data_5J7I # _model_server_result.job_id R5rBtAz3cTrJ4iQBQsUKcA _model_server_result.datetime_utc '2024-11-23 21:52:35' _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 5j7i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 5J7I # _exptl.entry_id 5J7I _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 3 _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 90 _cell.entry_id 5J7I _cell.length_a 93.054 _cell.length_b 109.543 _cell.length_c 204.149 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5J7I _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 H 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 ILE 272 A ILE 272 1_555 A N SCY 273 A SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C SCY 273 A SCY 273 1_555 A N ALA 274 A ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 B C ILE 272 B ILE 272 1_555 B N SCY 273 B SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 B C SCY 273 B SCY 273 1_555 B N ALA 274 B ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 C C ILE 272 C ILE 272 1_555 C N SCY 273 C SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 C C SCY 273 C SCY 273 1_555 C N ALA 274 C ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 D C ILE 272 D ILE 272 1_555 D N SCY 273 D SCY 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale8 D C SCY 273 D SCY 273 1_555 D N ALA 274 D ALA 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? # _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 5J7I _atom_sites.fract_transf_matrix[1][1] 0.010746 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009129 _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] 0.004898 _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 2 ADP A 1 501 1 ADP ADP . F 3 APR B 1 501 2 APR APR . G 2 ADP C 1 501 3 ADP ADP . H 2 ADP D 1 501 4 ADP ADP . # 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 . . . G 2 20.787 5.03 -6.632 1 50.77 ? PB ADP 501 C 1 HETATM 2 O O1B ADP . . . G 2 21.972 4.493 -7.416 1 50.77 ? O1B ADP 501 C 1 HETATM 3 O O2B ADP . . . G 2 20.528 4.258 -5.349 1 50.77 ? O2B ADP 501 C 1 HETATM 4 O O3B ADP . . . G 2 20.762 6.535 -6.446 1 50.77 ? O3B ADP 501 C 1 HETATM 5 P PA ADP . . . G 2 19.263 5.31 -9.096 1 50.77 ? PA ADP 501 C 1 HETATM 6 O O1A ADP . . . G 2 20.553 5.77 -9.746 1 50.77 ? O1A ADP 501 C 1 HETATM 7 O O2A ADP . . . G 2 18.065 6.239 -9.084 1 50.77 ? O2A ADP 501 C 1 HETATM 8 O O3A ADP . . . G 2 19.508 4.723 -7.594 1 50.77 ? O3A ADP 501 C 1 HETATM 9 O O5' ADP . . . G 2 18.819 3.957 -9.85 1 50.77 ? O5' ADP 501 C 1 HETATM 10 C C5' ADP . . . G 2 18.21 4.005 -11.133 1 50.77 ? C5' ADP 501 C 1 HETATM 11 C C4' ADP . . . G 2 19.023 3.162 -12.108 1 50.77 ? C4' ADP 501 C 1 HETATM 12 O O4' ADP . . . G 2 18.251 2.988 -13.292 1 50.77 ? O4' ADP 501 C 1 HETATM 13 C C3' ADP . . . G 2 20.307 3.861 -12.538 1 50.77 ? C3' ADP 501 C 1 HETATM 14 O O3' ADP . . . G 2 21.292 2.906 -12.959 1 50.77 ? O3' ADP 501 C 1 HETATM 15 C C2' ADP . . . G 2 19.841 4.747 -13.679 1 50.77 ? C2' ADP 501 C 1 HETATM 16 O O2' ADP . . . G 2 20.834 4.972 -14.69 1 50.77 ? O2' ADP 501 C 1 HETATM 17 C C1' ADP . . . G 2 18.645 3.987 -14.245 1 50.77 ? C1' ADP 501 C 1 HETATM 18 N N9 ADP . . . G 2 17.495 4.897 -14.455 1 50.77 ? N9 ADP 501 C 1 HETATM 19 C C8 ADP . . . G 2 16.263 4.726 -13.911 1 50.77 ? C8 ADP 501 C 1 HETATM 20 N N7 ADP . . . G 2 15.437 5.723 -14.312 1 50.77 ? N7 ADP 501 C 1 HETATM 21 C C5 ADP . . . G 2 16.146 6.533 -15.118 1 50.77 ? C5 ADP 501 C 1 HETATM 22 C C6 ADP . . . G 2 15.881 7.763 -15.884 1 50.77 ? C6 ADP 501 C 1 HETATM 23 N N6 ADP . . . G 2 14.667 8.317 -15.837 1 50.77 ? N6 ADP 501 C 1 HETATM 24 N N1 ADP . . . G 2 16.874 8.325 -16.606 1 50.77 ? N1 ADP 501 C 1 HETATM 25 C C2 ADP . . . G 2 18.096 7.781 -16.66 1 50.77 ? C2 ADP 501 C 1 HETATM 26 N N3 ADP . . . G 2 18.426 6.646 -15.993 1 50.77 ? N3 ADP 501 C 1 HETATM 27 C C4 ADP . . . G 2 17.501 5.995 -15.224 1 50.77 ? C4 ADP 501 C 1 HETATM 28 H "H5'1" ADP . . . G 2 18.166 5.038 -11.484 1 19.86 ? "H5'1" ADP 501 C 1 HETATM 29 H "H5'2" ADP . . . G 2 17.189 3.621 -11.074 1 19.86 ? "H5'2" ADP 501 C 1 HETATM 30 H H4' ADP . . . G 2 19.264 2.192 -11.651 1 19.86 ? H4' ADP 501 C 1 HETATM 31 H H3' ADP . . . G 2 20.685 4.483 -11.715 1 19.86 ? H3' ADP 501 C 1 HETATM 32 H HO3' ADP . . . G 2 22.097 3.371 -13.227 1 19.86 ? HO3' ADP 501 C 1 HETATM 33 H H2' ADP . . . G 2 19.493 5.705 -13.269 1 19.86 ? H2' ADP 501 C 1 HETATM 34 H HO2' ADP . . . G 2 21.596 5.421 -14.299 1 19.86 ? HO2' ADP 501 C 1 HETATM 35 H H1' ADP . . . G 2 18.934 3.514 -15.193 1 19.86 ? H1' ADP 501 C 1 HETATM 36 H H8 ADP . . . G 2 15.981 3.912 -13.254 1 19.86 ? H8 ADP 501 C 1 HETATM 37 H HN61 ADP . . . G 2 14.478 9.164 -16.353 1 19.86 ? HN61 ADP 501 C 1 HETATM 38 H HN62 ADP . . . G 2 13.937 7.889 -15.285 1 19.86 ? HN62 ADP 501 C 1 HETATM 39 H H2 ADP . . . G 2 18.854 8.268 -17.262 1 19.86 ? H2 ADP 501 C 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 91 _model_server_stats.query_time_ms 671 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #