data_5YZI # _model_server_result.job_id -0ssaACzrXeGli3dZUMDAw _model_server_result.datetime_utc '2024-11-05 00:41:20' _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 5yzi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 5YZI # _exptl.entry_id 5YZI _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 113.65 _cell.angle_gamma 90 _cell.entry_id 5YZI _cell.length_a 98.246 _cell.length_b 91.428 _cell.length_c 109.724 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YZI _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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,D,E,F,G,H,I _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 D N N ? 3 G N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 245 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 245 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id F _struct_conn.ptnr2_label_atom_id CD _struct_conn.ptnr2_label_comp_id CD _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CD _struct_conn.ptnr2_auth_seq_id 502 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 3.036 _struct_conn.pdbx_value_order ? # _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 5YZI _atom_sites.fract_transf_matrix[1][1] 0.010179 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004457 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010938 _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] 0.009949 _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 CD A 1 501 1 CD CD . D 3 NAP A 1 502 1 NAP NAP . E 2 CD B 1 501 2 CD CD . F 2 CD B 1 502 3 CD CD . G 3 NAP B 1 503 2 NAP NAP . H 4 HOH A 1 601 18 HOH HOH . H 4 HOH A 2 602 84 HOH HOH . H 4 HOH A 3 603 29 HOH HOH . H 4 HOH A 4 604 15 HOH HOH . H 4 HOH A 5 605 20 HOH HOH . H 4 HOH A 6 606 103 HOH HOH . H 4 HOH A 7 607 51 HOH HOH . H 4 HOH A 8 608 63 HOH HOH . H 4 HOH A 9 609 4 HOH HOH . H 4 HOH A 10 610 121 HOH HOH . H 4 HOH A 11 611 94 HOH HOH . H 4 HOH A 12 612 12 HOH HOH . H 4 HOH A 13 613 9 HOH HOH . H 4 HOH A 14 614 37 HOH HOH . H 4 HOH A 15 615 14 HOH HOH . H 4 HOH A 16 616 127 HOH HOH . H 4 HOH A 17 617 92 HOH HOH . H 4 HOH A 18 618 50 HOH HOH . H 4 HOH A 19 619 24 HOH HOH . H 4 HOH A 20 620 16 HOH HOH . H 4 HOH A 21 621 89 HOH HOH . H 4 HOH A 22 622 64 HOH HOH . H 4 HOH A 23 623 98 HOH HOH . H 4 HOH A 24 624 122 HOH HOH . H 4 HOH A 25 625 21 HOH HOH . H 4 HOH A 26 626 42 HOH HOH . H 4 HOH A 27 627 53 HOH HOH . H 4 HOH A 28 628 108 HOH HOH . H 4 HOH A 29 629 57 HOH HOH . H 4 HOH A 30 630 19 HOH HOH . H 4 HOH A 31 631 115 HOH HOH . H 4 HOH A 32 632 3 HOH HOH . H 4 HOH A 33 633 23 HOH HOH . H 4 HOH A 34 634 109 HOH HOH . H 4 HOH A 35 635 96 HOH HOH . H 4 HOH A 36 636 44 HOH HOH . H 4 HOH A 37 637 35 HOH HOH . H 4 HOH A 38 638 43 HOH HOH . H 4 HOH A 39 639 118 HOH HOH . H 4 HOH A 40 640 67 HOH HOH . H 4 HOH A 41 641 123 HOH HOH . H 4 HOH A 42 642 125 HOH HOH . H 4 HOH A 43 643 112 HOH HOH . H 4 HOH A 44 644 45 HOH HOH . H 4 HOH A 45 645 87 HOH HOH . H 4 HOH A 46 646 33 HOH HOH . H 4 HOH A 47 647 36 HOH HOH . H 4 HOH A 48 648 8 HOH HOH . H 4 HOH A 49 649 79 HOH HOH . H 4 HOH A 50 650 59 HOH HOH . H 4 HOH A 51 651 62 HOH HOH . H 4 HOH A 52 652 85 HOH HOH . H 4 HOH A 53 653 47 HOH HOH . H 4 HOH A 54 654 110 HOH HOH . H 4 HOH A 55 655 66 HOH HOH . H 4 HOH A 56 656 13 HOH HOH . H 4 HOH A 57 657 126 HOH HOH . H 4 HOH A 58 658 99 HOH HOH . H 4 HOH A 59 659 81 HOH HOH . H 4 HOH A 60 660 17 HOH HOH . H 4 HOH A 61 661 107 HOH HOH . H 4 HOH A 62 662 60 HOH HOH . H 4 HOH A 63 663 91 HOH HOH . H 4 HOH A 64 664 52 HOH HOH . H 4 HOH A 65 665 22 HOH HOH . H 4 HOH A 66 666 100 HOH HOH . H 4 HOH A 67 667 11 HOH HOH . H 4 HOH A 68 668 83 HOH HOH . H 4 HOH A 69 669 113 HOH HOH . H 4 HOH A 70 670 78 HOH HOH . H 4 HOH A 71 671 128 HOH HOH . H 4 HOH A 72 672 68 HOH HOH . H 4 HOH A 73 673 82 HOH HOH . H 4 HOH A 74 674 114 HOH HOH . H 4 HOH A 75 675 27 HOH HOH . H 4 HOH A 76 676 56 HOH HOH . H 4 HOH A 77 677 58 HOH HOH . H 4 HOH A 78 678 55 HOH HOH . H 4 HOH A 79 679 76 HOH HOH . H 4 HOH A 80 680 61 HOH HOH . H 4 HOH A 81 681 101 HOH HOH . H 4 HOH A 82 682 117 HOH HOH . H 4 HOH A 83 683 120 HOH HOH . H 4 HOH A 84 684 95 HOH HOH . H 4 HOH A 85 685 88 HOH HOH . H 4 HOH A 86 686 90 HOH HOH . H 4 HOH A 87 687 54 HOH HOH . I 4 HOH B 1 601 65 HOH HOH . I 4 HOH B 2 602 130 HOH HOH . I 4 HOH B 3 603 7 HOH HOH . I 4 HOH B 4 604 48 HOH HOH . I 4 HOH B 5 605 124 HOH HOH . I 4 HOH B 6 606 72 HOH HOH . I 4 HOH B 7 607 129 HOH HOH . I 4 HOH B 8 608 31 HOH HOH . I 4 HOH B 9 609 102 HOH HOH . I 4 HOH B 10 610 97 HOH HOH . I 4 HOH B 11 611 2 HOH HOH . I 4 HOH B 12 612 26 HOH HOH . I 4 HOH B 13 613 41 HOH HOH . I 4 HOH B 14 614 46 HOH HOH . I 4 HOH B 15 615 30 HOH HOH . I 4 HOH B 16 616 6 HOH HOH . I 4 HOH B 17 617 5 HOH HOH . I 4 HOH B 18 618 104 HOH HOH . I 4 HOH B 19 619 40 HOH HOH . I 4 HOH B 20 620 38 HOH HOH . I 4 HOH B 21 621 86 HOH HOH . I 4 HOH B 22 622 80 HOH HOH . I 4 HOH B 23 623 32 HOH HOH . I 4 HOH B 24 624 77 HOH HOH . I 4 HOH B 25 625 34 HOH HOH . I 4 HOH B 26 626 111 HOH HOH . I 4 HOH B 27 627 70 HOH HOH . I 4 HOH B 28 628 71 HOH HOH . I 4 HOH B 29 629 49 HOH HOH . I 4 HOH B 30 630 28 HOH HOH . I 4 HOH B 31 631 74 HOH HOH . I 4 HOH B 32 632 69 HOH HOH . I 4 HOH B 33 633 93 HOH HOH . I 4 HOH B 34 634 25 HOH HOH . I 4 HOH B 35 635 73 HOH HOH . I 4 HOH B 36 636 39 HOH HOH . I 4 HOH B 37 637 116 HOH HOH . I 4 HOH B 38 638 10 HOH HOH . I 4 HOH B 39 639 119 HOH HOH . I 4 HOH B 40 640 106 HOH HOH . I 4 HOH B 41 641 105 HOH HOH . I 4 HOH B 42 642 75 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 . . . D 3 -6.326 7.32 22.049 1 31.71 ? PA NAP 502 A 1 HETATM 2 O O1A NAP . . . D 3 -7.42 8.342 22.196 1 35.41 ? O1A NAP 502 A 1 HETATM 3 O O2A NAP . . . D 3 -6.506 5.96 22.675 1 32.57 ? O2A NAP 502 A 1 HETATM 4 O O5B NAP . . . D 3 -5.94 7.124 20.513 1 29.68 ? O5B NAP 502 A 1 HETATM 5 C C5B NAP . . . D 3 -6.925 7.385 19.556 1 31.84 ? C5B NAP 502 A 1 HETATM 6 C C4B NAP . . . D 3 -6.538 6.707 18.268 1 31.46 ? C4B NAP 502 A 1 HETATM 7 O O4B NAP . . . D 3 -6.507 5.286 18.449 1 29.27 ? O4B NAP 502 A 1 HETATM 8 C C3B NAP . . . D 3 -7.716 7.023 17.384 1 29.55 ? C3B NAP 502 A 1 HETATM 9 O O3B NAP . . . D 3 -7.331 8.086 16.509 1 29.74 ? O3B NAP 502 A 1 HETATM 10 C C2B NAP . . . D 3 -8.017 5.704 16.713 1 29.19 ? C2B NAP 502 A 1 HETATM 11 O O2B NAP . . . D 3 -7.112 5.561 15.633 1 27.87 ? O2B NAP 502 A 1 HETATM 12 C C1B NAP . . . D 3 -7.609 4.688 17.751 1 31.42 ? C1B NAP 502 A 1 HETATM 13 N N9A NAP . . . D 3 -8.732 4.444 18.704 1 36.62 ? N9A NAP 502 A 1 HETATM 14 C C8A NAP . . . D 3 -8.648 4.573 20.048 1 36.79 ? C8A NAP 502 A 1 HETATM 15 N N7A NAP . . . D 3 -9.824 4.274 20.655 1 36.41 ? N7A NAP 502 A 1 HETATM 16 C C5A NAP . . . D 3 -10.695 3.931 19.69 1 35.63 ? C5A NAP 502 A 1 HETATM 17 C C6A NAP . . . D 3 -12.114 3.508 19.659 1 36.45 ? C6A NAP 502 A 1 HETATM 18 N N6A NAP . . . D 3 -12.818 3.389 20.815 1 36.05 ? N6A NAP 502 A 1 HETATM 19 N N1A NAP . . . D 3 -12.672 3.245 18.454 1 35.7 ? N1A NAP 502 A 1 HETATM 20 C C2A NAP . . . D 3 -11.963 3.366 17.315 1 36.35 ? C2A NAP 502 A 1 HETATM 21 N N3A NAP . . . D 3 -10.671 3.751 17.268 1 37.41 ? N3A NAP 502 A 1 HETATM 22 C C4A NAP . . . D 3 -9.981 4.039 18.406 1 36.42 ? C4A NAP 502 A 1 HETATM 23 O O3 NAP . . . D 3 -4.899 7.91 22.495 1 34.36 ? O3 NAP 502 A 1 HETATM 24 P PN NAP . . . D 3 -4.292 9.268 21.88 1 32.07 ? PN NAP 502 A 1 HETATM 25 O O1N NAP . . . D 3 -5.065 9.744 20.674 1 30.36 ? O1N NAP 502 A 1 HETATM 26 O O2N NAP . . . D 3 -2.793 9.182 21.794 1 30.29 ? O2N NAP 502 A 1 HETATM 27 O O5D NAP . . . D 3 -4.581 10.166 23.173 1 35.76 ? O5D NAP 502 A 1 HETATM 28 C C5D NAP . . . D 3 -5.66 11.077 23.173 1 31.92 ? C5D NAP 502 A 1 HETATM 29 C C4D NAP . . . D 3 -5.924 11.638 24.563 1 31.94 ? C4D NAP 502 A 1 HETATM 30 O O4D NAP . . . D 3 -6.453 10.618 25.415 1 33.85 ? O4D NAP 502 A 1 HETATM 31 C C3D NAP . . . D 3 -4.67 12.185 25.224 1 31.74 ? C3D NAP 502 A 1 HETATM 32 O O3D NAP . . . D 3 -5.005 13.465 25.764 1 33.36 ? O3D NAP 502 A 1 HETATM 33 C C2D NAP . . . D 3 -4.353 11.208 26.347 1 32.89 ? C2D NAP 502 A 1 HETATM 34 O O2D NAP . . . D 3 -3.864 11.864 27.522 1 32.54 ? O2D NAP 502 A 1 HETATM 35 C C1D NAP . . . D 3 -5.692 10.553 26.63 1 33.3 ? C1D NAP 502 A 1 HETATM 36 N N1N NAP . . . D 3 -5.558 9.163 27.082 1 33.5 ? N1N NAP 502 A 1 HETATM 37 C C2N NAP . . . D 3 -6.297 8.761 28.13 1 33.35 ? C2N NAP 502 A 1 HETATM 38 C C3N NAP . . . D 3 -6.243 7.458 28.6 1 33.55 ? C3N NAP 502 A 1 HETATM 39 C C7N NAP . . . D 3 -7.088 7.065 29.781 1 35.6 ? C7N NAP 502 A 1 HETATM 40 O O7N NAP . . . D 3 -7.584 7.943 30.46 1 38.21 ? O7N NAP 502 A 1 HETATM 41 N N7N NAP . . . D 3 -7.287 5.78 30.065 1 35.25 ? N7N NAP 502 A 1 HETATM 42 C C4N NAP . . . D 3 -5.411 6.553 27.959 1 31.58 ? C4N NAP 502 A 1 HETATM 43 C C5N NAP . . . D 3 -4.659 6.988 26.872 1 31.27 ? C5N NAP 502 A 1 HETATM 44 C C6N NAP . . . D 3 -4.75 8.309 26.442 1 31.5 ? C6N NAP 502 A 1 HETATM 45 P P2B NAP . . . D 3 -7.549 6.118 14.195 1 30.85 ? P2B NAP 502 A 1 HETATM 46 O O1X NAP . . . D 3 -7.156 7.576 14.287 1 28.85 ? O1X NAP 502 A 1 HETATM 47 O O2X NAP . . . D 3 -9.036 5.868 14.146 1 31.8 ? O2X NAP 502 A 1 HETATM 48 O O3X NAP . . . D 3 -6.754 5.265 13.23 1 35.24 ? O3X NAP 502 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #