data_4DIN # _model_server_result.job_id QHfS3CqiBd91pGOiTPhyNA _model_server_result.datetime_utc '2024-11-04 22:49:58' _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 4din # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 4DIN # _exptl.entry_id 4DIN _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 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 4DIN _cell.length_a 172.194 _cell.length_b 172.194 _cell.length_c 146.646 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DIN _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 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 _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 3 _struct_asym.id C _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 TRP 196 A TRP 196 1_555 A N TPO 197 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C TPO 197 A TPO 197 1_555 A N LEU 198 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C VAL 337 A VAL 337 1_555 A N SEP 338 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C SEP 338 A SEP 338 1_555 A N ILE 339 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OD1 ASN 171 A ASN 171 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc2 A OD2 ASP 184 A ASP 184 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc3 A OD1 ASP 184 A ASP 184 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc4 A OD2 ASP 184 A ASP 184 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc5 C O2A ATP . A ATP 400 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc6 C O3G ATP . A ATP 400 1_555 D MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc7 C O3G ATP . A ATP 400 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc8 C O2B ATP . A ATP 400 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc9 C O2G ATP . A ATP 400 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? # _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 4DIN _atom_sites.fract_transf_matrix[1][1] 0.005807 _atom_sites.fract_transf_matrix[1][2] 0.003353 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006706 _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] 0.006819 _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 A 1 400 400 ATP ATP . D 4 MG A 1 401 401 MG MG . E 4 MG A 1 402 402 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 . . . C 3 60.869 43.859 -4.601 1 212.84 ? PG ATP 400 A 1 HETATM 2 O O1G ATP . . . C 3 59.36 43.79 -4.771 1 212.84 ? O1G ATP 400 A 1 HETATM 3 O O2G ATP . . . C 3 61.245 45.23 -4.058 1 212.84 ? O2G ATP 400 A 1 HETATM 4 O O3G ATP . . . C 3 61.307 42.786 -3.619 1 212.84 ? O3G ATP 400 A 1 HETATM 5 P PB ATP . . . C 3 63.113 44.116 -6.053 1 212.84 ? PB ATP 400 A 1 HETATM 6 O O1B ATP . . . C 3 63.137 45.601 -6.025 1 212.84 ? O1B ATP 400 A 1 HETATM 7 O O2B ATP . . . C 3 63.837 43.597 -4.865 1 212.84 ? O2B ATP 400 A 1 HETATM 8 O O3B ATP . . . C 3 61.576 43.602 -6.038 1 212.84 ? O3B ATP 400 A 1 HETATM 9 P PA ATP . . . C 3 64.489 42.142 -7.283 1 212.84 ? PA ATP 400 A 1 HETATM 10 O O1A ATP . . . C 3 65.563 42.162 -6.257 1 212.84 ? O1A ATP 400 A 1 HETATM 11 O O2A ATP . . . C 3 63.458 41.148 -6.889 1 212.84 ? O2A ATP 400 A 1 HETATM 12 O O3A ATP . . . C 3 63.817 43.609 -7.424 1 212.84 ? O3A ATP 400 A 1 HETATM 13 O O5' ATP . . . C 3 65.131 41.715 -8.679 1 212.84 ? O5' ATP 400 A 1 HETATM 14 C C5' ATP . . . C 3 64.311 41.634 -9.844 1 212.84 ? C5' ATP 400 A 1 HETATM 15 C C4' ATP . . . C 3 64.428 40.271 -10.493 1 212.84 ? C4' ATP 400 A 1 HETATM 16 O O4' ATP . . . C 3 65.822 39.964 -10.751 1 212.84 ? O4' ATP 400 A 1 HETATM 17 C C3' ATP . . . C 3 63.933 39.037 -9.763 1 212.84 ? C3' ATP 400 A 1 HETATM 18 O O3' ATP . . . C 3 62.517 38.911 -9.847 1 212.84 ? O3' ATP 400 A 1 HETATM 19 C C2' ATP . . . C 3 64.641 37.904 -10.507 1 212.84 ? C2' ATP 400 A 1 HETATM 20 O O2' ATP . . . C 3 63.977 37.49 -11.685 1 212.84 ? O2' ATP 400 A 1 HETATM 21 C C1' ATP . . . C 3 65.973 38.56 -10.886 1 212.84 ? C1' ATP 400 A 1 HETATM 22 N N9 ATP . . . C 3 67.118 38.11 -10.088 1 212.84 ? N9 ATP 400 A 1 HETATM 23 C C8 ATP . . . C 3 67.483 38.462 -8.808 1 212.84 ? C8 ATP 400 A 1 HETATM 24 N N7 ATP . . . C 3 68.559 37.85 -8.379 1 212.84 ? N7 ATP 400 A 1 HETATM 25 C C5 ATP . . . C 3 68.935 37.045 -9.445 1 212.84 ? C5 ATP 400 A 1 HETATM 26 C C6 ATP . . . C 3 70 36.144 -9.621 1 212.84 ? C6 ATP 400 A 1 HETATM 27 N N6 ATP . . . C 3 70.918 35.888 -8.686 1 212.84 ? N6 ATP 400 A 1 HETATM 28 N N1 ATP . . . C 3 70.092 35.504 -10.807 1 212.84 ? N1 ATP 400 A 1 HETATM 29 C C2 ATP . . . C 3 69.17 35.757 -11.744 1 212.84 ? C2 ATP 400 A 1 HETATM 30 N N3 ATP . . . C 3 68.124 36.577 -11.697 1 212.84 ? N3 ATP 400 A 1 HETATM 31 C C4 ATP . . . C 3 68.061 37.199 -10.506 1 212.84 ? C4 ATP 400 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #