data_1DYR # _model_server_result.job_id jMSv9Swtf2Z2yvbvjvvuoQ _model_server_result.datetime_utc '2024-11-24 15:48:09' _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 1dyr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":391}' # _entry.id 1DYR # _exptl.entry_id 1DYR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 745.421 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADPH DIHYDRO-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 117.7 _cell.angle_gamma 90 _cell.entry_id 1DYR _cell.length_a 69.9 _cell.length_b 43.6 _cell.length_c 37.6 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DYR _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H30 N7 O17 P3' _chem_comp.formula_weight 745.421 _chem_comp.id NDP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 PA O1A NDP doub 237 n n PA O2A NDP sing 238 n n PA O5B NDP sing 239 n n PA O3 NDP sing 240 n n O2A HOA2 NDP sing 241 n n O5B C5B NDP sing 242 n n C5B C4B NDP sing 243 n n C5B H51A NDP sing 244 n n C5B H52A NDP sing 245 n n C4B O4B NDP sing 246 n n C4B C3B NDP sing 247 n n C4B H4B NDP sing 248 n n O4B C1B NDP sing 249 n n C3B O3B NDP sing 250 n n C3B C2B NDP sing 251 n n C3B H3B NDP sing 252 n n O3B HO3A NDP sing 253 n n C2B O2B NDP sing 254 n n C2B C1B NDP sing 255 n n C2B H2B NDP sing 256 n n O2B P2B NDP sing 257 n n C1B N9A NDP sing 258 n n C1B H1B NDP sing 259 n n N9A C8A NDP sing 260 n y N9A C4A NDP sing 261 n y C8A N7A NDP doub 262 n y C8A H8A NDP sing 263 n n N7A C5A NDP sing 264 n y C5A C6A NDP sing 265 n y C5A C4A NDP doub 266 n y C6A N6A NDP sing 267 n n C6A N1A NDP doub 268 n y N6A H61A NDP sing 269 n n N6A H62A NDP sing 270 n n N1A C2A NDP sing 271 n y C2A N3A NDP doub 272 n y C2A H2A NDP sing 273 n n N3A C4A NDP sing 274 n y O3 PN NDP sing 275 n n PN O1N NDP doub 276 n n PN O2N NDP sing 277 n n PN O5D NDP sing 278 n n O2N H21N NDP sing 279 n n O5D C5D NDP sing 280 n n C5D C4D NDP sing 281 n n C5D H51N NDP sing 282 n n C5D H52N NDP sing 283 n n C4D O4D NDP sing 284 n n C4D C3D NDP sing 285 n n C4D H4D NDP sing 286 n n O4D C1D NDP sing 287 n n C3D O3D NDP sing 288 n n C3D C2D NDP sing 289 n n C3D H3D NDP sing 290 n n O3D HO3N NDP sing 291 n n C2D O2D NDP sing 292 n n C2D C1D NDP sing 293 n n C2D H2D NDP sing 294 n n O2D HO2N NDP sing 295 n n C1D N1N NDP sing 296 n n C1D H1D NDP sing 297 n n N1N C2N NDP sing 298 n n N1N C6N NDP sing 299 n n C2N C3N NDP doub 300 n n C2N H2N NDP sing 301 n n C3N C7N NDP sing 302 n n C3N C4N NDP sing 303 n n C7N O7N NDP doub 304 n n C7N N7N NDP sing 305 n n N7N H71N NDP sing 306 n n N7N H72N NDP sing 307 n n C4N C5N NDP sing 308 n n C4N H41N NDP sing 309 n n C4N H42N NDP sing 310 n n C5N C6N NDP doub 311 n n C5N H5N NDP sing 312 n n C6N H6N NDP sing 313 n n P2B O1X NDP doub 314 n n P2B O2X NDP sing 315 n n P2B O3X NDP sing 316 n n O2X HOP2 NDP sing 317 n n O3X HOP3 NDP sing 318 n n # _atom_sites.entry_id 1DYR _atom_sites.fract_transf_matrix[1][1] 0.014306 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007511 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022936 _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] 0.030038 _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 NDP A 1 391 391 NDP NDP . C 3 TOP A 1 407 407 TOP TOP . D 4 HOH A 1 408 408 HOH HOH . D 4 HOH A 2 502 502 HOH HOH . D 4 HOH A 3 503 503 HOH HOH . D 4 HOH A 4 504 504 HOH HOH . D 4 HOH A 5 506 506 HOH HOH . D 4 HOH A 6 508 508 HOH HOH . D 4 HOH A 7 509 509 HOH HOH . D 4 HOH A 8 513 513 HOH HOH . D 4 HOH A 9 514 514 HOH HOH . D 4 HOH A 10 515 515 HOH HOH . D 4 HOH A 11 516 516 HOH HOH . D 4 HOH A 12 517 517 HOH HOH . D 4 HOH A 13 518 518 HOH HOH . D 4 HOH A 14 519 519 HOH HOH . D 4 HOH A 15 520 520 HOH HOH . D 4 HOH A 16 521 521 HOH HOH . D 4 HOH A 17 522 522 HOH HOH . D 4 HOH A 18 523 523 HOH HOH . D 4 HOH A 19 524 524 HOH HOH . D 4 HOH A 20 525 525 HOH HOH . D 4 HOH A 21 526 526 HOH HOH . D 4 HOH A 22 527 527 HOH HOH . D 4 HOH A 23 528 528 HOH HOH . D 4 HOH A 24 529 529 HOH HOH . D 4 HOH A 25 530 530 HOH HOH . D 4 HOH A 26 531 531 HOH HOH . D 4 HOH A 27 532 532 HOH HOH . D 4 HOH A 28 533 533 HOH HOH . D 4 HOH A 29 534 534 HOH HOH . D 4 HOH A 30 535 535 HOH HOH . D 4 HOH A 31 536 536 HOH HOH . D 4 HOH A 32 537 537 HOH HOH . D 4 HOH A 33 538 538 HOH HOH . D 4 HOH A 34 539 539 HOH HOH . D 4 HOH A 35 540 540 HOH HOH . D 4 HOH A 36 542 542 HOH HOH . D 4 HOH A 37 543 543 HOH HOH . D 4 HOH A 38 544 544 HOH HOH . D 4 HOH A 39 545 545 HOH HOH . D 4 HOH A 40 547 547 HOH HOH . D 4 HOH A 41 548 548 HOH HOH . D 4 HOH A 42 549 549 HOH HOH . D 4 HOH A 43 550 550 HOH HOH . D 4 HOH A 44 551 551 HOH HOH . D 4 HOH A 45 552 552 HOH HOH . D 4 HOH A 46 553 553 HOH HOH . D 4 HOH A 47 554 554 HOH HOH . D 4 HOH A 48 555 555 HOH HOH . D 4 HOH A 49 556 556 HOH HOH . D 4 HOH A 50 557 557 HOH HOH . D 4 HOH A 51 558 558 HOH HOH . D 4 HOH A 52 559 559 HOH HOH . D 4 HOH A 53 560 560 HOH HOH . D 4 HOH A 54 561 561 HOH HOH . D 4 HOH A 55 562 562 HOH HOH . D 4 HOH A 56 563 563 HOH HOH . D 4 HOH A 57 564 564 HOH HOH . D 4 HOH A 58 565 565 HOH HOH . D 4 HOH A 59 566 566 HOH HOH . D 4 HOH A 60 567 567 HOH HOH . D 4 HOH A 61 568 568 HOH HOH . D 4 HOH A 62 569 569 HOH HOH . D 4 HOH A 63 570 570 HOH HOH . D 4 HOH A 64 572 572 HOH HOH . D 4 HOH A 65 573 573 HOH HOH . D 4 HOH A 66 574 574 HOH HOH . D 4 HOH A 67 575 575 HOH HOH . D 4 HOH A 68 576 576 HOH HOH . D 4 HOH A 69 577 577 HOH HOH . D 4 HOH A 70 578 578 HOH HOH . D 4 HOH A 71 584 584 HOH HOH . D 4 HOH A 72 585 585 HOH HOH . D 4 HOH A 73 588 588 HOH HOH . D 4 HOH A 74 589 589 HOH HOH . D 4 HOH A 75 591 591 HOH HOH . D 4 HOH A 76 592 592 HOH HOH . D 4 HOH A 77 594 594 HOH HOH . D 4 HOH A 78 596 596 HOH HOH . D 4 HOH A 79 598 598 HOH HOH . D 4 HOH A 80 602 602 HOH HOH . D 4 HOH A 81 603 603 HOH HOH . D 4 HOH A 82 605 605 HOH HOH . D 4 HOH A 83 606 606 HOH HOH . D 4 HOH A 84 609 609 HOH HOH . D 4 HOH A 85 612 612 HOH HOH . D 4 HOH A 86 619 619 HOH HOH . D 4 HOH A 87 620 620 HOH HOH . D 4 HOH A 88 622 622 HOH HOH . D 4 HOH A 89 623 623 HOH HOH . D 4 HOH A 90 624 624 HOH HOH . D 4 HOH A 91 626 626 HOH HOH . D 4 HOH A 92 631 631 HOH HOH . D 4 HOH A 93 632 632 HOH HOH . D 4 HOH A 94 634 634 HOH HOH . D 4 HOH A 95 637 637 HOH HOH . D 4 HOH A 96 640 640 HOH HOH . D 4 HOH A 97 641 641 HOH HOH . D 4 HOH A 98 645 645 HOH HOH . D 4 HOH A 99 654 654 HOH HOH . D 4 HOH A 100 658 658 HOH HOH . D 4 HOH A 101 672 672 HOH HOH . D 4 HOH A 102 673 673 HOH HOH . D 4 HOH A 103 674 674 HOH HOH . D 4 HOH A 104 676 676 HOH HOH . D 4 HOH A 105 678 678 HOH HOH . D 4 HOH A 106 680 680 HOH HOH . D 4 HOH A 107 681 681 HOH HOH . D 4 HOH A 108 682 682 HOH HOH . D 4 HOH A 109 684 684 HOH HOH . D 4 HOH A 110 685 685 HOH HOH . D 4 HOH A 111 686 686 HOH HOH . D 4 HOH A 112 688 688 HOH HOH . D 4 HOH A 113 690 690 HOH HOH . D 4 HOH A 114 691 691 HOH HOH . D 4 HOH A 115 692 692 HOH HOH . D 4 HOH A 116 694 694 HOH HOH . D 4 HOH A 117 699 699 HOH HOH . D 4 HOH A 118 700 700 HOH HOH . D 4 HOH A 119 703 703 HOH HOH . D 4 HOH A 120 704 704 HOH HOH . D 4 HOH A 121 705 705 HOH HOH . D 4 HOH A 122 706 706 HOH HOH . D 4 HOH A 123 707 707 HOH HOH . D 4 HOH A 124 708 708 HOH HOH . D 4 HOH A 125 710 710 HOH HOH . D 4 HOH A 126 713 713 HOH HOH . D 4 HOH A 127 715 715 HOH HOH . D 4 HOH A 128 718 718 HOH HOH . D 4 HOH A 129 719 719 HOH HOH . D 4 HOH A 130 722 722 HOH HOH . D 4 HOH A 131 725 725 HOH HOH . D 4 HOH A 132 726 726 HOH HOH . D 4 HOH A 133 727 727 HOH HOH . D 4 HOH A 134 728 728 HOH HOH . D 4 HOH A 135 729 729 HOH HOH . D 4 HOH A 136 732 732 HOH HOH . D 4 HOH A 137 733 733 HOH HOH . D 4 HOH A 138 736 736 HOH HOH . D 4 HOH A 139 740 740 HOH HOH . D 4 HOH A 140 741 741 HOH HOH . D 4 HOH A 141 742 742 HOH HOH . D 4 HOH A 142 746 746 HOH HOH . D 4 HOH A 143 747 747 HOH HOH . D 4 HOH A 144 748 748 HOH HOH . D 4 HOH A 145 749 749 HOH HOH . D 4 HOH A 146 750 750 HOH HOH . D 4 HOH A 147 751 751 HOH HOH . D 4 HOH A 148 752 752 HOH HOH . D 4 HOH A 149 753 753 HOH HOH . D 4 HOH A 150 754 754 HOH HOH . D 4 HOH A 151 755 755 HOH HOH . D 4 HOH A 152 758 758 HOH HOH . D 4 HOH A 153 759 759 HOH HOH . D 4 HOH A 154 760 760 HOH HOH . D 4 HOH A 155 762 762 HOH HOH . D 4 HOH A 156 763 763 HOH HOH . D 4 HOH A 157 764 764 HOH HOH . D 4 HOH A 158 766 766 HOH HOH . D 4 HOH A 159 767 767 HOH HOH . D 4 HOH A 160 769 769 HOH HOH . D 4 HOH A 161 770 770 HOH HOH . D 4 HOH A 162 771 771 HOH HOH . D 4 HOH A 163 772 772 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 NDP . . . B 2 28.087 9.71 -3.116 1 14.22 ? PA NDP 391 A 1 HETATM 2 O O1A NDP . . . B 2 28.001 9.362 -1.714 1 13.62 ? O1A NDP 391 A 1 HETATM 3 O O2A NDP . . . B 2 26.721 9.845 -3.722 1 14.13 ? O2A NDP 391 A 1 HETATM 4 O O5B NDP . . . B 2 28.825 11.113 -3.317 1 13.85 ? O5B NDP 391 A 1 HETATM 5 C C5B NDP . . . B 2 30.192 11.217 -2.848 1 14.09 ? C5B NDP 391 A 1 HETATM 6 C C4B NDP . . . B 2 30.455 12.69 -2.583 1 15.22 ? C4B NDP 391 A 1 HETATM 7 O O4B NDP . . . B 2 29.514 13.209 -1.628 1 15.42 ? O4B NDP 391 A 1 HETATM 8 C C3B NDP . . . B 2 31.873 12.997 -2.003 1 16.46 ? C3B NDP 391 A 1 HETATM 9 O O3B NDP . . . B 2 32.801 12.897 -3.092 1 16.74 ? O3B NDP 391 A 1 HETATM 10 C C2B NDP . . . B 2 31.553 14.359 -1.309 1 16.61 ? C2B NDP 391 A 1 HETATM 11 O O2B NDP . . . B 2 31.249 15.534 -2.131 1 17.72 ? O2B NDP 391 A 1 HETATM 12 C C1B NDP . . . B 2 30.21 13.963 -0.706 1 16.2 ? C1B NDP 391 A 1 HETATM 13 N N9A NDP . . . B 2 30.188 13.248 0.514 1 17.12 ? N9A NDP 391 A 1 HETATM 14 C C8A NDP . . . B 2 29.705 11.953 0.718 1 17.3 ? C8A NDP 391 A 1 HETATM 15 N N7A NDP . . . B 2 29.815 11.56 1.971 1 17.22 ? N7A NDP 391 A 1 HETATM 16 C C5A NDP . . . B 2 30.356 12.665 2.595 1 18.32 ? C5A NDP 391 A 1 HETATM 17 C C6A NDP . . . B 2 30.629 12.897 3.959 1 19.54 ? C6A NDP 391 A 1 HETATM 18 N N6A NDP . . . B 2 30.405 11.974 4.891 1 22.24 ? N6A NDP 391 A 1 HETATM 19 N N1A NDP . . . B 2 31.184 14.081 4.265 1 19.05 ? N1A NDP 391 A 1 HETATM 20 C C2A NDP . . . B 2 31.376 15.004 3.277 1 17.57 ? C2A NDP 391 A 1 HETATM 21 N N3A NDP . . . B 2 31.119 14.909 2.015 1 17.17 ? N3A NDP 391 A 1 HETATM 22 C C4A NDP . . . B 2 30.601 13.685 1.73 1 17.2 ? C4A NDP 391 A 1 HETATM 23 O O3 NDP . . . B 2 28.966 8.793 -3.957 1 16.14 ? O3 NDP 391 A 1 HETATM 24 P PN NDP . . . B 2 29.568 7.341 -4.254 1 15.79 ? PN NDP 391 A 1 HETATM 25 O O1N NDP . . . B 2 30.163 6.747 -3.063 1 16.56 ? O1N NDP 391 A 1 HETATM 26 O O2N NDP . . . B 2 30.584 7.503 -5.301 1 17.56 ? O2N NDP 391 A 1 HETATM 27 O O5D NDP . . . B 2 28.297 6.496 -4.727 1 16.51 ? O5D NDP 391 A 1 HETATM 28 C C5D NDP . . . B 2 27.78 6.722 -6.06 1 15.19 ? C5D NDP 391 A 1 HETATM 29 C C4D NDP . . . B 2 27.235 5.433 -6.588 1 13.99 ? C4D NDP 391 A 1 HETATM 30 O O4D NDP . . . B 2 26.2 4.925 -5.681 1 13.78 ? O4D NDP 391 A 1 HETATM 31 C C3D NDP . . . B 2 26.622 5.477 -7.989 1 14.1 ? C3D NDP 391 A 1 HETATM 32 O O3D NDP . . . B 2 27.027 4.289 -8.729 1 16.52 ? O3D NDP 391 A 1 HETATM 33 C C2D NDP . . . B 2 25.132 5.468 -7.664 1 13.74 ? C2D NDP 391 A 1 HETATM 34 O O2D NDP . . . B 2 24.35 4.984 -8.78 1 15.24 ? O2D NDP 391 A 1 HETATM 35 C C1D NDP . . . B 2 25.078 4.512 -6.511 1 13.34 ? C1D NDP 391 A 1 HETATM 36 N N1N NDP . . . B 2 23.836 4.568 -5.712 1 13.83 ? N1N NDP 391 A 1 HETATM 37 C C2N NDP . . . B 2 23.11 3.423 -5.507 1 12.96 ? C2N NDP 391 A 1 HETATM 38 C C3N NDP . . . B 2 21.979 3.435 -4.757 1 12.38 ? C3N NDP 391 A 1 HETATM 39 C C7N NDP . . . B 2 21.164 2.109 -4.551 1 10.2 ? C7N NDP 391 A 1 HETATM 40 O O7N NDP . . . B 2 20.193 2.183 -3.819 1 10.56 ? O7N NDP 391 A 1 HETATM 41 N N7N NDP . . . B 2 21.629 1.038 -5.197 1 8.71 ? N7N NDP 391 A 1 HETATM 42 C C4N NDP . . . B 2 21.489 4.585 -4.132 1 13.58 ? C4N NDP 391 A 1 HETATM 43 C C5N NDP . . . B 2 22.308 5.699 -4.398 1 14.04 ? C5N NDP 391 A 1 HETATM 44 C C6N NDP . . . B 2 23.429 5.778 -5.113 1 14.04 ? C6N NDP 391 A 1 HETATM 45 P P2B NDP . . . B 2 32.436 16.508 -2.754 1 18.57 ? P2B NDP 391 A 1 HETATM 46 O O1X NDP . . . B 2 33.431 15.491 -3.333 1 19.73 ? O1X NDP 391 A 1 HETATM 47 O O2X NDP . . . B 2 31.783 17.388 -3.696 1 19.21 ? O2X NDP 391 A 1 HETATM 48 O O3X NDP . . . B 2 32.973 17.208 -1.564 1 20.35 ? O3X NDP 391 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 48 #