data_3NBV # _model_server_result.job_id '_lXmVWHJt8nGFr2Cl9BmRQ' _model_server_result.datetime_utc '2024-11-02 21:38:36' _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 3nbv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":299}' # _entry.id 3NBV # _exptl.entry_id 3NBV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 2 _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 3NBV _cell.length_a 82.845 _cell.length_b 86.035 _cell.length_c 136.961 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NBV _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,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 3NBV _atom_sites.fract_transf_matrix[1][1] 0.012071 _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] 0.011623 _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] 0.007301 _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 2 ANP A 1 299 1 ANP ANP . D 3 FRU A 1 300 1 FRU FRU . E 2 ANP B 1 299 2 ANP ANP . F 4 SO4 B 1 300 2 SO4 SO4 . G 5 HOH A 1 301 3 HOH HOH . G 5 HOH A 2 302 4 HOH HOH . G 5 HOH A 3 303 5 HOH HOH . G 5 HOH A 4 304 10 HOH HOH . G 5 HOH A 5 305 11 HOH HOH . G 5 HOH A 6 306 16 HOH HOH . G 5 HOH A 7 307 19 HOH HOH . G 5 HOH A 8 308 21 HOH HOH . G 5 HOH A 9 309 24 HOH HOH . G 5 HOH A 10 310 29 HOH HOH . G 5 HOH A 11 311 30 HOH HOH . G 5 HOH A 12 312 34 HOH HOH . G 5 HOH A 13 313 36 HOH HOH . G 5 HOH A 14 314 37 HOH HOH . G 5 HOH A 15 315 41 HOH HOH . G 5 HOH A 16 316 42 HOH HOH . G 5 HOH A 17 317 44 HOH HOH . G 5 HOH A 18 318 47 HOH HOH . G 5 HOH A 19 319 50 HOH HOH . G 5 HOH A 20 320 52 HOH HOH . G 5 HOH A 21 321 53 HOH HOH . G 5 HOH A 22 322 54 HOH HOH . G 5 HOH A 23 323 55 HOH HOH . G 5 HOH A 24 324 61 HOH HOH . G 5 HOH A 25 325 62 HOH HOH . G 5 HOH A 26 326 69 HOH HOH . G 5 HOH A 27 327 73 HOH HOH . G 5 HOH A 28 328 75 HOH HOH . G 5 HOH A 29 329 77 HOH HOH . G 5 HOH A 30 330 81 HOH HOH . G 5 HOH A 31 331 82 HOH HOH . G 5 HOH A 32 332 84 HOH HOH . G 5 HOH A 33 333 90 HOH HOH . G 5 HOH A 34 334 97 HOH HOH . G 5 HOH A 35 335 101 HOH HOH . G 5 HOH A 36 336 104 HOH HOH . G 5 HOH A 37 337 105 HOH HOH . G 5 HOH A 38 338 108 HOH HOH . G 5 HOH A 39 339 109 HOH HOH . G 5 HOH A 40 340 113 HOH HOH . G 5 HOH A 41 341 115 HOH HOH . G 5 HOH A 42 342 116 HOH HOH . G 5 HOH A 43 343 118 HOH HOH . G 5 HOH A 44 344 119 HOH HOH . G 5 HOH A 45 345 120 HOH HOH . H 5 HOH B 1 301 1 HOH HOH . H 5 HOH B 2 302 2 HOH HOH . H 5 HOH B 3 303 6 HOH HOH . H 5 HOH B 4 304 7 HOH HOH . H 5 HOH B 5 305 8 HOH HOH . H 5 HOH B 6 306 9 HOH HOH . H 5 HOH B 7 307 12 HOH HOH . H 5 HOH B 8 308 13 HOH HOH . H 5 HOH B 9 309 14 HOH HOH . H 5 HOH B 10 310 15 HOH HOH . H 5 HOH B 11 311 17 HOH HOH . H 5 HOH B 12 312 18 HOH HOH . H 5 HOH B 13 313 20 HOH HOH . H 5 HOH B 14 314 22 HOH HOH . H 5 HOH B 15 315 23 HOH HOH . H 5 HOH B 16 316 25 HOH HOH . H 5 HOH B 17 317 26 HOH HOH . H 5 HOH B 18 318 27 HOH HOH . H 5 HOH B 19 319 28 HOH HOH . H 5 HOH B 20 320 31 HOH HOH . H 5 HOH B 21 321 32 HOH HOH . H 5 HOH B 22 322 33 HOH HOH . H 5 HOH B 23 323 35 HOH HOH . H 5 HOH B 24 324 38 HOH HOH . H 5 HOH B 25 325 39 HOH HOH . H 5 HOH B 26 326 40 HOH HOH . H 5 HOH B 27 327 43 HOH HOH . H 5 HOH B 28 328 45 HOH HOH . H 5 HOH B 29 329 46 HOH HOH . H 5 HOH B 30 330 48 HOH HOH . H 5 HOH B 31 331 49 HOH HOH . H 5 HOH B 32 332 51 HOH HOH . H 5 HOH B 33 333 56 HOH HOH . H 5 HOH B 34 334 57 HOH HOH . H 5 HOH B 35 335 58 HOH HOH . H 5 HOH B 36 336 59 HOH HOH . H 5 HOH B 37 337 60 HOH HOH . H 5 HOH B 38 338 63 HOH HOH . H 5 HOH B 39 339 64 HOH HOH . H 5 HOH B 40 340 65 HOH HOH . H 5 HOH B 41 341 66 HOH HOH . H 5 HOH B 42 342 67 HOH HOH . H 5 HOH B 43 343 68 HOH HOH . H 5 HOH B 44 344 70 HOH HOH . H 5 HOH B 45 345 71 HOH HOH . H 5 HOH B 46 346 72 HOH HOH . H 5 HOH B 47 347 74 HOH HOH . H 5 HOH B 48 348 76 HOH HOH . H 5 HOH B 49 349 78 HOH HOH . H 5 HOH B 50 350 79 HOH HOH . H 5 HOH B 51 351 80 HOH HOH . H 5 HOH B 52 352 83 HOH HOH . H 5 HOH B 53 353 85 HOH HOH . H 5 HOH B 54 354 86 HOH HOH . H 5 HOH B 55 355 87 HOH HOH . H 5 HOH B 56 356 88 HOH HOH . H 5 HOH B 57 357 89 HOH HOH . H 5 HOH B 58 358 91 HOH HOH . H 5 HOH B 59 359 92 HOH HOH . H 5 HOH B 60 360 93 HOH HOH . H 5 HOH B 61 361 94 HOH HOH . H 5 HOH B 62 362 95 HOH HOH . H 5 HOH B 63 363 96 HOH HOH . H 5 HOH B 64 364 98 HOH HOH . H 5 HOH B 65 365 99 HOH HOH . H 5 HOH B 66 366 100 HOH HOH . H 5 HOH B 67 367 102 HOH HOH . H 5 HOH B 68 368 103 HOH HOH . H 5 HOH B 69 369 106 HOH HOH . H 5 HOH B 70 370 107 HOH HOH . H 5 HOH B 71 371 110 HOH HOH . H 5 HOH B 72 372 111 HOH HOH . H 5 HOH B 73 373 112 HOH HOH . H 5 HOH B 74 374 114 HOH HOH . H 5 HOH B 75 375 117 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 ANP . . . E 2 -23.574 18.885 52.39 1 67.76 ? PG ANP 299 B 1 HETATM 2 O O1G ANP . . . E 2 -24.439 19.63 53.384 1 58.59 ? O1G ANP 299 B 1 HETATM 3 O O2G ANP . . . E 2 -23.907 18.93 50.907 1 64.85 ? O2G ANP 299 B 1 HETATM 4 O O3G ANP . . . E 2 -23.55 17.307 52.787 1 61.96 ? O3G ANP 299 B 1 HETATM 5 P PB ANP . . . E 2 -21.153 19.043 54.12 1 53.09 ? PB ANP 299 B 1 HETATM 6 O O1B ANP . . . E 2 -19.719 19.531 53.976 1 44.72 ? O1B ANP 299 B 1 HETATM 7 O O2B ANP . . . E 2 -21.42 17.577 54.422 1 47.66 ? O2B ANP 299 B 1 HETATM 8 N N3B ANP . . . E 2 -21.943 19.444 52.626 1 48.8 ? N3B ANP 299 B 1 HETATM 9 P PA ANP . . . E 2 -22.535 19.527 56.671 1 45.68 ? PA ANP 299 B 1 HETATM 10 O O1A ANP . . . E 2 -21.362 18.994 57.479 1 46.03 ? O1A ANP 299 B 1 HETATM 11 O O2A ANP . . . E 2 -23.794 18.693 56.563 1 42.23 ? O2A ANP 299 B 1 HETATM 12 O O3A ANP . . . E 2 -21.989 19.942 55.204 1 45.33 ? O3A ANP 299 B 1 HETATM 13 O O5' ANP . . . E 2 -23.028 20.967 57.225 1 44.25 ? O5' ANP 299 B 1 HETATM 14 C C5' ANP . . . E 2 -22.145 21.811 57.957 1 38.86 ? C5' ANP 299 B 1 HETATM 15 C C4' ANP . . . E 2 -22.86 23.149 58.124 1 34.81 ? C4' ANP 299 B 1 HETATM 16 O O4' ANP . . . E 2 -22.933 23.809 56.837 1 40.56 ? O4' ANP 299 B 1 HETATM 17 C C3' ANP . . . E 2 -24.329 23.029 58.587 1 36.22 ? C3' ANP 299 B 1 HETATM 18 O O3' ANP . . . E 2 -24.418 22.856 60.013 1 38.15 ? O3' ANP 299 B 1 HETATM 19 C C2' ANP . . . E 2 -24.91 24.398 58.147 1 34.61 ? C2' ANP 299 B 1 HETATM 20 O O2' ANP . . . E 2 -24.506 25.408 58.921 1 36.04 ? O2' ANP 299 B 1 HETATM 21 C C1' ANP . . . E 2 -24.21 24.496 56.76 1 34.52 ? C1' ANP 299 B 1 HETATM 22 N N9 ANP . . . E 2 -24.979 24.013 55.629 1 39.78 ? N9 ANP 299 B 1 HETATM 23 C C8 ANP . . . E 2 -24.809 22.838 54.935 1 39.02 ? C8 ANP 299 B 1 HETATM 24 N N7 ANP . . . E 2 -25.716 22.696 53.985 1 42.09 ? N7 ANP 299 B 1 HETATM 25 C C5 ANP . . . E 2 -26.501 23.829 54.086 1 41 ? C5 ANP 299 B 1 HETATM 26 C C6 ANP . . . E 2 -27.612 24.278 53.347 1 47.83 ? C6 ANP 299 B 1 HETATM 27 N N6 ANP . . . E 2 -28.131 23.548 52.302 1 45.19 ? N6 ANP 299 B 1 HETATM 28 N N1 ANP . . . E 2 -28.193 25.468 53.682 1 45.03 ? N1 ANP 299 B 1 HETATM 29 C C2 ANP . . . E 2 -27.657 26.174 54.709 1 41.93 ? C2 ANP 299 B 1 HETATM 30 N N3 ANP . . . E 2 -26.595 25.839 55.472 1 43.29 ? N3 ANP 299 B 1 HETATM 31 C C4 ANP . . . E 2 -26.072 24.65 55.105 1 37.62 ? C4 ANP 299 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 31 #