data_4YVP # _model_server_result.job_id Dw9KHZGLInKQLKXmmKhK4w _model_server_result.datetime_utc '2024-11-07 08:32:53' _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 4yvp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 4YVP # _exptl.entry_id 4YVP _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.88 _cell.angle_gamma 90 _cell.entry_id 4YVP _cell.length_a 49.545 _cell.length_b 76.168 _cell.length_c 88.706 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YVP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 ? 2 C N N ? 2 E N 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 300 n n PA O2A NAP sing 301 n n PA O5B NAP sing 302 n n PA O3 NAP sing 303 n n O2A HOA2 NAP sing 304 n n O5B C5B NAP sing 305 n n C5B C4B NAP sing 306 n n C5B H51A NAP sing 307 n n C5B H52A NAP sing 308 n n C4B O4B NAP sing 309 n n C4B C3B NAP sing 310 n n C4B H4B NAP sing 311 n n O4B C1B NAP sing 312 n n C3B O3B NAP sing 313 n n C3B C2B NAP sing 314 n n C3B H3B NAP sing 315 n n O3B HO3A NAP sing 316 n n C2B O2B NAP sing 317 n n C2B C1B NAP sing 318 n n C2B H2B NAP sing 319 n n O2B P2B NAP sing 320 n n C1B N9A NAP sing 321 n n C1B H1B NAP sing 322 n n N9A C8A NAP sing 323 n y N9A C4A NAP sing 324 n y C8A N7A NAP doub 325 n y C8A H8A NAP sing 326 n n N7A C5A NAP sing 327 n y C5A C6A NAP sing 328 n y C5A C4A NAP doub 329 n y C6A N6A NAP sing 330 n n C6A N1A NAP doub 331 n y N6A H61A NAP sing 332 n n N6A H62A NAP sing 333 n n N1A C2A NAP sing 334 n y C2A N3A NAP doub 335 n y C2A H2A NAP sing 336 n n N3A C4A NAP sing 337 n y O3 PN NAP sing 338 n n PN O1N NAP doub 339 n n PN O2N NAP sing 340 n n PN O5D NAP sing 341 n n O5D C5D NAP sing 342 n n C5D C4D NAP sing 343 n n C5D H51N NAP sing 344 n n C5D H52N NAP sing 345 n n C4D O4D NAP sing 346 n n C4D C3D NAP sing 347 n n C4D H4D NAP sing 348 n n O4D C1D NAP sing 349 n n C3D O3D NAP sing 350 n n C3D C2D NAP sing 351 n n C3D H3D NAP sing 352 n n O3D HO3N NAP sing 353 n n C2D O2D NAP sing 354 n n C2D C1D NAP sing 355 n n C2D H2D NAP sing 356 n n O2D HO2N NAP sing 357 n n C1D N1N NAP sing 358 n n C1D H1D NAP sing 359 n n N1N C2N NAP sing 360 n y N1N C6N NAP doub 361 n y C2N C3N NAP doub 362 n y C2N H2N NAP sing 363 n n C3N C7N NAP sing 364 n n C3N C4N NAP sing 365 n y C7N O7N NAP doub 366 n n C7N N7N NAP sing 367 n n N7N H71N NAP sing 368 n n N7N H72N NAP sing 369 n n C4N C5N NAP doub 370 n y C4N H4N NAP sing 371 n n C5N C6N NAP sing 372 n y C5N H5N NAP sing 373 n n C6N H6N NAP sing 374 n n P2B O1X NAP doub 375 n n P2B O2X NAP sing 376 n n P2B O3X NAP sing 377 n n O2X HOP2 NAP sing 378 n n O3X HOP3 NAP sing 379 n n # _atom_sites.entry_id 4YVP _atom_sites.fract_transf_matrix[1][1] 0.020184 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001723 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013129 _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] 0.011314 _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 NAP A 1 401 1 NAP NAP . D 3 GBM A 1 402 1 GBM GBM . E 2 NAP B 1 401 2 NAP NAP . F 3 GBM B 1 402 2 GBM GBM . G 4 HOH A 1 501 136 HOH HOH . G 4 HOH A 2 502 28 HOH HOH . G 4 HOH A 3 503 126 HOH HOH . G 4 HOH A 4 504 41 HOH HOH . G 4 HOH A 5 505 50 HOH HOH . G 4 HOH A 6 506 129 HOH HOH . G 4 HOH A 7 507 79 HOH HOH . G 4 HOH A 8 508 104 HOH HOH . G 4 HOH A 9 509 66 HOH HOH . G 4 HOH A 10 510 17 HOH HOH . G 4 HOH A 11 511 25 HOH HOH . G 4 HOH A 12 512 113 HOH HOH . G 4 HOH A 13 513 87 HOH HOH . G 4 HOH A 14 514 68 HOH HOH . G 4 HOH A 15 515 23 HOH HOH . G 4 HOH A 16 516 31 HOH HOH . G 4 HOH A 17 517 36 HOH HOH . G 4 HOH A 18 518 91 HOH HOH . G 4 HOH A 19 519 76 HOH HOH . G 4 HOH A 20 520 7 HOH HOH . G 4 HOH A 21 521 3 HOH HOH . G 4 HOH A 22 522 80 HOH HOH . G 4 HOH A 23 523 88 HOH HOH . G 4 HOH A 24 524 116 HOH HOH . G 4 HOH A 25 525 1 HOH HOH . G 4 HOH A 26 526 11 HOH HOH . G 4 HOH A 27 527 18 HOH HOH . G 4 HOH A 28 528 98 HOH HOH . G 4 HOH A 29 529 121 HOH HOH . G 4 HOH A 30 530 125 HOH HOH . G 4 HOH A 31 531 27 HOH HOH . G 4 HOH A 32 532 44 HOH HOH . G 4 HOH A 33 533 24 HOH HOH . G 4 HOH A 34 534 131 HOH HOH . G 4 HOH A 35 535 118 HOH HOH . G 4 HOH A 36 536 43 HOH HOH . G 4 HOH A 37 537 10 HOH HOH . G 4 HOH A 38 538 53 HOH HOH . G 4 HOH A 39 539 55 HOH HOH . G 4 HOH A 40 540 106 HOH HOH . G 4 HOH A 41 541 59 HOH HOH . G 4 HOH A 42 542 117 HOH HOH . G 4 HOH A 43 543 51 HOH HOH . G 4 HOH A 44 544 77 HOH HOH . G 4 HOH A 45 545 48 HOH HOH . G 4 HOH A 46 546 92 HOH HOH . G 4 HOH A 47 547 94 HOH HOH . G 4 HOH A 48 548 97 HOH HOH . G 4 HOH A 49 549 111 HOH HOH . G 4 HOH A 50 550 60 HOH HOH . G 4 HOH A 51 551 100 HOH HOH . G 4 HOH A 52 552 63 HOH HOH . G 4 HOH A 53 553 14 HOH HOH . G 4 HOH A 54 554 86 HOH HOH . G 4 HOH A 55 555 90 HOH HOH . G 4 HOH A 56 556 39 HOH HOH . G 4 HOH A 57 557 13 HOH HOH . G 4 HOH A 58 558 67 HOH HOH . G 4 HOH A 59 559 62 HOH HOH . G 4 HOH A 60 560 42 HOH HOH . G 4 HOH A 61 561 89 HOH HOH . G 4 HOH A 62 562 12 HOH HOH . G 4 HOH A 63 563 52 HOH HOH . G 4 HOH A 64 564 124 HOH HOH . G 4 HOH A 65 565 70 HOH HOH . G 4 HOH A 66 566 105 HOH HOH . G 4 HOH A 67 567 119 HOH HOH . G 4 HOH A 68 568 133 HOH HOH . G 4 HOH A 69 569 135 HOH HOH . G 4 HOH A 70 570 93 HOH HOH . G 4 HOH A 71 571 110 HOH HOH . H 4 HOH B 1 501 78 HOH HOH . H 4 HOH B 2 502 56 HOH HOH . H 4 HOH B 3 503 81 HOH HOH . H 4 HOH B 4 504 95 HOH HOH . H 4 HOH B 5 505 8 HOH HOH . H 4 HOH B 6 506 26 HOH HOH . H 4 HOH B 7 507 130 HOH HOH . H 4 HOH B 8 508 34 HOH HOH . H 4 HOH B 9 509 73 HOH HOH . H 4 HOH B 10 510 102 HOH HOH . H 4 HOH B 11 511 96 HOH HOH . H 4 HOH B 12 512 35 HOH HOH . H 4 HOH B 13 513 75 HOH HOH . H 4 HOH B 14 514 32 HOH HOH . H 4 HOH B 15 515 109 HOH HOH . H 4 HOH B 16 516 85 HOH HOH . H 4 HOH B 17 517 29 HOH HOH . H 4 HOH B 18 518 33 HOH HOH . H 4 HOH B 19 519 83 HOH HOH . H 4 HOH B 20 520 6 HOH HOH . H 4 HOH B 21 521 49 HOH HOH . H 4 HOH B 22 522 84 HOH HOH . H 4 HOH B 23 523 64 HOH HOH . H 4 HOH B 24 524 15 HOH HOH . H 4 HOH B 25 525 4 HOH HOH . H 4 HOH B 26 526 71 HOH HOH . H 4 HOH B 27 527 107 HOH HOH . H 4 HOH B 28 528 22 HOH HOH . H 4 HOH B 29 529 19 HOH HOH . H 4 HOH B 30 530 30 HOH HOH . H 4 HOH B 31 531 114 HOH HOH . H 4 HOH B 32 532 127 HOH HOH . H 4 HOH B 33 533 9 HOH HOH . H 4 HOH B 34 534 122 HOH HOH . H 4 HOH B 35 535 5 HOH HOH . H 4 HOH B 36 536 38 HOH HOH . H 4 HOH B 37 537 2 HOH HOH . H 4 HOH B 38 538 37 HOH HOH . H 4 HOH B 39 539 128 HOH HOH . H 4 HOH B 40 540 16 HOH HOH . H 4 HOH B 41 541 120 HOH HOH . H 4 HOH B 42 542 46 HOH HOH . H 4 HOH B 43 543 82 HOH HOH . H 4 HOH B 44 544 45 HOH HOH . H 4 HOH B 45 545 69 HOH HOH . H 4 HOH B 46 546 21 HOH HOH . H 4 HOH B 47 547 101 HOH HOH . H 4 HOH B 48 548 134 HOH HOH . H 4 HOH B 49 549 123 HOH HOH . H 4 HOH B 50 550 40 HOH HOH . H 4 HOH B 51 551 108 HOH HOH . H 4 HOH B 52 552 112 HOH HOH . H 4 HOH B 53 553 20 HOH HOH . H 4 HOH B 54 554 99 HOH HOH . H 4 HOH B 55 555 65 HOH HOH . H 4 HOH B 56 556 115 HOH HOH . H 4 HOH B 57 557 132 HOH HOH . H 4 HOH B 58 558 57 HOH HOH . H 4 HOH B 59 559 47 HOH HOH . H 4 HOH B 60 560 72 HOH HOH . H 4 HOH B 61 561 54 HOH HOH . H 4 HOH B 62 562 58 HOH HOH . H 4 HOH B 63 563 74 HOH HOH . H 4 HOH B 64 564 61 HOH HOH . H 4 HOH B 65 565 103 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 . . . E 2 -62.773 -9.501 2.354 1 9.69 ? PA NAP 401 B 1 HETATM 2 O O1A NAP . . . E 2 -62.206 -10.279 1.204 1 9.65 ? O1A NAP 401 B 1 HETATM 3 O O2A NAP . . . E 2 -63.342 -10.107 3.608 1 9.53 ? O2A NAP 401 B 1 HETATM 4 O O5B NAP . . . E 2 -61.676 -8.582 3.111 1 10.21 ? O5B NAP 401 B 1 HETATM 5 C C5B NAP . . . E 2 -61.114 -7.514 2.392 1 10.69 ? C5B NAP 401 B 1 HETATM 6 C C4B NAP . . . E 2 -60.302 -6.631 3.282 1 10.83 ? C4B NAP 401 B 1 HETATM 7 O O4B NAP . . . E 2 -59.073 -7.306 3.585 1 10.67 ? O4B NAP 401 B 1 HETATM 8 C C3B NAP . . . E 2 -59.96 -5.365 2.485 1 10.87 ? C3B NAP 401 B 1 HETATM 9 O O3B NAP . . . E 2 -60.089 -4.229 3.348 1 10.57 ? O3B NAP 401 B 1 HETATM 10 C C2B NAP . . . E 2 -58.528 -5.624 2.033 1 10.8 ? C2B NAP 401 B 1 HETATM 11 O O2B NAP . . . E 2 -57.83 -4.4 1.954 1 10.92 ? O2B NAP 401 B 1 HETATM 12 C C1B NAP . . . E 2 -57.971 -6.519 3.13 1 10.66 ? C1B NAP 401 B 1 HETATM 13 N N9A NAP . . . E 2 -56.928 -7.478 2.749 1 10.96 ? N9A NAP 401 B 1 HETATM 14 C C8A NAP . . . E 2 -56.937 -8.264 1.655 1 11.34 ? C8A NAP 401 B 1 HETATM 15 N N7A NAP . . . E 2 -55.854 -9.066 1.575 1 11.37 ? N7A NAP 401 B 1 HETATM 16 C C5A NAP . . . E 2 -55.122 -8.798 2.67 1 11.22 ? C5A NAP 401 B 1 HETATM 17 C C6A NAP . . . E 2 -53.843 -9.299 3.219 1 11.29 ? C6A NAP 401 B 1 HETATM 18 N N6A NAP . . . E 2 -53.149 -10.241 2.578 1 11.47 ? N6A NAP 401 B 1 HETATM 19 N N1A NAP . . . E 2 -53.389 -8.775 4.372 1 11.39 ? N1A NAP 401 B 1 HETATM 20 C C2A NAP . . . E 2 -54.1 -7.814 5.023 1 11.33 ? C2A NAP 401 B 1 HETATM 21 N N3A NAP . . . E 2 -55.283 -7.318 4.584 1 11.02 ? N3A NAP 401 B 1 HETATM 22 C C4A NAP . . . E 2 -55.836 -7.764 3.441 1 10.96 ? C4A NAP 401 B 1 HETATM 23 O O3 NAP . . . E 2 -63.623 -8.35 1.636 1 9.41 ? O3 NAP 401 B 1 HETATM 24 P PN NAP . . . E 2 -65.156 -8.304 1.282 1 8.93 ? PN NAP 401 B 1 HETATM 25 O O1N NAP . . . E 2 -65.268 -7.292 0.188 1 8.93 ? O1N NAP 401 B 1 HETATM 26 O O2N NAP . . . E 2 -65.933 -8.189 2.559 1 9 ? O2N NAP 401 B 1 HETATM 27 O O5D NAP . . . E 2 -65.33 -9.753 0.614 1 9.75 ? O5D NAP 401 B 1 HETATM 28 C C5D NAP . . . E 2 -64.73 -10.034 -0.659 1 10.01 ? C5D NAP 401 B 1 HETATM 29 C C4D NAP . . . E 2 -65.733 -10.1 -1.811 1 10.11 ? C4D NAP 401 B 1 HETATM 30 O O4D NAP . . . E 2 -66.833 -10.986 -1.592 1 10.28 ? O4D NAP 401 B 1 HETATM 31 C C3D NAP . . . E 2 -66.366 -8.77 -2.184 1 10.24 ? C3D NAP 401 B 1 HETATM 32 O O3D NAP . . . E 2 -65.436 -7.873 -2.804 1 9.75 ? O3D NAP 401 B 1 HETATM 33 C C2D NAP . . . E 2 -67.542 -9.255 -3.032 1 10.4 ? C2D NAP 401 B 1 HETATM 34 O O2D NAP . . . E 2 -67.125 -9.613 -4.354 1 10.59 ? O2D NAP 401 B 1 HETATM 35 C C1D NAP . . . E 2 -67.978 -10.532 -2.338 1 10.53 ? C1D NAP 401 B 1 HETATM 36 N N1N NAP . . . E 2 -69.116 -10.363 -1.402 1 11 ? N1N NAP 401 B 1 HETATM 37 C C2N NAP . . . E 2 -70.323 -10.902 -1.714 1 10.74 ? C2N NAP 401 B 1 HETATM 38 C C3N NAP . . . E 2 -71.422 -10.784 -0.856 1 10.95 ? C3N NAP 401 B 1 HETATM 39 C C7N NAP . . . E 2 -72.753 -11.425 -1.21 1 11.04 ? C7N NAP 401 B 1 HETATM 40 O O7N NAP . . . E 2 -72.815 -12.21 -2.157 1 11.43 ? O7N NAP 401 B 1 HETATM 41 N N7N NAP . . . E 2 -73.849 -11.258 -0.473 1 10.74 ? N7N NAP 401 B 1 HETATM 42 C C4N NAP . . . E 2 -71.227 -10.115 0.367 1 11.14 ? C4N NAP 401 B 1 HETATM 43 C C5N NAP . . . E 2 -69.977 -9.577 0.686 1 11.22 ? C5N NAP 401 B 1 HETATM 44 C C6N NAP . . . E 2 -68.924 -9.708 -0.214 1 11.11 ? C6N NAP 401 B 1 HETATM 45 P P2B NAP . . . E 2 -57.014 -4.006 0.638 1 11.59 ? P2B NAP 401 B 1 HETATM 46 O O1X NAP . . . E 2 -57.983 -4.003 -0.537 1 10.96 ? O1X NAP 401 B 1 HETATM 47 O O2X NAP . . . E 2 -56.444 -2.633 0.981 1 11.41 ? O2X NAP 401 B 1 HETATM 48 O O3X NAP . . . E 2 -55.94 -5.083 0.606 1 11.3 ? O3X NAP 401 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 48 #