data_2DBZ # _model_server_result.job_id mAbvf-ueZ6iil2KPujsbqQ _model_server_result.datetime_utc '2024-11-20 08:33:21' _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 2dbz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":402}' # _entry.id 2DBZ # _exptl.entry_id 2DBZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 120 _cell.entry_id 2DBZ _cell.length_a 104.472 _cell.length_b 104.472 _cell.length_c 182.079 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DBZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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,I,J _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 ? 3 E N N ? 3 H N N # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 PA O1A NAP doub 224 n n PA O2A NAP sing 225 n n PA O5B NAP sing 226 n n PA O3 NAP sing 227 n n O2A HOA2 NAP sing 228 n n O5B C5B NAP sing 229 n n C5B C4B NAP sing 230 n n C5B H51A NAP sing 231 n n C5B H52A NAP sing 232 n n C4B O4B NAP sing 233 n n C4B C3B NAP sing 234 n n C4B H4B NAP sing 235 n n O4B C1B NAP sing 236 n n C3B O3B NAP sing 237 n n C3B C2B NAP sing 238 n n C3B H3B NAP sing 239 n n O3B HO3A NAP sing 240 n n C2B O2B NAP sing 241 n n C2B C1B NAP sing 242 n n C2B H2B NAP sing 243 n n O2B P2B NAP sing 244 n n C1B N9A NAP sing 245 n n C1B H1B NAP sing 246 n n N9A C8A NAP sing 247 n y N9A C4A NAP sing 248 n y C8A N7A NAP doub 249 n y C8A H8A NAP sing 250 n n N7A C5A NAP sing 251 n y C5A C6A NAP sing 252 n y C5A C4A NAP doub 253 n y C6A N6A NAP sing 254 n n C6A N1A NAP doub 255 n y N6A H61A NAP sing 256 n n N6A H62A NAP sing 257 n n N1A C2A NAP sing 258 n y C2A N3A NAP doub 259 n y C2A H2A NAP sing 260 n n N3A C4A NAP sing 261 n y O3 PN NAP sing 262 n n PN O1N NAP doub 263 n n PN O2N NAP sing 264 n n PN O5D NAP sing 265 n n O5D C5D NAP sing 266 n n C5D C4D NAP sing 267 n n C5D H51N NAP sing 268 n n C5D H52N NAP sing 269 n n C4D O4D NAP sing 270 n n C4D C3D NAP sing 271 n n C4D H4D NAP sing 272 n n O4D C1D NAP sing 273 n n C3D O3D NAP sing 274 n n C3D C2D NAP sing 275 n n C3D H3D NAP sing 276 n n O3D HO3N NAP sing 277 n n C2D O2D NAP sing 278 n n C2D C1D NAP sing 279 n n C2D H2D NAP sing 280 n n O2D HO2N NAP sing 281 n n C1D N1N NAP sing 282 n n C1D H1D NAP sing 283 n n N1N C2N NAP sing 284 n y N1N C6N NAP doub 285 n y C2N C3N NAP doub 286 n y C2N H2N NAP sing 287 n n C3N C7N NAP sing 288 n n C3N C4N NAP sing 289 n y C7N O7N NAP doub 290 n n C7N N7N NAP sing 291 n n N7N H71N NAP sing 292 n n N7N H72N NAP sing 293 n n C4N C5N NAP doub 294 n y C4N H4N NAP sing 295 n n C5N C6N NAP sing 296 n y C5N H5N NAP sing 297 n n C6N H6N NAP sing 298 n n P2B O1X NAP doub 299 n n P2B O2X NAP sing 300 n n P2B O3X NAP sing 301 n n O2X HOP2 NAP sing 302 n n O3X HOP3 NAP sing 303 n n # _atom_sites.entry_id 2DBZ _atom_sites.fract_transf_matrix[1][1] 0.009572 _atom_sites.fract_transf_matrix[1][2] 0.005526 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011053 _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] 0.005492 _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 SO4 A 1 502 502 SO4 SO4 . D 2 SO4 A 1 504 504 SO4 SO4 . E 3 NAP A 1 401 401 NAP NAP . F 2 SO4 B 1 501 501 SO4 SO4 . G 2 SO4 B 1 503 503 SO4 SO4 . H 3 NAP B 1 402 402 NAP NAP . I 4 HOH A 1 505 1 HOH HOH . I 4 HOH A 2 506 3 HOH HOH . I 4 HOH A 3 507 5 HOH HOH . I 4 HOH A 4 508 6 HOH HOH . I 4 HOH A 5 509 7 HOH HOH . I 4 HOH A 6 510 8 HOH HOH . I 4 HOH A 7 511 9 HOH HOH . I 4 HOH A 8 512 15 HOH HOH . I 4 HOH A 9 513 16 HOH HOH . I 4 HOH A 10 514 21 HOH HOH . I 4 HOH A 11 515 23 HOH HOH . I 4 HOH A 12 516 24 HOH HOH . I 4 HOH A 13 517 27 HOH HOH . I 4 HOH A 14 518 28 HOH HOH . I 4 HOH A 15 519 29 HOH HOH . I 4 HOH A 16 520 30 HOH HOH . I 4 HOH A 17 521 31 HOH HOH . I 4 HOH A 18 522 32 HOH HOH . I 4 HOH A 19 523 33 HOH HOH . I 4 HOH A 20 524 34 HOH HOH . I 4 HOH A 21 525 35 HOH HOH . I 4 HOH A 22 526 36 HOH HOH . I 4 HOH A 23 527 38 HOH HOH . I 4 HOH A 24 528 41 HOH HOH . I 4 HOH A 25 529 43 HOH HOH . I 4 HOH A 26 530 44 HOH HOH . I 4 HOH A 27 531 45 HOH HOH . I 4 HOH A 28 532 47 HOH HOH . I 4 HOH A 29 533 50 HOH HOH . I 4 HOH A 30 534 52 HOH HOH . I 4 HOH A 31 535 53 HOH HOH . I 4 HOH A 32 536 55 HOH HOH . I 4 HOH A 33 537 58 HOH HOH . I 4 HOH A 34 538 61 HOH HOH . I 4 HOH A 35 539 62 HOH HOH . I 4 HOH A 36 540 63 HOH HOH . I 4 HOH A 37 541 64 HOH HOH . I 4 HOH A 38 542 65 HOH HOH . I 4 HOH A 39 543 66 HOH HOH . I 4 HOH A 40 544 68 HOH HOH . I 4 HOH A 41 545 70 HOH HOH . I 4 HOH A 42 546 72 HOH HOH . I 4 HOH A 43 547 73 HOH HOH . J 4 HOH B 1 504 2 HOH HOH . J 4 HOH B 2 505 4 HOH HOH . J 4 HOH B 3 506 10 HOH HOH . J 4 HOH B 4 507 11 HOH HOH . J 4 HOH B 5 508 12 HOH HOH . J 4 HOH B 6 509 13 HOH HOH . J 4 HOH B 7 510 14 HOH HOH . J 4 HOH B 8 511 17 HOH HOH . J 4 HOH B 9 512 18 HOH HOH . J 4 HOH B 10 513 19 HOH HOH . J 4 HOH B 11 514 20 HOH HOH . J 4 HOH B 12 515 22 HOH HOH . J 4 HOH B 13 516 25 HOH HOH . J 4 HOH B 14 517 26 HOH HOH . J 4 HOH B 15 518 37 HOH HOH . J 4 HOH B 16 519 39 HOH HOH . J 4 HOH B 17 520 40 HOH HOH . J 4 HOH B 18 521 42 HOH HOH . J 4 HOH B 19 522 46 HOH HOH . J 4 HOH B 20 523 48 HOH HOH . J 4 HOH B 21 524 49 HOH HOH . J 4 HOH B 22 525 51 HOH HOH . J 4 HOH B 23 526 54 HOH HOH . J 4 HOH B 24 527 56 HOH HOH . J 4 HOH B 25 528 57 HOH HOH . J 4 HOH B 26 529 59 HOH HOH . J 4 HOH B 27 530 60 HOH HOH . J 4 HOH B 28 531 67 HOH HOH . J 4 HOH B 29 532 69 HOH HOH . J 4 HOH B 30 533 71 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 PA NAP . . . H 3 73.065 1.657 -7.887 1 48.48 ? PA NAP 402 B 1 HETATM 2 O O1A NAP . . . H 3 74.514 1.456 -8.115 1 59.49 ? O1A NAP 402 B 1 HETATM 3 O O2A NAP . . . H 3 72.132 1.259 -8.963 1 34.41 ? O2A NAP 402 B 1 HETATM 4 O O5B NAP . . . H 3 72.857 3.197 -7.455 1 52.4 ? O5B NAP 402 B 1 HETATM 5 C C5B NAP . . . H 3 71.664 3.916 -7.776 1 63.24 ? C5B NAP 402 B 1 HETATM 6 C C4B NAP . . . H 3 71.986 5.314 -8.311 1 59.14 ? C4B NAP 402 B 1 HETATM 7 O O4B NAP . . . H 3 72.718 6.131 -7.381 1 60.62 ? O4B NAP 402 B 1 HETATM 8 C C3B NAP . . . H 3 72.829 5.281 -9.591 1 61.51 ? C3B NAP 402 B 1 HETATM 9 O O3B NAP . . . H 3 72.042 5.753 -10.688 1 58.28 ? O3B NAP 402 B 1 HETATM 10 C C2B NAP . . . H 3 73.959 6.269 -9.293 1 64.62 ? C2B NAP 402 B 1 HETATM 11 O O2B NAP . . . H 3 74.256 7.04 -10.461 1 77.29 ? O2B NAP 402 B 1 HETATM 12 C C1B NAP . . . H 3 73.278 7.14 -8.236 1 58.81 ? C1B NAP 402 B 1 HETATM 13 N N9A NAP . . . H 3 74.233 8.019 -7.513 1 56.33 ? N9A NAP 402 B 1 HETATM 14 C C8A NAP . . . H 3 75.37 7.658 -6.914 1 56.77 ? C8A NAP 402 B 1 HETATM 15 N N7A NAP . . . H 3 75.955 8.724 -6.367 1 56.06 ? N7A NAP 402 B 1 HETATM 16 C C5A NAP . . . H 3 75.165 9.772 -6.592 1 59.19 ? C5A NAP 402 B 1 HETATM 17 C C6A NAP . . . H 3 75.25 11.137 -6.313 1 59.84 ? C6A NAP 402 B 1 HETATM 18 N N6A NAP . . . H 3 76.276 11.626 -5.622 1 60.41 ? N6A NAP 402 B 1 HETATM 19 N N1A NAP . . . H 3 74.277 11.955 -6.751 1 58.17 ? N1A NAP 402 B 1 HETATM 20 C C2A NAP . . . H 3 73.242 11.49 -7.432 1 60.1 ? C2A NAP 402 B 1 HETATM 21 N N3A NAP . . . H 3 73.134 10.205 -7.73 1 53.35 ? N3A NAP 402 B 1 HETATM 22 C C4A NAP . . . H 3 74.073 9.328 -7.326 1 58.12 ? C4A NAP 402 B 1 HETATM 23 O O3 NAP . . . H 3 72.705 0.852 -6.537 1 60.22 ? O3 NAP 402 B 1 HETATM 24 P PN NAP . . . H 3 71.274 0.191 -6.186 1 52.53 ? PN NAP 402 B 1 HETATM 25 O O1N NAP . . . H 3 71.41 -1.273 -6.363 1 39.95 ? O1N NAP 402 B 1 HETATM 26 O O2N NAP . . . H 3 70.133 0.866 -6.846 1 48.96 ? O2N NAP 402 B 1 HETATM 27 O O5D NAP . . . H 3 71.204 0.519 -4.609 1 43.25 ? O5D NAP 402 B 1 HETATM 28 C C5D NAP . . . H 3 71.558 1.813 -4.115 1 41.64 ? C5D NAP 402 B 1 HETATM 29 C C4D NAP . . . H 3 71.679 1.788 -2.589 1 49.16 ? C4D NAP 402 B 1 HETATM 30 O O4D NAP . . . H 3 70.457 1.368 -1.965 1 45.79 ? O4D NAP 402 B 1 HETATM 31 C C3D NAP . . . H 3 72.671 0.739 -2.092 1 51.82 ? C3D NAP 402 B 1 HETATM 32 O O3D NAP . . . H 3 74.012 1.197 -2.28 1 44.49 ? O3D NAP 402 B 1 HETATM 33 C C2D NAP . . . H 3 72.321 0.722 -0.604 1 42.33 ? C2D NAP 402 B 1 HETATM 34 O O2D NAP . . . H 3 72.963 1.783 0.107 1 52.87 ? O2D NAP 402 B 1 HETATM 35 C C1D NAP . . . H 3 70.809 0.97 -0.626 1 50.6 ? C1D NAP 402 B 1 HETATM 36 N N1N NAP . . . H 3 70.057 -0.267 -0.319 1 48.86 ? N1N NAP 402 B 1 HETATM 37 C C2N NAP . . . H 3 69.225 -0.307 0.807 1 42.33 ? C2N NAP 402 B 1 HETATM 38 C C3N NAP . . . H 3 68.492 -1.46 1.075 1 41.13 ? C3N NAP 402 B 1 HETATM 39 C C7N NAP . . . H 3 67.607 -1.553 2.318 1 39.44 ? C7N NAP 402 B 1 HETATM 40 O O7N NAP . . . H 3 67.281 -2.651 2.774 1 49.01 ? O7N NAP 402 B 1 HETATM 41 N N7N NAP . . . H 3 67.247 -0.393 2.859 1 43.21 ? N7N NAP 402 B 1 HETATM 42 C C4N NAP . . . H 3 68.596 -2.552 0.218 1 37.67 ? C4N NAP 402 B 1 HETATM 43 C C5N NAP . . . H 3 69.416 -2.519 -0.902 1 34.44 ? C5N NAP 402 B 1 HETATM 44 C C6N NAP . . . H 3 70.157 -1.372 -1.175 1 38.95 ? C6N NAP 402 B 1 HETATM 45 P P2B NAP . . . H 3 75.476 6.641 -11.439 1 87.61 ? P2B NAP 402 B 1 HETATM 46 O O1X NAP . . . H 3 76.78 7.386 -10.86 1 95.49 ? O1X NAP 402 B 1 HETATM 47 O O2X NAP . . . H 3 75.742 5.062 -11.273 1 85.33 ? O2X NAP 402 B 1 HETATM 48 O O3X NAP . . . H 3 75.201 6.987 -12.851 1 95.17 ? O3X NAP 402 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 48 #