data_4YAC # _model_server_result.job_id ZkQpfpNe-OxR_txlp4ntqA _model_server_result.datetime_utc '2024-11-26 19:57:13' _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 4yac # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 4YAC # _exptl.entry_id 4YAC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 665.441 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' _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 4YAC _cell.length_a 79.298 _cell.length_b 79.298 _cell.length_c 71.973 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YAC _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 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 # _chem_comp.formula 'C21 H29 N7 O14 P2' _chem_comp.formula_weight 665.441 _chem_comp.id NAI _chem_comp.mon_nstd_flag . _chem_comp.name '1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms NADH # 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 NAI doub 237 n n PA O2A NAI sing 238 n n PA O5B NAI sing 239 n n PA O3 NAI sing 240 n n O2A HOA2 NAI sing 241 n n O5B C5B NAI sing 242 n n C5B C4B NAI sing 243 n n C5B H51A NAI sing 244 n n C5B H52A NAI sing 245 n n C4B O4B NAI sing 246 n n C4B C3B NAI sing 247 n n C4B H4B NAI sing 248 n n O4B C1B NAI sing 249 n n C3B O3B NAI sing 250 n n C3B C2B NAI sing 251 n n C3B H3B NAI sing 252 n n O3B HO3A NAI sing 253 n n C2B O2B NAI sing 254 n n C2B C1B NAI sing 255 n n C2B H2B NAI sing 256 n n O2B HO2A NAI sing 257 n n C1B N9A NAI sing 258 n n C1B H1B NAI sing 259 n n N9A C8A NAI sing 260 n y N9A C4A NAI sing 261 n y C8A N7A NAI doub 262 n y C8A H8A NAI sing 263 n n N7A C5A NAI sing 264 n y C5A C6A NAI sing 265 n y C5A C4A NAI doub 266 n y C6A N6A NAI sing 267 n n C6A N1A NAI doub 268 n y N6A H61A NAI sing 269 n n N6A H62A NAI sing 270 n n N1A C2A NAI sing 271 n y C2A N3A NAI doub 272 n y C2A H2A NAI sing 273 n n N3A C4A NAI sing 274 n y O3 PN NAI sing 275 n n PN O1N NAI sing 276 n n PN O2N NAI doub 277 n n PN O5D NAI sing 278 n n O1N HO1N NAI sing 279 n n O5D C5D NAI sing 280 n n C5D C4D NAI sing 281 n n C5D H51N NAI sing 282 n n C5D H52N NAI sing 283 n n C4D O4D NAI sing 284 n n C4D C3D NAI sing 285 n n C4D H4D NAI sing 286 n n O4D C1D NAI sing 287 n n C3D O3D NAI sing 288 n n C3D C2D NAI sing 289 n n C3D H3D NAI sing 290 n n O3D HO3N NAI sing 291 n n C2D O2D NAI sing 292 n n C2D C1D NAI sing 293 n n C2D H2D NAI sing 294 n n O2D HO2N NAI sing 295 n n C1D N1N NAI sing 296 n n C1D H1D NAI sing 297 n n N1N C2N NAI sing 298 n n N1N C6N NAI sing 299 n n C2N C3N NAI doub 300 n n C2N H2N NAI sing 301 n n C3N C7N NAI sing 302 n n C3N C4N NAI sing 303 n n C7N O7N NAI doub 304 n n C7N N7N NAI sing 305 n n N7N H71N NAI sing 306 n n N7N H72N NAI sing 307 n n C4N C5N NAI sing 308 n n C4N H4N NAI sing 309 n n C4N H42N NAI sing 310 n n C5N C6N NAI doub 311 n n C5N H5N NAI sing 312 n n C6N H6N NAI sing 313 n n # _atom_sites.entry_id 4YAC _atom_sites.fract_transf_matrix[1][1] 0.012611 _atom_sites.fract_transf_matrix[1][2] 0.007281 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014562 _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] 0.013894 _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 NAI A 1 500 500 NAI NAD . C 3 HOH A 1 601 51 HOH HOH . C 3 HOH A 2 602 40 HOH HOH . C 3 HOH A 3 603 105 HOH HOH . C 3 HOH A 4 604 18 HOH HOH . C 3 HOH A 5 605 35 HOH HOH . C 3 HOH A 6 606 49 HOH HOH . C 3 HOH A 7 607 77 HOH HOH . C 3 HOH A 8 608 72 HOH HOH . C 3 HOH A 9 609 32 HOH HOH . C 3 HOH A 10 610 102 HOH HOH . C 3 HOH A 11 611 3 HOH HOH . C 3 HOH A 12 612 45 HOH HOH . C 3 HOH A 13 613 48 HOH HOH . C 3 HOH A 14 614 100 HOH HOH . C 3 HOH A 15 615 5 HOH HOH . C 3 HOH A 16 616 42 HOH HOH . C 3 HOH A 17 617 63 HOH HOH . C 3 HOH A 18 618 24 HOH HOH . C 3 HOH A 19 619 13 HOH HOH . C 3 HOH A 20 620 2 HOH HOH . C 3 HOH A 21 621 58 HOH HOH . C 3 HOH A 22 622 87 HOH HOH . C 3 HOH A 23 623 16 HOH HOH . C 3 HOH A 24 624 17 HOH HOH . C 3 HOH A 25 625 55 HOH HOH . C 3 HOH A 26 626 82 HOH HOH . C 3 HOH A 27 627 10 HOH HOH . C 3 HOH A 28 628 27 HOH HOH . C 3 HOH A 29 629 34 HOH HOH . C 3 HOH A 30 630 107 HOH HOH . C 3 HOH A 31 631 39 HOH HOH . C 3 HOH A 32 632 44 HOH HOH . C 3 HOH A 33 633 47 HOH HOH . C 3 HOH A 34 634 43 HOH HOH . C 3 HOH A 35 635 23 HOH HOH . C 3 HOH A 36 636 114 HOH HOH . C 3 HOH A 37 637 33 HOH HOH . C 3 HOH A 38 638 71 HOH HOH . C 3 HOH A 39 639 41 HOH HOH . C 3 HOH A 40 640 122 HOH HOH . C 3 HOH A 41 641 31 HOH HOH . C 3 HOH A 42 642 79 HOH HOH . C 3 HOH A 43 643 113 HOH HOH . C 3 HOH A 44 644 62 HOH HOH . C 3 HOH A 45 645 22 HOH HOH . C 3 HOH A 46 646 118 HOH HOH . C 3 HOH A 47 647 90 HOH HOH . C 3 HOH A 48 648 20 HOH HOH . C 3 HOH A 49 649 106 HOH HOH . C 3 HOH A 50 650 116 HOH HOH . C 3 HOH A 51 651 94 HOH HOH . C 3 HOH A 52 652 115 HOH HOH . C 3 HOH A 53 653 25 HOH HOH . C 3 HOH A 54 654 83 HOH HOH . C 3 HOH A 55 655 76 HOH HOH . C 3 HOH A 56 656 50 HOH HOH . C 3 HOH A 57 657 96 HOH HOH . C 3 HOH A 58 658 19 HOH HOH . C 3 HOH A 59 659 46 HOH HOH . C 3 HOH A 60 660 11 HOH HOH . C 3 HOH A 61 661 92 HOH HOH . C 3 HOH A 62 662 129 HOH HOH . C 3 HOH A 63 663 86 HOH HOH . C 3 HOH A 64 664 125 HOH HOH . C 3 HOH A 65 665 70 HOH HOH . C 3 HOH A 66 666 99 HOH HOH . C 3 HOH A 67 667 80 HOH HOH . C 3 HOH A 68 668 98 HOH HOH . C 3 HOH A 69 669 68 HOH HOH . C 3 HOH A 70 670 119 HOH HOH . C 3 HOH A 71 671 124 HOH HOH . C 3 HOH A 72 672 56 HOH HOH . C 3 HOH A 73 673 128 HOH HOH . C 3 HOH A 74 674 81 HOH HOH . C 3 HOH A 75 675 57 HOH HOH . C 3 HOH A 76 676 121 HOH HOH . C 3 HOH A 77 677 117 HOH HOH . C 3 HOH A 78 678 123 HOH HOH . C 3 HOH A 79 679 1 HOH HOH . C 3 HOH A 80 680 4 HOH HOH . C 3 HOH A 81 681 6 HOH HOH . C 3 HOH A 82 682 7 HOH HOH . C 3 HOH A 83 683 8 HOH HOH . C 3 HOH A 84 684 9 HOH HOH . C 3 HOH A 85 685 12 HOH HOH . C 3 HOH A 86 686 14 HOH HOH . C 3 HOH A 87 687 15 HOH HOH . C 3 HOH A 88 688 21 HOH HOH . C 3 HOH A 89 689 26 HOH HOH . C 3 HOH A 90 690 28 HOH HOH . C 3 HOH A 91 691 29 HOH HOH . C 3 HOH A 92 692 30 HOH HOH . C 3 HOH A 93 693 36 HOH HOH . C 3 HOH A 94 694 37 HOH HOH . C 3 HOH A 95 695 38 HOH HOH . C 3 HOH A 96 696 52 HOH HOH . C 3 HOH A 97 697 53 HOH HOH . C 3 HOH A 98 698 54 HOH HOH . C 3 HOH A 99 699 59 HOH HOH . C 3 HOH A 100 700 60 HOH HOH . C 3 HOH A 101 701 61 HOH HOH . C 3 HOH A 102 702 64 HOH HOH . C 3 HOH A 103 703 65 HOH HOH . C 3 HOH A 104 704 66 HOH HOH . C 3 HOH A 105 705 67 HOH HOH . C 3 HOH A 106 706 69 HOH HOH . C 3 HOH A 107 707 73 HOH HOH . C 3 HOH A 108 708 74 HOH HOH . C 3 HOH A 109 709 75 HOH HOH . C 3 HOH A 110 710 78 HOH HOH . C 3 HOH A 111 711 84 HOH HOH . C 3 HOH A 112 712 85 HOH HOH . C 3 HOH A 113 713 88 HOH HOH . C 3 HOH A 114 714 89 HOH HOH . C 3 HOH A 115 715 91 HOH HOH . C 3 HOH A 116 716 93 HOH HOH . C 3 HOH A 117 717 95 HOH HOH . C 3 HOH A 118 718 97 HOH HOH . C 3 HOH A 119 719 101 HOH HOH . C 3 HOH A 120 720 103 HOH HOH . C 3 HOH A 121 721 104 HOH HOH . C 3 HOH A 122 722 108 HOH HOH . C 3 HOH A 123 723 109 HOH HOH . C 3 HOH A 124 724 110 HOH HOH . C 3 HOH A 125 725 111 HOH HOH . C 3 HOH A 126 726 112 HOH HOH . C 3 HOH A 127 727 120 HOH HOH . C 3 HOH A 128 728 126 HOH HOH . C 3 HOH A 129 729 127 HOH HOH . C 3 HOH A 130 730 130 HOH HOH . C 3 HOH A 131 731 131 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 NAI . . . B 2 -0.698 -37.932 9.689 1 39.03 ? PA NAI 500 A 1 HETATM 2 O O1A NAI . . . B 2 -0.795 -39.136 8.785 1 47.11 ? O1A NAI 500 A 1 HETATM 3 O O2A NAI . . . B 2 0.652 -37.962 10.428 1 43.31 -1 O2A NAI 500 A 1 HETATM 4 O O5B NAI . . . B 2 -1.874 -37.953 10.733 1 32.17 ? O5B NAI 500 A 1 HETATM 5 C C5B NAI . . . B 2 -3.188 -38.01 10.281 1 32.74 ? C5B NAI 500 A 1 HETATM 6 C C4B NAI . . . B 2 -4.023 -38.686 11.285 1 28.54 ? C4B NAI 500 A 1 HETATM 7 O O4B NAI . . . B 2 -5.43 -38.454 10.94 1 25.14 ? O4B NAI 500 A 1 HETATM 8 C C3B NAI . . . B 2 -3.798 -40.126 11.285 1 28.76 ? C3B NAI 500 A 1 HETATM 9 O O3B NAI . . . B 2 -3.628 -40.612 12.61 1 29.11 ? O3B NAI 500 A 1 HETATM 10 C C2B NAI . . . B 2 -4.966 -40.699 10.665 1 24.8 ? C2B NAI 500 A 1 HETATM 11 O O2B NAI . . . B 2 -5.221 -42.033 11.145 1 28.23 ? O2B NAI 500 A 1 HETATM 12 C C1B NAI . . . B 2 -6.034 -39.785 11.012 1 24.03 ? C1B NAI 500 A 1 HETATM 13 N N9A NAI . . . B 2 -7.182 -39.893 10.154 1 24.62 ? N9A NAI 500 A 1 HETATM 14 C C8A NAI . . . B 2 -7.226 -39.965 8.794 1 23.47 ? C8A NAI 500 A 1 HETATM 15 N N7A NAI . . . B 2 -8.498 -40.072 8.375 1 24.07 ? N7A NAI 500 A 1 HETATM 16 C C5A NAI . . . B 2 -9.326 -40.068 9.466 1 26.42 ? C5A NAI 500 A 1 HETATM 17 C C6A NAI . . . B 2 -10.697 -40.146 9.687 1 23.59 ? C6A NAI 500 A 1 HETATM 18 N N6A NAI . . . B 2 -11.628 -40.269 8.609 1 23.58 ? N6A NAI 500 A 1 HETATM 19 N N1A NAI . . . B 2 -11.177 -40.112 10.961 1 24.13 ? N1A NAI 500 A 1 HETATM 20 C C2A NAI . . . B 2 -10.354 -40.007 12.021 1 21.82 ? C2A NAI 500 A 1 HETATM 21 N N3A NAI . . . B 2 -9.023 -39.923 11.851 1 24.6 ? N3A NAI 500 A 1 HETATM 22 C C4A NAI . . . B 2 -8.486 -39.955 10.605 1 23.64 ? C4A NAI 500 A 1 HETATM 23 O O3 NAI . . . B 2 -0.828 -36.633 8.86 1 40.23 ? O3 NAI 500 A 1 HETATM 24 P PN NAI . . . B 2 -0.155 -35.254 9.325 1 48.21 ? PN NAI 500 A 1 HETATM 25 O O1N NAI . . . B 2 1.358 -35.406 9.323 1 56.63 -1 O1N NAI 500 A 1 HETATM 26 O O2N NAI . . . B 2 -0.586 -34.092 8.309 1 58.12 ? O2N NAI 500 A 1 HETATM 27 O O5D NAI . . . B 2 -0.634 -34.886 10.752 1 50.43 ? O5D NAI 500 A 1 HETATM 28 H H51A NAI . . . B 2 -3.223 -38.521 9.415 1 39.29 ? H51A NAI 500 A 1 HETATM 29 H H52A NAI . . . B 2 -3.532 -37.069 10.132 1 39.29 ? H52A NAI 500 A 1 HETATM 30 H H4B NAI . . . B 2 -3.83 -38.312 12.188 1 34.25 ? H4B NAI 500 A 1 HETATM 31 H H3B NAI . . . B 2 -3.005 -40.339 10.75 1 34.51 ? H3B NAI 500 A 1 HETATM 32 H HO3A NAI . . . B 2 -2.762 -40.641 12.806 1 34.93 ? HO3A NAI 500 A 1 HETATM 33 H H2B NAI . . . B 2 -4.85 -40.714 9.711 1 29.76 ? H2B NAI 500 A 1 HETATM 34 H HO2A NAI . . . B 2 -4.589 -42.562 10.879 1 33.88 ? HO2A NAI 500 A 1 HETATM 35 H H1B NAI . . . B 2 -6.305 -39.952 11.907 1 28.84 ? H1B NAI 500 A 1 HETATM 36 H H8A NAI . . . B 2 -6.413 -39.947 8.184 1 28.16 ? H8A NAI 500 A 1 HETATM 37 H H61A NAI . . . B 2 -11.541 -40.943 8.016 1 28.29 ? H61A NAI 500 A 1 HETATM 38 H H62A NAI . . . B 2 -12.306 -39.67 8.521 1 28.29 ? H62A NAI 500 A 1 HETATM 39 H H2A NAI . . . B 2 -10.73 -39.982 12.929 1 26.19 ? H2A NAI 500 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 1228 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 39 #