data_6N1X # _model_server_result.job_id mMrl78KHORR6kyecIPSB_Q _model_server_result.datetime_utc '2024-11-15 15:19:54' _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 6n1x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6N1X # _exptl.entry_id 6N1X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 6N1X _cell.length_a 135.143 _cell.length_b 135.143 _cell.length_c 135.143 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6N1X _symmetry.cell_setting ? _symmetry.Int_Tables_number 195 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 3' # _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,D _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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 135.143 0 0 3 'crystal symmetry operation' 3_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 135.143 0 135.143 4 'crystal symmetry operation' 4_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 135.143 # _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 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 N1 C2 UDP sing 360 n n N1 C6 UDP sing 361 n n N1 C1' UDP sing 362 n n C2 N3 UDP sing 363 n n C2 O2 UDP doub 364 n n N3 C4 UDP sing 365 n n N3 HN3 UDP sing 366 n n C4 C5 UDP sing 367 n n C4 O4 UDP doub 368 n n C5 C6 UDP doub 369 n n C5 H5 UDP sing 370 n n C6 H6 UDP sing 371 n n C1' C2' UDP sing 372 n n C1' O4' UDP sing 373 n n C1' H1' UDP sing 374 n n C2' O2' UDP sing 375 n n C2' C3' UDP sing 376 n n C2' H2' UDP sing 377 n n O2' HO2' UDP sing 378 n n C3' C4' UDP sing 379 n n C3' O3' UDP sing 380 n n C3' H3' UDP sing 381 n n C4' O4' UDP sing 382 n n C4' C5' UDP sing 383 n n C4' H4' UDP sing 384 n n O3' HO3' UDP sing 385 n n C5' O5' UDP sing 386 n n C5' "H5'1" UDP sing 387 n n C5' "H5'2" UDP sing 388 n n O5' PA UDP sing 389 n n PA O1A UDP doub 390 n n PA O2A UDP sing 391 n n PA O3A UDP sing 392 n n O2A HOA2 UDP sing 393 n n O3A PB UDP sing 394 n n PB O1B UDP doub 395 n n PB O2B UDP sing 396 n n PB O3B UDP sing 397 n n O2B HOB2 UDP sing 398 n n O3B HOB3 UDP sing 399 n n # _atom_sites.entry_id 6N1X _atom_sites.fract_transf_matrix[1][1] 0.0074 _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] 0.0074 _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] 0.0074 _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 UDP A 1 401 1 UDP UDP . C 3 NDG A 1 402 1 NDG NDG . D 4 HOH A 1 501 38 HOH HOH . D 4 HOH A 2 502 26 HOH HOH . D 4 HOH A 3 503 14 HOH HOH . D 4 HOH A 4 504 28 HOH HOH . D 4 HOH A 5 505 39 HOH HOH . D 4 HOH A 6 506 47 HOH HOH . D 4 HOH A 7 507 8 HOH HOH . D 4 HOH A 8 508 6 HOH HOH . D 4 HOH A 9 509 33 HOH HOH . D 4 HOH A 10 510 54 HOH HOH . D 4 HOH A 11 511 42 HOH HOH . D 4 HOH A 12 512 1 HOH HOH . D 4 HOH A 13 513 23 HOH HOH . D 4 HOH A 14 514 59 HOH HOH . D 4 HOH A 15 515 21 HOH HOH . D 4 HOH A 16 516 9 HOH HOH . D 4 HOH A 17 517 52 HOH HOH . D 4 HOH A 18 518 17 HOH HOH . D 4 HOH A 19 519 4 HOH HOH . D 4 HOH A 20 520 62 HOH HOH . D 4 HOH A 21 521 3 HOH HOH . D 4 HOH A 22 522 53 HOH HOH . D 4 HOH A 23 523 15 HOH HOH . D 4 HOH A 24 524 12 HOH HOH . D 4 HOH A 25 525 31 HOH HOH . D 4 HOH A 26 526 2 HOH HOH . D 4 HOH A 27 527 16 HOH HOH . D 4 HOH A 28 528 71 HOH HOH . D 4 HOH A 29 529 5 HOH HOH . D 4 HOH A 30 530 70 HOH HOH . D 4 HOH A 31 531 40 HOH HOH . D 4 HOH A 32 532 10 HOH HOH . D 4 HOH A 33 533 44 HOH HOH . D 4 HOH A 34 534 20 HOH HOH . D 4 HOH A 35 535 7 HOH HOH . D 4 HOH A 36 536 48 HOH HOH . D 4 HOH A 37 537 41 HOH HOH . D 4 HOH A 38 538 58 HOH HOH . D 4 HOH A 39 539 29 HOH HOH . D 4 HOH A 40 540 37 HOH HOH . D 4 HOH A 41 541 72 HOH HOH . D 4 HOH A 42 542 30 HOH HOH . D 4 HOH A 43 543 25 HOH HOH . D 4 HOH A 44 544 27 HOH HOH . D 4 HOH A 45 545 22 HOH HOH . D 4 HOH A 46 546 34 HOH HOH . D 4 HOH A 47 547 63 HOH HOH . D 4 HOH A 48 548 43 HOH HOH . D 4 HOH A 49 549 35 HOH HOH . D 4 HOH A 50 550 50 HOH HOH . D 4 HOH A 51 551 66 HOH HOH . D 4 HOH A 52 552 18 HOH HOH . D 4 HOH A 53 553 68 HOH HOH . D 4 HOH A 54 554 51 HOH HOH . D 4 HOH A 55 555 11 HOH HOH . D 4 HOH A 56 556 64 HOH HOH . D 4 HOH A 57 557 67 HOH HOH . D 4 HOH A 58 558 32 HOH HOH . D 4 HOH A 59 559 73 HOH HOH . D 4 HOH A 60 560 36 HOH HOH . D 4 HOH A 61 561 61 HOH HOH . D 4 HOH A 62 562 46 HOH HOH . D 4 HOH A 63 563 69 HOH HOH . D 4 HOH A 64 564 19 HOH HOH . D 4 HOH A 65 565 24 HOH HOH . D 4 HOH A 66 566 13 HOH HOH . D 4 HOH A 67 567 55 HOH HOH . D 4 HOH A 68 568 60 HOH HOH . D 4 HOH A 69 569 49 HOH HOH . D 4 HOH A 70 570 57 HOH HOH . D 4 HOH A 71 571 45 HOH HOH . D 4 HOH A 72 572 56 HOH HOH . D 4 HOH A 73 573 65 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 N N1 UDP . . . B 2 55.978 -21.589 68.358 1 36.55 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . B 2 56.937 -22.419 68.936 1 34.44 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . B 2 57.108 -22.427 70.246 1 32.49 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . B 2 56.372 -21.66 71.028 1 36.45 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . B 2 55.411 -20.829 70.491 1 33.7 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . B 2 55.226 -20.813 69.124 1 35.32 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . B 2 57.63 -23.141 68.218 1 38.3 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . B 2 56.554 -21.69 72.248 1 38.67 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . B 2 55.819 -21.626 66.916 1 34.83 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . B 2 54.583 -22.407 66.556 1 36.4 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . B 2 54.812 -23.803 66.658 1 37.62 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . B 2 54.32 -21.932 65.152 1 35.64 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . B 2 54.804 -20.501 65.17 1 36.13 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . B 2 55.603 -20.356 66.338 1 39.15 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . B 2 55.129 -22.651 64.241 1 37.22 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . B 2 53.649 -19.524 65.214 1 32.21 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . B 2 52.982 -19.558 63.967 1 34.77 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . B 2 51.489 -19.069 63.798 1 30.67 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . B 2 51.218 -18.9 62.364 1 32.17 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . B 2 50.637 -19.968 64.597 1 34.06 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . B 2 51.469 -17.64 64.509 1 39.29 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . B 2 52.307 -16.308 64.203 1 35.73 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . B 2 52.902 -16.414 62.853 1 33.34 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . B 2 51.252 -15.285 64.304 1 36.78 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . B 2 53.302 -16.258 65.286 1 39.27 ? O3B UDP 401 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #