data_2NYJ # _model_server_result.job_id j62PIL8PpGKm3WARsJKbsg _model_server_result.datetime_utc '2024-10-30 08:20:11' _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 2nyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 2NYJ # _exptl.entry_id 2NYJ _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 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 120 _cell.entry_id 2NYJ _cell.length_a 124.721 _cell.length_b 124.721 _cell.length_c 62.767 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NYJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 2 _struct_asym.id B _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 ALA 61 A ALA 161 1_555 A N MSE 62 A MSE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C MSE 62 A MSE 162 1_555 A N LEU 63 A LEU 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A C ASN 113 A ASN 213 1_555 A N MSE 114 A MSE 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale4 A C MSE 114 A MSE 214 1_555 A N THR 115 A THR 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A C SER 207 A SER 307 1_555 A N MSE 208 A MSE 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 A C MSE 208 A MSE 308 1_555 A N TYR 209 A TYR 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _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 2NYJ _atom_sites.fract_transf_matrix[1][1] 0.008018 _atom_sites.fract_transf_matrix[1][2] 0.004629 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009258 _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] 0.015932 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id ATP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id ATP _pdbx_nonpoly_scheme.auth_mon_id ATP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . B 2 -15.31 -30.434 -32.323 1 109.04 ? PG ATP 1 A 1 HETATM 2 O O1G ATP . . . B 2 -14.208 -31.335 -32.858 1 108.43 ? O1G ATP 1 A 1 HETATM 3 O O2G ATP . . . B 2 -15.955 -30.9 -31.036 1 109.39 ? O2G ATP 1 A 1 HETATM 4 O O3G ATP . . . B 2 -16.335 -29.992 -33.349 1 108.87 ? O3G ATP 1 A 1 HETATM 5 P PB ATP . . . B 2 -12.998 -29.062 -31.366 1 108.18 ? PB ATP 1 A 1 HETATM 6 O O1B ATP . . . B 2 -12.034 -29.295 -32.505 1 108.27 ? O1B ATP 1 A 1 HETATM 7 O O2B ATP . . . B 2 -12.846 -27.804 -30.541 1 108.37 ? O2B ATP 1 A 1 HETATM 8 O O3B ATP . . . B 2 -14.527 -29.079 -31.905 1 108.51 ? O3B ATP 1 A 1 HETATM 9 P PA ATP . . . B 2 -13.06 -30.296 -28.832 1 105.92 ? PA ATP 1 A 1 HETATM 10 O O1A ATP . . . B 2 -14.546 -30.255 -28.536 1 105.29 ? O1A ATP 1 A 1 HETATM 11 O O2A ATP . . . B 2 -12.119 -29.243 -28.3 1 105.57 ? O2A ATP 1 A 1 HETATM 12 O O3A ATP . . . B 2 -12.884 -30.372 -30.429 1 107.12 ? O3A ATP 1 A 1 HETATM 13 O O5' ATP . . . B 2 -12.467 -31.699 -28.344 1 105.67 ? O5' ATP 1 A 1 HETATM 14 C C5' ATP . . . B 2 -13.183 -32.885 -28.633 1 106.27 ? C5' ATP 1 A 1 HETATM 15 C C4' ATP . . . B 2 -12.361 -33.635 -29.656 1 106.79 ? C4' ATP 1 A 1 HETATM 16 O O4' ATP . . . B 2 -11.475 -34.546 -29.007 1 106.96 ? O4' ATP 1 A 1 HETATM 17 C C3' ATP . . . B 2 -13.279 -34.425 -30.561 1 107.35 ? C3' ATP 1 A 1 HETATM 18 O O3' ATP . . . B 2 -12.986 -34.044 -31.908 1 107.97 ? O3' ATP 1 A 1 HETATM 19 C C2' ATP . . . B 2 -12.963 -35.882 -30.296 1 107.56 ? C2' ATP 1 A 1 HETATM 20 O O2' ATP . . . B 2 -12.464 -36.531 -31.461 1 108.35 ? O2' ATP 1 A 1 HETATM 21 C C1' ATP . . . B 2 -11.877 -35.895 -29.24 1 108.21 ? C1' ATP 1 A 1 HETATM 22 N N9 ATP . . . B 2 -12.398 -36.487 -27.982 1 108.75 ? N9 ATP 1 A 1 HETATM 23 C C8 ATP . . . B 2 -13.669 -36.457 -27.51 1 109.09 ? C8 ATP 1 A 1 HETATM 24 N N7 ATP . . . B 2 -13.783 -37.103 -26.318 1 108.47 ? N7 ATP 1 A 1 HETATM 25 C C5 ATP . . . B 2 -12.555 -37.555 -26.025 1 108.54 ? C5 ATP 1 A 1 HETATM 26 C C6 ATP . . . B 2 -11.945 -38.32 -24.923 1 108.85 ? C6 ATP 1 A 1 HETATM 27 N N6 ATP . . . B 2 -12.714 -38.727 -23.891 1 108.78 ? N6 ATP 1 A 1 HETATM 28 N N1 ATP . . . B 2 -10.613 -38.591 -24.985 1 109.05 ? N1 ATP 1 A 1 HETATM 29 C C2 ATP . . . B 2 -9.847 -38.186 -26.02 1 108.76 ? C2 ATP 1 A 1 HETATM 30 N N3 ATP . . . B 2 -10.335 -37.484 -27.057 1 108.5 ? N3 ATP 1 A 1 HETATM 31 C C4 ATP . . . B 2 -11.648 -37.15 -27.112 1 108.56 ? C4 ATP 1 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 217 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #