data_3M9V # _model_server_result.job_id Jp2Zn6NWbOsu0xvfAsOoSw _model_server_result.datetime_utc '2024-10-10 22:32:46' _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 3m9v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 3M9V # _exptl.entry_id 3M9V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-DIPHOSPHATE" _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 3M9V _cell.length_a 72.948 _cell.length_b 82.487 _cell.length_c 153.22 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3M9V _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _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 _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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 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 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 TYD doub 334 n n PA O2A TYD sing 335 n n PA O3A TYD sing 336 n n PA O5' TYD sing 337 n n O2A HOA2 TYD sing 338 n n O3A PB TYD sing 339 n n PB O1B TYD doub 340 n n PB O2B TYD sing 341 n n PB O3B TYD sing 342 n n O2B HOB2 TYD sing 343 n n O3B HOB3 TYD sing 344 n n O5' C5' TYD sing 345 n n C5' C4' TYD sing 346 n n C5' "H5'1" TYD sing 347 n n C5' "H5'2" TYD sing 348 n n C4' O4' TYD sing 349 n n C4' C3' TYD sing 350 n n C4' H4' TYD sing 351 n n O4' C1' TYD sing 352 n n C3' O3' TYD sing 353 n n C3' C2' TYD sing 354 n n C3' H3' TYD sing 355 n n O3' HO3' TYD sing 356 n n C2' C1' TYD sing 357 n n C2' "H2'1" TYD sing 358 n n C2' "H2'2" TYD sing 359 n n C1' N1 TYD sing 360 n n C1' H1' TYD sing 361 n n N1 C2 TYD sing 362 n y N1 C6 TYD sing 363 n y C2 O2 TYD doub 364 n n C2 N3 TYD sing 365 n y N3 C4 TYD sing 366 n y N3 HN3 TYD sing 367 n n C4 O4 TYD doub 368 n n C4 C5 TYD sing 369 n y C5 C5M TYD sing 370 n n C5 C6 TYD doub 371 n y C5M H51 TYD sing 372 n n C5M H52 TYD sing 373 n n C5M H53 TYD sing 374 n n C6 H6 TYD sing 375 n n # _atom_sites.entry_id 3M9V _atom_sites.fract_transf_matrix[1][1] 0.013708 _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] 0.012123 _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] 0.006527 _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 TYD A 1 901 901 TYD TYD . C 3 HOH A 1 438 1 HOH HOH . C 3 HOH A 2 439 2 HOH HOH . C 3 HOH A 3 440 3 HOH HOH . C 3 HOH A 4 441 4 HOH HOH . C 3 HOH A 5 442 5 HOH HOH . C 3 HOH A 6 443 6 HOH HOH . C 3 HOH A 7 444 7 HOH HOH . C 3 HOH A 8 445 8 HOH HOH . C 3 HOH A 9 446 9 HOH HOH . C 3 HOH A 10 447 10 HOH HOH . C 3 HOH A 11 448 11 HOH HOH . C 3 HOH A 12 449 12 HOH HOH . C 3 HOH A 13 450 13 HOH HOH . C 3 HOH A 14 451 14 HOH HOH . C 3 HOH A 15 452 15 HOH HOH . C 3 HOH A 16 453 16 HOH HOH . C 3 HOH A 17 454 17 HOH HOH . C 3 HOH A 18 455 19 HOH HOH . C 3 HOH A 19 456 20 HOH HOH . C 3 HOH A 20 457 21 HOH HOH . C 3 HOH A 21 458 22 HOH HOH . C 3 HOH A 22 459 23 HOH HOH . C 3 HOH A 23 460 24 HOH HOH . C 3 HOH A 24 461 25 HOH HOH . C 3 HOH A 25 462 26 HOH HOH . C 3 HOH A 26 463 27 HOH HOH . C 3 HOH A 27 464 28 HOH HOH . C 3 HOH A 28 465 29 HOH HOH . C 3 HOH A 29 466 30 HOH HOH . C 3 HOH A 30 467 31 HOH HOH . C 3 HOH A 31 468 32 HOH HOH . C 3 HOH A 32 469 33 HOH HOH . C 3 HOH A 33 470 34 HOH HOH . C 3 HOH A 34 471 35 HOH HOH . C 3 HOH A 35 472 36 HOH HOH . C 3 HOH A 36 473 37 HOH HOH . C 3 HOH A 37 474 39 HOH HOH . C 3 HOH A 38 475 40 HOH HOH . C 3 HOH A 39 476 41 HOH HOH . C 3 HOH A 40 477 42 HOH HOH . C 3 HOH A 41 478 43 HOH HOH . C 3 HOH A 42 479 44 HOH HOH . C 3 HOH A 43 480 45 HOH HOH . C 3 HOH A 44 481 46 HOH HOH . C 3 HOH A 45 482 48 HOH HOH . C 3 HOH A 46 483 49 HOH HOH . C 3 HOH A 47 484 50 HOH HOH . C 3 HOH A 48 485 51 HOH HOH . C 3 HOH A 49 486 53 HOH HOH . C 3 HOH A 50 487 54 HOH HOH . C 3 HOH A 51 488 55 HOH HOH . C 3 HOH A 52 489 57 HOH HOH . C 3 HOH A 53 490 58 HOH HOH . C 3 HOH A 54 491 59 HOH HOH . C 3 HOH A 55 492 60 HOH HOH . C 3 HOH A 56 493 61 HOH HOH . C 3 HOH A 57 494 64 HOH HOH . C 3 HOH A 58 495 65 HOH HOH . C 3 HOH A 59 496 66 HOH HOH . C 3 HOH A 60 497 67 HOH HOH . C 3 HOH A 61 498 68 HOH HOH . C 3 HOH A 62 499 70 HOH HOH . C 3 HOH A 63 500 73 HOH HOH . C 3 HOH A 64 501 75 HOH HOH . C 3 HOH A 65 502 76 HOH HOH . C 3 HOH A 66 503 77 HOH HOH . C 3 HOH A 67 504 78 HOH HOH . C 3 HOH A 68 505 79 HOH HOH . C 3 HOH A 69 506 80 HOH HOH . C 3 HOH A 70 507 83 HOH HOH . C 3 HOH A 71 508 84 HOH HOH . C 3 HOH A 72 509 85 HOH HOH . C 3 HOH A 73 510 86 HOH HOH . C 3 HOH A 74 511 91 HOH HOH . C 3 HOH A 75 512 92 HOH HOH . C 3 HOH A 76 513 93 HOH HOH . C 3 HOH A 77 514 95 HOH HOH . C 3 HOH A 78 515 96 HOH HOH . C 3 HOH A 79 516 99 HOH HOH . C 3 HOH A 80 517 101 HOH HOH . C 3 HOH A 81 518 102 HOH HOH . C 3 HOH A 82 519 103 HOH HOH . C 3 HOH A 83 520 104 HOH HOH . C 3 HOH A 84 521 105 HOH HOH . C 3 HOH A 85 522 106 HOH HOH . C 3 HOH A 86 523 107 HOH HOH . C 3 HOH A 87 524 108 HOH HOH . C 3 HOH A 88 525 110 HOH HOH . C 3 HOH A 89 526 111 HOH HOH . C 3 HOH A 90 527 113 HOH HOH . C 3 HOH A 91 528 114 HOH HOH . C 3 HOH A 92 529 115 HOH HOH . C 3 HOH A 93 530 116 HOH HOH . C 3 HOH A 94 531 119 HOH HOH . C 3 HOH A 95 532 120 HOH HOH . C 3 HOH A 96 533 122 HOH HOH . C 3 HOH A 97 534 125 HOH HOH . C 3 HOH A 98 535 130 HOH HOH . C 3 HOH A 99 536 132 HOH HOH . C 3 HOH A 100 537 135 HOH HOH . C 3 HOH A 101 538 140 HOH HOH . C 3 HOH A 102 539 141 HOH HOH . C 3 HOH A 103 540 145 HOH HOH . C 3 HOH A 104 541 146 HOH HOH . C 3 HOH A 105 542 150 HOH HOH . C 3 HOH A 106 543 151 HOH HOH . C 3 HOH A 107 544 152 HOH HOH . C 3 HOH A 108 545 153 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 TYD . . . B 2 19.777 23.283 -16.262 1 58.48 ? PA TYD 901 A 1 HETATM 2 O O1A TYD . . . B 2 20.269 23.096 -17.685 1 60.8 ? O1A TYD 901 A 1 HETATM 3 O O2A TYD . . . B 2 18.601 22.48 -15.735 1 62.4 ? O2A TYD 901 A 1 HETATM 4 O O3A TYD . . . B 2 21.015 23.129 -15.251 1 63.19 ? O3A TYD 901 A 1 HETATM 5 P PB TYD . . . B 2 22.303 22.331 -15.789 1 70.29 ? PB TYD 901 A 1 HETATM 6 O O1B TYD . . . B 2 21.709 21.169 -16.564 1 71.46 ? O1B TYD 901 A 1 HETATM 7 O O2B TYD . . . B 2 22.891 21.941 -14.448 1 71.57 ? O2B TYD 901 A 1 HETATM 8 O O3B TYD . . . B 2 23.04 23.391 -16.587 1 70.58 ? O3B TYD 901 A 1 HETATM 9 O O5' TYD . . . B 2 19.546 24.842 -15.919 1 55.06 ? O5' TYD 901 A 1 HETATM 10 C C5' TYD . . . B 2 20.604 25.798 -15.884 1 43.96 ? C5' TYD 901 A 1 HETATM 11 C C4' TYD . . . B 2 19.763 27.043 -16.131 1 41.6 ? C4' TYD 901 A 1 HETATM 12 O O4' TYD . . . B 2 18.953 27.338 -15 1 31.81 ? O4' TYD 901 A 1 HETATM 13 C C3' TYD . . . B 2 20.559 28.298 -16.435 1 38.68 ? C3' TYD 901 A 1 HETATM 14 O O3' TYD . . . B 2 20.19 28.542 -17.794 1 44.05 ? O3' TYD 901 A 1 HETATM 15 C C2' TYD . . . B 2 19.887 29.386 -15.612 1 37.02 ? C2' TYD 901 A 1 HETATM 16 C C1' TYD . . . B 2 18.705 28.742 -14.893 1 33.08 ? C1' TYD 901 A 1 HETATM 17 N N1 TYD . . . B 2 18.704 29.105 -13.469 1 26.06 ? N1 TYD 901 A 1 HETATM 18 C C2 TYD . . . B 2 17.606 29.591 -12.893 1 27.73 ? C2 TYD 901 A 1 HETATM 19 O O2 TYD . . . B 2 16.571 29.752 -13.583 1 26.9 ? O2 TYD 901 A 1 HETATM 20 N N3 TYD . . . B 2 17.632 29.921 -11.583 1 27.04 ? N3 TYD 901 A 1 HETATM 21 C C4 TYD . . . B 2 18.75 29.751 -10.839 1 29.74 ? C4 TYD 901 A 1 HETATM 22 O O4 TYD . . . B 2 18.743 30.062 -9.629 1 30.15 ? O4 TYD 901 A 1 HETATM 23 C C5 TYD . . . B 2 19.898 29.25 -11.428 1 28.48 ? C5 TYD 901 A 1 HETATM 24 C C5M TYD . . . B 2 21.194 29.036 -10.692 1 27.73 ? C5M TYD 901 A 1 HETATM 25 C C6 TYD . . . B 2 19.835 28.926 -12.776 1 29.04 ? C6 TYD 901 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #