data_6U7Y # _model_server_result.job_id KiexTlug0JIGcNQMZnUjcw _model_server_result.datetime_utc '2024-11-13 18:06:28' _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 6u7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 6U7Y # _exptl.entry_id 6U7Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-MONOPHOSPHATE" _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 120 _cell.entry_id 6U7Y _cell.length_a 68.766 _cell.length_b 68.766 _cell.length_c 69.96 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6U7Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 A O3' C5P 1 A C5P 1 1_555 A P U 2 A U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.552 ? covale ? covale2 A O3' G 13 A G 13 1_555 A P TG 14 A TG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.615 ? covale ? covale3 A O2' TG 14 A TG 14 1_555 A P C 15 A C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.665 ? hydrog TYPE_16_PAIR hydrog1 A N3 U 2 A U 2 1_555 B O2 U 11 B U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog2 A O4 U 2 A U 2 1_555 B N3 U 11 B U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 G 3 A G 3 1_555 B N3 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 G 3 A G 3 1_555 B O2 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 G 3 A G 3 1_555 B N4 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 C 4 A C 4 1_555 B N1 G 9 B G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 C 4 A C 4 1_555 B O6 G 9 B G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 C 4 A C 4 1_555 B N2 G 9 B G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-U MISPAIR' hydrog9 A O4 U 5 A U 5 1_555 B N3 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 G 6 A G 6 1_555 B N3 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 G 6 A G 6 1_555 B O2 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 G 6 A G 6 1_555 B N4 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 G 7 A G 7 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N2 G 7 A G 7 1_555 B O2 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O6 G 7 A G 7 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 C 8 A C 8 1_555 B N1 G 5 B G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 C 8 A C 8 1_555 B O6 G 5 B G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 C 8 A C 8 1_555 B N2 G 5 B G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog19 A N3 U 9 A U 9 1_555 B N7 A 3 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog20 A O2 U 9 A U 9 1_555 B N6 A 3 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N1 A 11 A A 11 1_555 B N3 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N6 A 11 A A 11 1_555 B O4 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog23 A N1 G 12 A G 12 1_555 B O2 U 2 B U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog24 A O6 G 12 A G 12 1_555 B N3 U 2 B U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-U MISPAIR' hydrog25 A N2 G 12 A G 12 1_555 B O4 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N1 G 13 A G 13 1_555 B N3 C 1 B C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N2 G 13 A G 13 1_555 B O2 C 1 B C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O6 G 13 A G 13 1_555 B N4 C 1 B C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N3 C 15 A C 15 1_555 A N1 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N4 C 15 A C 15 1_555 A O6 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A O2 C 15 A C 15 1_555 A N2 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N3 C 16 A C 16 1_555 A N1 G 21 A G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N4 C 16 A C 16 1_555 A O6 G 21 A G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A O2 C 16 A C 16 1_555 A N2 G 21 A G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog35 A N2 G 17 A G 17 1_555 A N7 A 20 A A 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id C5P _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-MONOPHOSPHATE" _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 O3P P C5P sing 76 n n O3P HOP3 C5P sing 77 n n P O1P C5P doub 78 n n P O2P C5P sing 79 n n P O5' C5P sing 80 n n O2P HOP2 C5P sing 81 n n O5' C5' C5P sing 82 n n C5' C4' C5P sing 83 n n C5' "H5'1" C5P sing 84 n n C5' "H5'2" C5P sing 85 n n C4' O4' C5P sing 86 n n C4' C3' C5P sing 87 n n C4' H4' C5P sing 88 n n O4' C1' C5P sing 89 n n C3' O3' C5P sing 90 n n C3' C2' C5P sing 91 n n C3' H3' C5P sing 92 n n O3' HO3' C5P sing 93 n n C2' O2' C5P sing 94 n n C2' C1' C5P sing 95 n n C2' "H2'1" C5P sing 96 n n O2' HO2' C5P sing 97 n n C1' N1 C5P sing 98 n n C1' H1' C5P sing 99 n n N1 C2 C5P sing 100 n n N1 C6 C5P sing 101 n n C2 N3 C5P sing 102 n n C2 O2 C5P doub 103 n n N3 C4 C5P doub 104 n n C4 C5 C5P sing 105 n n C4 N4 C5P sing 106 n n C5 C6 C5P doub 107 n n C5 H5 C5P sing 108 n n C6 H6 C5P sing 109 n n N4 HN41 C5P sing 110 n n N4 HN42 C5P sing 111 n n # _atom_sites.entry_id 6U7Y _atom_sites.fract_transf_matrix[1][1] 0.014542 _atom_sites.fract_transf_matrix[1][2] 0.008396 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016792 _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] 0.014294 _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 3 C5P A 1 101 1 C5P C . D 4 HOH B 1 101 1 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 O O3P C5P . . . C 3 35.326 50.905 34.224 1 137.86 ? O3P C5P 101 A 1 HETATM 2 P P C5P . . . C 3 35.398 51.108 32.64 1 121.62 ? P C5P 101 A 1 HETATM 3 O O1P C5P . . . C 3 34.011 50.875 32.167 1 121.82 ? O1P C5P 101 A 1 HETATM 4 O O2P C5P . . . C 3 36.502 50.269 32.088 1 108.72 ? O2P C5P 101 A 1 HETATM 5 O O5' C5P . . . C 3 35.735 52.662 32.521 1 109.6 ? O5' C5P 101 A 1 HETATM 6 C C5' C5P . . . C 3 34.976 53.656 33.254 1 108.4 ? C5' C5P 101 A 1 HETATM 7 C C4' C5P . . . C 3 35.659 55.016 33.237 1 108.97 ? C4' C5P 101 A 1 HETATM 8 O O4' C5P . . . C 3 36.551 55.136 34.385 1 96.42 ? O4' C5P 101 A 1 HETATM 9 C C3' C5P . . . C 3 36.515 55.374 32.021 1 103.48 ? C3' C5P 101 A 1 HETATM 10 O O3' C5P . . . C 3 35.77 56.001 30.978 1 109.24 ? O3' C5P 101 A 1 HETATM 11 C C2' C5P . . . C 3 37.524 56.348 32.615 1 89.79 ? C2' C5P 101 A 1 HETATM 12 O O2' C5P . . . C 3 37.007 57.66 32.724 1 82.38 ? O2' C5P 101 A 1 HETATM 13 C C1' C5P . . . C 3 37.78 55.711 33.978 1 80.09 ? C1' C5P 101 A 1 HETATM 14 N N1 C5P . . . C 3 38.799 54.647 33.997 1 68.35 ? N1 C5P 101 A 1 HETATM 15 C C2 C5P . . . C 3 40.147 54.992 34.193 1 70.44 ? C2 C5P 101 A 1 HETATM 16 N N3 C5P . . . C 3 41.079 54.003 34.263 1 64.75 ? N3 C5P 101 A 1 HETATM 17 C C4 C5P . . . C 3 40.702 52.722 34.164 1 64.4 ? C4 C5P 101 A 1 HETATM 18 C C5 C5P . . . C 3 39.338 52.351 33.966 1 63.12 ? C5 C5P 101 A 1 HETATM 19 C C6 C5P . . . C 3 38.43 53.333 33.899 1 60.93 ? C6 C5P 101 A 1 HETATM 20 O O2 C5P . . . C 3 40.456 56.196 34.279 1 66.8 ? O2 C5P 101 A 1 HETATM 21 N N4 C5P . . . C 3 41.645 51.774 34.236 1 61.13 ? N4 C5P 101 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #