data_4Q1B # _model_server_result.job_id GsXnSLrd7CxcdfMkuoKK6w _model_server_result.datetime_utc '2024-11-22 20:41:29' _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 4q1b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 4Q1B # _exptl.entry_id 4Q1B _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 4Q1B _cell.length_a 68.968 _cell.length_b 68.968 _cell.length_c 121.944 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q1B _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 418 n n N1 C6 UDP sing 419 n n N1 C1' UDP sing 420 n n C2 N3 UDP sing 421 n n C2 O2 UDP doub 422 n n N3 C4 UDP sing 423 n n N3 HN3 UDP sing 424 n n C4 C5 UDP sing 425 n n C4 O4 UDP doub 426 n n C5 C6 UDP doub 427 n n C5 H5 UDP sing 428 n n C6 H6 UDP sing 429 n n C1' C2' UDP sing 430 n n C1' O4' UDP sing 431 n n C1' H1' UDP sing 432 n n C2' O2' UDP sing 433 n n C2' C3' UDP sing 434 n n C2' H2' UDP sing 435 n n O2' HO2' UDP sing 436 n n C3' C4' UDP sing 437 n n C3' O3' UDP sing 438 n n C3' H3' UDP sing 439 n n C4' O4' UDP sing 440 n n C4' C5' UDP sing 441 n n C4' H4' UDP sing 442 n n O3' HO3' UDP sing 443 n n C5' O5' UDP sing 444 n n C5' "H5'1" UDP sing 445 n n C5' "H5'2" UDP sing 446 n n O5' PA UDP sing 447 n n PA O1A UDP doub 448 n n PA O2A UDP sing 449 n n PA O3A UDP sing 450 n n O2A HOA2 UDP sing 451 n n O3A PB UDP sing 452 n n PB O1B UDP doub 453 n n PB O2B UDP sing 454 n n PB O3B UDP sing 455 n n O2B HOB2 UDP sing 456 n n O3B HOB3 UDP sing 457 n n # _atom_sites.entry_id 4Q1B _atom_sites.fract_transf_matrix[1][1] 0.014499 _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] 0.014499 _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] 0.0082 _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 2Y0 A 1 301 301 2Y0 DRG . D 3 UDP A 1 302 401 UDP UDP . E 2 2Y0 B 1 301 301 2Y0 DRG . F 3 UDP B 1 302 401 UDP UDP . G 4 HOH A 1 401 2 HOH HOH . G 4 HOH A 2 402 3 HOH HOH . G 4 HOH A 3 403 6 HOH HOH . G 4 HOH A 4 404 10 HOH HOH . G 4 HOH A 5 405 18 HOH HOH . G 4 HOH A 6 406 19 HOH HOH . G 4 HOH A 7 407 23 HOH HOH . G 4 HOH A 8 408 25 HOH HOH . G 4 HOH A 9 409 26 HOH HOH . G 4 HOH A 10 410 27 HOH HOH . G 4 HOH A 11 411 31 HOH HOH . G 4 HOH A 12 412 32 HOH HOH . G 4 HOH A 13 413 34 HOH HOH . G 4 HOH A 14 414 35 HOH HOH . G 4 HOH A 15 415 39 HOH HOH . G 4 HOH A 16 416 40 HOH HOH . G 4 HOH A 17 417 43 HOH HOH . G 4 HOH A 18 418 50 HOH HOH . G 4 HOH A 19 419 52 HOH HOH . G 4 HOH A 20 420 53 HOH HOH . G 4 HOH A 21 421 55 HOH HOH . G 4 HOH A 22 422 57 HOH HOH . G 4 HOH A 23 423 60 HOH HOH . G 4 HOH A 24 424 61 HOH HOH . G 4 HOH A 25 425 62 HOH HOH . G 4 HOH A 26 426 63 HOH HOH . G 4 HOH A 27 427 64 HOH HOH . G 4 HOH A 28 428 65 HOH HOH . G 4 HOH A 29 429 66 HOH HOH . G 4 HOH A 30 430 80 HOH HOH . G 4 HOH A 31 431 81 HOH HOH . G 4 HOH A 32 432 82 HOH HOH . G 4 HOH A 33 433 83 HOH HOH . G 4 HOH A 34 434 84 HOH HOH . G 4 HOH A 35 435 85 HOH HOH . G 4 HOH A 36 436 86 HOH HOH . G 4 HOH A 37 437 87 HOH HOH . G 4 HOH A 38 438 88 HOH HOH . G 4 HOH A 39 439 90 HOH HOH . H 4 HOH B 1 401 1 HOH HOH . H 4 HOH B 2 402 4 HOH HOH . H 4 HOH B 3 403 5 HOH HOH . H 4 HOH B 4 404 7 HOH HOH . H 4 HOH B 5 405 8 HOH HOH . H 4 HOH B 6 406 9 HOH HOH . H 4 HOH B 7 407 11 HOH HOH . H 4 HOH B 8 408 12 HOH HOH . H 4 HOH B 9 409 13 HOH HOH . H 4 HOH B 10 410 14 HOH HOH . H 4 HOH B 11 411 15 HOH HOH . H 4 HOH B 12 412 16 HOH HOH . H 4 HOH B 13 413 17 HOH HOH . H 4 HOH B 14 414 20 HOH HOH . H 4 HOH B 15 415 21 HOH HOH . H 4 HOH B 16 416 22 HOH HOH . H 4 HOH B 17 417 24 HOH HOH . H 4 HOH B 18 418 28 HOH HOH . H 4 HOH B 19 419 29 HOH HOH . H 4 HOH B 20 420 30 HOH HOH . H 4 HOH B 21 421 33 HOH HOH . H 4 HOH B 22 422 36 HOH HOH . H 4 HOH B 23 423 37 HOH HOH . H 4 HOH B 24 424 38 HOH HOH . H 4 HOH B 25 425 41 HOH HOH . H 4 HOH B 26 426 42 HOH HOH . H 4 HOH B 27 427 44 HOH HOH . H 4 HOH B 28 428 45 HOH HOH . H 4 HOH B 29 429 46 HOH HOH . H 4 HOH B 30 430 47 HOH HOH . H 4 HOH B 31 431 48 HOH HOH . H 4 HOH B 32 432 49 HOH HOH . H 4 HOH B 33 433 51 HOH HOH . H 4 HOH B 34 434 54 HOH HOH . H 4 HOH B 35 435 56 HOH HOH . H 4 HOH B 36 436 58 HOH HOH . H 4 HOH B 37 437 59 HOH HOH . H 4 HOH B 38 438 67 HOH HOH . H 4 HOH B 39 439 68 HOH HOH . H 4 HOH B 40 440 69 HOH HOH . H 4 HOH B 41 441 70 HOH HOH . H 4 HOH B 42 442 71 HOH HOH . H 4 HOH B 43 443 72 HOH HOH . H 4 HOH B 44 444 73 HOH HOH . H 4 HOH B 45 445 74 HOH HOH . H 4 HOH B 46 446 75 HOH HOH . H 4 HOH B 47 447 76 HOH HOH . H 4 HOH B 48 448 77 HOH HOH . H 4 HOH B 49 449 78 HOH HOH . H 4 HOH B 50 450 79 HOH HOH . H 4 HOH B 51 451 89 HOH HOH . H 4 HOH B 52 452 91 HOH HOH . H 4 HOH B 53 453 92 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 -25.066 28.92 3.712 1 63.52 ? N1 UDP 302 A 1 HETATM 2 C C2 UDP . . . D 3 -24.789 30.169 4.335 1 64.41 ? C2 UDP 302 A 1 HETATM 3 N N3 UDP . . . D 3 -23.814 30.275 5.274 1 57.46 ? N3 UDP 302 A 1 HETATM 4 C C4 UDP . . . D 3 -23.09 29.188 5.626 1 58.53 ? C4 UDP 302 A 1 HETATM 5 C C5 UDP . . . D 3 -23.336 27.952 5.029 1 52.08 ? C5 UDP 302 A 1 HETATM 6 C C6 UDP . . . D 3 -24.331 27.841 4.061 1 60.53 ? C6 UDP 302 A 1 HETATM 7 O O2 UDP . . . D 3 -25.464 31.169 4.007 1 59.79 ? O2 UDP 302 A 1 HETATM 8 O O4 UDP . . . D 3 -22.191 29.265 6.496 1 58.52 ? O4 UDP 302 A 1 HETATM 9 C C1' UDP . . . D 3 -26.108 28.826 2.677 1 62.6 ? C1' UDP 302 A 1 HETATM 10 C C2' UDP . . . D 3 -25.455 29.123 1.341 1 61.59 ? C2' UDP 302 A 1 HETATM 11 O O2' UDP . . . D 3 -25.436 30.526 1.085 1 67.64 ? O2' UDP 302 A 1 HETATM 12 C C3' UDP . . . D 3 -26.262 28.346 0.309 1 67.58 ? C3' UDP 302 A 1 HETATM 13 C C4' UDP . . . D 3 -26.936 27.25 1.136 1 64.62 ? C4' UDP 302 A 1 HETATM 14 O O4' UDP . . . D 3 -26.695 27.522 2.524 1 60.74 ? O4' UDP 302 A 1 HETATM 15 O O3' UDP . . . D 3 -27.238 29.159 -0.389 1 60.23 ? O3' UDP 302 A 1 HETATM 16 C C5' UDP . . . D 3 -26.447 25.848 0.752 1 74.96 ? C5' UDP 302 A 1 HETATM 17 O O5' UDP . . . D 3 -25.07 25.588 1.078 1 64.5 ? O5' UDP 302 A 1 HETATM 18 P PA UDP . . . D 3 -24.135 24.743 0.058 1 62.08 ? PA UDP 302 A 1 HETATM 19 O O1A UDP . . . D 3 -24.681 24.895 -1.344 1 55.1 ? O1A UDP 302 A 1 HETATM 20 O O2A UDP . . . D 3 -22.724 25.219 0.378 1 55.54 ? O2A UDP 302 A 1 HETATM 21 O O3A UDP . . . D 3 -24.406 23.234 0.622 1 50.94 ? O3A UDP 302 A 1 HETATM 22 P PB UDP . . . D 3 -23.79 21.77 0.252 1 44.14 ? PB UDP 302 A 1 HETATM 23 O O1B UDP . . . D 3 -22.754 21.903 -0.826 1 42.95 ? O1B UDP 302 A 1 HETATM 24 O O2B UDP . . . D 3 -24.925 20.874 -0.242 1 48.53 ? O2B UDP 302 A 1 HETATM 25 O O3B UDP . . . D 3 -23.366 21.354 1.63 1 41.35 ? O3B UDP 302 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #