data_8R6Y # _model_server_result.job_id VtUEc3-e98F3aupvNex7sQ _model_server_result.datetime_utc '2024-10-18 16:31:25' _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 8r6y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2101}' # _entry.id 8R6Y # _exptl.entry_id 8R6Y _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 483.156 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _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 8R6Y _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8R6Y _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 E O3B M7G 1 C M7G 1 1_555 E P A 2 C A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.629 ? metalc ? metalc1 A OD1 ASP 985 A ASP 985 1_555 G MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc2 A O ALA 986 A ALA 986 1_555 G MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc3 A OD2 ASP 1126 A ASP 1126 1_555 G MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc4 F O1A 2KH . A 2KH 2101 1_555 G MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc5 F O3B 2KH . A 2KH 2101 1_555 G MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? hydrog 'A-A MISPAIR' hydrog1 B N6 A 1 P A 1 1_555 B N1 A 9 P A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog2 B O2 C 2 P C 2 1_555 B N2 G 8 P G 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 G 11 P G 11 1_555 C N3 C 9 T C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 G 11 P G 11 1_555 C O2 C 9 T C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 G 11 P G 11 1_555 C N4 C 9 T C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 C 12 P C 12 1_555 C N1 G 8 T G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 C 12 P C 12 1_555 C O6 G 8 T G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 C 12 P C 12 1_555 C N2 G 8 T G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 C 13 P C 13 1_555 C N1 G 7 T G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 C 13 P C 13 1_555 C O6 G 7 T G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 C 13 P C 13 1_555 C N2 G 7 T G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 C 14 P C 14 1_555 C N1 G 6 T G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N4 C 14 P C 14 1_555 C O6 G 6 T G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O2 C 14 P C 14 1_555 C N2 G 6 T G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 A 15 P A 15 1_555 C N3 U 5 T U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N6 A 15 P A 15 1_555 C O4 U 5 T U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 G 16 P G 16 1_555 C N3 C 4 T C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N2 G 16 P G 16 1_555 C O2 C 4 T C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O6 G 16 P G 16 1_555 C N4 C 4 T C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog20 C N1 A 15 T A 21 1_555 D N6 A 3 G A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C N3 U 16 T U 22 1_555 D N1 A 3 G A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C O4 U 16 T U 22 1_555 D N6 A 3 G A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N1 G 17 T G 23 1_555 D N3 C 2 G C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C N2 G 17 T G 23 1_555 D O2 C 2 G C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C O6 G 17 T G 23 1_555 D N4 C 2 G C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N3 U 18 T U 24 1_555 D N1 A 1 G A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C O4 U 18 T U 24 1_555 D N6 A 1 G A 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id 2KH _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _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 O2' C2' 2KH sing 1 n n O3' C3' 2KH sing 2 n n C2' C3' 2KH sing 3 n n C2' C1' 2KH sing 4 n n O2 C2 2KH doub 5 n n C3' C4' 2KH sing 6 n n C1' N1 2KH sing 7 n n C1' O4' 2KH sing 8 n n C2 N1 2KH sing 9 n n C2 N3 2KH sing 10 n n C4' O4' 2KH sing 11 n n C4' C5' 2KH sing 12 n n N1 C6 2KH sing 13 n n N3 C4 2KH sing 14 n n C5' O5' 2KH sing 15 n n C6 C5 2KH doub 16 n n C4 C5 2KH sing 17 n n C4 O4 2KH doub 18 n n O2B PB 2KH doub 19 n n O5' PA 2KH sing 20 n n N3A PB 2KH sing 21 n n N3A PA 2KH sing 22 n n PB O1B 2KH sing 23 n n PB O3B 2KH sing 24 n n PA O1A 2KH doub 25 n n PA O2A 2KH sing 26 n n O3B PG 2KH sing 27 n n PG O2G 2KH doub 28 n n PG O1G 2KH sing 29 n n PG O3G 2KH sing 30 n n O2A H1 2KH sing 31 n n N3A H2 2KH sing 32 n n O1B H3 2KH sing 33 n n O1G H4 2KH sing 34 n n O3G H5 2KH sing 35 n n C5' H6 2KH sing 36 n n C5' H7 2KH sing 37 n n C4' H8 2KH sing 38 n n C1' H9 2KH sing 39 n n C2' H10 2KH sing 40 n n O2' H11 2KH sing 41 n n C3' H12 2KH sing 42 n n O3' H13 2KH sing 43 n n C6 H14 2KH sing 44 n n N3 H15 2KH sing 45 n n C5 H16 2KH sing 46 n n # _atom_sites.entry_id 8R6Y _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 F 6 2KH A 1 2101 2101 2KH 2KH . G 7 MG A 1 2102 1 MG MG . # 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 P PA 2KH . . . F 6 96.243 105.986 94.57 1 128.34 ? PA 2KH 2101 A 1 HETATM 2 O O1A 2KH . . . F 6 95.265 104.895 94.247 1 124.26 ? O1A 2KH 2101 A 1 HETATM 3 O O2A 2KH . . . F 6 97.625 105.463 94.287 1 122.22 ? O2A 2KH 2101 A 1 HETATM 4 N N3A 2KH . . . F 6 95.893 107.286 93.532 1 134.16 ? N3A 2KH 2101 A 1 HETATM 5 O O5' 2KH . . . F 6 96.062 106.453 96.153 1 124.72 ? O5' 2KH 2101 A 1 HETATM 6 P PB 2KH . . . F 6 94.407 107.344 92.707 1 139.1 ? PB 2KH 2101 A 1 HETATM 7 O O1B 2KH . . . F 6 93.31 107.413 93.733 1 130.31 ? O1B 2KH 2101 A 1 HETATM 8 O O2B 2KH . . . F 6 94.35 108.571 91.839 1 126.42 ? O2B 2KH 2101 A 1 HETATM 9 O O3B 2KH . . . F 6 94.196 105.994 91.79 1 125.14 ? O3B 2KH 2101 A 1 HETATM 10 P PG 2KH . . . F 6 94.831 105.78 90.29 1 124.59 ? PG 2KH 2101 A 1 HETATM 11 O O1G 2KH . . . F 6 94.101 104.643 89.626 1 129.58 ? O1G 2KH 2101 A 1 HETATM 12 O O2G 2KH . . . F 6 94.661 107.035 89.479 1 122.24 ? O2G 2KH 2101 A 1 HETATM 13 O O3G 2KH . . . F 6 96.302 105.48 90.382 1 122.38 ? O3G 2KH 2101 A 1 HETATM 14 C C5' 2KH . . . F 6 94.77 106.441 96.696 1 128.9 ? C5' 2KH 2101 A 1 HETATM 15 C C4' 2KH . . . F 6 94.659 107.494 97.788 1 125.09 ? C4' 2KH 2101 A 1 HETATM 16 O O4' 2KH . . . F 6 96.016 107.579 98.649 1 123.49 ? O4' 2KH 2101 A 1 HETATM 17 C C1' 2KH . . . F 6 96.076 108.789 99.132 1 122.39 ? C1' 2KH 2101 A 1 HETATM 18 C C2' 2KH . . . F 6 94.994 109.599 98.375 1 123.45 ? C2' 2KH 2101 A 1 HETATM 19 O O2' 2KH . . . F 6 93.947 109.805 99.204 1 126 ? O2' 2KH 2101 A 1 HETATM 20 C C3' 2KH . . . F 6 94.516 108.677 97.256 1 122.4 ? C3' 2KH 2101 A 1 HETATM 21 O O3' 2KH . . . F 6 93.078 108.921 96.947 1 117.54 ? O3' 2KH 2101 A 1 HETATM 22 N N1 2KH . . . F 6 97.401 109.386 98.862 1 123.38 ? N1 2KH 2101 A 1 HETATM 23 C C6 2KH . . . F 6 98.308 108.72 97.976 1 125.58 ? C6 2KH 2101 A 1 HETATM 24 C C2 2KH . . . F 6 97.783 110.653 99.501 1 123.63 ? C2 2KH 2101 A 1 HETATM 25 O O2 2KH . . . F 6 97.035 111.191 100.235 1 126.15 ? O2 2KH 2101 A 1 HETATM 26 N N3 2KH . . . F 6 99.105 111.239 99.214 1 123.41 ? N3 2KH 2101 A 1 HETATM 27 C C4 2KH . . . F 6 100.029 110.583 98.319 1 120.27 ? C4 2KH 2101 A 1 HETATM 28 O O4 2KH . . . F 6 101.083 111.063 98.097 1 120.59 ? O4 2KH 2101 A 1 HETATM 29 C C5 2KH . . . F 6 99.635 109.303 97.683 1 122.58 ? C5 2KH 2101 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #