data_6C7Y # _model_server_result.job_id qFcTSnMCUnbi1hgjyqAM6w _model_server_result.datetime_utc '2024-11-22 10:34:59' _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 6c7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1201}' # _entry.id 6C7Y # _exptl.entry_id 6C7Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 6C7Y _cell.length_a 83.926 _cell.length_b 83.926 _cell.length_c 161.438 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6C7Y _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,I,J,K _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 3 _struct_asym.id C _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 TYR 167 A TYR 1034 1_555 A N PTR 168 A PTR 1035 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C PTR 168 A PTR 1035 1_555 A N THR 169 A THR 1036 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD1 ASN 141 A ASN 1008 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc2 A OD2 ASP 154 A ASP 1021 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc3 A OD1 ASP 154 A ASP 1021 1_555 E MG MG . A MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc4 A OD2 ASP 154 A ASP 1021 1_555 E MG MG . A MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc5 C O3B ADP . A ADP 1201 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc6 C O1A ADP . A ADP 1201 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc7 C O2B ADP . A ADP 1201 1_555 E MG MG . A MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc8 C O3B ADP . A ADP 1201 1_555 E MG MG . A MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.829 ? metalc ? metalc9 D MG MG . A MG 1202 1_555 J O HOH . A HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc10 D MG MG . A MG 1202 1_555 J O HOH . A HOH 1317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc11 E MG MG . A MG 1203 1_555 J O HOH . A HOH 1325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? # _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 7 n n PB O2B ADP sing 8 n n PB O3B ADP sing 9 n n PB O3A ADP sing 10 n n O2B HOB2 ADP sing 11 n n O3B HOB3 ADP sing 12 n n PA O1A ADP doub 13 n n PA O2A ADP sing 14 n n PA O3A ADP sing 15 n n PA O5' ADP sing 16 n n O2A HOA2 ADP sing 17 n n O5' C5' ADP sing 18 n n C5' C4' ADP sing 19 n n C5' "H5'1" ADP sing 20 n n C5' "H5'2" ADP sing 21 n n C4' O4' ADP sing 22 n n C4' C3' ADP sing 23 n n C4' H4' ADP sing 24 n n O4' C1' ADP sing 25 n n C3' O3' ADP sing 26 n n C3' C2' ADP sing 27 n n C3' H3' ADP sing 28 n n O3' HO3' ADP sing 29 n n C2' O2' ADP sing 30 n n C2' C1' ADP sing 31 n n C2' H2' ADP sing 32 n n O2' HO2' ADP sing 33 n n C1' N9 ADP sing 34 n n C1' H1' ADP sing 35 n n N9 C8 ADP sing 36 n y N9 C4 ADP sing 37 n y C8 N7 ADP doub 38 n y C8 H8 ADP sing 39 n n N7 C5 ADP sing 40 n y C5 C6 ADP sing 41 n y C5 C4 ADP doub 42 n y C6 N6 ADP sing 43 n n C6 N1 ADP doub 44 n y N6 HN61 ADP sing 45 n n N6 HN62 ADP sing 46 n n N1 C2 ADP sing 47 n y C2 N3 ADP doub 48 n y C2 H2 ADP sing 49 n n N3 C4 ADP sing 50 n y # _atom_sites.entry_id 6C7Y _atom_sites.fract_transf_matrix[1][1] 0.011915 _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] 0.011915 _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] 0.006194 _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 3 ADP A 1 1201 300 ADP ADP . D 4 MG A 1 1202 301 MG MG . E 4 MG A 1 1203 302 MG MG . F 5 EDO A 1 1204 5 EDO EDO . G 5 EDO A 1 1205 7 EDO EDO . H 5 EDO B 1 201 1 EDO EDO . I 6 ACT B 1 202 4 ACT ACT . J 7 HOH A 1 1301 35 HOH HOH . J 7 HOH A 2 1302 29 HOH HOH . J 7 HOH A 3 1303 3 HOH HOH . J 7 HOH A 4 1304 5 HOH HOH . J 7 HOH A 5 1305 43 HOH HOH . J 7 HOH A 6 1306 9 HOH HOH . J 7 HOH A 7 1307 31 HOH HOH . J 7 HOH A 8 1308 2 HOH HOH . J 7 HOH A 9 1309 4 HOH HOH . J 7 HOH A 10 1310 25 HOH HOH . J 7 HOH A 11 1311 33 HOH HOH . J 7 HOH A 12 1312 38 HOH HOH . J 7 HOH A 13 1313 8 HOH HOH . J 7 HOH A 14 1314 44 HOH HOH . J 7 HOH A 15 1315 12 HOH HOH . J 7 HOH A 16 1316 20 HOH HOH . J 7 HOH A 17 1317 30 HOH HOH . J 7 HOH A 18 1318 39 HOH HOH . J 7 HOH A 19 1319 17 HOH HOH . J 7 HOH A 20 1320 32 HOH HOH . J 7 HOH A 21 1321 45 HOH HOH . J 7 HOH A 22 1322 18 HOH HOH . J 7 HOH A 23 1323 13 HOH HOH . J 7 HOH A 24 1324 41 HOH HOH . J 7 HOH A 25 1325 28 HOH HOH . J 7 HOH A 26 1326 42 HOH HOH . J 7 HOH A 27 1327 40 HOH HOH . K 7 HOH B 1 301 1 HOH HOH . K 7 HOH B 2 302 11 HOH HOH . K 7 HOH B 3 303 23 HOH HOH . K 7 HOH B 4 304 37 HOH HOH . K 7 HOH B 5 305 26 HOH HOH . K 7 HOH B 6 306 16 HOH HOH . K 7 HOH B 7 307 7 HOH HOH . K 7 HOH B 8 308 19 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 3 -6.415 34.178 -6.817 1 89.84 ? PB ADP 1201 A 1 HETATM 2 O O1B ADP . . . C 3 -4.965 34.124 -7.233 1 90.22 ? O1B ADP 1201 A 1 HETATM 3 O O2B ADP . . . C 3 -6.657 33.673 -5.417 1 100.6 ? O2B ADP 1201 A 1 HETATM 4 O O3B ADP . . . C 3 -7.122 35.471 -7.146 1 90.32 ? O3B ADP 1201 A 1 HETATM 5 P PA ADP . . . C 3 -8.046 31.894 -7.195 1 77.89 ? PA ADP 1201 A 1 HETATM 6 O O1A ADP . . . C 3 -9.368 32.499 -6.79 1 80.2 ? O1A ADP 1201 A 1 HETATM 7 O O2A ADP . . . C 3 -7.253 31.064 -6.216 1 70.4 ? O2A ADP 1201 A 1 HETATM 8 O O3A ADP . . . C 3 -7.131 33.093 -7.766 1 85.13 ? O3A ADP 1201 A 1 HETATM 9 O O5' ADP . . . C 3 -8.284 31.032 -8.532 1 82.82 ? O5' ADP 1201 A 1 HETATM 10 C C5' ADP . . . C 3 -8.559 31.709 -9.757 1 85.6 ? C5' ADP 1201 A 1 HETATM 11 C C4' ADP . . . C 3 -9.275 30.773 -10.719 1 87.75 ? C4' ADP 1201 A 1 HETATM 12 O O4' ADP . . . C 3 -8.786 29.439 -10.563 1 87.22 ? O4' ADP 1201 A 1 HETATM 13 C C3' ADP . . . C 3 -10.768 30.734 -10.441 1 90.45 ? C3' ADP 1201 A 1 HETATM 14 O O3' ADP . . . C 3 -11.479 31.478 -11.434 1 92.69 ? O3' ADP 1201 A 1 HETATM 15 C C2' ADP . . . C 3 -11.154 29.271 -10.501 1 91.3 ? C2' ADP 1201 A 1 HETATM 16 O O2' ADP . . . C 3 -12.001 29.036 -11.629 1 96.16 ? O2' ADP 1201 A 1 HETATM 17 C C1' ADP . . . C 3 -9.855 28.496 -10.654 1 91 ? C1' ADP 1201 A 1 HETATM 18 N N9 ADP . . . C 3 -9.752 27.51 -9.551 1 93.82 ? N9 ADP 1201 A 1 HETATM 19 C C8 ADP . . . C 3 -9.071 27.685 -8.403 1 94.09 ? C8 ADP 1201 A 1 HETATM 20 N N7 ADP . . . C 3 -9.177 26.596 -7.6 1 94.15 ? N7 ADP 1201 A 1 HETATM 21 C C5 ADP . . . C 3 -9.944 25.695 -8.241 1 95.8 ? C5 ADP 1201 A 1 HETATM 22 C C6 ADP . . . C 3 -10.453 24.333 -7.957 1 100.94 ? C6 ADP 1201 A 1 HETATM 23 N N6 ADP . . . C 3 -10.153 23.702 -6.796 1 104.16 ? N6 ADP 1201 A 1 HETATM 24 N N1 ADP . . . C 3 -11.226 23.743 -8.895 1 102.8 ? N1 ADP 1201 A 1 HETATM 25 C C2 ADP . . . C 3 -11.531 24.361 -10.051 1 101.95 ? C2 ADP 1201 A 1 HETATM 26 N N3 ADP . . . C 3 -11.104 25.595 -10.374 1 99.79 ? N3 ADP 1201 A 1 HETATM 27 C C4 ADP . . . C 3 -10.321 26.302 -9.526 1 95.54 ? C4 ADP 1201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #