data_2YUT # _model_server_result.job_id RhDT4lA7MYUiFwlQKambZw _model_server_result.datetime_utc '2024-11-05 00:23:41' _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 2yut # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 2YUT # _exptl.entry_id 2YUT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 2 _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 2YUT _cell.length_a 149.091 _cell.length_b 149.091 _cell.length_c 47.721 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YUT _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _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' 12_555 x,x-y,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 23.8605 # _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A C MSE 1 A MSE 1 1_555 A N ARG 2 A ARG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C GLU 92 A GLU 92 1_555 A N MSE 93 A MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C MSE 93 A MSE 93 1_555 A N LEU 94 A LEU 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _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 227 n n PA O2A NAP sing 228 n n PA O5B NAP sing 229 n n PA O3 NAP sing 230 n n O2A HOA2 NAP sing 231 n n O5B C5B NAP sing 232 n n C5B C4B NAP sing 233 n n C5B H51A NAP sing 234 n n C5B H52A NAP sing 235 n n C4B O4B NAP sing 236 n n C4B C3B NAP sing 237 n n C4B H4B NAP sing 238 n n O4B C1B NAP sing 239 n n C3B O3B NAP sing 240 n n C3B C2B NAP sing 241 n n C3B H3B NAP sing 242 n n O3B HO3A NAP sing 243 n n C2B O2B NAP sing 244 n n C2B C1B NAP sing 245 n n C2B H2B NAP sing 246 n n O2B P2B NAP sing 247 n n C1B N9A NAP sing 248 n n C1B H1B NAP sing 249 n n N9A C8A NAP sing 250 n y N9A C4A NAP sing 251 n y C8A N7A NAP doub 252 n y C8A H8A NAP sing 253 n n N7A C5A NAP sing 254 n y C5A C6A NAP sing 255 n y C5A C4A NAP doub 256 n y C6A N6A NAP sing 257 n n C6A N1A NAP doub 258 n y N6A H61A NAP sing 259 n n N6A H62A NAP sing 260 n n N1A C2A NAP sing 261 n y C2A N3A NAP doub 262 n y C2A H2A NAP sing 263 n n N3A C4A NAP sing 264 n y O3 PN NAP sing 265 n n PN O1N NAP doub 266 n n PN O2N NAP sing 267 n n PN O5D NAP sing 268 n n O5D C5D NAP sing 269 n n C5D C4D NAP sing 270 n n C5D H51N NAP sing 271 n n C5D H52N NAP sing 272 n n C4D O4D NAP sing 273 n n C4D C3D NAP sing 274 n n C4D H4D NAP sing 275 n n O4D C1D NAP sing 276 n n C3D O3D NAP sing 277 n n C3D C2D NAP sing 278 n n C3D H3D NAP sing 279 n n O3D HO3N NAP sing 280 n n C2D O2D NAP sing 281 n n C2D C1D NAP sing 282 n n C2D H2D NAP sing 283 n n O2D HO2N NAP sing 284 n n C1D N1N NAP sing 285 n n C1D H1D NAP sing 286 n n N1N C2N NAP sing 287 n y N1N C6N NAP doub 288 n y C2N C3N NAP doub 289 n y C2N H2N NAP sing 290 n n C3N C7N NAP sing 291 n n C3N C4N NAP sing 292 n y C7N O7N NAP doub 293 n n C7N N7N NAP sing 294 n n N7N H71N NAP sing 295 n n N7N H72N NAP sing 296 n n C4N C5N NAP doub 297 n y C4N H4N NAP sing 298 n n C5N C6N NAP sing 299 n y C5N H5N NAP sing 300 n n C6N H6N NAP sing 301 n n P2B O1X NAP doub 302 n n P2B O2X NAP sing 303 n n P2B O3X NAP sing 304 n n O2X HOP2 NAP sing 305 n n O3X HOP3 NAP sing 306 n n # _atom_sites.entry_id 2YUT _atom_sites.fract_transf_matrix[1][1] 0.006707 _atom_sites.fract_transf_matrix[1][2] 0.003872 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007745 _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] 0.020955 _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 NAP A 1 500 500 NAP NAP . C 3 HOH A 1 501 1 HOH HOH . C 3 HOH A 2 502 2 HOH HOH . C 3 HOH A 3 503 3 HOH HOH . C 3 HOH A 4 504 4 HOH HOH . C 3 HOH A 5 505 5 HOH HOH . C 3 HOH A 6 506 6 HOH HOH . C 3 HOH A 7 507 7 HOH HOH . C 3 HOH A 8 508 8 HOH HOH . C 3 HOH A 9 509 9 HOH HOH . C 3 HOH A 10 510 10 HOH HOH . C 3 HOH A 11 511 11 HOH HOH . C 3 HOH A 12 512 12 HOH HOH . C 3 HOH A 13 513 13 HOH HOH . C 3 HOH A 14 514 14 HOH HOH . C 3 HOH A 15 515 15 HOH HOH . C 3 HOH A 16 516 16 HOH HOH . C 3 HOH A 17 517 17 HOH HOH . C 3 HOH A 18 518 18 HOH HOH . C 3 HOH A 19 519 19 HOH HOH . C 3 HOH A 20 520 20 HOH HOH . C 3 HOH A 21 521 21 HOH HOH . C 3 HOH A 22 522 22 HOH HOH . C 3 HOH A 23 523 23 HOH HOH . C 3 HOH A 24 524 24 HOH HOH . C 3 HOH A 25 525 25 HOH HOH . C 3 HOH A 26 526 26 HOH HOH . C 3 HOH A 27 527 27 HOH HOH . C 3 HOH A 28 528 28 HOH HOH . C 3 HOH A 29 529 29 HOH HOH . C 3 HOH A 30 530 30 HOH HOH . C 3 HOH A 31 531 31 HOH HOH . C 3 HOH A 32 532 32 HOH HOH . C 3 HOH A 33 533 33 HOH HOH . C 3 HOH A 34 534 34 HOH HOH . C 3 HOH A 35 535 35 HOH HOH . C 3 HOH A 36 536 36 HOH HOH . C 3 HOH A 37 537 37 HOH HOH . C 3 HOH A 38 538 38 HOH HOH . C 3 HOH A 39 539 39 HOH HOH . C 3 HOH A 40 540 40 HOH HOH . C 3 HOH A 41 541 41 HOH HOH . C 3 HOH A 42 542 42 HOH HOH . C 3 HOH A 43 543 43 HOH HOH . C 3 HOH A 44 544 44 HOH HOH . C 3 HOH A 45 545 45 HOH HOH . C 3 HOH A 46 546 46 HOH HOH . C 3 HOH A 47 547 47 HOH HOH . C 3 HOH A 48 548 48 HOH HOH . C 3 HOH A 49 549 49 HOH HOH . C 3 HOH A 50 550 50 HOH HOH . C 3 HOH A 51 551 51 HOH HOH . C 3 HOH A 52 552 52 HOH HOH . C 3 HOH A 53 553 53 HOH HOH . C 3 HOH A 54 554 54 HOH HOH . C 3 HOH A 55 555 55 HOH HOH . C 3 HOH A 56 556 56 HOH HOH . C 3 HOH A 57 557 57 HOH HOH . C 3 HOH A 58 558 58 HOH HOH . C 3 HOH A 59 559 59 HOH HOH . C 3 HOH A 60 560 60 HOH HOH . C 3 HOH A 61 561 61 HOH HOH . C 3 HOH A 62 562 62 HOH HOH . C 3 HOH A 63 563 63 HOH HOH . C 3 HOH A 64 564 64 HOH HOH . C 3 HOH A 65 565 65 HOH HOH . C 3 HOH A 66 566 66 HOH HOH . C 3 HOH A 67 567 67 HOH HOH . C 3 HOH A 68 568 68 HOH HOH . C 3 HOH A 69 569 69 HOH HOH . C 3 HOH A 70 570 70 HOH HOH . C 3 HOH A 71 571 71 HOH HOH . C 3 HOH A 72 572 72 HOH HOH . C 3 HOH A 73 573 73 HOH HOH . C 3 HOH A 74 574 74 HOH HOH . C 3 HOH A 75 575 75 HOH HOH . C 3 HOH A 76 576 76 HOH HOH . C 3 HOH A 77 577 77 HOH HOH . C 3 HOH A 78 578 78 HOH HOH . C 3 HOH A 79 579 79 HOH HOH . C 3 HOH A 80 580 80 HOH HOH . C 3 HOH A 81 581 81 HOH HOH . C 3 HOH A 82 582 82 HOH HOH . C 3 HOH A 83 583 83 HOH HOH . C 3 HOH A 84 584 84 HOH HOH . C 3 HOH A 85 585 85 HOH HOH . C 3 HOH A 86 586 86 HOH HOH . C 3 HOH A 87 587 87 HOH HOH . C 3 HOH A 88 588 88 HOH HOH . C 3 HOH A 89 589 89 HOH HOH . C 3 HOH A 90 590 90 HOH HOH . C 3 HOH A 91 591 91 HOH HOH . C 3 HOH A 92 592 92 HOH HOH . C 3 HOH A 93 593 93 HOH HOH . C 3 HOH A 94 594 94 HOH HOH . C 3 HOH A 95 595 95 HOH HOH . C 3 HOH A 96 596 96 HOH HOH . C 3 HOH A 97 597 97 HOH HOH . C 3 HOH A 98 598 98 HOH HOH . C 3 HOH A 99 599 99 HOH HOH . C 3 HOH A 100 600 100 HOH HOH . C 3 HOH A 101 601 101 HOH HOH . C 3 HOH A 102 602 102 HOH HOH . C 3 HOH A 103 603 103 HOH HOH . C 3 HOH A 104 604 104 HOH HOH . C 3 HOH A 105 605 105 HOH HOH . C 3 HOH A 106 606 106 HOH HOH . C 3 HOH A 107 607 107 HOH HOH . C 3 HOH A 108 608 108 HOH HOH . C 3 HOH A 109 609 109 HOH HOH . C 3 HOH A 110 610 110 HOH HOH . C 3 HOH A 111 611 111 HOH HOH . C 3 HOH A 112 612 112 HOH HOH . C 3 HOH A 113 613 113 HOH HOH . C 3 HOH A 114 614 114 HOH HOH . C 3 HOH A 115 615 115 HOH HOH . C 3 HOH A 116 616 116 HOH HOH . C 3 HOH A 117 617 117 HOH HOH . C 3 HOH A 118 618 118 HOH HOH . C 3 HOH A 119 619 119 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 . . . B 2 41.868 43.506 2.176 1 17.2 ? PA NAP 500 A 1 HETATM 2 O O1A NAP . . . B 2 43.194 43.086 1.366 1 15.17 ? O1A NAP 500 A 1 HETATM 3 O O2A NAP . . . B 2 40.966 44.38 1.393 1 15.79 ? O2A NAP 500 A 1 HETATM 4 O O5B NAP . . . B 2 42.387 44.221 3.519 1 18.56 ? O5B NAP 500 A 1 HETATM 5 C C5B NAP . . . B 2 43.39 43.599 4.325 1 15.52 ? C5B NAP 500 A 1 HETATM 6 C C4B NAP . . . B 2 43.725 44.484 5.525 1 20.89 ? C4B NAP 500 A 1 HETATM 7 O O4B NAP . . . B 2 44.722 43.81 6.313 1 20.9 ? O4B NAP 500 A 1 HETATM 8 C C3B NAP . . . B 2 44.344 45.804 5.055 1 20.66 ? C3B NAP 500 A 1 HETATM 9 O O3B NAP . . . B 2 43.845 46.884 5.849 1 24.78 ? O3B NAP 500 A 1 HETATM 10 C C2B NAP . . . B 2 45.829 45.59 5.343 1 19.79 ? C2B NAP 500 A 1 HETATM 11 O O2B NAP . . . B 2 46.442 46.847 5.639 1 21.54 ? O2B NAP 500 A 1 HETATM 12 C C1B NAP . . . B 2 45.691 44.812 6.651 1 17.35 ? C1B NAP 500 A 1 HETATM 13 N N9A NAP . . . B 2 46.984 44.194 7.019 1 23.6 ? N9A NAP 500 A 1 HETATM 14 C C8A NAP . . . B 2 47.616 43.245 6.332 1 19.38 ? C8A NAP 500 A 1 HETATM 15 N N7A NAP . . . B 2 48.765 42.95 6.936 1 21.9 ? N7A NAP 500 A 1 HETATM 16 C C5A NAP . . . B 2 48.865 43.717 8.017 1 15.59 ? C5A NAP 500 A 1 HETATM 17 C C6A NAP . . . B 2 49.828 43.873 9.006 1 24.31 ? C6A NAP 500 A 1 HETATM 18 N N6A NAP . . . B 2 50.938 43.14 8.987 1 15.51 ? N6A NAP 500 A 1 HETATM 19 N N1A NAP . . . B 2 49.621 44.776 9.975 1 20.22 ? N1A NAP 500 A 1 HETATM 20 C C2A NAP . . . B 2 48.522 45.51 9.999 1 22.83 ? C2A NAP 500 A 1 HETATM 21 N N3A NAP . . . B 2 47.586 45.39 9.075 1 12.63 ? N3A NAP 500 A 1 HETATM 22 C C4A NAP . . . B 2 47.728 44.509 8.075 1 20.19 ? C4A NAP 500 A 1 HETATM 23 O O3 NAP . . . B 2 41.195 42.114 2.631 1 16.51 ? O3 NAP 500 A 1 HETATM 24 P PN NAP . . . B 2 39.657 41.993 3.094 1 19.25 ? PN NAP 500 A 1 HETATM 25 O O1N NAP . . . B 2 38.867 41.384 1.999 1 18.87 ? O1N NAP 500 A 1 HETATM 26 O O2N NAP . . . B 2 39.197 43.277 3.668 1 19.76 ? O2N NAP 500 A 1 HETATM 27 O O5D NAP . . . B 2 39.726 40.898 4.273 1 18.99 ? O5D NAP 500 A 1 HETATM 28 C C5D NAP . . . B 2 39.55 41.28 5.64 1 18.84 ? C5D NAP 500 A 1 HETATM 29 C C4D NAP . . . B 2 39.508 40.054 6.557 1 15.42 ? C4D NAP 500 A 1 HETATM 30 O O4D NAP . . . B 2 38.425 39.222 6.096 1 17.45 ? O4D NAP 500 A 1 HETATM 31 C C3D NAP . . . B 2 40.781 39.218 6.406 1 17.59 ? C3D NAP 500 A 1 HETATM 32 O O3D NAP . . . B 2 41.027 38.439 7.58 1 19.98 ? O3D NAP 500 A 1 HETATM 33 C C2D NAP . . . B 2 40.4 38.305 5.244 1 18.43 ? C2D NAP 500 A 1 HETATM 34 O O2D NAP . . . B 2 41.192 37.114 5.234 1 18.66 ? O2D NAP 500 A 1 HETATM 35 C C1D NAP . . . B 2 38.981 37.959 5.691 1 15.66 ? C1D NAP 500 A 1 HETATM 36 N N1N NAP . . . B 2 38.182 37.301 4.633 1 18.11 ? N1N NAP 500 A 1 HETATM 37 C C2N NAP . . . B 2 38.051 37.903 3.375 1 16.99 ? C2N NAP 500 A 1 HETATM 38 C C3N NAP . . . B 2 37.303 37.278 2.384 1 20.84 ? C3N NAP 500 A 1 HETATM 39 C C7N NAP . . . B 2 37.152 37.937 1.011 1 26.68 ? C7N NAP 500 A 1 HETATM 40 O O7N NAP . . . B 2 36.653 37.327 0.067 1 22.87 ? O7N NAP 500 A 1 HETATM 41 N N7N NAP . . . B 2 37.606 39.185 0.935 1 13.22 ? N7N NAP 500 A 1 HETATM 42 C C4N NAP . . . B 2 36.688 36.058 2.641 1 25.48 ? C4N NAP 500 A 1 HETATM 43 C C5N NAP . . . B 2 36.814 35.457 3.889 1 28.51 ? C5N NAP 500 A 1 HETATM 44 C C6N NAP . . . B 2 37.559 36.073 4.887 1 23.26 ? C6N NAP 500 A 1 HETATM 45 P P2B NAP . . . B 2 47.129 47.751 4.496 1 34.07 ? P2B NAP 500 A 1 HETATM 46 O O1X NAP . . . B 2 46.212 47.646 3.177 1 30.57 ? O1X NAP 500 A 1 HETATM 47 O O2X NAP . . . B 2 46.996 49.265 5.03 1 29.87 ? O2X NAP 500 A 1 HETATM 48 O O3X NAP . . . B 2 48.534 47.363 4.238 1 35.27 ? O3X NAP 500 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #