data_3GNI # _model_server_result.job_id oDXCqKLgXOTx8ljUh0mDzA _model_server_result.datetime_utc '2024-11-15 16:39:34' _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 3gni # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 3GNI # _exptl.entry_id 3GNI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _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 3GNI _cell.length_a 73.678 _cell.length_b 82.874 _cell.length_c 134.292 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GNI _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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 3GNI _atom_sites.fract_transf_matrix[1][1] 0.013572 _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] 0.012066 _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] 0.007446 _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 CIT A 1 342 2 CIT CIT . D 4 ATP B 1 1 1 ATP ATP . E 5 HOH A 1 343 1 HOH HOH . E 5 HOH A 2 344 2 HOH HOH . E 5 HOH A 3 345 3 HOH HOH . E 5 HOH A 4 346 4 HOH HOH . E 5 HOH A 5 347 5 HOH HOH . E 5 HOH A 6 348 6 HOH HOH . E 5 HOH A 7 349 7 HOH HOH . E 5 HOH A 8 350 8 HOH HOH . E 5 HOH A 9 351 9 HOH HOH . E 5 HOH A 10 352 10 HOH HOH . E 5 HOH A 11 353 11 HOH HOH . E 5 HOH A 12 354 12 HOH HOH . E 5 HOH A 13 355 13 HOH HOH . E 5 HOH A 14 356 14 HOH HOH . E 5 HOH A 15 357 15 HOH HOH . E 5 HOH A 16 358 16 HOH HOH . E 5 HOH A 17 359 17 HOH HOH . E 5 HOH A 18 360 18 HOH HOH . E 5 HOH A 19 361 19 HOH HOH . E 5 HOH A 20 362 20 HOH HOH . E 5 HOH A 21 363 21 HOH HOH . E 5 HOH A 22 364 22 HOH HOH . E 5 HOH A 23 365 23 HOH HOH . E 5 HOH A 24 366 24 HOH HOH . E 5 HOH A 25 367 25 HOH HOH . E 5 HOH A 26 368 26 HOH HOH . E 5 HOH A 27 369 27 HOH HOH . E 5 HOH A 28 370 28 HOH HOH . E 5 HOH A 29 371 29 HOH HOH . E 5 HOH A 30 372 30 HOH HOH . E 5 HOH A 31 373 31 HOH HOH . E 5 HOH A 32 374 32 HOH HOH . E 5 HOH A 33 375 33 HOH HOH . E 5 HOH A 34 376 34 HOH HOH . E 5 HOH A 35 377 35 HOH HOH . E 5 HOH A 36 378 36 HOH HOH . E 5 HOH A 37 379 37 HOH HOH . E 5 HOH A 38 380 38 HOH HOH . E 5 HOH A 39 381 39 HOH HOH . E 5 HOH A 40 382 40 HOH HOH . E 5 HOH A 41 383 41 HOH HOH . E 5 HOH A 42 384 42 HOH HOH . E 5 HOH A 43 385 43 HOH HOH . E 5 HOH A 44 386 44 HOH HOH . E 5 HOH A 45 387 46 HOH HOH . E 5 HOH A 46 388 47 HOH HOH . E 5 HOH A 47 389 48 HOH HOH . E 5 HOH A 48 390 49 HOH HOH . E 5 HOH A 49 391 50 HOH HOH . E 5 HOH A 50 392 51 HOH HOH . E 5 HOH A 51 393 52 HOH HOH . E 5 HOH A 52 394 53 HOH HOH . E 5 HOH A 53 395 54 HOH HOH . E 5 HOH A 54 396 55 HOH HOH . E 5 HOH A 55 397 56 HOH HOH . E 5 HOH A 56 398 57 HOH HOH . E 5 HOH A 57 399 58 HOH HOH . E 5 HOH A 58 400 59 HOH HOH . E 5 HOH A 59 401 60 HOH HOH . E 5 HOH A 60 402 62 HOH HOH . E 5 HOH A 61 403 63 HOH HOH . E 5 HOH A 62 404 64 HOH HOH . E 5 HOH A 63 405 65 HOH HOH . E 5 HOH A 64 406 66 HOH HOH . E 5 HOH A 65 407 67 HOH HOH . E 5 HOH A 66 408 68 HOH HOH . E 5 HOH A 67 409 69 HOH HOH . E 5 HOH A 68 410 70 HOH HOH . E 5 HOH A 69 411 71 HOH HOH . E 5 HOH A 70 412 72 HOH HOH . E 5 HOH A 71 413 73 HOH HOH . E 5 HOH A 72 414 74 HOH HOH . E 5 HOH A 73 415 75 HOH HOH . E 5 HOH A 74 416 76 HOH HOH . E 5 HOH A 75 417 77 HOH HOH . E 5 HOH A 76 418 78 HOH HOH . E 5 HOH A 77 419 79 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 . . . D 4 7.687 -24.902 -28.744 1 49.45 ? PG ATP 1 B 1 HETATM 2 O O1G ATP . . . D 4 7.495 -25.719 -30.012 1 47.68 ? O1G ATP 1 B 1 HETATM 3 O O2G ATP . . . D 4 7.911 -25.768 -27.519 1 49.5 ? O2G ATP 1 B 1 HETATM 4 O O3G ATP . . . D 4 8.657 -23.736 -28.85 1 51.16 ? O3G ATP 1 B 1 HETATM 5 P PB ATP . . . D 4 5.681 -23.477 -27.262 1 24.78 ? PB ATP 1 B 1 HETATM 6 O O1B ATP . . . D 4 5.776 -24.461 -26.13 1 21 ? O1B ATP 1 B 1 HETATM 7 O O2B ATP . . . D 4 6.285 -22.106 -27.11 1 25.44 ? O2B ATP 1 B 1 HETATM 8 O O3B ATP . . . D 4 6.25 -24.172 -28.596 1 34.29 ? O3B ATP 1 B 1 HETATM 9 P PA ATP . . . D 4 3.457 -21.991 -28.339 1 26.22 ? PA ATP 1 B 1 HETATM 10 O O1A ATP . . . D 4 2.95 -21.047 -27.28 1 32.82 ? O1A ATP 1 B 1 HETATM 11 O O2A ATP . . . D 4 4.373 -21.44 -29.397 1 23.84 ? O2A ATP 1 B 1 HETATM 12 O O3A ATP . . . D 4 4.109 -23.284 -27.614 1 27.48 ? O3A ATP 1 B 1 HETATM 13 O O5' ATP . . . D 4 2.202 -22.703 -29.019 1 27.19 ? O5' ATP 1 B 1 HETATM 14 C C5' ATP . . . D 4 2.415 -23.663 -30.059 1 26.09 ? C5' ATP 1 B 1 HETATM 15 C C4' ATP . . . D 4 1.632 -23.252 -31.288 1 20.96 ? C4' ATP 1 B 1 HETATM 16 O O4' ATP . . . D 4 0.243 -23.19 -30.951 1 27.2 ? O4' ATP 1 B 1 HETATM 17 C C3' ATP . . . D 4 1.943 -21.857 -31.808 1 20.97 ? C3' ATP 1 B 1 HETATM 18 O O3' ATP . . . D 4 3.093 -21.801 -32.648 1 20.88 ? O3' ATP 1 B 1 HETATM 19 C C2' ATP . . . D 4 0.677 -21.545 -32.575 1 25.84 ? C2' ATP 1 B 1 HETATM 20 O O2' ATP . . . D 4 0.671 -22.208 -33.853 1 25.44 ? O2' ATP 1 B 1 HETATM 21 C C1' ATP . . . D 4 -0.402 -22.139 -31.681 1 25.44 ? C1' ATP 1 B 1 HETATM 22 N N9 ATP . . . D 4 -0.874 -21.039 -30.801 1 27.69 ? N9 ATP 1 B 1 HETATM 23 C C8 ATP . . . D 4 -0.388 -20.701 -29.581 1 28.23 ? C8 ATP 1 B 1 HETATM 24 N N7 ATP . . . D 4 -1.041 -19.618 -29.078 1 31.33 ? N7 ATP 1 B 1 HETATM 25 C C5 ATP . . . D 4 -1.977 -19.234 -29.978 1 25.02 ? C5 ATP 1 B 1 HETATM 26 C C6 ATP . . . D 4 -3.007 -18.169 -30.073 1 25.43 ? C6 ATP 1 B 1 HETATM 27 N N6 ATP . . . D 4 -3.2 -17.251 -29.088 1 25.15 ? N6 ATP 1 B 1 HETATM 28 N N1 ATP . . . D 4 -3.769 -18.138 -31.186 1 27.72 ? N1 ATP 1 B 1 HETATM 29 C C2 ATP . . . D 4 -3.605 -19.021 -32.192 1 29.45 ? C2 ATP 1 B 1 HETATM 30 N N3 ATP . . . D 4 -2.691 -20.009 -32.177 1 26.64 ? N3 ATP 1 B 1 HETATM 31 C C4 ATP . . . D 4 -1.856 -20.167 -31.114 1 30.01 ? C4 ATP 1 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #