data_3FBB # _model_server_result.job_id iLepQpIVjjFy1rsHy21Heg _model_server_result.datetime_utc '2024-11-24 08:45:43' _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 3fbb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":201}' # _entry.id 3FBB # _exptl.entry_id 3FBB _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 6 _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 3FBB _cell.length_a 79.676 _cell.length_b 152.899 _cell.length_c 184.534 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3FBB _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G,H,K,L,O,P,S,U,W 1 1,2 B,D,F,I,J,M,N,Q,R,T,V,X 2 1,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 3_755 -x+2,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 159.352 0 92.267 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 R N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 L O3B UDP . C UDP 201 1_555 K MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc2 N O1A UDP . D UDP 201 1_555 M MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? # _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 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 3FBB _atom_sites.fract_transf_matrix[1][1] 0.012551 _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] 0.00654 _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] 0.005419 _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 MG A 1 202 202 MG MG . H 3 UDP A 1 201 201 UDP UDP . I 2 MG B 1 202 202 MG MG . J 3 UDP B 1 201 201 UDP UDP . K 2 MG C 1 202 202 MG MG . L 3 UDP C 1 201 201 UDP UDP . M 2 MG D 1 202 202 MG MG . N 3 UDP D 1 201 201 UDP UDP . O 2 MG E 1 202 202 MG MG . P 3 UDP E 1 201 201 UDP UDP . Q 2 MG F 1 202 202 MG MG . R 3 UDP F 1 201 201 UDP UDP . S 4 HOH A 1 138 3 HOH HOH . S 4 HOH A 2 139 5 HOH HOH . S 4 HOH A 3 140 9 HOH HOH . S 4 HOH A 4 141 13 HOH HOH . S 4 HOH A 5 142 142 HOH HOH . S 4 HOH A 6 143 22 HOH HOH . S 4 HOH A 7 144 144 HOH HOH . S 4 HOH A 8 145 23 HOH HOH . S 4 HOH A 9 146 26 HOH HOH . S 4 HOH A 10 147 27 HOH HOH . S 4 HOH A 11 148 28 HOH HOH . S 4 HOH A 12 149 31 HOH HOH . S 4 HOH A 13 150 49 HOH HOH . S 4 HOH A 14 151 151 HOH HOH . S 4 HOH A 15 152 50 HOH HOH . S 4 HOH A 16 153 153 HOH HOH . S 4 HOH A 17 154 74 HOH HOH . S 4 HOH A 18 155 97 HOH HOH . S 4 HOH A 19 156 156 HOH HOH . S 4 HOH A 20 157 157 HOH HOH . S 4 HOH A 21 158 98 HOH HOH . S 4 HOH A 22 159 100 HOH HOH . S 4 HOH A 23 160 160 HOH HOH . S 4 HOH A 24 161 108 HOH HOH . S 4 HOH A 25 162 115 HOH HOH . S 4 HOH A 26 163 128 HOH HOH . S 4 HOH A 27 164 131 HOH HOH . S 4 HOH A 28 165 132 HOH HOH . S 4 HOH A 29 166 134 HOH HOH . S 4 HOH A 30 171 171 HOH HOH . S 4 HOH A 31 176 176 HOH HOH . S 4 HOH A 32 180 180 HOH HOH . T 4 HOH B 1 138 24 HOH HOH . T 4 HOH B 2 139 139 HOH HOH . T 4 HOH B 3 140 34 HOH HOH . T 4 HOH B 4 141 141 HOH HOH . T 4 HOH B 5 142 36 HOH HOH . T 4 HOH B 6 143 37 HOH HOH . T 4 HOH B 7 144 38 HOH HOH . T 4 HOH B 8 145 145 HOH HOH . T 4 HOH B 9 146 53 HOH HOH . T 4 HOH B 10 147 56 HOH HOH . T 4 HOH B 11 148 64 HOH HOH . T 4 HOH B 12 149 149 HOH HOH . T 4 HOH B 13 150 73 HOH HOH . T 4 HOH B 14 151 78 HOH HOH . T 4 HOH B 15 152 82 HOH HOH . T 4 HOH B 16 153 83 HOH HOH . T 4 HOH B 17 154 154 HOH HOH . T 4 HOH B 18 155 86 HOH HOH . T 4 HOH B 19 156 104 HOH HOH . T 4 HOH B 20 157 106 HOH HOH . T 4 HOH B 21 158 111 HOH HOH . T 4 HOH B 22 159 159 HOH HOH . T 4 HOH B 23 160 112 HOH HOH . T 4 HOH B 24 161 129 HOH HOH . T 4 HOH B 25 162 137 HOH HOH . T 4 HOH B 26 166 166 HOH HOH . T 4 HOH B 27 168 168 HOH HOH . T 4 HOH B 28 172 172 HOH HOH . T 4 HOH B 29 173 173 HOH HOH . T 4 HOH B 30 178 178 HOH HOH . U 4 HOH C 1 138 4 HOH HOH . U 4 HOH C 2 139 6 HOH HOH . U 4 HOH C 3 140 7 HOH HOH . U 4 HOH C 4 141 8 HOH HOH . U 4 HOH C 5 142 10 HOH HOH . U 4 HOH C 6 143 12 HOH HOH . U 4 HOH C 7 144 16 HOH HOH . U 4 HOH C 8 145 17 HOH HOH . U 4 HOH C 9 146 20 HOH HOH . U 4 HOH C 10 147 21 HOH HOH . U 4 HOH C 11 148 25 HOH HOH . U 4 HOH C 12 149 39 HOH HOH . U 4 HOH C 13 150 41 HOH HOH . U 4 HOH C 14 151 47 HOH HOH . U 4 HOH C 15 152 66 HOH HOH . U 4 HOH C 16 153 81 HOH HOH . U 4 HOH C 17 154 87 HOH HOH . U 4 HOH C 18 155 88 HOH HOH . U 4 HOH C 19 156 89 HOH HOH . U 4 HOH C 20 157 90 HOH HOH . U 4 HOH C 21 158 92 HOH HOH . U 4 HOH C 22 159 96 HOH HOH . U 4 HOH C 23 160 99 HOH HOH . U 4 HOH C 24 161 101 HOH HOH . U 4 HOH C 25 162 162 HOH HOH . U 4 HOH C 26 163 113 HOH HOH . U 4 HOH C 27 164 114 HOH HOH . U 4 HOH C 28 165 119 HOH HOH . U 4 HOH C 29 166 122 HOH HOH . U 4 HOH C 30 167 125 HOH HOH . U 4 HOH C 31 169 169 HOH HOH . U 4 HOH C 32 179 179 HOH HOH . U 4 HOH C 33 181 181 HOH HOH . U 4 HOH C 34 182 182 HOH HOH . V 4 HOH D 1 138 138 HOH HOH . V 4 HOH D 2 139 15 HOH HOH . V 4 HOH D 3 140 140 HOH HOH . V 4 HOH D 4 141 32 HOH HOH . V 4 HOH D 5 142 46 HOH HOH . V 4 HOH D 6 143 48 HOH HOH . V 4 HOH D 7 144 51 HOH HOH . V 4 HOH D 8 145 52 HOH HOH . V 4 HOH D 9 146 54 HOH HOH . V 4 HOH D 10 147 57 HOH HOH . V 4 HOH D 11 148 68 HOH HOH . V 4 HOH D 12 149 69 HOH HOH . V 4 HOH D 13 150 75 HOH HOH . V 4 HOH D 14 151 76 HOH HOH . V 4 HOH D 15 152 152 HOH HOH . V 4 HOH D 16 153 77 HOH HOH . V 4 HOH D 17 154 93 HOH HOH . V 4 HOH D 18 155 94 HOH HOH . V 4 HOH D 19 156 102 HOH HOH . V 4 HOH D 20 157 103 HOH HOH . V 4 HOH D 21 158 105 HOH HOH . V 4 HOH D 22 159 107 HOH HOH . V 4 HOH D 23 160 118 HOH HOH . V 4 HOH D 24 161 161 HOH HOH . V 4 HOH D 25 162 121 HOH HOH . V 4 HOH D 26 163 123 HOH HOH . V 4 HOH D 27 164 130 HOH HOH . W 4 HOH E 1 138 1 HOH HOH . W 4 HOH E 2 139 14 HOH HOH . W 4 HOH E 3 140 18 HOH HOH . W 4 HOH E 4 141 30 HOH HOH . W 4 HOH E 5 142 33 HOH HOH . W 4 HOH E 6 143 40 HOH HOH . W 4 HOH E 7 144 42 HOH HOH . W 4 HOH E 8 145 43 HOH HOH . W 4 HOH E 9 146 146 HOH HOH . W 4 HOH E 10 147 147 HOH HOH . W 4 HOH E 11 148 44 HOH HOH . W 4 HOH E 12 149 45 HOH HOH . W 4 HOH E 13 150 150 HOH HOH . W 4 HOH E 14 151 61 HOH HOH . W 4 HOH E 15 152 62 HOH HOH . W 4 HOH E 16 153 63 HOH HOH . W 4 HOH E 17 154 65 HOH HOH . W 4 HOH E 18 155 67 HOH HOH . W 4 HOH E 19 156 71 HOH HOH . W 4 HOH E 20 157 72 HOH HOH . W 4 HOH E 21 158 158 HOH HOH . W 4 HOH E 22 159 79 HOH HOH . W 4 HOH E 23 160 84 HOH HOH . W 4 HOH E 24 161 85 HOH HOH . W 4 HOH E 25 162 91 HOH HOH . W 4 HOH E 26 163 120 HOH HOH . W 4 HOH E 27 164 164 HOH HOH . W 4 HOH E 28 165 127 HOH HOH . W 4 HOH E 29 166 133 HOH HOH . W 4 HOH E 30 170 170 HOH HOH . W 4 HOH E 31 174 174 HOH HOH . W 4 HOH E 32 175 175 HOH HOH . W 4 HOH E 33 177 177 HOH HOH . X 4 HOH F 1 138 2 HOH HOH . X 4 HOH F 2 139 11 HOH HOH . X 4 HOH F 3 140 19 HOH HOH . X 4 HOH F 4 141 29 HOH HOH . X 4 HOH F 5 142 35 HOH HOH . X 4 HOH F 6 143 143 HOH HOH . X 4 HOH F 7 144 55 HOH HOH . X 4 HOH F 8 145 58 HOH HOH . X 4 HOH F 9 146 59 HOH HOH . X 4 HOH F 10 147 60 HOH HOH . X 4 HOH F 11 148 148 HOH HOH . X 4 HOH F 12 149 70 HOH HOH . X 4 HOH F 13 150 80 HOH HOH . X 4 HOH F 14 151 95 HOH HOH . X 4 HOH F 15 152 109 HOH HOH . X 4 HOH F 16 153 110 HOH HOH . X 4 HOH F 17 154 116 HOH HOH . X 4 HOH F 18 155 155 HOH HOH . X 4 HOH F 19 156 117 HOH HOH . X 4 HOH F 20 157 124 HOH HOH . X 4 HOH F 21 158 126 HOH HOH . X 4 HOH F 22 159 135 HOH HOH . X 4 HOH F 23 160 136 HOH HOH . X 4 HOH F 24 163 163 HOH HOH . X 4 HOH F 25 165 165 HOH HOH . X 4 HOH F 26 167 167 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 . . . R 3 50.222 51.666 43.151 1 55.98 ? N1 UDP 201 F 1 HETATM 2 C C2 UDP . . . R 3 50.103 52.91 42.577 1 57.3 ? C2 UDP 201 F 1 HETATM 3 N N3 UDP . . . R 3 49.498 53.937 43.266 1 56.71 ? N3 UDP 201 F 1 HETATM 4 C C4 UDP . . . R 3 49.008 53.705 44.539 1 63.54 ? C4 UDP 201 F 1 HETATM 5 C C5 UDP . . . R 3 49.132 52.433 45.117 1 61.78 ? C5 UDP 201 F 1 HETATM 6 C C6 UDP . . . R 3 49.609 51.373 44.345 1 59.96 ? C6 UDP 201 F 1 HETATM 7 O O2 UDP . . . R 3 50.542 53.092 41.444 1 54.75 ? O2 UDP 201 F 1 HETATM 8 O O4 UDP . . . R 3 48.469 54.632 45.152 1 64.47 ? O4 UDP 201 F 1 HETATM 9 C C1' UDP . . . R 3 50.885 50.634 42.351 1 58.78 ? C1' UDP 201 F 1 HETATM 10 C C2' UDP . . . R 3 52.331 50.496 42.815 1 55.87 ? C2' UDP 201 F 1 HETATM 11 O O2' UDP . . . R 3 53.173 50.169 41.726 1 49.76 ? O2' UDP 201 F 1 HETATM 12 C C3' UDP . . . R 3 52.259 49.308 43.736 1 55.15 ? C3' UDP 201 F 1 HETATM 13 C C4' UDP . . . R 3 51.192 48.464 43.035 1 57.96 ? C4' UDP 201 F 1 HETATM 14 O O4' UDP . . . R 3 50.25 49.393 42.56 1 55.91 ? O4' UDP 201 F 1 HETATM 15 O O3' UDP . . . R 3 53.516 48.679 43.808 1 49.84 ? O3' UDP 201 F 1 HETATM 16 C C5' UDP . . . R 3 50.455 47.468 43.919 1 58.76 ? C5' UDP 201 F 1 HETATM 17 O O5' UDP . . . R 3 49.743 48.163 44.917 1 67.64 ? O5' UDP 201 F 1 HETATM 18 P PA UDP . . . R 3 49.957 47.649 46.43 1 75.04 ? PA UDP 201 F 1 HETATM 19 O O1A UDP . . . R 3 49.556 46.215 46.519 1 64.25 ? O1A UDP 201 F 1 HETATM 20 O O2A UDP . . . R 3 49.221 48.536 47.376 1 71.37 ? O2A UDP 201 F 1 HETATM 21 O O3A UDP . . . R 3 51.572 47.844 46.562 1 69.16 ? O3A UDP 201 F 1 HETATM 22 P PB UDP . . . R 3 52.654 46.646 46.743 1 60.35 ? PB UDP 201 F 1 HETATM 23 O O1B UDP . . . R 3 53.479 46.941 47.927 1 63.94 ? O1B UDP 201 F 1 HETATM 24 O O2B UDP . . . R 3 53.491 46.519 45.523 1 59.61 ? O2B UDP 201 F 1 HETATM 25 O O3B UDP . . . R 3 51.978 45.341 46.945 1 69.51 ? O3B UDP 201 F 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 25 #