data_6PRD # _model_server_result.job_id jXmNSKArn78Eo2jr_i13lA _model_server_result.datetime_utc '2025-02-23 10:17:54' _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 6prd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 6PRD # _exptl.entry_id 6PRD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 6PRD _cell.length_a 79.062 _cell.length_b 79.062 _cell.length_c 105.511 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PRD _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 237 n n PA O2A NAP sing 238 n n PA O5B NAP sing 239 n n PA O3 NAP sing 240 n n O2A HOA2 NAP sing 241 n n O5B C5B NAP sing 242 n n C5B C4B NAP sing 243 n n C5B H51A NAP sing 244 n n C5B H52A NAP sing 245 n n C4B O4B NAP sing 246 n n C4B C3B NAP sing 247 n n C4B H4B NAP sing 248 n n O4B C1B NAP sing 249 n n C3B O3B NAP sing 250 n n C3B C2B NAP sing 251 n n C3B H3B NAP sing 252 n n O3B HO3A NAP sing 253 n n C2B O2B NAP sing 254 n n C2B C1B NAP sing 255 n n C2B H2B NAP sing 256 n n O2B P2B NAP sing 257 n n C1B N9A NAP sing 258 n n C1B H1B NAP sing 259 n n N9A C8A NAP sing 260 n y N9A C4A NAP sing 261 n y C8A N7A NAP doub 262 n y C8A H8A NAP sing 263 n n N7A C5A NAP sing 264 n y C5A C6A NAP sing 265 n y C5A C4A NAP doub 266 n y C6A N6A NAP sing 267 n n C6A N1A NAP doub 268 n y N6A H61A NAP sing 269 n n N6A H62A NAP sing 270 n n N1A C2A NAP sing 271 n y C2A N3A NAP doub 272 n y C2A H2A NAP sing 273 n n N3A C4A NAP sing 274 n y O3 PN NAP sing 275 n n PN O1N NAP doub 276 n n PN O2N NAP sing 277 n n PN O5D NAP sing 278 n n O5D C5D NAP sing 279 n n C5D C4D NAP sing 280 n n C5D H51N NAP sing 281 n n C5D H52N NAP sing 282 n n C4D O4D NAP sing 283 n n C4D C3D NAP sing 284 n n C4D H4D NAP sing 285 n n O4D C1D NAP sing 286 n n C3D O3D NAP sing 287 n n C3D C2D NAP sing 288 n n C3D H3D NAP sing 289 n n O3D HO3N NAP sing 290 n n C2D O2D NAP sing 291 n n C2D C1D NAP sing 292 n n C2D H2D NAP sing 293 n n O2D HO2N NAP sing 294 n n C1D N1N NAP sing 295 n n C1D H1D NAP sing 296 n n N1N C2N NAP sing 297 n y N1N C6N NAP doub 298 n y C2N C3N NAP doub 299 n y C2N H2N NAP sing 300 n n C3N C7N NAP sing 301 n n C3N C4N NAP sing 302 n y C7N O7N NAP doub 303 n n C7N N7N NAP sing 304 n n N7N H71N NAP sing 305 n n N7N H72N NAP sing 306 n n C4N C5N NAP doub 307 n y C4N H4N NAP sing 308 n n C5N C6N NAP sing 309 n y C5N H5N NAP sing 310 n n C6N H6N NAP sing 311 n n P2B O1X NAP doub 312 n n P2B O2X NAP sing 313 n n P2B O3X NAP sing 314 n n O2X HOP2 NAP sing 315 n n O3X HOP3 NAP sing 316 n n # _atom_sites.entry_id 6PRD _atom_sites.fract_transf_matrix[1][1] 0.012648 _atom_sites.fract_transf_matrix[1][2] 0.007303 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014605 _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] 0.009478 _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 GOL A 1 401 401 GOL GOL . C 2 GOL A 1 402 501 GOL GOL . D 3 OWG A 1 403 301 OWG 007 . E 4 NAP A 1 404 201 NAP NAP . F 5 HOH A 1 501 67 HOH HOH . F 5 HOH A 2 502 136 HOH HOH . F 5 HOH A 3 503 70 HOH HOH . F 5 HOH A 4 504 85 HOH HOH . F 5 HOH A 5 505 24 HOH HOH . F 5 HOH A 6 506 61 HOH HOH . F 5 HOH A 7 507 37 HOH HOH . F 5 HOH A 8 508 109 HOH HOH . F 5 HOH A 9 509 71 HOH HOH . F 5 HOH A 10 510 75 HOH HOH . F 5 HOH A 11 511 39 HOH HOH . F 5 HOH A 12 512 10 HOH HOH . F 5 HOH A 13 513 108 HOH HOH . F 5 HOH A 14 514 1 HOH HOH . F 5 HOH A 15 515 59 HOH HOH . F 5 HOH A 16 516 2 HOH HOH . F 5 HOH A 17 517 23 HOH HOH . F 5 HOH A 18 518 51 HOH HOH . F 5 HOH A 19 519 6 HOH HOH . F 5 HOH A 20 520 41 HOH HOH . F 5 HOH A 21 521 8 HOH HOH . F 5 HOH A 22 522 27 HOH HOH . F 5 HOH A 23 523 9 HOH HOH . F 5 HOH A 24 524 5 HOH HOH . F 5 HOH A 25 525 81 HOH HOH . F 5 HOH A 26 526 46 HOH HOH . F 5 HOH A 27 527 16 HOH HOH . F 5 HOH A 28 528 89 HOH HOH . F 5 HOH A 29 529 31 HOH HOH . F 5 HOH A 30 530 18 HOH HOH . F 5 HOH A 31 531 68 HOH HOH . F 5 HOH A 32 532 90 HOH HOH . F 5 HOH A 33 533 4 HOH HOH . F 5 HOH A 34 534 43 HOH HOH . F 5 HOH A 35 535 11 HOH HOH . F 5 HOH A 36 536 62 HOH HOH . F 5 HOH A 37 537 48 HOH HOH . F 5 HOH A 38 538 29 HOH HOH . F 5 HOH A 39 539 126 HOH HOH . F 5 HOH A 40 540 36 HOH HOH . F 5 HOH A 41 541 72 HOH HOH . F 5 HOH A 42 542 127 HOH HOH . F 5 HOH A 43 543 47 HOH HOH . F 5 HOH A 44 544 129 HOH HOH . F 5 HOH A 45 545 122 HOH HOH . F 5 HOH A 46 546 137 HOH HOH . F 5 HOH A 47 547 128 HOH HOH . F 5 HOH A 48 548 14 HOH HOH . F 5 HOH A 49 549 130 HOH HOH . F 5 HOH A 50 550 92 HOH HOH . F 5 HOH A 51 551 73 HOH HOH . F 5 HOH A 52 552 80 HOH HOH . F 5 HOH A 53 553 125 HOH HOH . F 5 HOH A 54 554 42 HOH HOH . F 5 HOH A 55 555 3 HOH HOH . F 5 HOH A 56 556 78 HOH HOH . F 5 HOH A 57 557 40 HOH HOH . F 5 HOH A 58 558 20 HOH HOH . F 5 HOH A 59 559 82 HOH HOH . F 5 HOH A 60 560 84 HOH HOH . F 5 HOH A 61 561 35 HOH HOH . F 5 HOH A 62 562 114 HOH HOH . F 5 HOH A 63 563 52 HOH HOH . F 5 HOH A 64 564 79 HOH HOH . F 5 HOH A 65 565 33 HOH HOH . F 5 HOH A 66 566 32 HOH HOH . F 5 HOH A 67 567 93 HOH HOH . F 5 HOH A 68 568 60 HOH HOH . F 5 HOH A 69 569 97 HOH HOH . F 5 HOH A 70 570 22 HOH HOH . F 5 HOH A 71 571 12 HOH HOH . F 5 HOH A 72 572 15 HOH HOH . F 5 HOH A 73 573 25 HOH HOH . F 5 HOH A 74 574 77 HOH HOH . F 5 HOH A 75 575 38 HOH HOH . F 5 HOH A 76 576 119 HOH HOH . F 5 HOH A 77 577 49 HOH HOH . F 5 HOH A 78 578 13 HOH HOH . F 5 HOH A 79 579 19 HOH HOH . F 5 HOH A 80 580 86 HOH HOH . F 5 HOH A 81 581 107 HOH HOH . F 5 HOH A 82 582 105 HOH HOH . F 5 HOH A 83 583 28 HOH HOH . F 5 HOH A 84 584 104 HOH HOH . F 5 HOH A 85 585 7 HOH HOH . F 5 HOH A 86 586 66 HOH HOH . F 5 HOH A 87 587 116 HOH HOH . F 5 HOH A 88 588 57 HOH HOH . F 5 HOH A 89 589 101 HOH HOH . F 5 HOH A 90 590 53 HOH HOH . F 5 HOH A 91 591 133 HOH HOH . F 5 HOH A 92 592 44 HOH HOH . F 5 HOH A 93 593 65 HOH HOH . F 5 HOH A 94 594 74 HOH HOH . F 5 HOH A 95 595 30 HOH HOH . F 5 HOH A 96 596 112 HOH HOH . F 5 HOH A 97 597 103 HOH HOH . F 5 HOH A 98 598 91 HOH HOH . F 5 HOH A 99 599 63 HOH HOH . F 5 HOH A 100 600 99 HOH HOH . F 5 HOH A 101 601 120 HOH HOH . F 5 HOH A 102 602 45 HOH HOH . F 5 HOH A 103 603 131 HOH HOH . F 5 HOH A 104 604 135 HOH HOH . F 5 HOH A 105 605 88 HOH HOH . F 5 HOH A 106 606 111 HOH HOH . F 5 HOH A 107 607 55 HOH HOH . F 5 HOH A 108 608 134 HOH HOH . F 5 HOH A 109 609 26 HOH HOH . F 5 HOH A 110 610 54 HOH HOH . F 5 HOH A 111 611 83 HOH HOH . F 5 HOH A 112 612 113 HOH HOH . F 5 HOH A 113 613 102 HOH HOH . F 5 HOH A 114 614 124 HOH HOH . F 5 HOH A 115 615 34 HOH HOH . F 5 HOH A 116 616 50 HOH HOH . F 5 HOH A 117 617 100 HOH HOH . F 5 HOH A 118 618 64 HOH HOH . F 5 HOH A 119 619 117 HOH HOH . F 5 HOH A 120 620 121 HOH HOH . F 5 HOH A 121 621 94 HOH HOH . F 5 HOH A 122 622 123 HOH HOH . F 5 HOH A 123 623 132 HOH HOH . F 5 HOH A 124 624 58 HOH HOH . F 5 HOH A 125 625 115 HOH HOH . F 5 HOH A 126 626 76 HOH HOH . F 5 HOH A 127 627 69 HOH HOH . F 5 HOH A 128 628 56 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 . . . E 4 6.681 31.518 -6.003 1 25.18 ? PA NAP 404 A 1 HETATM 2 O O1A NAP . . . E 4 6.992 30.27 -5.249 1 21.21 ? O1A NAP 404 A 1 HETATM 3 O O2A NAP . . . E 4 5.38 32.226 -5.841 1 24.76 ? O2A NAP 404 A 1 HETATM 4 O O5B NAP . . . E 4 7.831 32.623 -5.767 1 26.17 ? O5B NAP 404 A 1 HETATM 5 C C5B NAP . . . E 4 9.185 32.265 -5.839 1 26.44 ? C5B NAP 404 A 1 HETATM 6 C C4B NAP . . . E 4 9.966 33.271 -5.03 1 24.94 ? C4B NAP 404 A 1 HETATM 7 O O4B NAP . . . E 4 9.746 33.075 -3.638 1 27.35 ? O4B NAP 404 A 1 HETATM 8 C C3B NAP . . . E 4 11.469 33.085 -5.159 1 26.89 ? C3B NAP 404 A 1 HETATM 9 O O3B NAP . . . E 4 11.94 33.619 -6.398 1 26.7 ? O3B NAP 404 A 1 HETATM 10 C C2B NAP . . . E 4 11.946 33.851 -3.959 1 30.88 ? C2B NAP 404 A 1 HETATM 11 O O2B NAP . . . E 4 11.735 35.234 -4.195 1 31.12 ? O2B NAP 404 A 1 HETATM 12 C C1B NAP . . . E 4 10.903 33.475 -2.924 1 28.74 ? C1B NAP 404 A 1 HETATM 13 N N9A NAP . . . E 4 11.384 32.335 -2.162 1 27.17 ? N9A NAP 404 A 1 HETATM 14 C C8A NAP . . . E 4 10.955 31.05 -2.291 1 32.86 ? C8A NAP 404 A 1 HETATM 15 N N7A NAP . . . E 4 11.614 30.246 -1.428 1 25.85 ? N7A NAP 404 A 1 HETATM 16 C C5A NAP . . . E 4 12.472 31.028 -0.722 1 28.07 ? C5A NAP 404 A 1 HETATM 17 C C6A NAP . . . E 4 13.448 30.851 0.374 1 31.08 ? C6A NAP 404 A 1 HETATM 18 N N6A NAP . . . E 4 13.69 29.638 0.913 1 33.34 ? N6A NAP 404 A 1 HETATM 19 N N1A NAP . . . E 4 14.13 31.952 0.806 1 33.62 ? N1A NAP 404 A 1 HETATM 20 C C2A NAP . . . E 4 13.919 33.179 0.292 1 28.44 ? C2A NAP 404 A 1 HETATM 21 N N3A NAP . . . E 4 13.035 33.427 -0.689 1 30.41 ? N3A NAP 404 A 1 HETATM 22 C C4A NAP . . . E 4 12.302 32.408 -1.214 1 29.35 ? C4A NAP 404 A 1 HETATM 23 O O3 NAP . . . E 4 6.914 31.355 -7.599 1 27.87 ? O3 NAP 404 A 1 HETATM 24 P PN NAP . . . E 4 6.822 30.064 -8.569 1 27.74 ? PN NAP 404 A 1 HETATM 25 O O1N NAP . . . E 4 7.438 28.871 -7.964 1 26.71 ? O1N NAP 404 A 1 HETATM 26 O O2N NAP . . . E 4 7.243 30.508 -9.938 1 31.19 ? O2N NAP 404 A 1 HETATM 27 O O5D NAP . . . E 4 5.22 29.832 -8.671 1 23.51 ? O5D NAP 404 A 1 HETATM 28 C C5D NAP . . . E 4 4.391 30.849 -9.257 1 21.42 ? C5D NAP 404 A 1 HETATM 29 C C4D NAP . . . E 4 3.176 30.256 -9.963 1 30.43 ? C4D NAP 404 A 1 HETATM 30 O O4D NAP . . . E 4 2.301 29.552 -9.045 1 23.68 ? O4D NAP 404 A 1 HETATM 31 C C3D NAP . . . E 4 2.323 31.357 -10.624 1 21.6 ? C3D NAP 404 A 1 HETATM 32 O O3D NAP . . . E 4 1.954 30.979 -11.953 1 22.29 ? O3D NAP 404 A 1 HETATM 33 C C2D NAP . . . E 4 1.008 31.381 -9.891 1 19.37 ? C2D NAP 404 A 1 HETATM 34 O O2D NAP . . . E 4 -0.039 31.584 -10.841 1 23.05 ? O2D NAP 404 A 1 HETATM 35 C C1D NAP . . . E 4 0.945 29.979 -9.32 1 17.28 ? C1D NAP 404 A 1 HETATM 36 N N1N NAP . . . E 4 0.16 29.764 -8.108 1 23.68 ? N1N NAP 404 A 1 HETATM 37 C C2N NAP . . . E 4 -0.823 28.858 -8.201 1 19.37 ? C2N NAP 404 A 1 HETATM 38 C C3N NAP . . . E 4 -1.58 28.504 -7.107 1 22.96 ? C3N NAP 404 A 1 HETATM 39 C C7N NAP . . . E 4 -2.671 27.485 -7.263 1 22.11 ? C7N NAP 404 A 1 HETATM 40 O O7N NAP . . . E 4 -3.035 27.115 -8.375 1 20.9 ? O7N NAP 404 A 1 HETATM 41 N N7N NAP . . . E 4 -3.209 27.031 -6.153 1 16.41 ? N7N NAP 404 A 1 HETATM 42 C C4N NAP . . . E 4 -1.314 29.099 -5.88 1 25.62 ? C4N NAP 404 A 1 HETATM 43 C C5N NAP . . . E 4 -0.296 30.071 -5.804 1 28.06 ? C5N NAP 404 A 1 HETATM 44 C C6N NAP . . . E 4 0.457 30.374 -6.942 1 23.83 ? C6N NAP 404 A 1 HETATM 45 P P2B NAP . . . E 4 12.971 36.283 -4.555 1 27.36 ? P2B NAP 404 A 1 HETATM 46 O O1X NAP . . . E 4 12.193 37.595 -4.577 1 27.77 ? O1X NAP 404 A 1 HETATM 47 O O2X NAP . . . E 4 13.963 36.031 -3.454 1 25.84 ? O2X NAP 404 A 1 HETATM 48 O O3X NAP . . . E 4 13.366 35.781 -5.929 1 26.52 ? O3X NAP 404 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 547 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 48 #