data_4Q1D # _model_server_result.job_id 2TpiTpQKSDfEkbDvBmgccw _model_server_result.datetime_utc '2024-11-22 20:39:40' _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 4q1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 4Q1D # _exptl.entry_id 4Q1D _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 4Q1D _cell.length_a 68.734 _cell.length_b 68.734 _cell.length_c 120.623 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q1D _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 _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 D 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 417 n n N1 C6 UDP sing 418 n n N1 C1' UDP sing 419 n n C2 N3 UDP sing 420 n n C2 O2 UDP doub 421 n n N3 C4 UDP sing 422 n n N3 HN3 UDP sing 423 n n C4 C5 UDP sing 424 n n C4 O4 UDP doub 425 n n C5 C6 UDP doub 426 n n C5 H5 UDP sing 427 n n C6 H6 UDP sing 428 n n C1' C2' UDP sing 429 n n C1' O4' UDP sing 430 n n C1' H1' UDP sing 431 n n C2' O2' UDP sing 432 n n C2' C3' UDP sing 433 n n C2' H2' UDP sing 434 n n O2' HO2' UDP sing 435 n n C3' C4' UDP sing 436 n n C3' O3' UDP sing 437 n n C3' H3' UDP sing 438 n n C4' O4' UDP sing 439 n n C4' C5' UDP sing 440 n n C4' H4' UDP sing 441 n n O3' HO3' UDP sing 442 n n C5' O5' UDP sing 443 n n C5' "H5'1" UDP sing 444 n n C5' "H5'2" UDP sing 445 n n O5' PA UDP sing 446 n n PA O1A UDP doub 447 n n PA O2A UDP sing 448 n n PA O3A UDP sing 449 n n O2A HOA2 UDP sing 450 n n O3A PB UDP sing 451 n n PB O1B UDP doub 452 n n PB O2B UDP sing 453 n n PB O3B UDP sing 454 n n O2B HOB2 UDP sing 455 n n O3B HOB3 UDP sing 456 n n # _atom_sites.entry_id 4Q1D _atom_sites.fract_transf_matrix[1][1] 0.014549 _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] 0.014549 _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] 0.00829 _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 2Y1 A 1 301 301 2Y1 DRR . D 3 UDP A 1 302 401 UDP UDP . E 2 2Y1 B 1 301 301 2Y1 DRR . F 3 UDP B 1 302 401 UDP UDP . G 4 HOH A 1 401 1 HOH HOH . G 4 HOH A 2 402 3 HOH HOH . G 4 HOH A 3 403 4 HOH HOH . G 4 HOH A 4 404 5 HOH HOH . G 4 HOH A 5 405 6 HOH HOH . G 4 HOH A 6 406 7 HOH HOH . G 4 HOH A 7 407 8 HOH HOH . G 4 HOH A 8 408 9 HOH HOH . G 4 HOH A 9 409 10 HOH HOH . G 4 HOH A 10 410 11 HOH HOH . G 4 HOH A 11 411 12 HOH HOH . G 4 HOH A 12 412 13 HOH HOH . G 4 HOH A 13 413 14 HOH HOH . G 4 HOH A 14 414 15 HOH HOH . G 4 HOH A 15 415 16 HOH HOH . G 4 HOH A 16 416 17 HOH HOH . G 4 HOH A 17 417 18 HOH HOH . G 4 HOH A 18 418 19 HOH HOH . G 4 HOH A 19 419 20 HOH HOH . G 4 HOH A 20 420 21 HOH HOH . G 4 HOH A 21 421 22 HOH HOH . G 4 HOH A 22 422 23 HOH HOH . G 4 HOH A 23 423 24 HOH HOH . G 4 HOH A 24 424 25 HOH HOH . G 4 HOH A 25 425 26 HOH HOH . G 4 HOH A 26 426 27 HOH HOH . G 4 HOH A 27 427 28 HOH HOH . G 4 HOH A 28 428 29 HOH HOH . G 4 HOH A 29 429 30 HOH HOH . G 4 HOH A 30 430 31 HOH HOH . G 4 HOH A 31 431 32 HOH HOH . G 4 HOH A 32 432 33 HOH HOH . G 4 HOH A 33 433 34 HOH HOH . G 4 HOH A 34 434 35 HOH HOH . G 4 HOH A 35 435 36 HOH HOH . G 4 HOH A 36 436 37 HOH HOH . G 4 HOH A 37 437 38 HOH HOH . G 4 HOH A 38 438 40 HOH HOH . G 4 HOH A 39 439 60 HOH HOH . G 4 HOH A 40 440 80 HOH HOH . G 4 HOH A 41 441 81 HOH HOH . G 4 HOH A 42 442 82 HOH HOH . G 4 HOH A 43 443 83 HOH HOH . G 4 HOH A 44 444 84 HOH HOH . G 4 HOH A 45 445 85 HOH HOH . G 4 HOH A 46 446 86 HOH HOH . G 4 HOH A 47 447 90 HOH HOH . G 4 HOH A 48 448 91 HOH HOH . G 4 HOH A 49 449 92 HOH HOH . H 4 HOH B 1 401 2 HOH HOH . H 4 HOH B 2 402 39 HOH HOH . H 4 HOH B 3 403 41 HOH HOH . H 4 HOH B 4 404 42 HOH HOH . H 4 HOH B 5 405 43 HOH HOH . H 4 HOH B 6 406 44 HOH HOH . H 4 HOH B 7 407 45 HOH HOH . H 4 HOH B 8 408 46 HOH HOH . H 4 HOH B 9 409 47 HOH HOH . H 4 HOH B 10 410 48 HOH HOH . H 4 HOH B 11 411 49 HOH HOH . H 4 HOH B 12 412 50 HOH HOH . H 4 HOH B 13 413 51 HOH HOH . H 4 HOH B 14 414 52 HOH HOH . H 4 HOH B 15 415 53 HOH HOH . H 4 HOH B 16 416 54 HOH HOH . H 4 HOH B 17 417 55 HOH HOH . H 4 HOH B 18 418 56 HOH HOH . H 4 HOH B 19 419 57 HOH HOH . H 4 HOH B 20 420 58 HOH HOH . H 4 HOH B 21 421 59 HOH HOH . H 4 HOH B 22 422 61 HOH HOH . H 4 HOH B 23 423 62 HOH HOH . H 4 HOH B 24 424 63 HOH HOH . H 4 HOH B 25 425 64 HOH HOH . H 4 HOH B 26 426 65 HOH HOH . H 4 HOH B 27 427 66 HOH HOH . H 4 HOH B 28 428 67 HOH HOH . H 4 HOH B 29 429 68 HOH HOH . H 4 HOH B 30 430 69 HOH HOH . H 4 HOH B 31 431 70 HOH HOH . H 4 HOH B 32 432 71 HOH HOH . H 4 HOH B 33 433 72 HOH HOH . H 4 HOH B 34 434 73 HOH HOH . H 4 HOH B 35 435 74 HOH HOH . H 4 HOH B 36 436 75 HOH HOH . H 4 HOH B 37 437 76 HOH HOH . H 4 HOH B 38 438 77 HOH HOH . H 4 HOH B 39 439 78 HOH HOH . H 4 HOH B 40 440 79 HOH HOH . H 4 HOH B 41 441 87 HOH HOH . H 4 HOH B 42 442 88 HOH HOH . H 4 HOH B 43 443 89 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 . . . D 3 28.936 25.163 3.382 1 55.46 ? N1 UDP 302 A 1 HETATM 2 C C2 UDP . . . D 3 30.139 24.963 4.101 1 55.57 ? C2 UDP 302 A 1 HETATM 3 N N3 UDP . . . D 3 30.195 24.088 5.123 1 52.58 ? N3 UDP 302 A 1 HETATM 4 C C4 UDP . . . D 3 29.105 23.382 5.475 1 53.48 ? C4 UDP 302 A 1 HETATM 5 C C5 UDP . . . D 3 27.903 23.556 4.798 1 50.04 ? C5 UDP 302 A 1 HETATM 6 C C6 UDP . . . D 3 27.836 24.462 3.744 1 55.46 ? C6 UDP 302 A 1 HETATM 7 O O2 UDP . . . D 3 31.158 25.598 3.779 1 59.26 ? O2 UDP 302 A 1 HETATM 8 O O4 UDP . . . D 3 29.157 22.564 6.424 1 54.56 ? O4 UDP 302 A 1 HETATM 9 C C1' UDP . . . D 3 28.864 26.129 2.285 1 53.2 ? C1' UDP 302 A 1 HETATM 10 C C2' UDP . . . D 3 28.831 25.526 0.896 1 56.47 ? C2' UDP 302 A 1 HETATM 11 O O2' UDP . . . D 3 30.108 25.504 0.272 1 57.83 ? O2' UDP 302 A 1 HETATM 12 C C3' UDP . . . D 3 27.931 26.466 0.107 1 59.39 ? C3' UDP 302 A 1 HETATM 13 C C4' UDP . . . D 3 26.978 27.022 1.159 1 54.9 ? C4' UDP 302 A 1 HETATM 14 O O4' UDP . . . D 3 27.644 26.878 2.413 1 52.59 ? O4' UDP 302 A 1 HETATM 15 O O3' UDP . . . D 3 28.705 27.49 -0.541 1 56.88 ? O3' UDP 302 A 1 HETATM 16 C C5' UDP . . . D 3 25.649 26.269 1.202 1 53.72 ? C5' UDP 302 A 1 HETATM 17 O O5' UDP . . . D 3 25.861 25.046 0.506 1 54.56 ? O5' UDP 302 A 1 HETATM 18 P PA UDP . . . D 3 24.767 24.153 -0.224 1 51.52 ? PA UDP 302 A 1 HETATM 19 O O1A UDP . . . D 3 24.555 24.714 -1.604 1 50.68 ? O1A UDP 302 A 1 HETATM 20 O O2A UDP . . . D 3 25.289 22.725 -0.153 1 50.25 ? O2A UDP 302 A 1 HETATM 21 O O3A UDP . . . D 3 23.462 24.273 0.748 1 50.11 ? O3A UDP 302 A 1 HETATM 22 P PB UDP . . . D 3 21.964 23.824 0.293 1 43.44 ? PB UDP 302 A 1 HETATM 23 O O1B UDP . . . D 3 22.167 22.888 -0.875 1 49.42 ? O1B UDP 302 A 1 HETATM 24 O O2B UDP . . . D 3 21.403 25.136 -0.167 1 55.78 ? O2B UDP 302 A 1 HETATM 25 O O3B UDP . . . D 3 21.173 23.323 1.46 1 45.85 ? O3B UDP 302 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #