data_2YVJ # _model_server_result.job_id nzHp8J8_BIEp5KMvUxnVwQ _model_server_result.datetime_utc '2024-11-27 20:05:20' _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 2yvj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":503}' # _entry.id 2YVJ # _exptl.entry_id 2YVJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 665.441 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' _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 115.81 _cell.angle_gamma 90 _cell.entry_id 2YVJ _cell.length_a 60.596 _cell.length_b 173.715 _cell.length_c 60.976 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YVJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,J,K _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 ? 4 E N N ? 4 H N 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 metalc ? metalc1 B SG CYS 43 B CYS 43 1_555 F FE1 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc2 B ND1 HIS 45 B HIS 45 1_555 F FE2 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc3 B SG CYS 63 B CYS 63 1_555 F FE1 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? metalc ? metalc4 B ND1 HIS 66 B HIS 66 1_555 F FE2 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.659 ? # _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 332 n n PA O2A NAI sing 333 n n PA O5B NAI sing 334 n n PA O3 NAI sing 335 n n O2A HOA2 NAI sing 336 n n O5B C5B NAI sing 337 n n C5B C4B NAI sing 338 n n C5B H51A NAI sing 339 n n C5B H52A NAI sing 340 n n C4B O4B NAI sing 341 n n C4B C3B NAI sing 342 n n C4B H4B NAI sing 343 n n O4B C1B NAI sing 344 n n C3B O3B NAI sing 345 n n C3B C2B NAI sing 346 n n C3B H3B NAI sing 347 n n O3B HO3A NAI sing 348 n n C2B O2B NAI sing 349 n n C2B C1B NAI sing 350 n n C2B H2B NAI sing 351 n n O2B HO2A NAI sing 352 n n C1B N9A NAI sing 353 n n C1B H1B NAI sing 354 n n N9A C8A NAI sing 355 n y N9A C4A NAI sing 356 n y C8A N7A NAI doub 357 n y C8A H8A NAI sing 358 n n N7A C5A NAI sing 359 n y C5A C6A NAI sing 360 n y C5A C4A NAI doub 361 n y C6A N6A NAI sing 362 n n C6A N1A NAI doub 363 n y N6A H61A NAI sing 364 n n N6A H62A NAI sing 365 n n N1A C2A NAI sing 366 n y C2A N3A NAI doub 367 n y C2A H2A NAI sing 368 n n N3A C4A NAI sing 369 n y O3 PN NAI sing 370 n n PN O1N NAI sing 371 n n PN O2N NAI doub 372 n n PN O5D NAI sing 373 n n O1N HO1N NAI sing 374 n n O5D C5D NAI sing 375 n n C5D C4D NAI sing 376 n n C5D H51N NAI sing 377 n n C5D H52N NAI sing 378 n n C4D O4D NAI sing 379 n n C4D C3D NAI sing 380 n n C4D H4D NAI sing 381 n n O4D C1D NAI sing 382 n n C3D O3D NAI sing 383 n n C3D C2D NAI sing 384 n n C3D H3D NAI sing 385 n n O3D HO3N NAI sing 386 n n C2D O2D NAI sing 387 n n C2D C1D NAI sing 388 n n C2D H2D NAI sing 389 n n O2D HO2N NAI sing 390 n n C1D N1N NAI sing 391 n n C1D H1D NAI sing 392 n n N1N C2N NAI sing 393 n n N1N C6N NAI sing 394 n n C2N C3N NAI doub 395 n n C2N H2N NAI sing 396 n n C3N C7N NAI sing 397 n n C3N C4N NAI sing 398 n n C7N O7N NAI doub 399 n n C7N N7N NAI sing 400 n n N7N H71N NAI sing 401 n n N7N H72N NAI sing 402 n n C4N C5N NAI sing 403 n n C4N H4N NAI sing 404 n n C4N H42N NAI sing 405 n n C5N C6N NAI doub 406 n n C5N H5N NAI sing 407 n n C6N H6N NAI sing 408 n n # _atom_sites.entry_id 2YVJ _atom_sites.fract_transf_matrix[1][1] 0.016503 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007981 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005757 _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] 0.018217 _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 D 3 FAD A 1 501 501 FAD FAD . E 4 NAI A 1 503 503 NAI NAI . F 5 FES B 1 500 500 FES FES . G 3 FAD P 1 502 502 FAD FAD . H 4 NAI P 1 504 504 NAI NAI . I 6 HOH A 1 504 1 HOH HOH . I 6 HOH A 2 505 2 HOH HOH . I 6 HOH A 3 506 3 HOH HOH . I 6 HOH A 4 507 4 HOH HOH . I 6 HOH A 5 508 7 HOH HOH . I 6 HOH A 6 509 10 HOH HOH . I 6 HOH A 7 510 11 HOH HOH . I 6 HOH A 8 511 13 HOH HOH . I 6 HOH A 9 512 16 HOH HOH . I 6 HOH A 10 513 19 HOH HOH . I 6 HOH A 11 514 21 HOH HOH . I 6 HOH A 12 515 24 HOH HOH . I 6 HOH A 13 516 25 HOH HOH . I 6 HOH A 14 517 28 HOH HOH . I 6 HOH A 15 518 31 HOH HOH . I 6 HOH A 16 519 33 HOH HOH . I 6 HOH A 17 520 43 HOH HOH . I 6 HOH A 18 521 44 HOH HOH . I 6 HOH A 19 522 46 HOH HOH . I 6 HOH A 20 523 50 HOH HOH . I 6 HOH A 21 524 51 HOH HOH . I 6 HOH A 22 525 52 HOH HOH . I 6 HOH A 23 526 54 HOH HOH . I 6 HOH A 24 527 55 HOH HOH . I 6 HOH A 25 528 57 HOH HOH . I 6 HOH A 26 529 60 HOH HOH . I 6 HOH A 27 530 61 HOH HOH . I 6 HOH A 28 531 62 HOH HOH . I 6 HOH A 29 532 66 HOH HOH . I 6 HOH A 30 533 68 HOH HOH . I 6 HOH A 31 534 70 HOH HOH . I 6 HOH A 32 535 77 HOH HOH . J 6 HOH B 1 501 5 HOH HOH . J 6 HOH B 2 502 56 HOH HOH . J 6 HOH B 3 503 64 HOH HOH . J 6 HOH B 4 504 78 HOH HOH . K 6 HOH P 1 505 6 HOH HOH . K 6 HOH P 2 506 8 HOH HOH . K 6 HOH P 3 507 9 HOH HOH . K 6 HOH P 4 508 12 HOH HOH . K 6 HOH P 5 509 14 HOH HOH . K 6 HOH P 6 510 15 HOH HOH . K 6 HOH P 7 511 17 HOH HOH . K 6 HOH P 8 512 18 HOH HOH . K 6 HOH P 9 513 20 HOH HOH . K 6 HOH P 10 514 22 HOH HOH . K 6 HOH P 11 515 23 HOH HOH . K 6 HOH P 12 516 26 HOH HOH . K 6 HOH P 13 517 27 HOH HOH . K 6 HOH P 14 518 29 HOH HOH . K 6 HOH P 15 519 30 HOH HOH . K 6 HOH P 16 520 32 HOH HOH . K 6 HOH P 17 521 34 HOH HOH . K 6 HOH P 18 522 35 HOH HOH . K 6 HOH P 19 523 36 HOH HOH . K 6 HOH P 20 524 37 HOH HOH . K 6 HOH P 21 525 38 HOH HOH . K 6 HOH P 22 526 39 HOH HOH . K 6 HOH P 23 527 40 HOH HOH . K 6 HOH P 24 528 41 HOH HOH . K 6 HOH P 25 529 42 HOH HOH . K 6 HOH P 26 530 45 HOH HOH . K 6 HOH P 27 531 47 HOH HOH . K 6 HOH P 28 532 48 HOH HOH . K 6 HOH P 29 533 49 HOH HOH . K 6 HOH P 30 534 53 HOH HOH . K 6 HOH P 31 535 58 HOH HOH . K 6 HOH P 32 536 59 HOH HOH . K 6 HOH P 33 537 63 HOH HOH . K 6 HOH P 34 538 65 HOH HOH . K 6 HOH P 35 539 67 HOH HOH . K 6 HOH P 36 540 69 HOH HOH . K 6 HOH P 37 541 71 HOH HOH . K 6 HOH P 38 542 72 HOH HOH . K 6 HOH P 39 543 73 HOH HOH . K 6 HOH P 40 544 74 HOH HOH . K 6 HOH P 41 545 75 HOH HOH . K 6 HOH P 42 546 76 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 . . . E 4 -2.945 -17.867 24.544 1 36.71 ? PA NAI 503 A 1 HETATM 2 O O1A NAI . . . E 4 -2.318 -16.58 24.919 1 27.72 ? O1A NAI 503 A 1 HETATM 3 O O2A NAI . . . E 4 -3.596 -17.871 23.178 1 42.85 ? O2A NAI 503 A 1 HETATM 4 O O5B NAI . . . E 4 -4.018 -18.241 25.671 1 49.98 ? O5B NAI 503 A 1 HETATM 5 C C5B NAI . . . E 4 -3.672 -18.451 27.02 1 51 ? C5B NAI 503 A 1 HETATM 6 C C4B NAI . . . E 4 -5.006 -18.48 27.79 1 58.48 ? C4B NAI 503 A 1 HETATM 7 O O4B NAI . . . E 4 -4.824 -18.952 29.118 1 61.36 ? O4B NAI 503 A 1 HETATM 8 C C3B NAI . . . E 4 -5.671 -17.106 27.903 1 50.09 ? C3B NAI 503 A 1 HETATM 9 O O3B NAI . . . E 4 -7.058 -17.251 27.632 1 73.12 ? O3B NAI 503 A 1 HETATM 10 C C2B NAI . . . E 4 -5.435 -16.695 29.346 1 43.11 ? C2B NAI 503 A 1 HETATM 11 O O2B NAI . . . E 4 -6.427 -15.828 29.872 1 61.35 ? O2B NAI 503 A 1 HETATM 12 C C1B NAI . . . E 4 -5.425 -18.033 30.045 1 42.26 ? C1B NAI 503 A 1 HETATM 13 N N9A NAI . . . E 4 -4.609 -18.114 31.269 1 40.76 ? N9A NAI 503 A 1 HETATM 14 C C8A NAI . . . E 4 -3.548 -17.316 31.627 1 28.68 ? C8A NAI 503 A 1 HETATM 15 N N7A NAI . . . E 4 -3.086 -17.747 32.827 1 31.77 ? N7A NAI 503 A 1 HETATM 16 C C5A NAI . . . E 4 -3.849 -18.782 33.244 1 37.75 ? C5A NAI 503 A 1 HETATM 17 C C6A NAI . . . E 4 -3.772 -19.622 34.355 1 43.37 ? C6A NAI 503 A 1 HETATM 18 N N6A NAI . . . E 4 -2.873 -19.359 35.298 1 61.54 ? N6A NAI 503 A 1 HETATM 19 N N1A NAI . . . E 4 -4.677 -20.666 34.497 1 44.36 ? N1A NAI 503 A 1 HETATM 20 C C2A NAI . . . E 4 -5.705 -20.819 33.575 1 41.88 ? C2A NAI 503 A 1 HETATM 21 N N3A NAI . . . E 4 -5.756 -20.004 32.453 1 44.5 ? N3A NAI 503 A 1 HETATM 22 C C4A NAI . . . E 4 -4.826 -19.019 32.276 1 40.35 ? C4A NAI 503 A 1 HETATM 23 O O3 NAI . . . E 4 -1.753 -18.971 24.728 1 28.93 ? O3 NAI 503 A 1 HETATM 24 P PN NAI . . . E 4 -1.653 -20.517 24.273 1 39.51 ? PN NAI 503 A 1 HETATM 25 O O1N NAI . . . E 4 -2.992 -20.973 23.869 1 67.92 ? O1N NAI 503 A 1 HETATM 26 O O2N NAI . . . E 4 -0.84 -21.199 25.351 1 48.05 ? O2N NAI 503 A 1 HETATM 27 O O5D NAI . . . E 4 -0.777 -20.45 22.907 1 44.69 ? O5D NAI 503 A 1 HETATM 28 C C5D NAI . . . E 4 0.635 -20.37 22.987 1 48.5 ? C5D NAI 503 A 1 HETATM 29 C C4D NAI . . . E 4 1.219 -19.824 21.691 1 63.95 ? C4D NAI 503 A 1 HETATM 30 O O4D NAI . . . E 4 0.887 -20.655 20.587 1 68.77 ? O4D NAI 503 A 1 HETATM 31 C C3D NAI . . . E 4 0.63 -18.46 21.387 1 71.56 ? C3D NAI 503 A 1 HETATM 32 O O3D NAI . . . E 4 1.647 -17.623 20.9 1 98.38 ? O3D NAI 503 A 1 HETATM 33 C C2D NAI . . . E 4 -0.376 -18.759 20.29 1 70.7 ? C2D NAI 503 A 1 HETATM 34 O O2D NAI . . . E 4 -0.596 -17.645 19.449 1 81.44 ? O2D NAI 503 A 1 HETATM 35 C C1D NAI . . . E 4 0.236 -19.953 19.558 1 65.72 ? C1D NAI 503 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #