data_8C1M # _model_server_result.job_id jWY7YD28pL8y1wKWR5dyMg _model_server_result.datetime_utc '2024-10-10 03:23:48' _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 8c1m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 8C1M # _exptl.entry_id 8C1M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 90 _cell.angle_gamma 90 _cell.entry_id 8C1M _cell.length_a 82.82 _cell.length_b 82.82 _cell.length_c 139 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8C1M _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _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 covale ? covale1 A C THR 169 A THR 287 1_555 A N TPO 170 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C TPO 170 A TPO 288 1_555 A N LEU 171 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? metalc ? metalc1 A OD2 ASP 156 A ASP 274 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc2 A OD1 ASP 156 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc3 B MG MG . A MG 401 1_555 E O2B ADP . A ADP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc4 B MG MG . A MG 401 1_555 E O2A ADP . A ADP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc5 D MG MG . A MG 403 1_555 E O3B ADP . A ADP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? # _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 8C1M _atom_sites.fract_transf_matrix[1][1] 0.012074 _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] 0.012074 _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] 0.007194 _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 1 401 1 MG MG . C 3 T4X A 1 402 1 T4X LIG . D 2 MG A 1 403 1 MG MG . E 4 ADP A 1 404 1 ADP ATP . # 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 4 25.515 1.787 5.407 1 67.58 ? PB ADP 404 A 1 HETATM 2 O O1B ADP . . . E 4 25.226 1.253 4.056 1 67.64 ? O1B ADP 404 A 1 HETATM 3 O O2B ADP . . . E 4 24.394 2.327 6.203 1 67.89 ? O2B ADP 404 A 1 HETATM 4 O O3B ADP . . . E 4 26.643 2.917 5.286 1 67.74 ? O3B ADP 404 A 1 HETATM 5 P PA ADP . . . E 4 26.85 0.534 7.761 1 67.1 ? PA ADP 404 A 1 HETATM 6 O O1A ADP . . . E 4 28.325 0.375 7.711 1 66.86 ? O1A ADP 404 A 1 HETATM 7 O O2A ADP . . . E 4 26.255 1.59 8.61 1 66.83 ? O2A ADP 404 A 1 HETATM 8 O O3A ADP . . . E 4 26.294 0.677 6.262 1 67.45 ? O3A ADP 404 A 1 HETATM 9 O O5' ADP . . . E 4 26.219 -0.865 8.213 1 66.88 ? O5' ADP 404 A 1 HETATM 10 C C5' ADP . . . E 4 24.787 -1.049 8.228 1 66.63 ? C5' ADP 404 A 1 HETATM 11 C C4' ADP . . . E 4 24.412 -1.827 9.464 1 66.37 ? C4' ADP 404 A 1 HETATM 12 O O4' ADP . . . E 4 25.218 -3.022 9.533 1 66.14 ? O4' ADP 404 A 1 HETATM 13 C C3' ADP . . . E 4 24.689 -1.117 10.78 1 66.48 ? C3' ADP 404 A 1 HETATM 14 O O3' ADP . . . E 4 23.668 -0.177 11.101 1 66.34 ? O3' ADP 404 A 1 HETATM 15 C C2' ADP . . . E 4 24.834 -2.294 11.751 1 66.61 ? C2' ADP 404 A 1 HETATM 16 O O2' ADP . . . E 4 23.585 -2.856 12.139 1 67.14 ? O2' ADP 404 A 1 HETATM 17 C C1' ADP . . . E 4 25.538 -3.333 10.877 1 66.02 ? C1' ADP 404 A 1 HETATM 18 N N9 ADP . . . E 4 26.989 -3.36 11.01 1 65.75 ? N9 ADP 404 A 1 HETATM 19 C C8 ADP . . . E 4 27.895 -2.67 10.248 1 65.65 ? C8 ADP 404 A 1 HETATM 20 N N7 ADP . . . E 4 29.146 -2.913 10.55 1 65.8 ? N7 ADP 404 A 1 HETATM 21 C C5 ADP . . . E 4 29.06 -3.832 11.586 1 66.02 ? C5 ADP 404 A 1 HETATM 22 C C6 ADP . . . E 4 30.039 -4.523 12.327 1 66.06 ? C6 ADP 404 A 1 HETATM 23 N N6 ADP . . . E 4 31.355 -4.373 12.142 1 66.15 ? N6 ADP 404 A 1 HETATM 24 N N1 ADP . . . E 4 29.617 -5.396 13.268 1 66.03 ? N1 ADP 404 A 1 HETATM 25 C C2 ADP . . . E 4 28.303 -5.56 13.448 1 66.02 ? C2 ADP 404 A 1 HETATM 26 N N3 ADP . . . E 4 27.289 -4.969 12.809 1 66.12 ? N3 ADP 404 A 1 HETATM 27 C C4 ADP . . . E 4 27.736 -4.114 11.881 1 66.03 ? C4 ADP 404 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #