data_5HGM # _model_server_result.job_id VDgQApAS5Kx6SQnwtHfBNA _model_server_result.datetime_utc '2024-10-26 10:25:11' _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 5hgm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5HGM # _exptl.entry_id 5HGM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 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 5HGM _cell.length_a 90.81 _cell.length_b 90.81 _cell.length_c 56.68 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HGM _symmetry.cell_setting ? _symmetry.Int_Tables_number 168 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_765 -y+2,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 136.215 78.643767 0 3 'crystal symmetry operation' 3_675 -x+y+1,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 157.287534 0 4 'crystal symmetry operation' 4_775 -x+2,-y+2,z -1 0 0 0 -1 0 0 0 1 90.81 157.287534 0 5 'crystal symmetry operation' 5_565 y,-x+y+1,z 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 -45.405 78.643767 0 6 'crystal symmetry operation' 6_655 x-y+1,x,z 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 90.81 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 14 A CYS 14 1_555 A SG CYS 45 A CYS 45 5_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? disulf ? disulf2 A SG CYS 198 A CYS 198 1_555 A SG CYS 218 A CYS 218 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.046 ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DTP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 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 DTP doub 83 n n PG O2G DTP sing 84 n n PG O3G DTP sing 85 n n PG O3B DTP sing 86 n n O2G HOG2 DTP sing 87 n n O3G HOG3 DTP sing 88 n n PB O1B DTP doub 89 n n PB O2B DTP sing 90 n n PB O3B DTP sing 91 n n PB O3A DTP sing 92 n n O2B HOB2 DTP sing 93 n n PA O1A DTP doub 94 n n PA O2A DTP sing 95 n n PA O3A DTP sing 96 n n PA O5' DTP sing 97 n n O2A HOA2 DTP sing 98 n n O5' C5' DTP sing 99 n n C5' C4' DTP sing 100 n n C5' "H5'1" DTP sing 101 n n C5' "H5'2" DTP sing 102 n n C4' O4' DTP sing 103 n n C4' C3' DTP sing 104 n n C4' H4' DTP sing 105 n n O4' C1' DTP sing 106 n n C3' O3' DTP sing 107 n n C3' C2' DTP sing 108 n n C3' H3' DTP sing 109 n n O3' HO3' DTP sing 110 n n C2' C1' DTP sing 111 n n C2' "H2'1" DTP sing 112 n n C2' "H2'2" DTP sing 113 n n C1' N9 DTP sing 114 n n C1' H1' DTP sing 115 n n N9 C8 DTP sing 116 n y N9 C4 DTP sing 117 n y C8 N7 DTP doub 118 n y C8 H8 DTP sing 119 n n N7 C5 DTP sing 120 n y C5 C6 DTP sing 121 n y C5 C4 DTP doub 122 n y C6 N6 DTP sing 123 n n C6 N1 DTP doub 124 n y N6 HN61 DTP sing 125 n n N6 HN62 DTP sing 126 n n N1 C2 DTP sing 127 n y C2 N3 DTP doub 128 n y C2 H2 DTP sing 129 n n N3 C4 DTP sing 130 n y # _atom_sites.entry_id 5HGM _atom_sites.fract_transf_matrix[1][1] 0.011012 _atom_sites.fract_transf_matrix[1][2] 0.006358 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012716 _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] 0.017643 _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 B 2 DTP A 1 301 1 DTP DTP . C 3 HOH A 1 401 11 HOH HOH . C 3 HOH A 2 402 28 HOH HOH . C 3 HOH A 3 403 55 HOH HOH . C 3 HOH A 4 404 35 HOH HOH . C 3 HOH A 5 405 10 HOH HOH . C 3 HOH A 6 406 40 HOH HOH . C 3 HOH A 7 407 47 HOH HOH . C 3 HOH A 8 408 22 HOH HOH . C 3 HOH A 9 409 32 HOH HOH . C 3 HOH A 10 410 62 HOH HOH . C 3 HOH A 11 411 45 HOH HOH . C 3 HOH A 12 412 9 HOH HOH . C 3 HOH A 13 413 6 HOH HOH . C 3 HOH A 14 414 29 HOH HOH . C 3 HOH A 15 415 64 HOH HOH . C 3 HOH A 16 416 31 HOH HOH . C 3 HOH A 17 417 36 HOH HOH . C 3 HOH A 18 418 18 HOH HOH . C 3 HOH A 19 419 66 HOH HOH . C 3 HOH A 20 420 58 HOH HOH . C 3 HOH A 21 421 5 HOH HOH . C 3 HOH A 22 422 49 HOH HOH . C 3 HOH A 23 423 8 HOH HOH . C 3 HOH A 24 424 56 HOH HOH . C 3 HOH A 25 425 57 HOH HOH . C 3 HOH A 26 426 90 HOH HOH . C 3 HOH A 27 427 15 HOH HOH . C 3 HOH A 28 428 76 HOH HOH . C 3 HOH A 29 429 53 HOH HOH . C 3 HOH A 30 430 1 HOH HOH . C 3 HOH A 31 431 84 HOH HOH . C 3 HOH A 32 432 41 HOH HOH . C 3 HOH A 33 433 2 HOH HOH . C 3 HOH A 34 434 25 HOH HOH . C 3 HOH A 35 435 33 HOH HOH . C 3 HOH A 36 436 24 HOH HOH . C 3 HOH A 37 437 63 HOH HOH . C 3 HOH A 38 438 59 HOH HOH . C 3 HOH A 39 439 16 HOH HOH . C 3 HOH A 40 440 88 HOH HOH . C 3 HOH A 41 441 78 HOH HOH . C 3 HOH A 42 442 48 HOH HOH . C 3 HOH A 43 443 46 HOH HOH . C 3 HOH A 44 444 37 HOH HOH . C 3 HOH A 45 445 80 HOH HOH . C 3 HOH A 46 446 20 HOH HOH . C 3 HOH A 47 447 52 HOH HOH . C 3 HOH A 48 448 60 HOH HOH . C 3 HOH A 49 449 65 HOH HOH . C 3 HOH A 50 450 34 HOH HOH . C 3 HOH A 51 451 69 HOH HOH . C 3 HOH A 52 452 12 HOH HOH . C 3 HOH A 53 453 68 HOH HOH . C 3 HOH A 54 454 50 HOH HOH . C 3 HOH A 55 455 74 HOH HOH . C 3 HOH A 56 456 79 HOH HOH . C 3 HOH A 57 457 91 HOH HOH . C 3 HOH A 58 458 21 HOH HOH . C 3 HOH A 59 459 54 HOH HOH . C 3 HOH A 60 460 42 HOH HOH . C 3 HOH A 61 461 61 HOH HOH . C 3 HOH A 62 462 14 HOH HOH . C 3 HOH A 63 463 75 HOH HOH . C 3 HOH A 64 464 4 HOH HOH . C 3 HOH A 65 465 51 HOH HOH . C 3 HOH A 66 466 23 HOH HOH . C 3 HOH A 67 467 19 HOH HOH . C 3 HOH A 68 468 71 HOH HOH . C 3 HOH A 69 469 7 HOH HOH . C 3 HOH A 70 470 26 HOH HOH . C 3 HOH A 71 471 87 HOH HOH . C 3 HOH A 72 472 30 HOH HOH . C 3 HOH A 73 473 73 HOH HOH . C 3 HOH A 74 474 81 HOH HOH . C 3 HOH A 75 475 38 HOH HOH . C 3 HOH A 76 476 83 HOH HOH . C 3 HOH A 77 477 89 HOH HOH . C 3 HOH A 78 478 44 HOH HOH . C 3 HOH A 79 479 27 HOH HOH . C 3 HOH A 80 480 82 HOH HOH . C 3 HOH A 81 481 72 HOH HOH . C 3 HOH A 82 482 70 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 DTP . . . B 2 45.137 78.522 1.281 0.17 121.54 ? PG DTP 301 A 1 HETATM 2 O O1G DTP . . . B 2 46.638 78.511 1.121 0.17 121.38 ? O1G DTP 301 A 1 HETATM 3 O O2G DTP . . . B 2 44.568 77.272 1.908 0.17 121.03 ? O2G DTP 301 A 1 HETATM 4 O O3G DTP . . . B 2 44.579 79.809 1.84 0.17 121.24 ? O3G DTP 301 A 1 HETATM 5 P PB DTP . . . B 2 45.566 78.803 -1.467 0.17 119.6 ? PB DTP 301 A 1 HETATM 6 O O1B DTP . . . B 2 45.8 80.294 -1.512 0.17 120.01 ? O1B DTP 301 A 1 HETATM 7 O O2B DTP . . . B 2 46.741 77.858 -1.394 0.17 119.91 ? O2B DTP 301 A 1 HETATM 8 O O3B DTP . . . B 2 44.585 78.483 -0.231 0.17 120.09 ? O3B DTP 301 A 1 HETATM 9 P PA DTP . . . B 2 45.139 78.798 -4.229 0.17 121.69 ? PA DTP 301 A 1 HETATM 10 O O1A DTP . . . B 2 46.05 77.711 -4.747 0.17 121.76 ? O1A DTP 301 A 1 HETATM 11 O O2A DTP . . . B 2 45.615 80.231 -4.202 0.17 121.05 ? O2A DTP 301 A 1 HETATM 12 O O3A DTP . . . B 2 44.671 78.396 -2.742 0.17 120.71 ? O3A DTP 301 A 1 HETATM 13 O O5' DTP . . . B 2 43.761 78.74 -5.059 0.17 121.44 ? O5' DTP 301 A 1 HETATM 14 C C5' DTP . . . B 2 43.783 79.057 -6.599 0 105.66 ? C5' DTP 301 A 1 HETATM 15 C C4' DTP . . . B 2 43.376 77.835 -7.412 0 103.56 ? C4' DTP 301 A 1 HETATM 16 O O4' DTP . . . B 2 42.004 77.941 -7.807 0 101.83 ? O4' DTP 301 A 1 HETATM 17 C C3' DTP . . . B 2 44.214 77.698 -8.674 0 102.54 ? C3' DTP 301 A 1 HETATM 18 O O3' DTP . . . B 2 44.987 76.494 -8.64 0 102.35 ? O3' DTP 301 A 1 HETATM 19 C C2' DTP . . . B 2 43.237 77.673 -9.835 0 101.76 ? C2' DTP 301 A 1 HETATM 20 C C1' DTP . . . B 2 41.855 77.871 -9.228 0 100.75 ? C1' DTP 301 A 1 HETATM 21 N N9 DTP . . . B 2 41.251 79.129 -9.737 0 99.39 ? N9 DTP 301 A 1 HETATM 22 C C8 DTP . . . B 2 40.822 80.155 -8.977 0 98.91 ? C8 DTP 301 A 1 HETATM 23 N N7 DTP . . . B 2 40.322 81.151 -9.755 0 98.34 ? N7 DTP 301 A 1 HETATM 24 C C5 DTP . . . B 2 40.43 80.763 -11.038 0 98.3 ? C5 DTP 301 A 1 HETATM 25 C C6 DTP . . . B 2 40.094 81.337 -12.362 0 97.71 ? C6 DTP 301 A 1 HETATM 26 N N6 DTP . . . B 2 39.526 82.562 -12.471 0 97.54 ? N6 DTP 301 A 1 HETATM 27 N N1 DTP . . . B 2 40.374 80.596 -13.457 0 97.31 ? N1 DTP 301 A 1 HETATM 28 C C2 DTP . . . B 2 40.938 79.376 -13.373 0 97.39 ? C2 DTP 301 A 1 HETATM 29 N N3 DTP . . . B 2 41.266 78.801 -12.201 0 97.96 ? N3 DTP 301 A 1 HETATM 30 C C4 DTP . . . B 2 41.043 79.428 -11.022 0 98.46 ? C4 DTP 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 209 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 30 #