data_2Y4I # _model_server_result.job_id Fu4BzzOonwmMYGdhojATUw _model_server_result.datetime_utc '2024-11-29 17:59:29' _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 2y4i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1932}' # _entry.id 2Y4I # _exptl.entry_id 2Y4I _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 120 _cell.entry_id 2Y4I _cell.length_a 130.565 _cell.length_b 130.565 _cell.length_c 221.005 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Y4I _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 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 _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 C N N ? 3 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 OD1 ASN 160 B ASN 791 1_555 D MG MG . B MG 1933 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc2 A OD2 ASP 172 B ASP 803 1_555 D MG MG . B MG 1933 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc3 C O1B ATP . B ATP 1932 1_555 D MG MG . B MG 1933 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc4 C O2A ATP . B ATP 1932 1_555 D MG MG . B MG 1933 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc5 B O SER 196 C SER 194 1_555 F MG MG . C MG 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc6 B OD1 ASN 197 C ASN 195 1_555 F MG MG . C MG 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc7 B OD2 ASP 210 C ASP 208 1_555 F MG MG . C MG 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc8 E O1B ATP . C ATP 1382 1_555 F MG MG . C MG 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc9 E O2A ATP . C ATP 1382 1_555 F MG MG . C MG 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? # _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 2Y4I _atom_sites.fract_transf_matrix[1][1] 0.007659 _atom_sites.fract_transf_matrix[1][2] 0.004422 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008844 _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] 0.004525 _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 3 ATP B 1 1932 1932 ATP ATP . D 4 MG B 1 1933 1933 MG MG . E 3 ATP C 1 1382 1382 ATP ATP . F 4 MG C 1 1383 1383 MG MG . G 5 CL C 1 1384 1384 CL CL . # 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 . . . C 3 -12.986 59.971 -3.755 1 127.97 ? PG ATP 1932 B 1 HETATM 2 O O1G ATP . . . C 3 -11.904 59.108 -3.149 1 127.56 ? O1G ATP 1932 B 1 HETATM 3 O O2G ATP . . . C 3 -14.229 60.097 -2.908 1 134.28 ? O2G ATP 1932 B 1 HETATM 4 O O3G ATP . . . C 3 -13.266 59.682 -5.211 1 121.39 ? O3G ATP 1932 B 1 HETATM 5 P PB ATP . . . C 3 -10.765 61.649 -3.827 1 102.68 ? PB ATP 1932 B 1 HETATM 6 O O1B ATP . . . C 3 -10.443 63.093 -4.138 1 99.47 ? O1B ATP 1932 B 1 HETATM 7 O O2B ATP . . . C 3 -10.157 61.005 -2.606 1 102.93 ? O2B ATP 1932 B 1 HETATM 8 O O3B ATP . . . C 3 -12.361 61.458 -3.758 1 265.64 ? O3B ATP 1932 B 1 HETATM 9 P PA ATP . . . C 3 -9.539 61.117 -6.367 1 102.98 ? PA ATP 1932 B 1 HETATM 10 O O1A ATP . . . C 3 -9.918 60.193 -7.505 1 96.05 ? O1A ATP 1932 B 1 HETATM 11 O O2A ATP . . . C 3 -9.591 62.615 -6.552 1 105.7 ? O2A ATP 1932 B 1 HETATM 12 O O3A ATP . . . C 3 -10.479 60.726 -5.12 1 268.14 ? O3A ATP 1932 B 1 HETATM 13 O O5' ATP . . . C 3 -8.06 60.735 -5.865 1 107.72 ? O5' ATP 1932 B 1 HETATM 14 C C5' ATP . . . C 3 -7.777 60.732 -4.471 1 110.6 ? C5' ATP 1932 B 1 HETATM 15 C C4' ATP . . . C 3 -6.376 61.258 -4.218 1 109.22 ? C4' ATP 1932 B 1 HETATM 16 O O4' ATP . . . C 3 -5.858 61.864 -5.403 1 101.19 ? O4' ATP 1932 B 1 HETATM 17 C C3' ATP . . . C 3 -6.416 62.307 -3.118 1 117.73 ? C3' ATP 1932 B 1 HETATM 18 O O3' ATP . . . C 3 -5.674 61.849 -1.984 1 123.1 ? O3' ATP 1932 B 1 HETATM 19 C C2' ATP . . . C 3 -5.772 63.539 -3.717 1 118.99 ? C2' ATP 1932 B 1 HETATM 20 O O2' ATP . . . C 3 -4.712 64.024 -2.885 1 126.28 ? O2' ATP 1932 B 1 HETATM 21 C C1' ATP . . . C 3 -5.241 63.109 -5.077 1 107.31 ? C1' ATP 1932 B 1 HETATM 22 N N9 ATP . . . C 3 -5.649 64.115 -6.078 1 98.46 ? N9 ATP 1932 B 1 HETATM 23 C C8 ATP . . . C 3 -6.663 63.956 -6.943 1 102.1 ? C8 ATP 1932 B 1 HETATM 24 N N7 ATP . . . C 3 -6.796 65.052 -7.731 1 106.87 ? N7 ATP 1932 B 1 HETATM 25 C C5 ATP . . . C 3 -5.85 65.937 -7.367 1 101.26 ? C5 ATP 1932 B 1 HETATM 26 C C6 ATP . . . C 3 -5.44 67.293 -7.8 1 104.26 ? C6 ATP 1932 B 1 HETATM 27 N N6 ATP . . . C 3 -6.095 67.927 -8.806 1 108.98 ? N6 ATP 1932 B 1 HETATM 28 N N1 ATP . . . C 3 -4.396 67.867 -7.157 1 98.39 ? N1 ATP 1932 B 1 HETATM 29 C C2 ATP . . . C 3 -3.749 67.236 -6.16 1 90.28 ? C2 ATP 1932 B 1 HETATM 30 N N3 ATP . . . C 3 -4.071 66.006 -5.72 1 86.11 ? N3 ATP 1932 B 1 HETATM 31 C C4 ATP . . . C 3 -5.093 65.314 -6.274 1 92.27 ? C4 ATP 1932 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 31 #