data_6S5D # _model_server_result.job_id rc9GoossQFn4nRv9Xr1F0g _model_server_result.datetime_utc '2024-11-04 22:47:38' _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 6s5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 6S5D # _exptl.entry_id 6S5D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 6S5D _cell.length_a 121.572 _cell.length_b 121.572 _cell.length_c 83.726 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S5D _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 1 2 A,B,C,D,E,F,G 1 3 A,B,C,D,E,F,G 1 4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_775 -x+2,-y+2,z -1 0 0 0 -1 0 0 0 1 243.144 243.144 0 3 'crystal symmetry operation' 3_755 -y+2,x,z 0 -1 0 1 0 0 0 0 1 243.144 0 0 4 'crystal symmetry operation' 4_575 y,-x+2,z 0 1 0 -1 0 0 0 0 1 0 243.144 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 metalc ? metalc1 A OE2 GLU 125 A GLU 125 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc2 C O2G ATP . A ATP 601 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc3 D MG MG . A MG 602 1_555 F O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc4 D MG MG . A MG 602 1_555 B OE2 GLU 125 B GLU 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc5 D MG MG . A MG 602 1_555 E O2G ATP . B ATP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc6 D MG MG . A MG 602 1_555 G O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _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 6S5D _atom_sites.fract_transf_matrix[1][1] 0.008226 _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] 0.008226 _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] 0.011944 _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 2 ATP A 1 601 601 ATP ATP . D 3 MG A 1 602 1 MG MG . E 2 ATP B 1 601 601 ATP ATP . F 4 HOH A 1 701 2 HOH HOH . G 4 HOH B 1 701 1 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 PG ATP . . . E 2 142.394 109.51 -1.876 1 181.99 ? PG ATP 601 B 1 HETATM 2 O O1G ATP . . . E 2 142.131 110.997 -1.889 1 160.25 ? O1G ATP 601 B 1 HETATM 3 O O2G ATP . . . E 2 142.893 108.995 -0.546 1 157.47 ? O2G ATP 601 B 1 HETATM 4 O O3G ATP . . . E 2 143.165 109.013 -3.075 1 165.35 ? O3G ATP 601 B 1 HETATM 5 P PB ATP . . . E 2 139.586 109.347 -1.411 1 173.16 ? PB ATP 601 B 1 HETATM 6 O O1B ATP . . . E 2 139.347 108.631 -0.103 1 162.96 ? O1B ATP 601 B 1 HETATM 7 O O2B ATP . . . E 2 139.556 110.856 -1.453 1 193.73 ? O2B ATP 601 B 1 HETATM 8 O O3B ATP . . . E 2 140.962 108.784 -2.034 1 166.29 ? O3B ATP 601 B 1 HETATM 9 P PA ATP . . . E 2 137.952 109.785 -3.605 1 174.86 ? PA ATP 601 B 1 HETATM 10 O O1A ATP . . . E 2 139.135 110.543 -4.164 1 166.09 ? O1A ATP 601 B 1 HETATM 11 O O2A ATP . . . E 2 136.766 110.552 -3.076 1 178.44 ? O2A ATP 601 B 1 HETATM 12 O O3A ATP . . . E 2 138.52 108.79 -2.478 1 151.77 ? O3A ATP 601 B 1 HETATM 13 O O5' ATP . . . E 2 137.457 108.788 -4.762 1 142.52 ? O5' ATP 601 B 1 HETATM 14 C C5' ATP . . . E 2 138.336 108.587 -5.863 1 161.85 ? C5' ATP 601 B 1 HETATM 15 C C4' ATP . . . E 2 137.627 108.846 -7.184 1 142.73 ? C4' ATP 601 B 1 HETATM 16 O O4' ATP . . . E 2 136.65 107.847 -7.466 1 152.95 ? O4' ATP 601 B 1 HETATM 17 C C3' ATP . . . E 2 136.896 110.177 -7.206 1 138.38 ? C3' ATP 601 B 1 HETATM 18 O O3' ATP . . . E 2 137.682 111.134 -7.917 1 146.2 ? O3' ATP 601 B 1 HETATM 19 C C2' ATP . . . E 2 135.604 109.905 -7.95 1 141.07 ? C2' ATP 601 B 1 HETATM 20 O O2' ATP . . . E 2 135.545 110.699 -9.136 1 152.28 ? O2' ATP 601 B 1 HETATM 21 C C1' ATP . . . E 2 135.661 108.43 -8.313 1 142.73 ? C1' ATP 601 B 1 HETATM 22 N N9 ATP . . . E 2 134.346 107.771 -8.125 1 145.18 ? N9 ATP 601 B 1 HETATM 23 C C8 ATP . . . E 2 133.618 107.753 -6.993 1 145.95 ? C8 ATP 601 B 1 HETATM 24 N N7 ATP . . . E 2 132.463 107.062 -7.167 1 129.78 ? N7 ATP 601 B 1 HETATM 25 C C5 ATP . . . E 2 132.443 106.626 -8.439 1 120.42 ? C5 ATP 601 B 1 HETATM 26 C C6 ATP . . . E 2 131.516 105.838 -9.282 1 135.36 ? C6 ATP 601 B 1 HETATM 27 N N6 ATP . . . E 2 130.349 105.367 -8.781 1 145.67 ? N6 ATP 601 B 1 HETATM 28 N N1 ATP . . . E 2 131.876 105.606 -10.565 1 144.4 ? N1 ATP 601 B 1 HETATM 29 C C2 ATP . . . E 2 133.033 106.069 -11.073 1 142.67 ? C2 ATP 601 B 1 HETATM 30 N N3 ATP . . . E 2 133.919 106.792 -10.366 1 140.76 ? N3 ATP 601 B 1 HETATM 31 C C4 ATP . . . E 2 133.684 107.099 -9.067 1 134.68 ? C4 ATP 601 B 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #