data_2RK2 # _model_server_result.job_id aL6ZK9EnpvzNHNiQaLtOLA _model_server_result.datetime_utc '2024-11-05 01:54:46' _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 2rk2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 2RK2 # _exptl.entry_id 2RK2 _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 90 _cell.entry_id 2RK2 _cell.length_a 67.52 _cell.length_b 67.52 _cell.length_c 52.07 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RK2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2,3,4 # 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' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 10_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 4 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 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 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 258 n n PA O2A NAP sing 259 n n PA O5B NAP sing 260 n n PA O3 NAP sing 261 n n O2A HOA2 NAP sing 262 n n O5B C5B NAP sing 263 n n C5B C4B NAP sing 264 n n C5B H51A NAP sing 265 n n C5B H52A NAP sing 266 n n C4B O4B NAP sing 267 n n C4B C3B NAP sing 268 n n C4B H4B NAP sing 269 n n O4B C1B NAP sing 270 n n C3B O3B NAP sing 271 n n C3B C2B NAP sing 272 n n C3B H3B NAP sing 273 n n O3B HO3A NAP sing 274 n n C2B O2B NAP sing 275 n n C2B C1B NAP sing 276 n n C2B H2B NAP sing 277 n n O2B P2B NAP sing 278 n n C1B N9A NAP sing 279 n n C1B H1B NAP sing 280 n n N9A C8A NAP sing 281 n y N9A C4A NAP sing 282 n y C8A N7A NAP doub 283 n y C8A H8A NAP sing 284 n n N7A C5A NAP sing 285 n y C5A C6A NAP sing 286 n y C5A C4A NAP doub 287 n y C6A N6A NAP sing 288 n n C6A N1A NAP doub 289 n y N6A H61A NAP sing 290 n n N6A H62A NAP sing 291 n n N1A C2A NAP sing 292 n y C2A N3A NAP doub 293 n y C2A H2A NAP sing 294 n n N3A C4A NAP sing 295 n y O3 PN NAP sing 296 n n PN O1N NAP doub 297 n n PN O2N NAP sing 298 n n PN O5D NAP sing 299 n n O5D C5D NAP sing 300 n n C5D C4D NAP sing 301 n n C5D H51N NAP sing 302 n n C5D H52N NAP sing 303 n n C4D O4D NAP sing 304 n n C4D C3D NAP sing 305 n n C4D H4D NAP sing 306 n n O4D C1D NAP sing 307 n n C3D O3D NAP sing 308 n n C3D C2D NAP sing 309 n n C3D H3D NAP sing 310 n n O3D HO3N NAP sing 311 n n C2D O2D NAP sing 312 n n C2D C1D NAP sing 313 n n C2D H2D NAP sing 314 n n O2D HO2N NAP sing 315 n n C1D N1N NAP sing 316 n n C1D H1D NAP sing 317 n n N1N C2N NAP sing 318 n y N1N C6N NAP doub 319 n y C2N C3N NAP doub 320 n y C2N H2N NAP sing 321 n n C3N C7N NAP sing 322 n n C3N C4N NAP sing 323 n y C7N O7N NAP doub 324 n n C7N N7N NAP sing 325 n n N7N H71N NAP sing 326 n n N7N H72N NAP sing 327 n n C4N C5N NAP doub 328 n y C4N H4N NAP sing 329 n n C5N C6N NAP sing 330 n y C5N H5N NAP sing 331 n n C6N H6N NAP sing 332 n n P2B O1X NAP doub 333 n n P2B O2X NAP sing 334 n n P2B O3X NAP sing 335 n n O2X HOP2 NAP sing 336 n n O3X HOP3 NAP sing 337 n n # _atom_sites.entry_id 2RK2 _atom_sites.fract_transf_matrix[1][1] 0.01481 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01481 _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] 0.019205 _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 1 1 NAP NAP . C 3 MRD A 1 500 500 MRD MRD . D 3 MRD A 1 501 501 MRD MRD . E 3 MRD A 1 502 502 MRD MRD . F 4 HOH A 1 503 503 HOH HOH . F 4 HOH A 2 504 504 HOH HOH . F 4 HOH A 3 505 505 HOH HOH . F 4 HOH A 4 506 506 HOH HOH . F 4 HOH A 5 507 507 HOH HOH . F 4 HOH A 6 508 508 HOH HOH . F 4 HOH A 7 509 509 HOH HOH . F 4 HOH A 8 510 510 HOH HOH . F 4 HOH A 9 511 511 HOH HOH . F 4 HOH A 10 512 512 HOH HOH . F 4 HOH A 11 513 513 HOH HOH . F 4 HOH A 12 514 514 HOH HOH . F 4 HOH A 13 515 515 HOH HOH . F 4 HOH A 14 516 516 HOH HOH . F 4 HOH A 15 517 517 HOH HOH . F 4 HOH A 16 518 518 HOH HOH . F 4 HOH A 17 519 519 HOH HOH . F 4 HOH A 18 520 520 HOH HOH . F 4 HOH A 19 521 521 HOH HOH . F 4 HOH A 20 522 522 HOH HOH . F 4 HOH A 21 523 523 HOH HOH . F 4 HOH A 22 524 524 HOH HOH . F 4 HOH A 23 525 525 HOH HOH . F 4 HOH A 24 526 526 HOH HOH . F 4 HOH A 25 527 527 HOH HOH . F 4 HOH A 26 528 528 HOH HOH . F 4 HOH A 27 529 529 HOH HOH . F 4 HOH A 28 530 530 HOH HOH . F 4 HOH A 29 531 531 HOH HOH . F 4 HOH A 30 532 532 HOH HOH . F 4 HOH A 31 533 533 HOH HOH . F 4 HOH A 32 534 534 HOH HOH . F 4 HOH A 33 535 535 HOH HOH . F 4 HOH A 34 536 536 HOH HOH . F 4 HOH A 35 537 537 HOH HOH . F 4 HOH A 36 538 538 HOH HOH . F 4 HOH A 37 539 539 HOH HOH . F 4 HOH A 38 540 540 HOH HOH . F 4 HOH A 39 541 541 HOH HOH . F 4 HOH A 40 542 542 HOH HOH . F 4 HOH A 41 543 543 HOH HOH . F 4 HOH A 42 544 544 HOH HOH . F 4 HOH A 43 545 545 HOH HOH . F 4 HOH A 44 546 546 HOH HOH . F 4 HOH A 45 547 547 HOH HOH . F 4 HOH A 46 548 548 HOH HOH . F 4 HOH A 47 549 549 HOH HOH . F 4 HOH A 48 550 550 HOH HOH . F 4 HOH A 49 551 551 HOH HOH . F 4 HOH A 50 552 552 HOH HOH . F 4 HOH A 51 553 553 HOH HOH . F 4 HOH A 52 554 554 HOH HOH . F 4 HOH A 53 555 555 HOH HOH . F 4 HOH A 54 556 556 HOH HOH . F 4 HOH A 55 557 557 HOH HOH . F 4 HOH A 56 558 558 HOH HOH . F 4 HOH A 57 559 559 HOH HOH . F 4 HOH A 58 560 560 HOH HOH . F 4 HOH A 59 561 561 HOH HOH . F 4 HOH A 60 562 562 HOH HOH . F 4 HOH A 61 563 563 HOH HOH . F 4 HOH A 62 564 564 HOH HOH . F 4 HOH A 63 565 565 HOH HOH . F 4 HOH A 64 566 566 HOH HOH . F 4 HOH A 65 567 567 HOH HOH . F 4 HOH A 66 568 568 HOH HOH . F 4 HOH A 67 569 569 HOH HOH . F 4 HOH A 68 570 570 HOH HOH . F 4 HOH A 69 571 571 HOH HOH . F 4 HOH A 70 572 572 HOH HOH . F 4 HOH A 71 573 573 HOH HOH . F 4 HOH A 72 574 574 HOH HOH . F 4 HOH A 73 575 575 HOH HOH . F 4 HOH A 74 576 576 HOH HOH . F 4 HOH A 75 577 577 HOH HOH . F 4 HOH A 76 578 578 HOH HOH . F 4 HOH A 77 579 579 HOH HOH . F 4 HOH A 78 580 580 HOH HOH . F 4 HOH A 79 581 581 HOH HOH . F 4 HOH A 80 582 582 HOH HOH . F 4 HOH A 81 583 583 HOH HOH . F 4 HOH A 82 584 584 HOH HOH . F 4 HOH A 83 585 585 HOH HOH . F 4 HOH A 84 586 586 HOH HOH . F 4 HOH A 85 587 587 HOH HOH . F 4 HOH A 86 588 588 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 . A . B 2 8.431 -5.903 -4.014 0.25 18.37 ? PA NAP 1 A 1 HETATM 2 O O1A NAP . A . B 2 7.292 -4.999 -4.483 0.25 10.95 ? O1A NAP 1 A 1 HETATM 3 O O2A NAP . A . B 2 9.683 -6.149 -4.829 0.25 18.67 ? O2A NAP 1 A 1 HETATM 4 O O5B NAP . A . B 2 7.791 -7.355 -3.686 0.25 14.8 ? O5B NAP 1 A 1 HETATM 5 C C5B NAP . A . B 2 6.44 -7.356 -3.244 0.25 11.88 ? C5B NAP 1 A 1 HETATM 6 C C4B NAP . A . B 2 6.099 -8.581 -2.43 0.25 12.59 ? C4B NAP 1 A 1 HETATM 7 O O4B NAP . A . B 2 5.8 -9.662 -3.324 0.25 11.42 ? O4B NAP 1 A 1 HETATM 8 C C3B NAP . A . B 2 7.233 -9.046 -1.533 0.25 13.69 ? C3B NAP 1 A 1 HETATM 9 O O3B NAP . A . B 2 7.164 -8.454 -0.22 0.25 13.51 ? O3B NAP 1 A 1 HETATM 10 C C2B NAP . A . B 2 6.928 -10.514 -1.518 0.25 13.45 ? C2B NAP 1 A 1 HETATM 11 O O2B NAP . A . B 2 5.599 -10.597 -1.113 0.25 14.66 ? O2B NAP 1 A 1 HETATM 12 C C1B NAP . A . B 2 6.529 -10.822 -2.917 0.25 14.64 ? C1B NAP 1 A 1 HETATM 13 N N9A NAP . A . B 2 7.685 -11.08 -3.79 0.25 15.05 ? N9A NAP 1 A 1 HETATM 14 C C8A NAP . A . B 2 8.528 -10.211 -4.372 0.25 14.83 ? C8A NAP 1 A 1 HETATM 15 N N7A NAP . A . B 2 9.406 -10.937 -5.111 0.25 15.52 ? N7A NAP 1 A 1 HETATM 16 C C5A NAP . A . B 2 9.086 -12.252 -4.982 0.25 15.64 ? C5A NAP 1 A 1 HETATM 17 C C6A NAP . A . B 2 9.57 -13.444 -5.487 0.25 15.5 ? C6A NAP 1 A 1 HETATM 18 N N6A NAP . A . B 2 10.642 -13.487 -6.301 0.25 14.91 ? N6A NAP 1 A 1 HETATM 19 N N1A NAP . A . B 2 8.986 -14.602 -5.134 0.25 16.83 ? N1A NAP 1 A 1 HETATM 20 C C2A NAP . A . B 2 7.932 -14.625 -4.326 0.25 15.53 ? C2A NAP 1 A 1 HETATM 21 N N3A NAP . A . B 2 7.425 -13.502 -3.838 0.25 15.98 ? N3A NAP 1 A 1 HETATM 22 C C4A NAP . A . B 2 7.998 -12.316 -4.147 0.25 16.67 ? C4A NAP 1 A 1 HETATM 23 O O3 NAP . A . B 2 8.862 -5.593 -2.492 0.25 14.16 ? O3 NAP 1 A 1 HETATM 24 P PN NAP . A . B 2 9.632 -4.247 -2.071 0.25 10.29 ? PN NAP 1 A 1 HETATM 25 O O1N NAP . A . B 2 10.95 -4.254 -2.841 0.25 7.98 ? O1N NAP 1 A 1 HETATM 26 O O2N NAP . A . B 2 9.564 -4.142 -0.554 0.25 9.67 ? O2N NAP 1 A 1 HETATM 27 O O5D NAP . A . B 2 8.616 -3.173 -2.609 0.25 8.56 ? O5D NAP 1 A 1 HETATM 28 C C5D NAP . A . B 2 7.603 -2.649 -1.746 0.25 9.61 ? C5D NAP 1 A 1 HETATM 29 C C4D NAP . A . B 2 6.615 -2.016 -2.709 0.25 7.17 ? C4D NAP 1 A 1 HETATM 30 O O4D NAP . A . B 2 5.269 -2.118 -2.243 0.25 9.87 ? O4D NAP 1 A 1 HETATM 31 C C3D NAP . A . B 2 6.963 -0.568 -2.954 0.25 6.35 ? C3D NAP 1 A 1 HETATM 32 O O3D NAP . A . B 2 6.866 -0.366 -4.379 0.25 1 ? O3D NAP 1 A 1 HETATM 33 C C2D NAP . A . B 2 5.902 0.059 -2.049 0.25 7.21 ? C2D NAP 1 A 1 HETATM 34 O O2D NAP . A . B 2 5.689 1.504 -2.112 0.25 2.49 ? O2D NAP 1 A 1 HETATM 35 C C1D NAP . A . B 2 4.66 -0.84 -2.243 0.25 8.12 ? C1D NAP 1 A 1 HETATM 36 N N1N NAP . A . B 2 3.764 -0.55 -1.129 0.25 5.9 ? N1N NAP 1 A 1 HETATM 37 C C2N NAP . A . B 2 4.078 -0.93 0.103 0.25 6.56 ? C2N NAP 1 A 1 HETATM 38 C C3N NAP . A . B 2 3.258 -0.546 1.141 0.25 5.29 ? C3N NAP 1 A 1 HETATM 39 C C7N NAP . A . B 2 3.617 -0.95 2.538 0.25 5.35 ? C7N NAP 1 A 1 HETATM 40 O O7N NAP . A . B 2 2.935 -0.534 3.427 0.25 1 ? O7N NAP 1 A 1 HETATM 41 N N7N NAP . A . B 2 4.728 -1.677 2.742 0.25 4.23 ? N7N NAP 1 A 1 HETATM 42 C C4N NAP . A . B 2 2.116 0.201 0.906 0.25 6.78 ? C4N NAP 1 A 1 HETATM 43 C C5N NAP . A . B 2 1.78 0.555 -0.39 0.25 2.84 ? C5N NAP 1 A 1 HETATM 44 C C6N NAP . A . B 2 2.671 0.184 -1.383 0.25 6.94 ? C6N NAP 1 A 1 HETATM 45 P P2B NAP . A . B 2 5.24 -11.321 0.252 0.25 17.69 ? P2B NAP 1 A 1 HETATM 46 O O1X NAP . A . B 2 6.298 -12.41 0.378 0.25 18.46 ? O1X NAP 1 A 1 HETATM 47 O O2X NAP . A . B 2 5.406 -10.151 1.194 0.25 16.08 ? O2X NAP 1 A 1 HETATM 48 O O3X NAP . A . B 2 3.821 -11.804 0.082 0.25 16.22 ? O3X NAP 1 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 48 #