data_6MW8 # _model_server_result.job_id dB_zTpDzyYtJJu7PcKMcXQ _model_server_result.datetime_utc '2025-04-23 06:38:46' _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 6mw8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6MW8 # _exptl.entry_id 6MW8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _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 6MW8 _cell.length_a 84.055 _cell.length_b 84.055 _cell.length_c 76.076 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MW8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 OD2 ASP 117 A ASP 117 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc2 A OD1 ASP 119 A ASP 119 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc3 A OD2 ASP 119 A ASP 119 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc4 A NE2 HIS 231 A HIS 231 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc5 B MN MN . A MN 301 1_555 C O3B UDP . A UDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc6 B MN MN . A MN 301 1_555 C O1A UDP . A UDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? # _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 373 n n N1 C6 UDP sing 374 n n N1 C1' UDP sing 375 n n C2 N3 UDP sing 376 n n C2 O2 UDP doub 377 n n N3 C4 UDP sing 378 n n N3 HN3 UDP sing 379 n n C4 C5 UDP sing 380 n n C4 O4 UDP doub 381 n n C5 C6 UDP doub 382 n n C5 H5 UDP sing 383 n n C6 H6 UDP sing 384 n n C1' C2' UDP sing 385 n n C1' O4' UDP sing 386 n n C1' H1' UDP sing 387 n n C2' O2' UDP sing 388 n n C2' C3' UDP sing 389 n n C2' H2' UDP sing 390 n n O2' HO2' UDP sing 391 n n C3' C4' UDP sing 392 n n C3' O3' UDP sing 393 n n C3' H3' UDP sing 394 n n C4' O4' UDP sing 395 n n C4' C5' UDP sing 396 n n C4' H4' UDP sing 397 n n O3' HO3' UDP sing 398 n n C5' O5' UDP sing 399 n n C5' "H5'1" UDP sing 400 n n C5' "H5'2" UDP sing 401 n n O5' PA UDP sing 402 n n PA O1A UDP doub 403 n n PA O2A UDP sing 404 n n PA O3A UDP sing 405 n n O2A HOA2 UDP sing 406 n n O3A PB UDP sing 407 n n PB O1B UDP doub 408 n n PB O2B UDP sing 409 n n PB O3B UDP sing 410 n n O2B HOB2 UDP sing 411 n n O3B HOB3 UDP sing 412 n n # _atom_sites.entry_id 6MW8 _atom_sites.fract_transf_matrix[1][1] 0.011897 _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] 0.011897 _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] 0.013145 _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 MN A 1 301 301 MN MN . C 3 UDP A 1 302 302 UDP UDP . D 4 ACT A 1 303 303 ACT ACT . E 4 ACT A 1 304 304 ACT ACT . F 4 ACT A 1 305 305 ACT ACT . G 5 EDO A 1 306 306 EDO EDO . H 6 HOH A 1 401 471 HOH HOH . H 6 HOH A 2 402 464 HOH HOH . H 6 HOH A 3 403 416 HOH HOH . H 6 HOH A 4 404 465 HOH HOH . H 6 HOH A 5 405 485 HOH HOH . H 6 HOH A 6 406 446 HOH HOH . H 6 HOH A 7 407 470 HOH HOH . H 6 HOH A 8 408 510 HOH HOH . H 6 HOH A 9 409 430 HOH HOH . H 6 HOH A 10 410 489 HOH HOH . H 6 HOH A 11 411 450 HOH HOH . H 6 HOH A 12 412 439 HOH HOH . H 6 HOH A 13 413 408 HOH HOH . H 6 HOH A 14 414 422 HOH HOH . H 6 HOH A 15 415 444 HOH HOH . H 6 HOH A 16 416 492 HOH HOH . H 6 HOH A 17 417 501 HOH HOH . H 6 HOH A 18 418 437 HOH HOH . H 6 HOH A 19 419 469 HOH HOH . H 6 HOH A 20 420 402 HOH HOH . H 6 HOH A 21 421 477 HOH HOH . H 6 HOH A 22 422 516 HOH HOH . H 6 HOH A 23 423 406 HOH HOH . H 6 HOH A 24 424 436 HOH HOH . H 6 HOH A 25 425 445 HOH HOH . H 6 HOH A 26 426 419 HOH HOH . H 6 HOH A 27 427 425 HOH HOH . H 6 HOH A 28 428 415 HOH HOH . H 6 HOH A 29 429 412 HOH HOH . H 6 HOH A 30 430 493 HOH HOH . H 6 HOH A 31 431 479 HOH HOH . H 6 HOH A 32 432 500 HOH HOH . H 6 HOH A 33 433 512 HOH HOH . H 6 HOH A 34 434 429 HOH HOH . H 6 HOH A 35 435 509 HOH HOH . H 6 HOH A 36 436 452 HOH HOH . H 6 HOH A 37 437 417 HOH HOH . H 6 HOH A 38 438 508 HOH HOH . H 6 HOH A 39 439 467 HOH HOH . H 6 HOH A 40 440 474 HOH HOH . H 6 HOH A 41 441 494 HOH HOH . H 6 HOH A 42 442 490 HOH HOH . H 6 HOH A 43 443 404 HOH HOH . H 6 HOH A 44 444 411 HOH HOH . H 6 HOH A 45 445 473 HOH HOH . H 6 HOH A 46 446 456 HOH HOH . H 6 HOH A 47 447 407 HOH HOH . H 6 HOH A 48 448 409 HOH HOH . H 6 HOH A 49 449 427 HOH HOH . H 6 HOH A 50 450 519 HOH HOH . H 6 HOH A 51 451 414 HOH HOH . H 6 HOH A 52 452 457 HOH HOH . H 6 HOH A 53 453 405 HOH HOH . H 6 HOH A 54 454 447 HOH HOH . H 6 HOH A 55 455 505 HOH HOH . H 6 HOH A 56 456 434 HOH HOH . H 6 HOH A 57 457 421 HOH HOH . H 6 HOH A 58 458 426 HOH HOH . H 6 HOH A 59 459 506 HOH HOH . H 6 HOH A 60 460 401 HOH HOH . H 6 HOH A 61 461 428 HOH HOH . H 6 HOH A 62 462 432 HOH HOH . H 6 HOH A 63 463 461 HOH HOH . H 6 HOH A 64 464 442 HOH HOH . H 6 HOH A 65 465 475 HOH HOH . H 6 HOH A 66 466 481 HOH HOH . H 6 HOH A 67 467 441 HOH HOH . H 6 HOH A 68 468 418 HOH HOH . H 6 HOH A 69 469 499 HOH HOH . H 6 HOH A 70 470 403 HOH HOH . H 6 HOH A 71 471 435 HOH HOH . H 6 HOH A 72 472 472 HOH HOH . H 6 HOH A 73 473 458 HOH HOH . H 6 HOH A 74 474 443 HOH HOH . H 6 HOH A 75 475 410 HOH HOH . H 6 HOH A 76 476 460 HOH HOH . H 6 HOH A 77 477 420 HOH HOH . H 6 HOH A 78 478 514 HOH HOH . H 6 HOH A 79 479 486 HOH HOH . H 6 HOH A 80 480 455 HOH HOH . H 6 HOH A 81 481 424 HOH HOH . H 6 HOH A 82 482 504 HOH HOH . H 6 HOH A 83 483 433 HOH HOH . H 6 HOH A 84 484 451 HOH HOH . H 6 HOH A 85 485 478 HOH HOH . H 6 HOH A 86 486 502 HOH HOH . H 6 HOH A 87 487 483 HOH HOH . H 6 HOH A 88 488 431 HOH HOH . H 6 HOH A 89 489 440 HOH HOH . H 6 HOH A 90 490 466 HOH HOH . H 6 HOH A 91 491 511 HOH HOH . H 6 HOH A 92 492 480 HOH HOH . H 6 HOH A 93 493 453 HOH HOH . H 6 HOH A 94 494 438 HOH HOH . H 6 HOH A 95 495 496 HOH HOH . H 6 HOH A 96 496 476 HOH HOH . H 6 HOH A 97 497 413 HOH HOH . H 6 HOH A 98 498 448 HOH HOH . H 6 HOH A 99 499 484 HOH HOH . H 6 HOH A 100 500 518 HOH HOH . H 6 HOH A 101 501 462 HOH HOH . H 6 HOH A 102 502 482 HOH HOH . H 6 HOH A 103 503 454 HOH HOH . H 6 HOH A 104 504 507 HOH HOH . H 6 HOH A 105 505 495 HOH HOH . H 6 HOH A 106 506 497 HOH HOH . H 6 HOH A 107 507 488 HOH HOH . H 6 HOH A 108 508 498 HOH HOH . H 6 HOH A 109 509 513 HOH HOH . H 6 HOH A 110 510 449 HOH HOH . H 6 HOH A 111 511 520 HOH HOH . H 6 HOH A 112 512 468 HOH HOH . H 6 HOH A 113 513 487 HOH HOH . H 6 HOH A 114 514 459 HOH HOH . H 6 HOH A 115 515 503 HOH HOH . H 6 HOH A 116 516 463 HOH HOH . H 6 HOH A 117 517 517 HOH HOH . H 6 HOH A 118 518 423 HOH HOH . H 6 HOH A 119 519 491 HOH HOH . H 6 HOH A 120 520 515 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 . . . C 3 33.242 35.712 22.931 1 29.81 ? N1 UDP 302 A 1 HETATM 2 C C2 UDP . . . C 3 33.324 36.59 23.981 1 27.44 ? C2 UDP 302 A 1 HETATM 3 N N3 UDP . . . C 3 34.516 37.164 24.302 1 34.19 ? N3 UDP 302 A 1 HETATM 4 C C4 UDP . . . C 3 35.624 36.875 23.575 1 37.42 ? C4 UDP 302 A 1 HETATM 5 C C5 UDP . . . C 3 35.535 35.97 22.491 1 39.52 ? C5 UDP 302 A 1 HETATM 6 C C6 UDP . . . C 3 34.347 35.403 22.199 1 30.3 ? C6 UDP 302 A 1 HETATM 7 O O2 UDP . . . C 3 32.334 36.847 24.652 1 31.46 ? O2 UDP 302 A 1 HETATM 8 O O4 UDP . . . C 3 36.692 37.394 23.853 1 40.49 ? O4 UDP 302 A 1 HETATM 9 C C1' UDP . . . C 3 31.957 35.087 22.587 1 28.21 ? C1' UDP 302 A 1 HETATM 10 C C2' UDP . . . C 3 31.022 36.101 21.892 1 26.28 ? C2' UDP 302 A 1 HETATM 11 O O2' UDP . . . C 3 29.669 35.651 21.941 1 29.64 ? O2' UDP 302 A 1 HETATM 12 C C3' UDP . . . C 3 31.533 35.991 20.456 1 28.59 ? C3' UDP 302 A 1 HETATM 13 C C4' UDP . . . C 3 31.605 34.465 20.347 1 33.75 ? C4' UDP 302 A 1 HETATM 14 O O4' UDP . . . C 3 32.166 34.031 21.61 1 35.06 ? O4' UDP 302 A 1 HETATM 15 O O3' UDP . . . C 3 30.581 36.533 19.548 1 28.79 ? O3' UDP 302 A 1 HETATM 16 C C5' UDP . . . C 3 32.492 34.027 19.172 1 33.09 ? C5' UDP 302 A 1 HETATM 17 O O5' UDP . . . C 3 33.708 34.78 19.132 1 33.73 ? O5' UDP 302 A 1 HETATM 18 P PA UDP . . . C 3 33.951 35.883 18.003 1 34.18 ? PA UDP 302 A 1 HETATM 19 O O1A UDP . . . C 3 32.64 36.431 17.584 1 32.28 ? O1A UDP 302 A 1 HETATM 20 O O2A UDP . . . C 3 34.898 37.019 18.542 1 32.88 ? O2A UDP 302 A 1 HETATM 21 O O3A UDP . . . C 3 34.625 35.2 16.754 1 35.99 ? O3A UDP 302 A 1 HETATM 22 P PB UDP . . . C 3 34.55 35.505 15.209 1 37.5 ? PB UDP 302 A 1 HETATM 23 O O1B UDP . . . C 3 35.254 34.321 14.433 1 37.76 ? O1B UDP 302 A 1 HETATM 24 O O2B UDP . . . C 3 35.274 36.874 14.919 1 38.84 ? O2B UDP 302 A 1 HETATM 25 O O3B UDP . . . C 3 33.122 35.631 14.796 1 30.21 ? O3B UDP 302 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #