data_4GOM # _model_server_result.job_id Wo_iDy1ldbmS2d8zDrjAvw _model_server_result.datetime_utc '2024-11-15 00:37:13' _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 4gom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 4GOM # _exptl.entry_id 4GOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 367.36 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-{[(3S)-3-amino-3-carboxypropyl]amino}-5'-deoxyadenosine" _entity.pdbx_number_of_molecules 3 _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 4GOM _cell.length_a 161.038 _cell.length_b 161.038 _cell.length_c 95.293 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GOM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 PISA monomeric 1 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1 A,D,G 2 1 B,E,H 3 1 C,F,I 4 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 ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C14 H21 N7 O5' _chem_comp.formula_weight 367.36 _chem_comp.id 0Y0 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl]amino}-5'-deoxyadenosine" _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 OXT C 0Y0 doub 1 n n C CA 0Y0 sing 2 n n C O 0Y0 sing 3 n n CA N 0Y0 sing 4 n n CA CB 0Y0 sing 5 n n CB CAS 0Y0 sing 6 n n CAS NAR 0Y0 sing 7 n n NAR CAF 0Y0 sing 8 n n CAF CAA 0Y0 sing 9 n n CAB CAA 0Y0 sing 10 n n CAB OAH 0Y0 sing 11 n n CAB CAC 0Y0 sing 12 n n CAA OAE 0Y0 sing 13 n n CAC OAI 0Y0 sing 14 n n CAC CAD 0Y0 sing 15 n n OAE CAD 0Y0 sing 16 n n CAD N9 0Y0 sing 17 n n C8 N9 0Y0 sing 18 n y C8 N7 0Y0 doub 19 n y N9 C4 0Y0 sing 20 n y N7 C5 0Y0 sing 21 n y C4 N3 0Y0 doub 22 n y C4 C5 0Y0 sing 23 n y N3 C2 0Y0 sing 24 n y C5 C6 0Y0 doub 25 n y C2 N1 0Y0 doub 26 n y C6 N1 0Y0 sing 27 n y C6 N6 0Y0 sing 28 n n O H1 0Y0 sing 29 n n CA H2 0Y0 sing 30 n n N H3 0Y0 sing 31 n n N H4 0Y0 sing 32 n n CB H6 0Y0 sing 33 n n CB H7 0Y0 sing 34 n n CAS H8 0Y0 sing 35 n n CAS H9 0Y0 sing 36 n n NAR H10 0Y0 sing 37 n n CAF H12 0Y0 sing 38 n n CAF H13 0Y0 sing 39 n n CAA H14 0Y0 sing 40 n n CAB H15 0Y0 sing 41 n n OAH H16 0Y0 sing 42 n n CAC H17 0Y0 sing 43 n n OAI H18 0Y0 sing 44 n n CAD H19 0Y0 sing 45 n n C8 H20 0Y0 sing 46 n n C2 H21 0Y0 sing 47 n n N6 H22 0Y0 sing 48 n n N6 H23 0Y0 sing 49 n n # _atom_sites.entry_id 4GOM _atom_sites.fract_transf_matrix[1][1] 0.00621 _atom_sites.fract_transf_matrix[1][2] 0.003585 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00717 _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] 0.010494 _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 D 2 0Y0 D 1 301 1 0Y0 0Y0 . E 2 0Y0 E 1 301 1 0Y0 0Y0 . F 2 0Y0 F 1 301 1 0Y0 0Y0 . G 3 HOH D 1 401 13 HOH HOH . G 3 HOH D 2 402 19 HOH HOH . G 3 HOH D 3 403 26 HOH HOH . G 3 HOH D 4 404 27 HOH HOH . G 3 HOH D 5 405 28 HOH HOH . G 3 HOH D 6 406 29 HOH HOH . G 3 HOH D 7 407 31 HOH HOH . G 3 HOH D 8 408 33 HOH HOH . G 3 HOH D 9 409 35 HOH HOH . G 3 HOH D 10 410 36 HOH HOH . G 3 HOH D 11 411 37 HOH HOH . G 3 HOH D 12 412 39 HOH HOH . G 3 HOH D 13 413 40 HOH HOH . G 3 HOH D 14 414 41 HOH HOH . G 3 HOH D 15 415 46 HOH HOH . G 3 HOH D 16 416 47 HOH HOH . G 3 HOH D 17 417 48 HOH HOH . G 3 HOH D 18 418 55 HOH HOH . G 3 HOH D 19 419 57 HOH HOH . G 3 HOH D 20 420 58 HOH HOH . G 3 HOH D 21 421 59 HOH HOH . G 3 HOH D 22 422 63 HOH HOH . G 3 HOH D 23 423 64 HOH HOH . G 3 HOH D 24 424 65 HOH HOH . G 3 HOH D 25 425 71 HOH HOH . G 3 HOH D 26 426 72 HOH HOH . G 3 HOH D 27 427 74 HOH HOH . G 3 HOH D 28 428 76 HOH HOH . G 3 HOH D 29 429 81 HOH HOH . G 3 HOH D 30 430 82 HOH HOH . G 3 HOH D 31 431 84 HOH HOH . G 3 HOH D 32 432 85 HOH HOH . G 3 HOH D 33 433 86 HOH HOH . G 3 HOH D 34 434 87 HOH HOH . G 3 HOH D 35 435 89 HOH HOH . G 3 HOH D 36 436 93 HOH HOH . G 3 HOH D 37 437 95 HOH HOH . G 3 HOH D 38 438 96 HOH HOH . G 3 HOH D 39 439 97 HOH HOH . G 3 HOH D 40 440 98 HOH HOH . G 3 HOH D 41 441 100 HOH HOH . G 3 HOH D 42 442 101 HOH HOH . G 3 HOH D 43 443 102 HOH HOH . G 3 HOH D 44 444 103 HOH HOH . G 3 HOH D 45 445 104 HOH HOH . G 3 HOH D 46 446 107 HOH HOH . G 3 HOH D 47 447 109 HOH HOH . G 3 HOH D 48 448 110 HOH HOH . G 3 HOH D 49 449 117 HOH HOH . G 3 HOH D 50 450 122 HOH HOH . G 3 HOH D 51 451 123 HOH HOH . G 3 HOH D 52 452 125 HOH HOH . G 3 HOH D 53 453 126 HOH HOH . G 3 HOH D 54 454 129 HOH HOH . G 3 HOH D 55 455 132 HOH HOH . G 3 HOH D 56 456 133 HOH HOH . G 3 HOH D 57 457 136 HOH HOH . G 3 HOH D 58 458 139 HOH HOH . G 3 HOH D 59 459 140 HOH HOH . G 3 HOH D 60 460 144 HOH HOH . G 3 HOH D 61 461 146 HOH HOH . G 3 HOH D 62 462 147 HOH HOH . G 3 HOH D 63 463 153 HOH HOH . G 3 HOH D 64 464 155 HOH HOH . G 3 HOH D 65 465 156 HOH HOH . G 3 HOH D 66 466 157 HOH HOH . H 3 HOH E 1 401 12 HOH HOH . H 3 HOH E 2 402 14 HOH HOH . H 3 HOH E 3 403 15 HOH HOH . H 3 HOH E 4 404 17 HOH HOH . H 3 HOH E 5 405 23 HOH HOH . H 3 HOH E 6 406 25 HOH HOH . H 3 HOH E 7 407 32 HOH HOH . H 3 HOH E 8 408 34 HOH HOH . H 3 HOH E 9 409 49 HOH HOH . H 3 HOH E 10 410 53 HOH HOH . H 3 HOH E 11 411 54 HOH HOH . H 3 HOH E 12 412 60 HOH HOH . H 3 HOH E 13 413 61 HOH HOH . H 3 HOH E 14 414 69 HOH HOH . H 3 HOH E 15 415 73 HOH HOH . H 3 HOH E 16 416 78 HOH HOH . H 3 HOH E 17 417 90 HOH HOH . H 3 HOH E 18 418 91 HOH HOH . H 3 HOH E 19 419 92 HOH HOH . H 3 HOH E 20 420 106 HOH HOH . H 3 HOH E 21 421 111 HOH HOH . H 3 HOH E 22 422 114 HOH HOH . H 3 HOH E 23 423 115 HOH HOH . H 3 HOH E 24 424 116 HOH HOH . H 3 HOH E 25 425 121 HOH HOH . H 3 HOH E 26 426 124 HOH HOH . H 3 HOH E 27 427 130 HOH HOH . H 3 HOH E 28 428 134 HOH HOH . H 3 HOH E 29 429 141 HOH HOH . H 3 HOH E 30 430 142 HOH HOH . H 3 HOH E 31 431 148 HOH HOH . H 3 HOH E 32 432 149 HOH HOH . H 3 HOH E 33 433 154 HOH HOH . I 3 HOH F 1 401 16 HOH HOH . I 3 HOH F 2 402 18 HOH HOH . I 3 HOH F 3 403 20 HOH HOH . I 3 HOH F 4 404 21 HOH HOH . I 3 HOH F 5 405 22 HOH HOH . I 3 HOH F 6 406 38 HOH HOH . I 3 HOH F 7 407 43 HOH HOH . I 3 HOH F 8 408 44 HOH HOH . I 3 HOH F 9 409 45 HOH HOH . I 3 HOH F 10 410 51 HOH HOH . I 3 HOH F 11 411 52 HOH HOH . I 3 HOH F 12 412 56 HOH HOH . I 3 HOH F 13 413 62 HOH HOH . I 3 HOH F 14 414 67 HOH HOH . I 3 HOH F 15 415 75 HOH HOH . I 3 HOH F 16 416 77 HOH HOH . I 3 HOH F 17 417 79 HOH HOH . I 3 HOH F 18 418 80 HOH HOH . I 3 HOH F 19 419 83 HOH HOH . I 3 HOH F 20 420 88 HOH HOH . I 3 HOH F 21 421 94 HOH HOH . I 3 HOH F 22 422 105 HOH HOH . I 3 HOH F 23 423 108 HOH HOH . I 3 HOH F 24 424 112 HOH HOH . I 3 HOH F 25 425 113 HOH HOH . I 3 HOH F 26 426 119 HOH HOH . I 3 HOH F 27 427 120 HOH HOH . I 3 HOH F 28 428 131 HOH HOH . I 3 HOH F 29 429 137 HOH HOH . I 3 HOH F 30 430 143 HOH HOH . I 3 HOH F 31 431 150 HOH HOH . I 3 HOH F 32 432 151 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 O O 0Y0 . . . D 2 70.52 4.986 61.3 1 62.46 ? O 0Y0 301 D 1 HETATM 2 C C 0Y0 . . . D 2 70.216 3.811 61.579 1 62.29 ? C 0Y0 301 D 1 HETATM 3 O OXT 0Y0 . . . D 2 70.94 3.167 62.433 1 62.14 ? OXT 0Y0 301 D 1 HETATM 4 C CA 0Y0 . . . D 2 69.041 3.216 60.948 1 62.07 ? CA 0Y0 301 D 1 HETATM 5 N N 0Y0 . . . D 2 69.4 2.148 60.027 1 61.7 ? N 0Y0 301 D 1 HETATM 6 C CB 0Y0 . . . D 2 68.276 2.568 62.09 1 61.48 ? CB 0Y0 301 D 1 HETATM 7 C CAS 0Y0 . . . D 2 67.228 3.275 62.896 1 59.72 ? CAS 0Y0 301 D 1 HETATM 8 N NAR 0Y0 . . . D 2 66.203 2.397 63.369 1 57.04 ? NAR 0Y0 301 D 1 HETATM 9 C CAF 0Y0 . . . D 2 66.314 2.213 64.796 1 52.32 ? CAF 0Y0 301 D 1 HETATM 10 C CAA 0Y0 . . . D 2 65.105 2.303 65.558 1 53.36 ? CAA 0Y0 301 D 1 HETATM 11 O OAE 0Y0 . . . D 2 65.139 1.175 66.407 1 51.29 ? OAE 0Y0 301 D 1 HETATM 12 C CAB 0Y0 . . . D 2 65.175 3.433 66.464 1 52.93 ? CAB 0Y0 301 D 1 HETATM 13 O OAH 0Y0 . . . D 2 64.046 4.12 66.45 1 51.23 ? OAH 0Y0 301 D 1 HETATM 14 C CAC 0Y0 . . . D 2 65.329 2.888 67.774 1 51.82 ? CAC 0Y0 301 D 1 HETATM 15 O OAI 0Y0 . . . D 2 64.613 3.656 68.63 1 53.02 ? OAI 0Y0 301 D 1 HETATM 16 C CAD 0Y0 . . . D 2 64.767 1.548 67.664 1 51.82 ? CAD 0Y0 301 D 1 HETATM 17 N N9 0Y0 . . . D 2 65.364 0.587 68.553 1 53.02 ? N9 0Y0 301 D 1 HETATM 18 C C8 0Y0 . . . D 2 66.576 0.627 69.049 1 50.26 ? C8 0Y0 301 D 1 HETATM 19 N N7 0Y0 . . . D 2 66.739 -0.434 69.803 1 51.25 ? N7 0Y0 301 D 1 HETATM 20 C C5 0Y0 . . . D 2 65.638 -1.147 69.787 1 51.34 ? C5 0Y0 301 D 1 HETATM 21 C C4 0Y0 . . . D 2 64.749 -0.491 68.985 1 52.15 ? C4 0Y0 301 D 1 HETATM 22 N N3 0Y0 . . . D 2 63.555 -1.008 68.804 1 48.04 ? N3 0Y0 301 D 1 HETATM 23 C C2 0Y0 . . . D 2 63.221 -2.131 69.374 1 48.9 ? C2 0Y0 301 D 1 HETATM 24 N N1 0Y0 . . . D 2 64.058 -2.787 70.146 1 50.3 ? N1 0Y0 301 D 1 HETATM 25 C C6 0Y0 . . . D 2 65.259 -2.329 70.373 1 48.4 ? C6 0Y0 301 D 1 HETATM 26 N N6 0Y0 . . . D 2 66.18 -3.06 71.256 1 45.42 ? N6 0Y0 301 D 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 378 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 26 #