data_1S5G # _model_server_result.job_id 5mfJyHb2et-q37hLKDHfPA _model_server_result.datetime_utc '2024-10-18 14:35:44' _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 1s5g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":995}' # _entry.id 1S5G # _exptl.entry_id 1S5G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 98.36 _cell.angle_gamma 90 _cell.entry_id 1S5G _cell.length_a 84.051 _cell.length_b 50.935 _cell.length_c 161.59 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1S5G _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 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,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 # _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 metalc ? metalc1 B OD2 ASP 30 Y ASP 30 1_555 F MG MG . Y MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc2 B OD2 ASP 32 Y ASP 32 1_555 F MG MG . Y MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.997 ? metalc ? metalc3 B OD1 ASP 32 Y ASP 32 1_555 F MG MG . Y MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.84 ? metalc ? metalc4 B OD2 ASP 39 Y ASP 39 1_555 F MG MG . Y MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc5 C OD1 ASP 19 Z ASP 19 1_555 G CA CA . Z CA 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? metalc ? metalc6 C O ASP 19 Z ASP 19 1_555 G CA CA . Z CA 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? metalc ? metalc7 C OD2 ASP 22 Z ASP 22 1_555 G CA CA . Z CA 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc8 C O GLY 23 Z GLY 23 1_555 G CA CA . Z CA 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc9 C OD1 ASP 25 Z ASP 25 1_555 G CA CA . Z CA 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.163 ? metalc ? metalc10 C OD2 ASP 25 Z ASP 25 1_555 G CA CA . Z CA 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc11 C O ALA 27 Z ALA 27 1_555 G CA CA . Z CA 998 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? # _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 1S5G _atom_sites.fract_transf_matrix[1][1] 0.011898 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001748 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019633 _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] 0.006255 _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 D 4 SO4 A 1 996 996 SO4 SO4 . E 5 ADP A 1 995 995 ADP ADP . F 6 MG Y 1 999 999 MG MG . G 7 CA Z 1 998 998 CA CA . H 8 HOH A 1 997 997 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 . . . E 5 -10.091 -2.412 12.148 1 102.15 ? PB ADP 995 A 1 HETATM 2 O O1B ADP . . . E 5 -9.551 -1.111 11.829 1 71.79 ? O1B ADP 995 A 1 HETATM 3 O O2B ADP . . . E 5 -11.54 -2.58 11.514 1 97.59 ? O2B ADP 995 A 1 HETATM 4 O O3B ADP . . . E 5 -9.196 -3.604 11.696 1 60.94 ? O3B ADP 995 A 1 HETATM 5 P PA ADP . . . E 5 -11.434 -1.864 14.692 1 92.04 ? PA ADP 995 A 1 HETATM 6 O O1A ADP . . . E 5 -12.506 -1.036 13.99 1 73.02 ? O1A ADP 995 A 1 HETATM 7 O O2A ADP . . . E 5 -12.101 -3.003 15.408 1 79.06 ? O2A ADP 995 A 1 HETATM 8 O O3A ADP . . . E 5 -10.369 -2.451 13.719 1 90.85 ? O3A ADP 995 A 1 HETATM 9 O O5' ADP . . . E 5 -10.664 -0.954 15.805 1 91.46 ? O5' ADP 995 A 1 HETATM 10 C C5' ADP . . . E 5 -9.202 -0.777 15.702 1 88.32 ? C5' ADP 995 A 1 HETATM 11 C C4' ADP . . . E 5 -8.88 0.247 16.814 1 82.6 ? C4' ADP 995 A 1 HETATM 12 O O4' ADP . . . E 5 -7.929 -0.326 17.705 1 70.85 ? O4' ADP 995 A 1 HETATM 13 C C3' ADP . . . E 5 -8.239 1.559 16.299 1 75.69 ? C3' ADP 995 A 1 HETATM 14 O O3' ADP . . . E 5 -8.833 2.738 16.877 1 72.85 ? O3' ADP 995 A 1 HETATM 15 C C2' ADP . . . E 5 -6.748 1.436 16.613 1 65.18 ? C2' ADP 995 A 1 HETATM 16 O O2' ADP . . . E 5 -6.089 2.71 16.777 1 53.53 ? O2' ADP 995 A 1 HETATM 17 C C1' ADP . . . E 5 -6.749 0.511 17.835 1 60.77 ? C1' ADP 995 A 1 HETATM 18 N N9 ADP . . . E 5 -5.546 -0.429 17.982 1 72.53 ? N9 ADP 995 A 1 HETATM 19 C C8 ADP . . . E 5 -5.583 -1.583 18.699 1 84.83 ? C8 ADP 995 A 1 HETATM 20 N N7 ADP . . . E 5 -4.41 -2.187 18.663 1 78.8 ? N7 ADP 995 A 1 HETATM 21 C C5 ADP . . . E 5 -3.591 -1.469 17.945 1 79.44 ? C5 ADP 995 A 1 HETATM 22 C C6 ADP . . . E 5 -2.243 -1.587 17.552 1 81.9 ? C6 ADP 995 A 1 HETATM 23 N N6 ADP . . . E 5 -1.522 -2.641 17.951 1 77.01 ? N6 ADP 995 A 1 HETATM 24 N N1 ADP . . . E 5 -1.659 -0.61 16.758 1 90.25 ? N1 ADP 995 A 1 HETATM 25 C C2 ADP . . . E 5 -2.353 0.483 16.327 1 85.21 ? C2 ADP 995 A 1 HETATM 26 N N3 ADP . . . E 5 -3.663 0.613 16.7 1 79.18 ? N3 ADP 995 A 1 HETATM 27 C C4 ADP . . . E 5 -4.311 -0.32 17.488 1 82.06 ? C4 ADP 995 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #