data_3RTD # _model_server_result.job_id ms6HAI_NgtSBEikUlPnE9A _model_server_result.datetime_utc '2024-10-19 03:45:14' _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 3rtd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":495}' # _entry.id 3RTD # _exptl.entry_id 3RTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 683.456 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' _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 3RTD _cell.length_a 121.81 _cell.length_b 121.81 _cell.length_c 155.221 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RTD _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 6 'crystal symmetry operation' 6_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 7 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _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 metalc ? metalc1 A OD1 ASN 64 A ASN 52 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc2 A O ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc3 A OD2 ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.466 ? metalc ? metalc4 A O PHE 129 A PHE 117 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc5 A O VAL 158 A VAL 146 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc6 A O VAL 160 A VAL 148 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc7 A OG SER 162 A SER 150 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.919 ? metalc ? metalc8 D MG MG . A MG 492 1_555 F O1A ADP . A ADP 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc9 D MG MG . A MG 492 1_555 F O1B ADP . A ADP 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc10 D MG MG . A MG 492 1_555 H O HOH . A HOH 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc11 D MG MG . A MG 492 1_555 H O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc12 D MG MG . A MG 492 1_555 H O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? # _chem_comp.formula 'C21 H31 N7 O15 P2' _chem_comp.formula_weight 683.456 _chem_comp.id NAX _chem_comp.mon_nstd_flag . _chem_comp.name 'BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 NAX doub 358 n n PA O2A NAX sing 359 n n PA O5B NAX sing 360 n n PA O3 NAX sing 361 n n O2A HOA2 NAX sing 362 n n O5B C5B NAX sing 363 n n C5B C4B NAX sing 364 n n C5B H51A NAX sing 365 n n C5B H52A NAX sing 366 n n C4B O4B NAX sing 367 n n C4B C3B NAX sing 368 n n C4B H4B NAX sing 369 n n O4B C1B NAX sing 370 n n C3B O3B NAX sing 371 n n C3B C2B NAX sing 372 n n C3B H3B NAX sing 373 n n O3B HO3A NAX sing 374 n n C2B O2B NAX sing 375 n n C2B C1B NAX sing 376 n n C2B H2B NAX sing 377 n n O2B HO2A NAX sing 378 n n C1B N9A NAX sing 379 n n C1B H1B NAX sing 380 n n N9A C8A NAX sing 381 n y N9A C4A NAX sing 382 n y C8A N7A NAX doub 383 n y C8A H8A NAX sing 384 n n N7A C5A NAX sing 385 n y C5A C6A NAX sing 386 n y C5A C4A NAX doub 387 n y C6A N6A NAX sing 388 n n C6A N1A NAX doub 389 n y N6A H61A NAX sing 390 n n N6A H62A NAX sing 391 n n N1A C2A NAX sing 392 n y C2A N3A NAX doub 393 n y C2A H2A NAX sing 394 n n N3A C4A NAX sing 395 n y O3 PN NAX sing 396 n n PN O1N NAX doub 397 n n PN O2N NAX sing 398 n n PN O5D NAX sing 399 n n O2N HNO2 NAX sing 400 n n O5D C5D NAX sing 401 n n C5D C4D NAX sing 402 n n C5D "H5'1" NAX sing 403 n n C5D "H5'2" NAX sing 404 n n C4D O4D NAX sing 405 n n C4D C3D NAX sing 406 n n C4D H4D NAX sing 407 n n O4D C1D NAX sing 408 n n C3D O3D NAX sing 409 n n C3D C2D NAX sing 410 n n C3D H3D NAX sing 411 n n O3D HO3N NAX sing 412 n n C2D O2D NAX sing 413 n n C2D C1D NAX sing 414 n n C2D H2D NAX sing 415 n n O2D HO2N NAX sing 416 n n C1D N1N NAX sing 417 n n C1D H1D NAX sing 418 n n N1N C2N NAX sing 419 n n N1N C6N NAX sing 420 n n C2N C3N NAX doub 421 n n C2N H2N NAX sing 422 n n C3N C7N NAX sing 423 n n C3N C4N NAX sing 424 n n C7N O7N NAX doub 425 n n C7N N7N NAX sing 426 n n N7N H71N NAX sing 427 n n N7N H72N NAX sing 428 n n C4N C5N NAX sing 429 n n C4N H41N NAX sing 430 n n C4N H42N NAX sing 431 n n C5N C6N NAX sing 432 n n C5N H51N NAX sing 433 n n C5N H52N NAX sing 434 n n C6N O6N NAX sing 435 n n C6N H6N NAX sing 436 n n O6N HO6N NAX sing 437 n n # _atom_sites.entry_id 3RTD _atom_sites.fract_transf_matrix[1][1] 0.00821 _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] 0.00821 _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] 0.006442 _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 3 K A 1 491 491 K K . D 4 MG A 1 492 492 MG MG . E 5 NAI A 1 493 493 NAI NAI . F 6 ADP A 1 494 494 ADP ADP . G 7 NAX A 1 495 495 NAX NAX . H 8 HOH A 1 496 496 HOH HOH . H 8 HOH A 2 497 497 HOH HOH . H 8 HOH A 3 498 498 HOH HOH . H 8 HOH A 4 499 499 HOH HOH . H 8 HOH A 5 500 500 HOH HOH . H 8 HOH A 6 501 501 HOH HOH . H 8 HOH A 7 502 502 HOH HOH . H 8 HOH A 8 503 503 HOH HOH . H 8 HOH A 9 504 504 HOH HOH . H 8 HOH A 10 505 505 HOH HOH . H 8 HOH A 11 506 506 HOH HOH . H 8 HOH A 12 507 507 HOH HOH . H 8 HOH A 13 508 508 HOH HOH . H 8 HOH A 14 509 509 HOH HOH . H 8 HOH A 15 510 510 HOH HOH . H 8 HOH A 16 511 511 HOH HOH . H 8 HOH A 17 512 512 HOH HOH . H 8 HOH A 18 513 513 HOH HOH . H 8 HOH A 19 514 514 HOH HOH . H 8 HOH A 20 515 515 HOH HOH . H 8 HOH A 21 516 516 HOH HOH . H 8 HOH A 22 517 517 HOH HOH . H 8 HOH A 23 518 518 HOH HOH . H 8 HOH A 24 519 519 HOH HOH . H 8 HOH A 25 520 520 HOH HOH . H 8 HOH A 26 521 521 HOH HOH . H 8 HOH A 27 522 522 HOH HOH . H 8 HOH A 28 523 523 HOH HOH . H 8 HOH A 29 524 524 HOH HOH . H 8 HOH A 30 525 525 HOH HOH . H 8 HOH A 31 526 526 HOH HOH . H 8 HOH A 32 527 527 HOH HOH . H 8 HOH A 33 528 528 HOH HOH . H 8 HOH A 34 529 529 HOH HOH . H 8 HOH A 35 530 530 HOH HOH . H 8 HOH A 36 531 531 HOH HOH . H 8 HOH A 37 532 532 HOH HOH . H 8 HOH A 38 533 533 HOH HOH . H 8 HOH A 39 534 534 HOH HOH . H 8 HOH A 40 535 535 HOH HOH . H 8 HOH A 41 536 536 HOH HOH . H 8 HOH A 42 537 537 HOH HOH . H 8 HOH A 43 538 538 HOH HOH . H 8 HOH A 44 539 539 HOH HOH . H 8 HOH A 45 540 540 HOH HOH . H 8 HOH A 46 541 541 HOH HOH . H 8 HOH A 47 542 542 HOH HOH . H 8 HOH A 48 543 543 HOH HOH . H 8 HOH A 49 544 544 HOH HOH . H 8 HOH A 50 545 545 HOH HOH . H 8 HOH A 51 546 546 HOH HOH . H 8 HOH A 52 547 547 HOH HOH . H 8 HOH A 53 548 548 HOH HOH . H 8 HOH A 54 549 549 HOH HOH . H 8 HOH A 55 550 550 HOH HOH . H 8 HOH A 56 551 551 HOH HOH . H 8 HOH A 57 552 552 HOH HOH . H 8 HOH A 58 553 553 HOH HOH . H 8 HOH A 59 554 554 HOH HOH . H 8 HOH A 60 555 555 HOH HOH . H 8 HOH A 61 556 556 HOH HOH . H 8 HOH A 62 557 557 HOH HOH . H 8 HOH A 63 558 558 HOH HOH . H 8 HOH A 64 559 559 HOH HOH . H 8 HOH A 65 560 560 HOH HOH . H 8 HOH A 66 561 561 HOH HOH . H 8 HOH A 67 562 562 HOH HOH . H 8 HOH A 68 563 563 HOH HOH . H 8 HOH A 69 564 564 HOH HOH . H 8 HOH A 70 565 565 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 NAX . . . G 7 -8.06 25.762 47.818 1 44.11 ? PA NAX 495 A 1 HETATM 2 O O1A NAX . . . G 7 -8.625 25.9 49.195 1 46.05 ? O1A NAX 495 A 1 HETATM 3 O O2A NAX . . . G 7 -6.527 25.956 47.744 1 41.26 ? O2A NAX 495 A 1 HETATM 4 O O5B NAX . . . G 7 -8.842 26.696 46.816 1 48.63 ? O5B NAX 495 A 1 HETATM 5 C C5B NAX . . . G 7 -9.791 27.651 47.292 1 57.12 ? C5B NAX 495 A 1 HETATM 6 C C4B NAX . . . G 7 -11.089 27.554 46.493 1 60.61 ? C4B NAX 495 A 1 HETATM 7 O O4B NAX . . . G 7 -10.918 28.186 45.236 1 60.97 ? O4B NAX 495 A 1 HETATM 8 C C3B NAX . . . G 7 -11.547 26.131 46.197 1 63.96 ? C3B NAX 495 A 1 HETATM 9 O O3B NAX . . . G 7 -12.601 25.814 47.113 1 67.38 ? O3B NAX 495 A 1 HETATM 10 C C2B NAX . . . G 7 -12.093 26.155 44.79 1 65.56 ? C2B NAX 495 A 1 HETATM 11 O O2B NAX . . . G 7 -13.539 26.102 44.697 1 69.87 ? O2B NAX 495 A 1 HETATM 12 C C1B NAX . . . G 7 -11.7 27.517 44.261 1 64.01 ? C1B NAX 495 A 1 HETATM 13 N N9A NAX . . . G 7 -10.967 27.359 43.003 1 65.04 ? N9A NAX 495 A 1 HETATM 14 C C8A NAX . . . G 7 -10.139 26.347 42.643 1 65.33 ? C8A NAX 495 A 1 HETATM 15 N N7A NAX . . . G 7 -9.655 26.567 41.399 1 64.18 ? N7A NAX 495 A 1 HETATM 16 C C5A NAX . . . G 7 -10.189 27.714 40.972 1 62.84 ? C5A NAX 495 A 1 HETATM 17 C C6A NAX . . . G 7 -10.107 28.481 39.757 1 62.97 ? C6A NAX 495 A 1 HETATM 18 N N6A NAX . . . G 7 -9.32 28.034 38.766 1 63.82 ? N6A NAX 495 A 1 HETATM 19 N N1A NAX . . . G 7 -10.827 29.612 39.667 1 65.89 ? N1A NAX 495 A 1 HETATM 20 C C2A NAX . . . G 7 -11.603 30.039 40.677 1 66.37 ? C2A NAX 495 A 1 HETATM 21 N N3A NAX . . . G 7 -11.72 29.381 41.833 1 65.87 ? N3A NAX 495 A 1 HETATM 22 C C4A NAX . . . G 7 -11.048 28.236 42.019 1 64.54 ? C4A NAX 495 A 1 HETATM 23 O O3 NAX . . . G 7 -8.663 24.395 47.259 1 40.9 ? O3 NAX 495 A 1 HETATM 24 P PN NAX . . . G 7 -7.967 23.316 46.294 1 35.7 ? PN NAX 495 A 1 HETATM 25 O O1N NAX . . . G 7 -7.552 23.949 44.986 1 35.65 ? O1N NAX 495 A 1 HETATM 26 O O2N NAX . . . G 7 -9.047 22.284 46.198 1 36.25 ? O2N NAX 495 A 1 HETATM 27 O O5D NAX . . . G 7 -6.69 22.777 47.091 1 37.29 ? O5D NAX 495 A 1 HETATM 28 C C5D NAX . . . G 7 -6.788 22.313 48.452 1 35.4 ? C5D NAX 495 A 1 HETATM 29 C C4D NAX . . . G 7 -5.752 21.202 48.706 1 34.14 ? C4D NAX 495 A 1 HETATM 30 O O4D NAX . . . G 7 -6.114 19.996 47.947 1 33.95 ? O4D NAX 495 A 1 HETATM 31 C C3D NAX . . . G 7 -4.329 21.572 48.272 1 32.57 ? C3D NAX 495 A 1 HETATM 32 O O3D NAX . . . G 7 -3.387 21.19 49.312 1 31.75 ? O3D NAX 495 A 1 HETATM 33 C C2D NAX . . . G 7 -4.092 20.741 46.986 1 31.54 ? C2D NAX 495 A 1 HETATM 34 O O2D NAX . . . G 7 -2.711 20.356 46.762 1 29.65 ? O2D NAX 495 A 1 HETATM 35 C C1D NAX . . . G 7 -4.917 19.515 47.344 1 28.69 ? C1D NAX 495 A 1 HETATM 36 N N1N NAX . . . G 7 -5.223 18.659 46.236 1 31.85 ? N1N NAX 495 A 1 HETATM 37 C C2N NAX . . . G 7 -5.052 17.386 46.468 1 31.39 ? C2N NAX 495 A 1 HETATM 38 C C3N NAX . . . G 7 -5.221 16.426 45.544 1 30.51 ? C3N NAX 495 A 1 HETATM 39 C C7N NAX . . . G 7 -4.778 15.037 45.81 1 29.62 ? C7N NAX 495 A 1 HETATM 40 O O7N NAX . . . G 7 -4.23 14.712 46.858 1 30.21 ? O7N NAX 495 A 1 HETATM 41 N N7N NAX . . . G 7 -4.941 14.107 44.872 1 32.31 ? N7N NAX 495 A 1 HETATM 42 C C4N NAX . . . G 7 -5.818 16.829 44.206 1 28.86 ? C4N NAX 495 A 1 HETATM 43 C C5N NAX . . . G 7 -6.535 18.206 44.345 1 28.8 ? C5N NAX 495 A 1 HETATM 44 C C6N NAX . . . G 7 -5.628 19.223 44.942 1 29.87 ? C6N NAX 495 A 1 HETATM 45 O O6N NAX . . . G 7 -4.399 19.381 44.18 1 28.67 ? O6N NAX 495 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 45 #