data_1ZYD # _model_server_result.job_id 856BbOxsRRQTCH-cOZCsfQ _model_server_result.datetime_utc '2024-11-28 19:02:38' _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 1zyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":303}' # _entry.id 1ZYD # _exptl.entry_id 1ZYD _exptl.method 'X-RAY DIFFRACTION' # _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 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 1ZYD _cell.length_a 82.11 _cell.length_b 175.21 _cell.length_c 47.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 H 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 E O2G ATP . A ATP 303 1_555 C MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc2 E O3B ATP . A ATP 303 1_555 C MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? metalc ? metalc3 E O3G ATP . A ATP 303 1_555 C MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? metalc ? metalc4 E O1A ATP . A ATP 303 1_555 C MG MG . A MG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc5 E O3B ATP . A ATP 303 1_555 D MG MG . A MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc6 C MG MG . A MG 305 1_555 A OD1 ASP 159 A ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc7 C MG MG . A MG 305 1_555 A OD2 ASP 159 A ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc8 D MG MG . A MG 306 1_555 A OD1 ASN 146 A ASN 840 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc9 D MG MG . A MG 306 1_555 A OD2 ASP 159 A ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc10 H O3G ATP . B ATP 304 1_555 F MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc11 H O2G ATP . B ATP 304 1_555 F MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.115 ? metalc ? metalc12 H O3B ATP . B ATP 304 1_555 F MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.049 ? metalc ? metalc13 H O1A ATP . B ATP 304 1_555 F MG MG . B MG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc14 H O3B ATP . B ATP 304 1_555 G MG MG . B MG 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc15 F MG MG . B MG 307 1_555 B OD1 ASP 159 B ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc16 F MG MG . B MG 307 1_555 B OD2 ASP 159 B ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc17 G MG MG . B MG 308 1_555 B OD1 ASN 146 B ASN 840 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc18 G MG MG . B MG 308 1_555 B OD2 ASP 159 B ASP 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? # _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 1ZYD _atom_sites.fract_transf_matrix[1][1] 0.012179 _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] 0.005707 _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] 0.021022 _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 MG A 1 305 305 MG MG2 . D 2 MG A 1 306 306 MG MG2 . E 3 ATP A 1 303 304 ATP ATP . F 2 MG B 1 307 305 MG MG2 . G 2 MG B 1 308 306 MG MG2 . H 3 ATP B 1 304 304 ATP ATP . I 4 HOH A 1 1 1 HOH HOH . I 4 HOH A 2 2 2 HOH HOH . I 4 HOH A 3 3 3 HOH HOH . I 4 HOH A 4 4 4 HOH HOH . I 4 HOH A 5 5 5 HOH HOH . I 4 HOH A 6 6 6 HOH HOH . I 4 HOH A 7 7 7 HOH HOH . I 4 HOH A 8 10 10 HOH HOH . I 4 HOH A 9 11 11 HOH HOH . I 4 HOH A 10 16 16 HOH HOH . I 4 HOH A 11 17 17 HOH HOH . I 4 HOH A 12 18 18 HOH HOH . I 4 HOH A 13 23 23 HOH HOH . I 4 HOH A 14 28 28 HOH HOH . I 4 HOH A 15 29 29 HOH HOH . I 4 HOH A 16 32 32 HOH HOH . I 4 HOH A 17 35 35 HOH HOH . I 4 HOH A 18 36 36 HOH HOH . I 4 HOH A 19 43 43 HOH HOH . I 4 HOH A 20 44 44 HOH HOH . I 4 HOH A 21 49 49 HOH HOH . I 4 HOH A 22 51 51 HOH HOH . I 4 HOH A 23 54 54 HOH HOH . I 4 HOH A 24 55 55 HOH HOH . I 4 HOH A 25 57 57 HOH HOH . I 4 HOH A 26 58 58 HOH HOH . I 4 HOH A 27 60 60 HOH HOH . I 4 HOH A 28 61 61 HOH HOH . I 4 HOH A 29 62 62 HOH HOH . I 4 HOH A 30 64 64 HOH HOH . I 4 HOH A 31 65 65 HOH HOH . I 4 HOH A 32 66 66 HOH HOH . I 4 HOH A 33 68 68 HOH HOH . I 4 HOH A 34 69 69 HOH HOH . I 4 HOH A 35 70 70 HOH HOH . I 4 HOH A 36 71 71 HOH HOH . I 4 HOH A 37 73 73 HOH HOH . J 4 HOH B 1 8 8 HOH HOH . J 4 HOH B 2 9 9 HOH HOH . J 4 HOH B 3 12 12 HOH HOH . J 4 HOH B 4 13 13 HOH HOH . J 4 HOH B 5 14 14 HOH HOH . J 4 HOH B 6 15 15 HOH HOH . J 4 HOH B 7 20 20 HOH HOH . J 4 HOH B 8 21 21 HOH HOH . J 4 HOH B 9 22 22 HOH HOH . J 4 HOH B 10 24 24 HOH HOH . J 4 HOH B 11 25 25 HOH HOH . J 4 HOH B 12 26 26 HOH HOH . J 4 HOH B 13 27 27 HOH HOH . J 4 HOH B 14 31 31 HOH HOH . J 4 HOH B 15 33 33 HOH HOH . J 4 HOH B 16 34 34 HOH HOH . J 4 HOH B 17 37 37 HOH HOH . J 4 HOH B 18 38 38 HOH HOH . J 4 HOH B 19 39 39 HOH HOH . J 4 HOH B 20 40 40 HOH HOH . J 4 HOH B 21 41 41 HOH HOH . J 4 HOH B 22 42 42 HOH HOH . J 4 HOH B 23 45 45 HOH HOH . J 4 HOH B 24 47 47 HOH HOH . J 4 HOH B 25 48 48 HOH HOH . J 4 HOH B 26 52 52 HOH HOH . J 4 HOH B 27 53 53 HOH HOH . J 4 HOH B 28 56 56 HOH HOH . J 4 HOH B 29 63 63 HOH HOH . J 4 HOH B 30 67 67 HOH HOH . J 4 HOH B 31 72 72 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 3 0.529 61.086 9.18 1 49.31 ? PG ATP 303 A 1 HETATM 2 O O1G ATP . . . E 3 -0.194 62.212 8.467 1 52.49 ? O1G ATP 303 A 1 HETATM 3 O O2G ATP . . . E 3 -0.246 59.791 8.966 1 51.98 ? O2G ATP 303 A 1 HETATM 4 O O3G ATP . . . E 3 1.913 60.9 8.621 1 60.12 ? O3G ATP 303 A 1 HETATM 5 P PB ATP . . . E 3 -0.728 61.755 11.702 1 48.46 ? PB ATP 303 A 1 HETATM 6 O O1B ATP . . . E 3 -2.118 61.275 11.421 1 63.24 ? O1B ATP 303 A 1 HETATM 7 O O2B ATP . . . E 3 -0.663 63.08 12.4 1 52.31 ? O2B ATP 303 A 1 HETATM 8 O O3B ATP . . . E 3 0.549 61.282 10.81 1 54.91 ? O3B ATP 303 A 1 HETATM 9 P PA ATP . . . E 3 -0.134 59.244 13.032 1 46.23 ? PA ATP 303 A 1 HETATM 10 O O1A ATP . . . E 3 0.93 58.719 12.144 1 47.61 ? O1A ATP 303 A 1 HETATM 11 O O2A ATP . . . E 3 -1.424 58.544 12.81 1 45.04 ? O2A ATP 303 A 1 HETATM 12 O O3A ATP . . . E 3 -0.312 60.861 12.934 1 46.62 ? O3A ATP 303 A 1 HETATM 13 O O5' ATP . . . E 3 0.328 59.151 14.551 1 51.04 ? O5' ATP 303 A 1 HETATM 14 C C5' ATP . . . E 3 -0.609 59.617 15.566 1 40.15 ? C5' ATP 303 A 1 HETATM 15 C C4' ATP . . . E 3 -0.214 60.865 16.353 1 29.9 ? C4' ATP 303 A 1 HETATM 16 O O4' ATP . . . E 3 0.9 60.656 17.273 1 38.4 ? O4' ATP 303 A 1 HETATM 17 C C3' ATP . . . E 3 0.169 62.152 15.593 1 35.93 ? C3' ATP 303 A 1 HETATM 18 O O3' ATP . . . E 3 -0.371 63.305 16.255 1 38.11 ? O3' ATP 303 A 1 HETATM 19 C C2' ATP . . . E 3 1.685 62.107 15.583 1 37.94 ? C2' ATP 303 A 1 HETATM 20 O O2' ATP . . . E 3 2.338 63.371 15.504 1 40.66 ? O2' ATP 303 A 1 HETATM 21 C C1' ATP . . . E 3 2.019 61.427 16.888 1 34.32 ? C1' ATP 303 A 1 HETATM 22 N N9 ATP . . . E 3 3.249 60.632 16.874 1 35 ? N9 ATP 303 A 1 HETATM 23 C C8 ATP . . . E 3 3.684 59.661 15.985 1 30.67 ? C8 ATP 303 A 1 HETATM 24 N N7 ATP . . . E 3 4.86 59.168 16.287 1 35.91 ? N7 ATP 303 A 1 HETATM 25 C C5 ATP . . . E 3 5.225 59.843 17.442 1 33.35 ? C5 ATP 303 A 1 HETATM 26 C C6 ATP . . . E 3 6.38 59.788 18.273 1 32.22 ? C6 ATP 303 A 1 HETATM 27 N N6 ATP . . . E 3 7.402 58.965 18.037 1 36.42 ? N6 ATP 303 A 1 HETATM 28 N N1 ATP . . . E 3 6.432 60.618 19.374 1 34.98 ? N1 ATP 303 A 1 HETATM 29 C C2 ATP . . . E 3 5.393 61.456 19.617 1 36.2 ? C2 ATP 303 A 1 HETATM 30 N N3 ATP . . . E 3 4.258 61.591 18.895 1 43.66 ? N3 ATP 303 A 1 HETATM 31 C C4 ATP . . . E 3 4.241 60.754 17.811 1 36.24 ? C4 ATP 303 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #