data_3U4L # _model_server_result.job_id Mi_o_KImrPPKPJAeHyYENA _model_server_result.datetime_utc '2025-01-11 09:10:16' _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 3u4l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 3U4L # _exptl.entry_id 3U4L _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 90 _cell.entry_id 3U4L _cell.length_a 38.3 _cell.length_b 71.1 _cell.length_c 171.5 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U4L _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _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 B C ACE 1 P ACE 0 1_555 B N ALA 2 P ALA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? metalc ? metalc1 A OD2 ASP 288 A ASP 288 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc2 C O3B ATP . A ATP 401 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc3 C O2G ATP . A ATP 401 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc4 D CA CA . A CA 402 1_555 F O HOH . A HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc5 E CA CA . A CA 403 1_555 G O HOH . P HOH 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? # _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 76 n n PG O2G ATP sing 77 n n PG O3G ATP sing 78 n n PG O3B ATP sing 79 n n O2G HOG2 ATP sing 80 n n O3G HOG3 ATP sing 81 n n PB O1B ATP doub 82 n n PB O2B ATP sing 83 n n PB O3B ATP sing 84 n n PB O3A ATP sing 85 n n O2B HOB2 ATP sing 86 n n PA O1A ATP doub 87 n n PA O2A ATP sing 88 n n PA O3A ATP sing 89 n n PA O5' ATP sing 90 n n O2A HOA2 ATP sing 91 n n O5' C5' ATP sing 92 n n C5' C4' ATP sing 93 n n C5' "H5'1" ATP sing 94 n n C5' "H5'2" ATP sing 95 n n C4' O4' ATP sing 96 n n C4' C3' ATP sing 97 n n C4' H4' ATP sing 98 n n O4' C1' ATP sing 99 n n C3' O3' ATP sing 100 n n C3' C2' ATP sing 101 n n C3' H3' ATP sing 102 n n O3' HO3' ATP sing 103 n n C2' O2' ATP sing 104 n n C2' C1' ATP sing 105 n n C2' H2' ATP sing 106 n n O2' HO2' ATP sing 107 n n C1' N9 ATP sing 108 n n C1' H1' ATP sing 109 n n N9 C8 ATP sing 110 n y N9 C4 ATP sing 111 n y C8 N7 ATP doub 112 n y C8 H8 ATP sing 113 n n N7 C5 ATP sing 114 n y C5 C6 ATP sing 115 n y C5 C4 ATP doub 116 n y C6 N6 ATP sing 117 n n C6 N1 ATP doub 118 n y N6 HN61 ATP sing 119 n n N6 HN62 ATP sing 120 n n N1 C2 ATP sing 121 n y C2 N3 ATP doub 122 n y C2 H2 ATP sing 123 n n N3 C4 ATP sing 124 n y # _atom_sites.entry_id 3U4L _atom_sites.fract_transf_matrix[1][1] 0.02611 _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] 0.014065 _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] 0.005831 _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 1 401 376 ATP ATP . D 4 CA A 1 402 377 CA CA . E 4 CA A 1 403 378 CA CA . F 5 HOH A 1 501 379 HOH HOH . F 5 HOH A 2 502 380 HOH HOH . F 5 HOH A 3 503 381 HOH HOH . F 5 HOH A 4 504 382 HOH HOH . F 5 HOH A 5 505 383 HOH HOH . F 5 HOH A 6 506 384 HOH HOH . F 5 HOH A 7 507 385 HOH HOH . F 5 HOH A 8 508 386 HOH HOH . F 5 HOH A 9 509 387 HOH HOH . F 5 HOH A 10 510 388 HOH HOH . F 5 HOH A 11 511 389 HOH HOH . F 5 HOH A 12 512 390 HOH HOH . F 5 HOH A 13 513 391 HOH HOH . F 5 HOH A 14 514 392 HOH HOH . F 5 HOH A 15 515 393 HOH HOH . F 5 HOH A 16 516 394 HOH HOH . G 5 HOH P 1 201 141 HOH HOH . G 5 HOH P 2 202 142 HOH HOH . G 5 HOH P 3 203 143 HOH HOH . G 5 HOH P 4 204 144 HOH HOH . G 5 HOH P 5 205 145 HOH HOH . G 5 HOH P 6 206 146 HOH HOH . G 5 HOH P 7 207 147 HOH HOH . G 5 HOH P 8 208 148 HOH HOH . G 5 HOH P 9 209 149 HOH HOH . G 5 HOH P 10 210 150 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 . . . C 3 -10.412 -15.768 25.625 1 49.41 ? PG ATP 401 A 1 HETATM 2 O O1G ATP . . . C 3 -11.414 -15.109 26.54 1 48.68 ? O1G ATP 401 A 1 HETATM 3 O O2G ATP . . . C 3 -10.204 -15.14 24.268 1 49 ? O2G ATP 401 A 1 HETATM 4 O O3G ATP . . . C 3 -10.7 -17.228 25.557 1 53.31 ? O3G ATP 401 A 1 HETATM 5 P PB ATP . . . C 3 -7.983 -16.7 26.709 1 48.69 ? PB ATP 401 A 1 HETATM 6 O O1B ATP . . . C 3 -7.809 -16.773 28.219 1 47.81 ? O1B ATP 401 A 1 HETATM 7 O O2B ATP . . . C 3 -8.621 -17.842 26.004 1 49.28 ? O2B ATP 401 A 1 HETATM 8 O O3B ATP . . . C 3 -8.936 -15.476 26.274 1 48.66 ? O3B ATP 401 A 1 HETATM 9 P PA ATP . . . C 3 -5.867 -17.657 25.026 1 45.21 ? PA ATP 401 A 1 HETATM 10 O O1A ATP . . . C 3 -4.39 -17.764 25.335 1 49.95 ? O1A ATP 401 A 1 HETATM 11 O O2A ATP . . . C 3 -6.264 -17.323 23.627 1 49.3 ? O2A ATP 401 A 1 HETATM 12 O O3A ATP . . . C 3 -6.531 -16.555 26.032 1 47.37 ? O3A ATP 401 A 1 HETATM 13 O O5' ATP . . . C 3 -6.485 -19.1 25.298 1 51.45 ? O5' ATP 401 A 1 HETATM 14 C C5' ATP . . . C 3 -5.638 -20.232 25.507 1 53.24 ? C5' ATP 401 A 1 HETATM 15 C C4' ATP . . . C 3 -6.333 -21.512 25.052 1 54.48 ? C4' ATP 401 A 1 HETATM 16 O O4' ATP . . . C 3 -5.589 -22.038 23.953 1 56.19 ? O4' ATP 401 A 1 HETATM 17 C C3' ATP . . . C 3 -6.321 -22.596 26.116 1 58.73 ? C3' ATP 401 A 1 HETATM 18 O O3' ATP . . . C 3 -7.58 -23.287 26.109 1 63.98 ? O3' ATP 401 A 1 HETATM 19 C C2' ATP . . . C 3 -5.237 -23.553 25.672 1 54.64 ? C2' ATP 401 A 1 HETATM 20 O O2' ATP . . . C 3 -5.573 -24.892 26.028 1 53.14 ? O2' ATP 401 A 1 HETATM 21 C C1' ATP . . . C 3 -5.213 -23.389 24.163 1 51.13 ? C1' ATP 401 A 1 HETATM 22 N N9 ATP . . . C 3 -3.862 -23.742 23.669 1 51.17 ? N9 ATP 401 A 1 HETATM 23 C C8 ATP . . . C 3 -2.697 -23.256 24.154 1 48.56 ? C8 ATP 401 A 1 HETATM 24 N N7 ATP . . . C 3 -1.636 -23.813 23.527 1 44.65 ? N7 ATP 401 A 1 HETATM 25 C C5 ATP . . . C 3 -2.113 -24.685 22.615 1 50.19 ? C5 ATP 401 A 1 HETATM 26 C C6 ATP . . . C 3 -1.532 -25.624 21.603 1 49.72 ? C6 ATP 401 A 1 HETATM 27 N N6 ATP . . . C 3 -0.192 -25.706 21.467 1 45.72 ? N6 ATP 401 A 1 HETATM 28 N N1 ATP . . . C 3 -2.381 -26.376 20.827 1 50.73 ? N1 ATP 401 A 1 HETATM 29 C C2 ATP . . . C 3 -3.729 -26.295 20.97 1 47.74 ? C2 ATP 401 A 1 HETATM 30 N N3 ATP . . . C 3 -4.319 -25.458 21.872 1 51.31 ? N3 ATP 401 A 1 HETATM 31 C C4 ATP . . . C 3 -3.591 -24.642 22.707 1 49.98 ? C4 ATP 401 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 326 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 31 #