data_8G27 # _model_server_result.job_id GGt4-vprcNfmA39aQzEd6g _model_server_result.datetime_utc '2024-10-11 02:19:11' _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 8g27 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1001}' # _entry.id 8G27 # _exptl.entry_id 8G27 _exptl.method 'ELECTRON MICROSCOPY' # _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 3 _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 8G27 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8G27 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 ? _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 G N N ? 3 H N N ? 3 I N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 BGC _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n D BGC 1 E 1 BGC E 12 BGC 2 n D BGC 2 E 2 BGC E 11 BGC 2 n E BGC 1 A 1 BGC E 13 BGC 2 n E BGC 2 A 2 BGC E 14 BGC 2 n F BGC 1 B 1 BGC E 15 BGC 2 n F BGC 2 B 2 BGC E 16 BGC # 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 covale ? covale1 D O4 BGC . E BGC 1 1_555 D C1 BGC . E BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 E O4 BGC . A BGC 1 1_555 E C1 BGC . A BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 F O4 BGC . B BGC 1 1_555 F C1 BGC . B BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 380 n n N1 C6 UDP sing 381 n n N1 C1' UDP sing 382 n n C2 N3 UDP sing 383 n n C2 O2 UDP doub 384 n n N3 C4 UDP sing 385 n n N3 HN3 UDP sing 386 n n C4 C5 UDP sing 387 n n C4 O4 UDP doub 388 n n C5 C6 UDP doub 389 n n C5 H5 UDP sing 390 n n C6 H6 UDP sing 391 n n C1' C2' UDP sing 392 n n C1' O4' UDP sing 393 n n C1' H1' UDP sing 394 n n C2' O2' UDP sing 395 n n C2' C3' UDP sing 396 n n C2' H2' UDP sing 397 n n O2' HO2' UDP sing 398 n n C3' C4' UDP sing 399 n n C3' O3' UDP sing 400 n n C3' H3' UDP sing 401 n n C4' O4' UDP sing 402 n n C4' C5' UDP sing 403 n n C4' H4' UDP sing 404 n n O3' HO3' UDP sing 405 n n C5' O5' UDP sing 406 n n C5' "H5'1" UDP sing 407 n n C5' "H5'2" UDP sing 408 n n O5' PA UDP sing 409 n n PA O1A UDP doub 410 n n PA O2A UDP sing 411 n n PA O3A UDP sing 412 n n O2A HOA2 UDP sing 413 n n O3A PB UDP sing 414 n n PB O1B UDP doub 415 n n PB O2B UDP sing 416 n n PB O3B UDP sing 417 n n O2B HOB2 UDP sing 418 n n O3B HOB3 UDP sing 419 n n # _atom_sites.entry_id 8G27 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 3 UDP D 1 1001 1001 UDP UDP . H 3 UDP I 1 1001 1001 UDP UDP . I 3 UDP C 1 1001 1001 UDP UDP . # 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 . . . H 3 158.035 145.818 153.008 1 100.44 ? N1 UDP 1001 I 1 HETATM 2 C C2 UDP . . . H 3 157.296 144.867 152.331 1 105.03 ? C2 UDP 1001 I 1 HETATM 3 N N3 UDP . . . H 3 157.57 143.564 152.673 1 108.75 ? N3 UDP 1001 I 1 HETATM 4 C C4 UDP . . . H 3 158.494 143.134 153.606 1 105.25 ? C4 UDP 1001 I 1 HETATM 5 C C5 UDP . . . H 3 159.218 144.179 154.262 1 105.49 ? C5 UDP 1001 I 1 HETATM 6 C C6 UDP . . . H 3 158.973 145.462 153.949 1 104.7 ? C6 UDP 1001 I 1 HETATM 7 O O2 UDP . . . H 3 156.457 145.153 151.489 1 107.29 ? O2 UDP 1001 I 1 HETATM 8 O O4 UDP . . . H 3 158.635 141.918 153.812 1 104.8 ? O4 UDP 1001 I 1 HETATM 9 C C1' UDP . . . H 3 157.787 147.232 152.683 1 102.22 ? C1' UDP 1001 I 1 HETATM 10 C C2' UDP . . . H 3 157.411 148.083 153.903 1 107.33 ? C2' UDP 1001 I 1 HETATM 11 O O2' UDP . . . H 3 156.442 149.064 153.554 1 107.34 ? O2' UDP 1001 I 1 HETATM 12 C C3' UDP . . . H 3 158.753 148.711 154.281 1 110.96 ? C3' UDP 1001 I 1 HETATM 13 C C4' UDP . . . H 3 159.41 148.909 152.922 1 108.25 ? C4' UDP 1001 I 1 HETATM 14 O O4' UDP . . . H 3 158.977 147.779 152.138 1 105.1 ? O4' UDP 1001 I 1 HETATM 15 O O3' UDP . . . H 3 158.589 149.954 154.953 1 105.79 ? O3' UDP 1001 I 1 HETATM 16 C C5' UDP . . . H 3 160.917 148.954 152.943 1 112.36 ? C5' UDP 1001 I 1 HETATM 17 O O5' UDP . . . H 3 161.346 150.02 153.815 1 112.47 ? O5' UDP 1001 I 1 HETATM 18 P PA UDP . . . H 3 162.788 150.021 154.463 1 118.48 ? PA UDP 1001 I 1 HETATM 19 O O1A UDP . . . H 3 162.806 148.941 155.477 1 109.23 ? O1A UDP 1001 I 1 HETATM 20 O O2A UDP . . . H 3 163.873 149.985 153.389 1 105.46 ? O2A UDP 1001 I 1 HETATM 21 O O3A UDP . . . H 3 162.908 151.435 155.167 1 113.14 ? O3A UDP 1001 I 1 HETATM 22 P PB UDP . . . H 3 163.876 151.72 156.388 1 122.33 ? PB UDP 1001 I 1 HETATM 23 O O1B UDP . . . H 3 163.276 150.868 157.509 1 113.02 ? O1B UDP 1001 I 1 HETATM 24 O O2B UDP . . . H 3 165.202 151.112 155.926 1 105.88 ? O2B UDP 1001 I 1 HETATM 25 O O3B UDP . . . H 3 163.958 153.176 156.713 1 111.2 ? O3B UDP 1001 I 1 HETATM 26 H HN3 UDP . . . H 3 157.121 142.955 152.264 1 105.92 ? HN3 UDP 1001 I 1 HETATM 27 H H5 UDP . . . H 3 159.858 143.968 154.903 1 105.86 ? H5 UDP 1001 I 1 HETATM 28 H H6 UDP . . . H 3 159.452 146.129 154.385 1 105.9 ? H6 UDP 1001 I 1 HETATM 29 H H1' UDP . . . H 3 157.078 147.294 152.025 1 104.47 ? H1' UDP 1001 I 1 HETATM 30 H H2' UDP . . . H 3 157.088 147.519 154.623 1 105.08 ? H2' UDP 1001 I 1 HETATM 31 H HO2' UDP . . . H 3 156.692 149.473 152.851 1 104.83 ? HO2' UDP 1001 I 1 HETATM 32 H H3' UDP . . . H 3 159.273 148.096 154.821 1 106.6 ? H3' UDP 1001 I 1 HETATM 33 H H4' UDP . . . H 3 159.067 149.723 152.521 1 104.9 ? H4' UDP 1001 I 1 HETATM 34 H HO3' UDP . . . H 3 157.768 150.175 154.942 1 105.22 ? HO3' UDP 1001 I 1 HETATM 35 H "H5'1" UDP . . . H 3 161.263 148.11 153.272 1 107.19 ? "H5'1" UDP 1001 I 1 HETATM 36 H "H5'2" UDP . . . H 3 161.25 149.114 152.046 1 106.46 ? "H5'2" UDP 1001 I 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #