ADP 336 B 1 HETATM 20 N N7 ADP . . . D 2 11.751 37.42 150.108 1 44.25 ? N7 ADP 336 B 1 HETATM 21 C C5 ADP . . . D 2 12.521 38.523 150.158 1 38.65 ? C5 ADP 336 B 1 HETATM 22 C C6 ADP . . . D 2 12.325 39.836 149.781 1 35.4 ? C6 ADP 336 B 1 HETATM 23 N N6 ADP . . . D 2 11.151 40.216 149.237 1 42.27 ? N6 ADP 336 B 1 HETATM 24 N N1 ADP . . . D 2 13.315 40.731 149.961 1 41.25 ? N1 ADP 336 B 1 HETATM 25 C C2 ADP . . . D 2 14.484 40.355 150.499 1 42.77 ? C2 ADP 336 B 1 HETATM 26 N N3 ADP . . . D 2 14.697 39.088 150.873 1 42.85 ? N3 ADP 336 B 1 HETATM 27 C C4 ADP . . . D 2 13.731 38.159 150.709 1 39.85 ? C4 ADP 336 B 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #