data_5D00 # _model_server_result.job_id bWOLAVoGQ9ijjQSJtmqwQQ _model_server_result.datetime_utc '2024-12-07 08:22:04' _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 5d00 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 5D00 # _exptl.entry_id 5D00 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 5D00 _cell.length_a 90.66 _cell.length_b 164.627 _cell.length_c 97.729 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D00 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 # _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 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 N1 C2 U5P sing 376 n n N1 C6 U5P sing 377 n n N1 C1' U5P sing 378 n n C2 N3 U5P sing 379 n n C2 O2 U5P doub 380 n n N3 C4 U5P sing 381 n n N3 HN3 U5P sing 382 n n C4 C5 U5P sing 383 n n C4 O4 U5P doub 384 n n C5 C6 U5P doub 385 n n C5 H5 U5P sing 386 n n C6 H6 U5P sing 387 n n C1' C2' U5P sing 388 n n C1' O4' U5P sing 389 n n C1' H1' U5P sing 390 n n C2' O2' U5P sing 391 n n C2' C3' U5P sing 392 n n C2' H2' U5P sing 393 n n O2' HO2' U5P sing 394 n n C3' C4' U5P sing 395 n n C3' O3' U5P sing 396 n n C3' H3' U5P sing 397 n n C4' O4' U5P sing 398 n n C4' C5' U5P sing 399 n n C4' H4' U5P sing 400 n n O3' HO3' U5P sing 401 n n C5' O5' U5P sing 402 n n C5' "H5'1" U5P sing 403 n n C5' "H5'2" U5P sing 404 n n O5' P U5P sing 405 n n P O1P U5P doub 406 n n P O2P U5P sing 407 n n P O3P U5P sing 408 n n O2P HOP2 U5P sing 409 n n O3P HOP3 U5P sing 410 n n # _atom_sites.entry_id 5D00 _atom_sites.fract_transf_matrix[1][1] 0.01103 _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] 0.006074 _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] 0.010232 _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 GMT A 1 401 2 GMT GMT . D 3 PO4 A 1 402 1 PO4 PO4 . E 2 GMT B 1 401 1 GMT GMT . F 4 U5P B 1 402 1 U5P U5P . G 5 HOH A 1 501 81 HOH HOH . G 5 HOH A 2 502 36 HOH HOH . G 5 HOH A 3 503 3 HOH HOH . G 5 HOH A 4 504 30 HOH HOH . G 5 HOH A 5 505 5 HOH HOH . G 5 HOH A 6 506 7 HOH HOH . G 5 HOH A 7 507 20 HOH HOH . G 5 HOH A 8 508 73 HOH HOH . G 5 HOH A 9 509 8 HOH HOH . G 5 HOH A 10 510 83 HOH HOH . G 5 HOH A 11 511 14 HOH HOH . G 5 HOH A 12 512 39 HOH HOH . G 5 HOH A 13 513 70 HOH HOH . G 5 HOH A 14 514 21 HOH HOH . G 5 HOH A 15 515 76 HOH HOH . G 5 HOH A 16 516 64 HOH HOH . G 5 HOH A 17 517 52 HOH HOH . G 5 HOH A 18 518 35 HOH HOH . G 5 HOH A 19 519 12 HOH HOH . G 5 HOH A 20 520 50 HOH HOH . G 5 HOH A 21 521 28 HOH HOH . G 5 HOH A 22 522 46 HOH HOH . G 5 HOH A 23 523 84 HOH HOH . G 5 HOH A 24 524 19 HOH HOH . G 5 HOH A 25 525 26 HOH HOH . G 5 HOH A 26 526 56 HOH HOH . G 5 HOH A 27 527 38 HOH HOH . G 5 HOH A 28 528 1 HOH HOH . G 5 HOH A 29 529 66 HOH HOH . G 5 HOH A 30 530 10 HOH HOH . G 5 HOH A 31 531 67 HOH HOH . G 5 HOH A 32 532 27 HOH HOH . G 5 HOH A 33 533 78 HOH HOH . G 5 HOH A 34 534 40 HOH HOH . G 5 HOH A 35 535 68 HOH HOH . G 5 HOH A 36 536 34 HOH HOH . G 5 HOH A 37 537 77 HOH HOH . G 5 HOH A 38 538 42 HOH HOH . G 5 HOH A 39 539 24 HOH HOH . G 5 HOH A 40 540 58 HOH HOH . G 5 HOH A 41 541 55 HOH HOH . G 5 HOH A 42 542 37 HOH HOH . G 5 HOH A 43 543 65 HOH HOH . H 5 HOH B 1 501 82 HOH HOH . H 5 HOH B 2 502 75 HOH HOH . H 5 HOH B 3 503 74 HOH HOH . H 5 HOH B 4 504 72 HOH HOH . H 5 HOH B 5 505 85 HOH HOH . H 5 HOH B 6 506 4 HOH HOH . H 5 HOH B 7 507 15 HOH HOH . H 5 HOH B 8 508 54 HOH HOH . H 5 HOH B 9 509 80 HOH HOH . H 5 HOH B 10 510 6 HOH HOH . H 5 HOH B 11 511 69 HOH HOH . H 5 HOH B 12 512 25 HOH HOH . H 5 HOH B 13 513 18 HOH HOH . H 5 HOH B 14 514 48 HOH HOH . H 5 HOH B 15 515 13 HOH HOH . H 5 HOH B 16 516 23 HOH HOH . H 5 HOH B 17 517 2 HOH HOH . H 5 HOH B 18 518 16 HOH HOH . H 5 HOH B 19 519 41 HOH HOH . H 5 HOH B 20 520 51 HOH HOH . H 5 HOH B 21 521 45 HOH HOH . H 5 HOH B 22 522 59 HOH HOH . H 5 HOH B 23 523 32 HOH HOH . H 5 HOH B 24 524 31 HOH HOH . H 5 HOH B 25 525 57 HOH HOH . H 5 HOH B 26 526 33 HOH HOH . H 5 HOH B 27 527 60 HOH HOH . H 5 HOH B 28 528 87 HOH HOH . H 5 HOH B 29 529 22 HOH HOH . H 5 HOH B 30 530 86 HOH HOH . H 5 HOH B 31 531 79 HOH HOH . H 5 HOH B 32 532 11 HOH HOH . H 5 HOH B 33 533 9 HOH HOH . H 5 HOH B 34 534 47 HOH HOH . H 5 HOH B 35 535 71 HOH HOH . H 5 HOH B 36 536 88 HOH HOH . H 5 HOH B 37 537 49 HOH HOH . H 5 HOH B 38 538 44 HOH HOH . H 5 HOH B 39 539 17 HOH HOH . H 5 HOH B 40 540 29 HOH HOH . H 5 HOH B 41 541 53 HOH HOH . H 5 HOH B 42 542 63 HOH HOH . H 5 HOH B 43 543 61 HOH HOH . H 5 HOH B 44 544 62 HOH HOH . H 5 HOH B 45 545 89 HOH HOH . H 5 HOH B 46 546 43 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 U5P . . . F 4 -13.889 14.599 26.068 0.8 51.23 ? N1 U5P 402 B 1 HETATM 2 C C2 U5P . . . F 4 -13.047 13.734 26.824 0.8 51.03 ? C2 U5P 402 B 1 HETATM 3 N N3 U5P . . . F 4 -12.999 13.843 28.159 0.8 51.05 ? N3 U5P 402 B 1 HETATM 4 C C4 U5P . . . F 4 -13.738 14.774 28.793 0.8 48.06 ? C4 U5P 402 B 1 HETATM 5 C C5 U5P . . . F 4 -14.567 15.667 28.084 0.8 48.36 ? C5 U5P 402 B 1 HETATM 6 C C6 U5P . . . F 4 -14.631 15.543 26.694 0.8 51.08 ? C6 U5P 402 B 1 HETATM 7 O O2 U5P . . . F 4 -12.362 12.847 26.268 0.8 44.3 ? O2 U5P 402 B 1 HETATM 8 O O4 U5P . . . F 4 -13.644 14.83 30.023 0.8 44.67 ? O4 U5P 402 B 1 HETATM 9 C C1' U5P . . . F 4 -13.907 14.424 24.599 0.8 50.63 ? C1' U5P 402 B 1 HETATM 10 C C2' U5P . . . F 4 -15.129 13.651 24.142 0.8 46.75 ? C2' U5P 402 B 1 HETATM 11 O O2' U5P . . . F 4 -15.019 12.268 24.479 0.8 40.25 ? O2' U5P 402 B 1 HETATM 12 C C3' U5P . . . F 4 -15.182 14.004 22.64 0.8 50.43 ? C3' U5P 402 B 1 HETATM 13 C C4' U5P . . . F 4 -14.694 15.453 22.637 0.8 51.09 ? C4' U5P 402 B 1 HETATM 14 O O3' U5P . . . F 4 -14.355 13.19 21.769 0.8 47.86 ? O3' U5P 402 B 1 HETATM 15 O O4' U5P . . . F 4 -13.931 15.644 23.849 0.8 51.66 ? O4' U5P 402 B 1 HETATM 16 C C5' U5P . . . F 4 -15.819 16.474 22.598 0.8 52.17 ? C5' U5P 402 B 1 HETATM 17 O O5' U5P . . . F 4 -16.304 16.599 21.256 0.8 58.56 ? O5' U5P 402 B 1 HETATM 18 P P U5P . . . F 4 -17.609 17.507 20.911 0.8 54.72 ? P U5P 402 B 1 HETATM 19 O O1P U5P . . . F 4 -17.721 17.45 19.403 0.8 55.95 ? O1P U5P 402 B 1 HETATM 20 O O2P U5P . . . F 4 -18.827 16.917 21.587 0.8 54.63 ? O2P U5P 402 B 1 HETATM 21 O O3P U5P . . . F 4 -17.2 18.892 21.403 0.8 66.72 ? O3P U5P 402 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #