data_8OI6 # _model_server_result.job_id jDZwgF27wdlKXUQUZNiQCQ _model_server_result.datetime_utc '2024-11-14 19:37:39' _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 8oi6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 8OI6 # _exptl.entry_id 8OI6 _exptl.method 'ELECTRON MICROSCOPY' # _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 4 _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 8OI6 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OI6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _pdbx_struct_assembly.details author_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,L,M,N,O _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 ? _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 ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N 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 72 A GLU 72 1_555 A N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C HIC 73 A HIC 73 1_555 A N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C GLU 72 B GLU 72 1_555 B N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 B C HIC 73 B HIC 73 1_555 B N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 E C TRP 1 H TRP 1 1_555 E N EEP 2 H EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 E N TRP 1 H TRP 1 1_555 E C ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale11 E C EEP 2 H EEP 2 1_555 E N ALA 3 H ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale12 E C ALA 3 H ALA 3 1_555 E N DTH 4 H DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale13 E C DTH 4 H DTH 4 1_555 E N CYS 5 H CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale14 E C CYS 5 H CYS 5 1_555 E N HYP 6 H HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale15 E C HYP 6 H HYP 6 1_555 E N ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale16 F C TRP 1 I TRP 1 1_555 F N EEP 2 I EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale17 F N TRP 1 I TRP 1 1_555 F C ALA 7 I ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale18 F C EEP 2 I EEP 2 1_555 F N ALA 3 I ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale19 F C ALA 3 I ALA 3 1_555 F N DTH 4 I DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale20 F C DTH 4 I DTH 4 1_555 F N CYS 5 I CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale21 F C CYS 5 I CYS 5 1_555 F N HYP 6 I HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale22 F C HYP 6 I HYP 6 1_555 F N ALA 7 I ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale23 G C TRP 1 J TRP 1 1_555 G N EEP 2 J EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale24 G N TRP 1 J TRP 1 1_555 G C ALA 7 J ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale25 G C EEP 2 J EEP 2 1_555 G N ALA 3 J ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale26 G C ALA 3 J ALA 3 1_555 G N DTH 4 J DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale27 G C DTH 4 J DTH 4 1_555 G N CYS 5 J CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale28 G C CYS 5 J CYS 5 1_555 G N HYP 6 J HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale29 G C HYP 6 J HYP 6 1_555 G N ALA 7 J ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 H O1B ADP . A ADP 401 1_555 I MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc2 J O1B ADP . B ADP 401 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc3 L O1B ADP . C ADP 401 1_555 M MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc4 N O1B ADP . D ADP 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? # _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 8OI6 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 H 3 ADP A 1 401 376 ADP ADP . I 4 MG A 1 402 377 MG MG . J 3 ADP B 1 401 376 ADP ADP . K 4 MG B 1 402 377 MG MG . L 3 ADP C 1 401 376 ADP ADP . M 4 MG C 1 402 377 MG MG . N 3 ADP D 1 401 376 ADP ADP . O 4 MG D 1 402 377 MG MG . # 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 . . . J 3 216.424 227.666 258.608 1 61.34 ? PB ADP 401 B 1 HETATM 2 O O1B ADP . . . J 3 215.991 226.612 257.619 1 61.34 ? O1B ADP 401 B 1 HETATM 3 O O2B ADP . . . J 3 217.099 227.134 259.847 1 61.34 ? O2B ADP 401 B 1 HETATM 4 O O3B ADP . . . J 3 217.147 228.823 257.973 1 61.34 ? O3B ADP 401 B 1 HETATM 5 P PA ADP . . . J 3 214.672 229.841 259.236 1 61.34 ? PA ADP 401 B 1 HETATM 6 O O1A ADP . . . J 3 214.916 230.471 257.886 1 61.34 ? O1A ADP 401 B 1 HETATM 7 O O2A ADP . . . J 3 213.291 229.937 259.836 1 61.34 ? O2A ADP 401 B 1 HETATM 8 O O3A ADP . . . J 3 215.033 228.27 259.156 1 61.34 ? O3A ADP 401 B 1 HETATM 9 O O5' ADP . . . J 3 215.687 230.505 260.297 1 61.34 ? O5' ADP 401 B 1 HETATM 10 C C5' ADP . . . J 3 216.853 231.191 259.846 1 61.34 ? C5' ADP 401 B 1 HETATM 11 C C4' ADP . . . J 3 217.329 232.218 260.865 1 61.34 ? C4' ADP 401 B 1 HETATM 12 O O4' ADP . . . J 3 216.697 233.479 260.641 1 61.34 ? O4' ADP 401 B 1 HETATM 13 C C3' ADP . . . J 3 217.02 231.821 262.299 1 61.34 ? C3' ADP 401 B 1 HETATM 14 O O3' ADP . . . J 3 218.193 231.309 262.934 1 61.34 ? O3' ADP 401 B 1 HETATM 15 C C2' ADP . . . J 3 216.579 233.1 262.98 1 61.34 ? C2' ADP 401 B 1 HETATM 16 O O2' ADP . . . J 3 217.54 233.478 263.969 1 61.34 ? O2' ADP 401 B 1 HETATM 17 C C1' ADP . . . J 3 216.523 234.155 261.886 1 61.34 ? C1' ADP 401 B 1 HETATM 18 N N9 ADP . . . J 3 215.213 234.85 261.923 1 61.34 ? N9 ADP 401 B 1 HETATM 19 C C8 ADP . . . J 3 214.011 234.263 261.788 1 61.34 ? C8 ADP 401 B 1 HETATM 20 N N7 ADP . . . J 3 213.008 235.173 261.875 1 61.34 ? N7 ADP 401 B 1 HETATM 21 C C5 ADP . . . J 3 213.573 236.376 262.074 1 61.34 ? C5 ADP 401 B 1 HETATM 22 C C6 ADP . . . J 3 213.089 237.764 262.252 1 61.34 ? C6 ADP 401 B 1 HETATM 23 N N6 ADP . . . J 3 211.767 238.053 262.235 1 61.34 ? N6 ADP 401 B 1 HETATM 24 N N1 ADP . . . J 3 214.013 238.731 262.433 1 61.34 ? N1 ADP 401 B 1 HETATM 25 C C2 ADP . . . J 3 215.329 238.456 262.451 1 61.34 ? C2 ADP 401 B 1 HETATM 26 N N3 ADP . . . J 3 215.838 237.222 262.296 1 61.34 ? N3 ADP 401 B 1 HETATM 27 C C4 ADP . . . J 3 215.026 236.157 262.109 1 61.34 ? C4 ADP 401 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 675 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #