data_8DGF # _model_server_result.job_id EXWf0_QBsRLDYBXMIH0wdA _model_server_result.datetime_utc '2024-11-27 14:45:38' _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 8dgf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1601}' # _entry.id 8DGF # _exptl.entry_id 8DGF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 8DGF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DGF _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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,P _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 I N N ? 3 K N N ? 3 M N N ? 3 O 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 disulf ? disulf1 A SG CYS 1439 A CYS 1439 1_555 A SG CYS 1490 A CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 B SG CYS 1439 B CYS 1439 1_555 B SG CYS 1490 B CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 C SG CYS 1439 C CYS 1439 1_555 C SG CYS 1490 C CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf4 D SG CYS 1439 D CYS 1439 1_555 D SG CYS 1490 D CYS 1490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A C FME 1 A FME 1 1_555 A N VAL 2 A VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 C C FME 1 C FME 1 1_555 C N VAL 2 C VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A OG1 THR 240 A THR 240 1_555 J MG MG . A MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc2 I O1G ATP . A ATP 1601 1_555 J MG MG . A MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc3 I O2B ATP . A ATP 1601 1_555 J MG MG . A MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc4 B OG1 THR 240 B THR 240 1_555 L MG MG . B MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc5 K O1G ATP . B ATP 1601 1_555 L MG MG . B MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc6 K O2B ATP . B ATP 1601 1_555 L MG MG . B MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc7 C OG1 THR 240 C THR 240 1_555 N MG MG . C MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc8 M O1G ATP . C ATP 1601 1_555 N MG MG . C MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc9 M O2B ATP . C ATP 1601 1_555 N MG MG . C MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc10 D OG1 THR 240 D THR 240 1_555 P MG MG . D MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc11 O O1G ATP . D ATP 1601 1_555 P MG MG . D MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc12 O O2B ATP . D ATP 1601 1_555 P MG MG . D MG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 8DGF _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 I 3 ATP A 1 1601 1601 ATP ATP . J 4 MG A 1 1602 1602 MG MG . K 3 ATP B 1 1601 1601 ATP ATP . L 4 MG B 1 1602 1602 MG MG . M 3 ATP C 1 1601 1601 ATP ATP . N 4 MG C 1 1602 1602 MG MG . O 3 ATP D 1 1601 1601 ATP ATP . P 4 MG D 1 1602 1602 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 PG ATP . . . I 3 175.183 209.517 173.874 1 32.19 ? PG ATP 1601 A 1 HETATM 2 O O1G ATP . . . I 3 175.551 209.035 172.525 1 71.74 ? O1G ATP 1601 A 1 HETATM 3 O O2G ATP . . . I 3 174.331 208.54 174.644 1 54.24 ? O2G ATP 1601 A 1 HETATM 4 O O3G ATP . . . I 3 176.392 209.911 174.686 1 68.6 ? O3G ATP 1601 A 1 HETATM 5 P PB ATP . . . I 3 174.24 212.216 173.04 1 9.19 ? PB ATP 1601 A 1 HETATM 6 O O1B ATP . . . I 3 174.867 213.28 173.827 1 52.17 ? O1B ATP 1601 A 1 HETATM 7 O O2B ATP . . . I 3 174.808 211.966 171.64 1 65.44 ? O2B ATP 1601 A 1 HETATM 8 O O3B ATP . . . I 3 174.29 210.85 173.787 1 57.82 ? O3B ATP 1601 A 1 HETATM 9 P PA ATP . . . I 3 171.69 212.553 171.646 1 16.41 ? PA ATP 1601 A 1 HETATM 10 O O1A ATP . . . I 3 171.354 211.246 171.053 1 60.08 ? O1A ATP 1601 A 1 HETATM 11 O O2A ATP . . . I 3 172.313 213.535 170.661 1 68.43 ? O2A ATP 1601 A 1 HETATM 12 O O3A ATP . . . I 3 172.671 212.427 172.841 1 56.36 ? O3A ATP 1601 A 1 HETATM 13 O O5' ATP . . . I 3 170.397 213.257 172.22 1 61.86 ? O5' ATP 1601 A 1 HETATM 14 C C5' ATP . . . I 3 169.667 212.677 173.316 1 66.22 ? C5' ATP 1601 A 1 HETATM 15 C C4' ATP . . . I 3 168.255 213.19 173.337 1 59.61 ? C4' ATP 1601 A 1 HETATM 16 O O4' ATP . . . I 3 168.241 214.587 173.68 1 64.61 ? O4' ATP 1601 A 1 HETATM 17 C C3' ATP . . . I 3 167.502 213.108 172.017 1 59.82 ? C3' ATP 1601 A 1 HETATM 18 O O3' ATP . . . I 3 166.97 211.799 171.855 1 65.96 ? O3' ATP 1601 A 1 HETATM 19 C C2' ATP . . . I 3 166.425 214.18 172.181 1 58.79 ? C2' ATP 1601 A 1 HETATM 20 O O2' ATP . . . I 3 165.332 213.617 172.886 1 65.73 ? O2' ATP 1601 A 1 HETATM 21 C C1' ATP . . . I 3 167.115 215.213 173.081 1 59.47 ? C1' ATP 1601 A 1 HETATM 22 N N9 ATP . . . I 3 167.55 216.438 172.418 1 60.66 ? N9 ATP 1601 A 1 HETATM 23 C C8 ATP . . . I 3 168.709 216.618 171.711 1 65.54 ? C8 ATP 1601 A 1 HETATM 24 N N7 ATP . . . I 3 168.862 217.83 171.232 1 66.43 ? N7 ATP 1601 A 1 HETATM 25 C C5 ATP . . . I 3 167.716 218.494 171.645 1 62.21 ? C5 ATP 1601 A 1 HETATM 26 C C6 ATP . . . I 3 167.268 219.816 171.46 1 61.92 ? C6 ATP 1601 A 1 HETATM 27 N N6 ATP . . . I 3 167.962 220.747 170.789 1 65.64 ? N6 ATP 1601 A 1 HETATM 28 N N1 ATP . . . I 3 166.071 220.152 172.007 1 63.73 ? N1 ATP 1601 A 1 HETATM 29 C C2 ATP . . . I 3 165.387 219.221 172.684 1 62.95 ? C2 ATP 1601 A 1 HETATM 30 N N3 ATP . . . I 3 165.711 217.945 172.922 1 66.46 ? N3 ATP 1601 A 1 HETATM 31 C C4 ATP . . . I 3 166.894 217.645 172.373 1 63.28 ? C4 ATP 1601 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 92 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 31 #