data_8GAE # _model_server_result.job_id FI1nlXetlCPPEiL2XCw18A _model_server_result.datetime_utc '2025-03-09 02:02:20' _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 8gae # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":803}' # _entry.id 8GAE # _exptl.entry_id 8GAE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 7 _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 8GAE _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GAE _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id H _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 C C VAL 12 C VAL 12 1_555 C N SEP 13 C SEP 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 C C SEP 13 C SEP 13 1_555 C N ASP 14 C ASP 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 A OD1 ASN 49 A ASN 46 1_555 G MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc2 A O ASN 104 A ASN 101 1_555 F K K . A K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc3 A O THR 107 A THR 104 1_555 F K K . A K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.949 ? metalc ? metalc4 A O LYS 110 A LYS 107 1_555 F K K . A K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.062 ? metalc ? metalc5 A O GLY 133 A GLY 130 1_555 F K K . A K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.761 ? metalc ? metalc6 A OH TYR 137 A TYR 134 1_555 F K K . A K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.153 ? metalc ? metalc7 G MG MG . A MG 802 1_555 H O2B ADP . A ADP 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc8 G MG MG . A MG 802 1_555 H O2A ADP . A ADP 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc9 B OD1 ASN 49 B ASN 46 1_555 J MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc10 B O ASN 104 B ASN 101 1_555 I K K . B K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc11 B O THR 107 B THR 104 1_555 I K K . B K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.088 ? metalc ? metalc12 B O LYS 110 B LYS 107 1_555 I K K . B K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.027 ? metalc ? metalc13 B O GLY 133 B GLY 130 1_555 I K K . B K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc14 B OH TYR 137 B TYR 134 1_555 I K K . B K 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.448 ? metalc ? metalc15 J MG MG . B MG 802 1_555 K O3G ATP . B ATP 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc16 J MG MG . B MG 802 1_555 K O1B ATP . B ATP 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc17 J MG MG . B MG 802 1_555 K O2A ATP . B ATP 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc18 E OD1 ASP 246 E ASP 242 1_555 L MN MN . E MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc19 E NE2 HIS 248 E HIS 244 1_555 L MN MN . E MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc20 E OD2 ASP 275 E ASP 271 1_555 L MN MN . E MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc21 E OD1 ASP 275 E ASP 271 1_555 M MN MN . E MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc22 E OD2 ASP 275 E ASP 271 1_555 M MN MN . E MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc23 E OD1 ASN 307 E ASN 303 1_555 M MN MN . E MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? # _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 8GAE _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 F 5 K A 1 801 997 K K . G 6 MG A 1 802 998 MG MG . H 7 ADP A 1 803 999 ADP ADP . I 5 K B 1 801 997 K K . J 6 MG B 1 802 998 MG MG . K 8 ATP B 1 803 999 ATP ATP . L 9 MN E 1 501 998 MN MN . M 9 MN E 1 502 999 MN MN . # 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 . . . H 7 131.504 142.463 99.22 1 119.35 ? PB ADP 803 A 1 HETATM 2 O O1B ADP . . . H 7 131.948 142.45 97.81 1 119.35 ? O1B ADP 803 A 1 HETATM 3 O O2B ADP . . . H 7 132.67 142.668 100.11 1 119.35 ? O2B ADP 803 A 1 HETATM 4 O O3B ADP . . . H 7 130.933 141.142 99.538 1 119.35 ? O3B ADP 803 A 1 HETATM 5 P PA ADP . . . H 7 130.693 144.957 100.026 1 119.35 ? PA ADP 803 A 1 HETATM 6 O O1A ADP . . . H 7 129.463 145.696 100.377 1 119.35 ? O1A ADP 803 A 1 HETATM 7 O O2A ADP . . . H 7 131.589 144.97 101.209 1 119.35 ? O2A ADP 803 A 1 HETATM 8 O O3A ADP . . . H 7 130.402 143.531 99.484 1 119.35 ? O3A ADP 803 A 1 HETATM 9 O O5' ADP . . . H 7 131.379 145.576 98.749 1 119.35 ? O5' ADP 803 A 1 HETATM 10 C C5' ADP . . . H 7 130.56 145.918 97.639 1 119.35 ? C5' ADP 803 A 1 HETATM 11 C C4' ADP . . . H 7 131.437 146.597 96.592 1 119.35 ? C4' ADP 803 A 1 HETATM 12 O O4' ADP . . . H 7 132.231 147.615 97.211 1 119.35 ? O4' ADP 803 A 1 HETATM 13 C C3' ADP . . . H 7 132.46 145.651 95.949 1 119.35 ? C3' ADP 803 A 1 HETATM 14 O O3' ADP . . . H 7 132.081 145.346 94.628 1 119.35 ? O3' ADP 803 A 1 HETATM 15 C C2' ADP . . . H 7 133.739 146.472 95.915 1 119.35 ? C2' ADP 803 A 1 HETATM 16 O O2' ADP . . . H 7 134.374 146.48 94.629 1 119.35 ? O2' ADP 803 A 1 HETATM 17 C C1' ADP . . . H 7 133.294 147.872 96.311 1 119.35 ? C1' ADP 803 A 1 HETATM 18 N N9 ADP . . . H 7 134.326 148.613 96.965 1 119.35 ? N9 ADP 803 A 1 HETATM 19 C C8 ADP . . . H 7 134.41 149.044 98.284 1 119.35 ? C8 ADP 803 A 1 HETATM 20 N N7 ADP . . . H 7 135.603 149.594 98.57 1 119.35 ? N7 ADP 803 A 1 HETATM 21 C C5 ADP . . . H 7 136.239 149.5 97.367 1 119.35 ? C5 ADP 803 A 1 HETATM 22 C C6 ADP . . . H 7 137.509 149.922 97.019 1 119.35 ? C6 ADP 803 A 1 HETATM 23 N N6 ADP . . . H 7 138.36 150.404 97.921 1 119.35 ? N6 ADP 803 A 1 HETATM 24 N N1 ADP . . . H 7 137.984 149.831 95.79 1 119.35 ? N1 ADP 803 A 1 HETATM 25 C C2 ADP . . . H 7 137.175 149.225 94.918 1 119.35 ? C2 ADP 803 A 1 HETATM 26 N N3 ADP . . . H 7 135.948 148.741 95.163 1 119.35 ? N3 ADP 803 A 1 HETATM 27 C C4 ADP . . . H 7 135.512 148.93 96.405 1 119.35 ? C4 ADP 803 A 1 HETATM 28 H "H5'1" ADP . . . H 7 130.103 145.015 97.216 1 119.35 ? "H5'1" ADP 803 A 1 HETATM 29 H "H5'2" ADP . . . H 7 129.781 146.62 97.959 1 119.35 ? "H5'2" ADP 803 A 1 HETATM 30 H H4' ADP . . . H 7 130.802 147.044 95.817 1 119.35 ? H4' ADP 803 A 1 HETATM 31 H H3' ADP . . . H 7 132.608 144.745 96.552 1 119.35 ? H3' ADP 803 A 1 HETATM 32 H HO3' ADP . . . H 7 132.839 145.695 94.126 1 119.35 ? HO3' ADP 803 A 1 HETATM 33 H H2' ADP . . . H 7 134.428 146.083 96.676 1 119.35 ? H2' ADP 803 A 1 HETATM 34 H HO2' ADP . . . H 7 134.99 147.232 94.651 1 119.35 ? HO2' ADP 803 A 1 HETATM 35 H H1' ADP . . . H 7 132.925 148.437 95.445 1 119.35 ? H1' ADP 803 A 1 HETATM 36 H H8 ADP . . . H 7 133.592 148.915 98.98 1 119.35 ? H8 ADP 803 A 1 HETATM 37 H HN61 ADP . . . H 7 137.939 150.361 98.84 1 119.35 ? HN61 ADP 803 A 1 HETATM 38 H HN62 ADP . . . H 7 138.679 151.334 97.684 1 119.35 ? HN62 ADP 803 A 1 HETATM 39 H H2 ADP . . . H 7 137.55 149.115 93.902 1 119.35 ? H2 ADP 803 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 57 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #