data_3NWY # _model_server_result.job_id -acRKlrB05vA9wPfsIq3lA _model_server_result.datetime_utc '2024-11-22 05:53:42' _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 3nwy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":263}' # _entry.id 3NWY # _exptl.entry_id 3NWY _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 3NWY _cell.length_a 136.71 _cell.length_b 175.48 _cell.length_c 65.41 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NWY _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I,J,K,L,M,N,O,P,Q,R,S _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id I _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 380 n n N1 C6 UDP sing 381 n n N1 C1' UDP sing 382 n n C2 N3 UDP sing 383 n n C2 O2 UDP doub 384 n n N3 C4 UDP sing 385 n n N3 HN3 UDP sing 386 n n C4 C5 UDP sing 387 n n C4 O4 UDP doub 388 n n C5 C6 UDP doub 389 n n C5 H5 UDP sing 390 n n C6 H6 UDP sing 391 n n C1' C2' UDP sing 392 n n C1' O4' UDP sing 393 n n C1' H1' UDP sing 394 n n C2' O2' UDP sing 395 n n C2' C3' UDP sing 396 n n C2' H2' UDP sing 397 n n O2' HO2' UDP sing 398 n n C3' C4' UDP sing 399 n n C3' O3' UDP sing 400 n n C3' H3' UDP sing 401 n n C4' O4' UDP sing 402 n n C4' C5' UDP sing 403 n n C4' H4' UDP sing 404 n n O3' HO3' UDP sing 405 n n C5' O5' UDP sing 406 n n C5' "H5'1" UDP sing 407 n n C5' "H5'2" UDP sing 408 n n O5' PA UDP sing 409 n n PA O1A UDP doub 410 n n PA O2A UDP sing 411 n n PA O3A UDP sing 412 n n O2A HOA2 UDP sing 413 n n O3A PB UDP sing 414 n n PB O1B UDP doub 415 n n PB O2B UDP sing 416 n n PB O3B UDP sing 417 n n O2B HOB2 UDP sing 418 n n O3B HOB3 UDP sing 419 n n # _atom_sites.entry_id 3NWY _atom_sites.fract_transf_matrix[1][1] 0.007315 _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] 0.005699 _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] 0.015288 _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 G 2 GTP A 1 262 262 GTP GTP . H 2 GTP B 1 262 262 GTP GTP . I 3 UDP B 1 263 263 UDP UDP . J 2 GTP C 1 262 262 GTP GTP . K 2 GTP D 1 262 262 GTP GTP . L 2 GTP E 1 262 262 GTP GTP . M 2 GTP F 1 262 262 GTP GTP . N 4 HOH A 1 263 21 HOH HOH . N 4 HOH A 2 264 36 HOH HOH . N 4 HOH A 3 265 42 HOH HOH . N 4 HOH A 4 266 66 HOH HOH . N 4 HOH A 5 267 73 HOH HOH . N 4 HOH A 6 268 75 HOH HOH . N 4 HOH A 7 269 86 HOH HOH . N 4 HOH A 8 270 124 HOH HOH . N 4 HOH A 9 271 217 HOH HOH . N 4 HOH A 10 302 302 HOH HOH . N 4 HOH A 11 357 357 HOH HOH . N 4 HOH A 12 395 395 HOH HOH . N 4 HOH A 13 397 397 HOH HOH . N 4 HOH A 14 409 409 HOH HOH . N 4 HOH A 15 410 410 HOH HOH . N 4 HOH A 16 411 411 HOH HOH . N 4 HOH A 17 412 412 HOH HOH . N 4 HOH A 18 505 505 HOH HOH . N 4 HOH A 19 506 506 HOH HOH . N 4 HOH A 20 509 509 HOH HOH . N 4 HOH A 21 510 510 HOH HOH . N 4 HOH A 22 513 513 HOH HOH . N 4 HOH A 23 514 514 HOH HOH . N 4 HOH A 24 515 515 HOH HOH . N 4 HOH A 25 521 521 HOH HOH . N 4 HOH A 26 522 522 HOH HOH . N 4 HOH A 27 523 523 HOH HOH . N 4 HOH A 28 524 524 HOH HOH . N 4 HOH A 29 538 538 HOH HOH . N 4 HOH A 30 539 539 HOH HOH . N 4 HOH A 31 540 540 HOH HOH . N 4 HOH A 32 541 541 HOH HOH . N 4 HOH A 33 542 542 HOH HOH . N 4 HOH A 34 543 543 HOH HOH . N 4 HOH A 35 544 544 HOH HOH . N 4 HOH A 36 545 545 HOH HOH . N 4 HOH A 37 546 546 HOH HOH . N 4 HOH A 38 548 548 HOH HOH . N 4 HOH A 39 569 569 HOH HOH . N 4 HOH A 40 570 570 HOH HOH . N 4 HOH A 41 571 571 HOH HOH . O 4 HOH B 1 264 16 HOH HOH . O 4 HOH B 2 265 67 HOH HOH . O 4 HOH B 3 266 69 HOH HOH . O 4 HOH B 4 267 121 HOH HOH . O 4 HOH B 5 268 125 HOH HOH . O 4 HOH B 6 269 194 HOH HOH . O 4 HOH B 7 390 390 HOH HOH . O 4 HOH B 8 398 398 HOH HOH . O 4 HOH B 9 399 399 HOH HOH . O 4 HOH B 10 400 400 HOH HOH . O 4 HOH B 11 402 402 HOH HOH . O 4 HOH B 12 403 403 HOH HOH . O 4 HOH B 13 413 413 HOH HOH . O 4 HOH B 14 415 415 HOH HOH . O 4 HOH B 15 416 416 HOH HOH . O 4 HOH B 16 417 417 HOH HOH . O 4 HOH B 17 418 418 HOH HOH . O 4 HOH B 18 419 419 HOH HOH . O 4 HOH B 19 421 421 HOH HOH . O 4 HOH B 20 422 422 HOH HOH . O 4 HOH B 21 423 423 HOH HOH . O 4 HOH B 22 424 424 HOH HOH . O 4 HOH B 23 507 507 HOH HOH . O 4 HOH B 24 511 511 HOH HOH . O 4 HOH B 25 525 525 HOH HOH . O 4 HOH B 26 526 526 HOH HOH . O 4 HOH B 27 527 527 HOH HOH . O 4 HOH B 28 528 528 HOH HOH . O 4 HOH B 29 547 547 HOH HOH . O 4 HOH B 30 550 550 HOH HOH . O 4 HOH B 31 551 551 HOH HOH . O 4 HOH B 32 562 562 HOH HOH . P 4 HOH C 1 263 23 HOH HOH . P 4 HOH C 2 264 48 HOH HOH . P 4 HOH C 3 265 74 HOH HOH . P 4 HOH C 4 266 201 HOH HOH . P 4 HOH C 5 267 244 HOH HOH . P 4 HOH C 6 372 372 HOH HOH . P 4 HOH C 7 383 383 HOH HOH . P 4 HOH C 8 389 389 HOH HOH . P 4 HOH C 9 394 394 HOH HOH . P 4 HOH C 10 404 404 HOH HOH . P 4 HOH C 11 405 405 HOH HOH . P 4 HOH C 12 406 406 HOH HOH . P 4 HOH C 13 407 407 HOH HOH . P 4 HOH C 14 432 432 HOH HOH . P 4 HOH C 15 512 512 HOH HOH . P 4 HOH C 16 520 520 HOH HOH . P 4 HOH C 17 529 529 HOH HOH . P 4 HOH C 18 530 530 HOH HOH . P 4 HOH C 19 531 531 HOH HOH . P 4 HOH C 20 532 532 HOH HOH . P 4 HOH C 21 552 552 HOH HOH . P 4 HOH C 22 553 553 HOH HOH . P 4 HOH C 23 554 554 HOH HOH . Q 4 HOH D 1 263 9 HOH HOH . Q 4 HOH D 2 264 31 HOH HOH . Q 4 HOH D 3 393 393 HOH HOH . Q 4 HOH D 4 429 429 HOH HOH . Q 4 HOH D 5 430 430 HOH HOH . Q 4 HOH D 6 431 431 HOH HOH . Q 4 HOH D 7 503 503 HOH HOH . Q 4 HOH D 8 516 516 HOH HOH . Q 4 HOH D 9 517 517 HOH HOH . Q 4 HOH D 10 518 518 HOH HOH . Q 4 HOH D 11 519 519 HOH HOH . Q 4 HOH D 12 555 555 HOH HOH . Q 4 HOH D 13 556 556 HOH HOH . Q 4 HOH D 14 557 557 HOH HOH . R 4 HOH E 1 263 20 HOH HOH . R 4 HOH E 2 391 391 HOH HOH . R 4 HOH E 3 392 392 HOH HOH . R 4 HOH E 4 408 408 HOH HOH . R 4 HOH E 5 427 427 HOH HOH . R 4 HOH E 6 533 533 HOH HOH . R 4 HOH E 7 534 534 HOH HOH . R 4 HOH E 8 535 535 HOH HOH . R 4 HOH E 9 536 536 HOH HOH . R 4 HOH E 10 537 537 HOH HOH . R 4 HOH E 11 558 558 HOH HOH . R 4 HOH E 12 559 559 HOH HOH . R 4 HOH E 13 560 560 HOH HOH . R 4 HOH E 14 561 561 HOH HOH . S 4 HOH F 1 263 10 HOH HOH . S 4 HOH F 2 264 25 HOH HOH . S 4 HOH F 3 401 401 HOH HOH . S 4 HOH F 4 414 414 HOH HOH . S 4 HOH F 5 420 420 HOH HOH . S 4 HOH F 6 425 425 HOH HOH . S 4 HOH F 7 426 426 HOH HOH . S 4 HOH F 8 501 501 HOH HOH . S 4 HOH F 9 502 502 HOH HOH . S 4 HOH F 10 504 504 HOH HOH . S 4 HOH F 11 508 508 HOH HOH . S 4 HOH F 12 549 549 HOH HOH . S 4 HOH F 13 563 563 HOH HOH . S 4 HOH F 14 564 564 HOH HOH . S 4 HOH F 15 565 565 HOH HOH . S 4 HOH F 16 566 566 HOH HOH . S 4 HOH F 17 567 567 HOH HOH . S 4 HOH F 18 568 568 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 . . . I 3 59.21 32.569 40.311 1 39.67 ? N1 UDP 263 B 1 HETATM 2 C C2 UDP . . . I 3 59.606 31.89 39.17 1 40 ? C2 UDP 263 B 1 HETATM 3 N N3 UDP . . . I 3 60.32 30.705 39.272 1 40.09 ? N3 UDP 263 B 1 HETATM 4 C C4 UDP . . . I 3 60.652 30.184 40.502 1 37.92 ? C4 UDP 263 B 1 HETATM 5 C C5 UDP . . . I 3 60.249 30.864 41.641 1 38.14 ? C5 UDP 263 B 1 HETATM 6 C C6 UDP . . . I 3 59.341 31.91 41.508 1 38.64 ? C6 UDP 263 B 1 HETATM 7 O O2 UDP . . . I 3 59.327 32.306 38.049 1 39.83 ? O2 UDP 263 B 1 HETATM 8 O O4 UDP . . . I 3 61.293 29.141 40.575 1 35.89 ? O4 UDP 263 B 1 HETATM 9 C C1' UDP . . . I 3 58.458 33.86 40.211 1 41.65 ? C1' UDP 263 B 1 HETATM 10 C C2' UDP . . . I 3 57.023 33.693 39.722 1 42.44 ? C2' UDP 263 B 1 HETATM 11 O O2' UDP . . . I 3 56.723 34.684 38.771 1 42.81 ? O2' UDP 263 B 1 HETATM 12 C C3' UDP . . . I 3 56.201 33.906 40.966 1 43.63 ? C3' UDP 263 B 1 HETATM 13 C C4' UDP . . . I 3 57.035 34.951 41.684 1 43.91 ? C4' UDP 263 B 1 HETATM 14 O O4' UDP . . . I 3 58.374 34.539 41.469 1 42.21 ? O4' UDP 263 B 1 HETATM 15 O O3' UDP . . . I 3 54.898 34.372 40.725 1 45.96 ? O3' UDP 263 B 1 HETATM 16 C C5' UDP . . . I 3 56.697 35.118 43.161 1 44.87 ? C5' UDP 263 B 1 HETATM 17 O O5' UDP . . . I 3 56.679 33.872 43.829 1 46.14 ? O5' UDP 263 B 1 HETATM 18 P PA UDP . . . I 3 55.285 33.225 44.314 1 46.51 ? PA UDP 263 B 1 HETATM 19 O O1A UDP . . . I 3 54.213 33.392 43.288 1 44.92 ? O1A UDP 263 B 1 HETATM 20 O O2A UDP . . . I 3 55.483 31.795 44.656 1 45.13 ? O2A UDP 263 B 1 HETATM 21 O O3A UDP . . . I 3 55.014 34.145 45.603 0.9 47.57 ? O3A UDP 263 B 1 HETATM 22 P PB UDP . . . I 3 53.916 33.768 46.723 0.9 50.83 ? PB UDP 263 B 1 HETATM 23 O O1B UDP . . . I 3 53.686 35.006 47.53 0.9 50.38 ? O1B UDP 263 B 1 HETATM 24 O O2B UDP . . . I 3 54.43 32.643 47.544 0.9 49.66 ? O2B UDP 263 B 1 HETATM 25 O O3B UDP . . . I 3 52.633 33.316 46.123 0.9 49.93 ? O3B UDP 263 B 1 # _model_server_stats.io_time_ms 87 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #