data_4Q18 # _model_server_result.job_id z64RHxeuPidIUXOPdDZsoQ _model_server_result.datetime_utc '2024-10-13 04:22:28' _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 4q18 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 4Q18 # _exptl.entry_id 4Q18 _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 2 _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 4Q18 _cell.length_a 68.75 _cell.length_b 68.75 _cell.length_c 122.45 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q18 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _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,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N 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 421 n n N1 C6 UDP sing 422 n n N1 C1' UDP sing 423 n n C2 N3 UDP sing 424 n n C2 O2 UDP doub 425 n n N3 C4 UDP sing 426 n n N3 HN3 UDP sing 427 n n C4 C5 UDP sing 428 n n C4 O4 UDP doub 429 n n C5 C6 UDP doub 430 n n C5 H5 UDP sing 431 n n C6 H6 UDP sing 432 n n C1' C2' UDP sing 433 n n C1' O4' UDP sing 434 n n C1' H1' UDP sing 435 n n C2' O2' UDP sing 436 n n C2' C3' UDP sing 437 n n C2' H2' UDP sing 438 n n O2' HO2' UDP sing 439 n n C3' C4' UDP sing 440 n n C3' O3' UDP sing 441 n n C3' H3' UDP sing 442 n n C4' O4' UDP sing 443 n n C4' C5' UDP sing 444 n n C4' H4' UDP sing 445 n n O3' HO3' UDP sing 446 n n C5' O5' UDP sing 447 n n C5' "H5'1" UDP sing 448 n n C5' "H5'2" UDP sing 449 n n O5' PA UDP sing 450 n n PA O1A UDP doub 451 n n PA O2A UDP sing 452 n n PA O3A UDP sing 453 n n O2A HOA2 UDP sing 454 n n O3A PB UDP sing 455 n n PB O1B UDP doub 456 n n PB O2B UDP sing 457 n n PB O3B UDP sing 458 n n O2B HOB2 UDP sing 459 n n O3B HOB3 UDP sing 460 n n # _atom_sites.entry_id 4Q18 _atom_sites.fract_transf_matrix[1][1] 0.014545 _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] 0.014545 _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] 0.008167 _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 2 2XJ A 1 301 301 2XJ 2XJ . D 2 2XJ A 1 302 302 2XJ 2XJ . E 3 UDP A 1 303 401 UDP UDP . F 3 UDP B 1 401 401 UDP UDP . G 2 2XJ B 1 402 301 2XJ 2XJ . H 2 2XJ B 1 403 302 2XJ 2XJ . I 4 HOH A 1 401 1 HOH HOH . I 4 HOH A 2 402 4 HOH HOH . I 4 HOH A 3 403 5 HOH HOH . I 4 HOH A 4 404 6 HOH HOH . I 4 HOH A 5 405 7 HOH HOH . I 4 HOH A 6 406 10 HOH HOH . I 4 HOH A 7 407 11 HOH HOH . I 4 HOH A 8 408 14 HOH HOH . I 4 HOH A 9 409 17 HOH HOH . I 4 HOH A 10 410 18 HOH HOH . I 4 HOH A 11 411 19 HOH HOH . I 4 HOH A 12 412 22 HOH HOH . I 4 HOH A 13 413 23 HOH HOH . I 4 HOH A 14 414 25 HOH HOH . I 4 HOH A 15 415 26 HOH HOH . I 4 HOH A 16 416 29 HOH HOH . I 4 HOH A 17 417 30 HOH HOH . I 4 HOH A 18 418 32 HOH HOH . I 4 HOH A 19 419 33 HOH HOH . I 4 HOH A 20 420 34 HOH HOH . I 4 HOH A 21 421 35 HOH HOH . I 4 HOH A 22 422 36 HOH HOH . I 4 HOH A 23 423 46 HOH HOH . I 4 HOH A 24 424 49 HOH HOH . I 4 HOH A 25 425 50 HOH HOH . I 4 HOH A 26 426 59 HOH HOH . I 4 HOH A 27 427 60 HOH HOH . I 4 HOH A 28 428 61 HOH HOH . I 4 HOH A 29 429 62 HOH HOH . I 4 HOH A 30 430 63 HOH HOH . I 4 HOH A 31 431 64 HOH HOH . I 4 HOH A 32 432 65 HOH HOH . I 4 HOH A 33 433 66 HOH HOH . I 4 HOH A 34 434 67 HOH HOH . I 4 HOH A 35 435 68 HOH HOH . I 4 HOH A 36 436 69 HOH HOH . I 4 HOH A 37 437 70 HOH HOH . I 4 HOH A 38 438 71 HOH HOH . I 4 HOH A 39 439 72 HOH HOH . I 4 HOH A 40 440 73 HOH HOH . I 4 HOH A 41 441 78 HOH HOH . I 4 HOH A 42 442 79 HOH HOH . I 4 HOH A 43 443 80 HOH HOH . I 4 HOH A 44 444 83 HOH HOH . J 4 HOH B 1 501 2 HOH HOH . J 4 HOH B 2 502 3 HOH HOH . J 4 HOH B 3 503 8 HOH HOH . J 4 HOH B 4 504 9 HOH HOH . J 4 HOH B 5 505 12 HOH HOH . J 4 HOH B 6 506 13 HOH HOH . J 4 HOH B 7 507 15 HOH HOH . J 4 HOH B 8 508 16 HOH HOH . J 4 HOH B 9 509 20 HOH HOH . J 4 HOH B 10 510 21 HOH HOH . J 4 HOH B 11 511 24 HOH HOH . J 4 HOH B 12 512 27 HOH HOH . J 4 HOH B 13 513 28 HOH HOH . J 4 HOH B 14 514 31 HOH HOH . J 4 HOH B 15 515 37 HOH HOH . J 4 HOH B 16 516 38 HOH HOH . J 4 HOH B 17 517 39 HOH HOH . J 4 HOH B 18 518 40 HOH HOH . J 4 HOH B 19 519 41 HOH HOH . J 4 HOH B 20 520 42 HOH HOH . J 4 HOH B 21 521 43 HOH HOH . J 4 HOH B 22 522 44 HOH HOH . J 4 HOH B 23 523 45 HOH HOH . J 4 HOH B 24 524 47 HOH HOH . J 4 HOH B 25 525 48 HOH HOH . J 4 HOH B 26 526 51 HOH HOH . J 4 HOH B 27 527 52 HOH HOH . J 4 HOH B 28 528 53 HOH HOH . J 4 HOH B 29 529 54 HOH HOH . J 4 HOH B 30 530 55 HOH HOH . J 4 HOH B 31 531 56 HOH HOH . J 4 HOH B 32 532 57 HOH HOH . J 4 HOH B 33 533 58 HOH HOH . J 4 HOH B 34 534 74 HOH HOH . J 4 HOH B 35 535 75 HOH HOH . J 4 HOH B 36 536 76 HOH HOH . J 4 HOH B 37 537 77 HOH HOH . J 4 HOH B 38 538 81 HOH HOH . J 4 HOH B 39 539 82 HOH HOH . J 4 HOH B 40 540 84 HOH HOH . J 4 HOH B 41 541 85 HOH HOH . J 4 HOH B 42 542 86 HOH HOH . J 4 HOH B 43 543 87 HOH HOH . J 4 HOH B 44 544 88 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 . . . F 3 -25.358 -28.792 -30.759 1 51.95 ? N1 UDP 401 B 1 HETATM 2 C C2 UDP . . . F 3 -25.386 -29.98 -31.531 1 52.35 ? C2 UDP 401 B 1 HETATM 3 N N3 UDP . . . F 3 -24.399 -30.244 -32.385 1 52.02 ? N3 UDP 401 B 1 HETATM 4 C C4 UDP . . . F 3 -23.37 -29.409 -32.522 1 53.93 ? C4 UDP 401 B 1 HETATM 5 C C5 UDP . . . F 3 -23.3 -28.238 -31.769 1 51.38 ? C5 UDP 401 B 1 HETATM 6 C C6 UDP . . . F 3 -24.323 -27.943 -30.874 1 50.68 ? C6 UDP 401 B 1 HETATM 7 O O2 UDP . . . F 3 -26.326 -30.804 -31.431 1 52.5 ? O2 UDP 401 B 1 HETATM 8 O O4 UDP . . . F 3 -22.472 -29.707 -33.333 1 57.09 ? O4 UDP 401 B 1 HETATM 9 C C1' UDP . . . F 3 -26.441 -28.544 -29.809 1 50.6 ? C1' UDP 401 B 1 HETATM 10 C C2' UDP . . . F 3 -25.895 -28.653 -28.391 1 49.19 ? C2' UDP 401 B 1 HETATM 11 O O2' UDP . . . F 3 -25.824 -29.971 -27.863 1 40.36 ? O2' UDP 401 B 1 HETATM 12 C C3' UDP . . . F 3 -26.912 -27.872 -27.612 1 52.45 ? C3' UDP 401 B 1 HETATM 13 C C4' UDP . . . F 3 -27.371 -26.807 -28.595 1 51.59 ? C4' UDP 401 B 1 HETATM 14 O O4' UDP . . . F 3 -27.037 -27.252 -29.921 1 49.38 ? O4' UDP 401 B 1 HETATM 15 O O3' UDP . . . F 3 -27.977 -28.743 -27.205 1 57.58 ? O3' UDP 401 B 1 HETATM 16 C C5' UDP . . . F 3 -26.702 -25.471 -28.294 1 54.67 ? C5' UDP 401 B 1 HETATM 17 O O5' UDP . . . F 3 -25.3 -25.641 -28.063 1 51 ? O5' UDP 401 B 1 HETATM 18 P PA UDP . . . F 3 -24.478 -24.698 -27.046 1 47.6 ? PA UDP 401 B 1 HETATM 19 O O1A UDP . . . F 3 -25.013 -24.724 -25.645 1 44.62 ? O1A UDP 401 B 1 HETATM 20 O O2A UDP . . . F 3 -23.009 -25.04 -27.243 1 47.91 ? O2A UDP 401 B 1 HETATM 21 O O3A UDP . . . F 3 -24.818 -23.285 -27.755 1 43.65 ? O3A UDP 401 B 1 HETATM 22 P PB UDP . . . F 3 -24.21 -21.85 -27.273 1 39.63 ? PB UDP 401 B 1 HETATM 23 O O1B UDP . . . F 3 -23.221 -22.189 -26.251 1 37.69 ? O1B UDP 401 B 1 HETATM 24 O O2B UDP . . . F 3 -25.387 -21.091 -26.708 1 47.64 ? O2B UDP 401 B 1 HETATM 25 O O3B UDP . . . F 3 -23.719 -21.274 -28.583 1 39.05 ? O3B UDP 401 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #