data_3RTD # _model_server_result.job_id BvaT8qw84LDv6cjsBVEa_A _model_server_result.datetime_utc '2024-11-22 08:10:48' _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":"E","auth_seq_id":493}' # _entry.id 3RTD # _exptl.entry_id 3RTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 665.441 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,4-DIHYDRONICOTINAMIDE 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 5 _struct_asym.id E _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 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 281 n n PA O2A NAI sing 282 n n PA O5B NAI sing 283 n n PA O3 NAI sing 284 n n O2A HOA2 NAI sing 285 n n O5B C5B NAI sing 286 n n C5B C4B NAI sing 287 n n C5B H51A NAI sing 288 n n C5B H52A NAI sing 289 n n C4B O4B NAI sing 290 n n C4B C3B NAI sing 291 n n C4B H4B NAI sing 292 n n O4B C1B NAI sing 293 n n C3B O3B NAI sing 294 n n C3B C2B NAI sing 295 n n C3B H3B NAI sing 296 n n O3B HO3A NAI sing 297 n n C2B O2B NAI sing 298 n n C2B C1B NAI sing 299 n n C2B H2B NAI sing 300 n n O2B HO2A NAI sing 301 n n C1B N9A NAI sing 302 n n C1B H1B NAI sing 303 n n N9A C8A NAI sing 304 n y N9A C4A NAI sing 305 n y C8A N7A NAI doub 306 n y C8A H8A NAI sing 307 n n N7A C5A NAI sing 308 n y C5A C6A NAI sing 309 n y C5A C4A NAI doub 310 n y C6A N6A NAI sing 311 n n C6A N1A NAI doub 312 n y N6A H61A NAI sing 313 n n N6A H62A NAI sing 314 n n N1A C2A NAI sing 315 n y C2A N3A NAI doub 316 n y C2A H2A NAI sing 317 n n N3A C4A NAI sing 318 n y O3 PN NAI sing 319 n n PN O1N NAI sing 320 n n PN O2N NAI doub 321 n n PN O5D NAI sing 322 n n O1N HO1N NAI sing 323 n n O5D C5D NAI sing 324 n n C5D C4D NAI sing 325 n n C5D H51N NAI sing 326 n n C5D H52N NAI sing 327 n n C4D O4D NAI sing 328 n n C4D C3D NAI sing 329 n n C4D H4D NAI sing 330 n n O4D C1D NAI sing 331 n n C3D O3D NAI sing 332 n n C3D C2D NAI sing 333 n n C3D H3D NAI sing 334 n n O3D HO3N NAI sing 335 n n C2D O2D NAI sing 336 n n C2D C1D NAI sing 337 n n C2D H2D NAI sing 338 n n O2D HO2N NAI sing 339 n n C1D N1N NAI sing 340 n n C1D H1D NAI sing 341 n n N1N C2N NAI sing 342 n n N1N C6N NAI sing 343 n n C2N C3N NAI doub 344 n n C2N H2N NAI sing 345 n n C3N C7N NAI sing 346 n n C3N C4N NAI sing 347 n n C7N O7N NAI doub 348 n n C7N N7N NAI sing 349 n n N7N H71N NAI sing 350 n n N7N H72N NAI sing 351 n n C4N C5N NAI sing 352 n n C4N H4N NAI sing 353 n n C4N H42N NAI sing 354 n n C5N C6N NAI doub 355 n n C5N H5N NAI sing 356 n n C6N H6N NAI sing 357 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 NAI . . . E 5 -11.828 51.489 15.415 1 41.18 ? PA NAI 493 A 1 HETATM 2 O O1A NAI . . . E 5 -11.533 50.246 16.226 1 43.39 ? O1A NAI 493 A 1 HETATM 3 O O2A NAI . . . E 5 -12.116 51.486 13.905 1 42.06 ? O2A NAI 493 A 1 HETATM 4 O O5B NAI . . . E 5 -13.197 51.979 16.057 1 45.88 ? O5B NAI 493 A 1 HETATM 5 C C5B NAI . . . E 5 -13.41 53.373 16.213 1 48.86 ? C5B NAI 493 A 1 HETATM 6 C C4B NAI . . . E 5 -14.837 53.623 15.783 1 49.74 ? C4B NAI 493 A 1 HETATM 7 O O4B NAI . . . E 5 -15.753 52.981 16.647 1 46.64 ? O4B NAI 493 A 1 HETATM 8 C C3B NAI . . . E 5 -15.194 55.086 15.826 1 53.57 ? C3B NAI 493 A 1 HETATM 9 O O3B NAI . . . E 5 -15.944 55.311 14.603 1 53.25 ? O3B NAI 493 A 1 HETATM 10 C C2B NAI . . . E 5 -16.016 55.221 17.121 1 53.61 ? C2B NAI 493 A 1 HETATM 11 O O2B NAI . . . E 5 -16.977 56.274 17.091 1 51.63 ? O2B NAI 493 A 1 HETATM 12 C C1B NAI . . . E 5 -16.707 53.87 17.151 1 51.54 ? C1B NAI 493 A 1 HETATM 13 N N9A NAI . . . E 5 -16.993 53.318 18.499 1 54.17 ? N9A NAI 493 A 1 HETATM 14 C C8A NAI . . . E 5 -16.038 53.011 19.415 1 54 ? C8A NAI 493 A 1 HETATM 15 N N7A NAI . . . E 5 -16.614 52.478 20.521 1 54.25 ? N7A NAI 493 A 1 HETATM 16 C C5A NAI . . . E 5 -17.949 52.443 20.282 1 52.39 ? C5A NAI 493 A 1 HETATM 17 C C6A NAI . . . E 5 -19.11 52.029 21.074 1 52.06 ? C6A NAI 493 A 1 HETATM 18 N N6A NAI . . . E 5 -18.88 51.523 22.315 1 51.1 ? N6A NAI 493 A 1 HETATM 19 N N1A NAI . . . E 5 -20.325 52.15 20.505 1 50.96 ? N1A NAI 493 A 1 HETATM 20 C C2A NAI . . . E 5 -20.489 52.648 19.245 1 52.27 ? C2A NAI 493 A 1 HETATM 21 N N3A NAI . . . E 5 -19.47 53.069 18.474 1 49.41 ? N3A NAI 493 A 1 HETATM 22 C C4A NAI . . . E 5 -18.207 52.99 18.958 1 50.27 ? C4A NAI 493 A 1 HETATM 23 O O3 NAI . . . E 5 -10.794 52.562 15.967 1 41.1 ? O3 NAI 493 A 1 HETATM 24 P PN NAI . . . E 5 -9.634 53.217 15.13 1 39.54 ? PN NAI 493 A 1 HETATM 25 O O1N NAI . . . E 5 -8.628 53.553 16.132 1 34.08 ? O1N NAI 493 A 1 HETATM 26 O O2N NAI . . . E 5 -10.252 54.143 14.082 1 42.06 ? O2N NAI 493 A 1 HETATM 27 O O5D NAI . . . E 5 -8.994 51.981 14.307 1 42.54 ? O5D NAI 493 A 1 HETATM 28 C C5D NAI . . . E 5 -8.126 50.972 14.881 1 39.49 ? C5D NAI 493 A 1 HETATM 29 C C4D NAI . . . E 5 -8.169 49.805 13.887 1 41.4 ? C4D NAI 493 A 1 HETATM 30 O O4D NAI . . . E 5 -7.587 50.163 12.594 1 40.64 ? O4D NAI 493 A 1 HETATM 31 C C3D NAI . . . E 5 -7.403 48.576 14.382 1 38.91 ? C3D NAI 493 A 1 HETATM 32 O O3D NAI . . . E 5 -8.293 47.663 15.009 1 33.67 ? O3D NAI 493 A 1 HETATM 33 C C2D NAI . . . E 5 -6.859 48.033 13.072 1 40.53 ? C2D NAI 493 A 1 HETATM 34 O O2D NAI . . . E 5 -7.926 47.334 12.41 1 33.44 ? O2D NAI 493 A 1 HETATM 35 C C1D NAI . . . E 5 -6.512 49.288 12.272 1 41.19 ? C1D NAI 493 A 1 HETATM 36 N N1N NAI . . . E 5 -5.253 49.849 12.723 1 40.27 ? N1N NAI 493 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 36 #