data_4BES # _model_server_result.job_id hU7BCBgI_IhbwA1_lF9Uyw _model_server_result.datetime_utc '2024-12-02 04:16:28' _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 4bes # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1000}' # _entry.id 4BES # _exptl.entry_id 4BES _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 2 _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 90 _cell.entry_id 4BES _cell.length_a 84.275 _cell.length_b 122.304 _cell.length_c 54.985 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BES _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 70 n n O3P HOP3 C5P sing 71 n n P O1P C5P doub 72 n n P O2P C5P sing 73 n n P O5' C5P sing 74 n n O2P HOP2 C5P sing 75 n n O5' C5' C5P sing 76 n n C5' C4' C5P sing 77 n n C5' "H5'1" C5P sing 78 n n C5' "H5'2" C5P sing 79 n n C4' O4' C5P sing 80 n n C4' C3' C5P sing 81 n n C4' H4' C5P sing 82 n n O4' C1' C5P sing 83 n n C3' O3' C5P sing 84 n n C3' C2' C5P sing 85 n n C3' H3' C5P sing 86 n n O3' HO3' C5P sing 87 n n C2' O2' C5P sing 88 n n C2' C1' C5P sing 89 n n C2' "H2'1" C5P sing 90 n n O2' HO2' C5P sing 91 n n C1' N1 C5P sing 92 n n C1' H1' C5P sing 93 n n N1 C2 C5P sing 94 n n N1 C6 C5P sing 95 n n C2 N3 C5P sing 96 n n C2 O2 C5P doub 97 n n N3 C4 C5P doub 98 n n C4 C5 C5P sing 99 n n C4 N4 C5P sing 100 n n C5 C6 C5P doub 101 n n C5 H5 C5P sing 102 n n C6 H6 C5P sing 103 n n N4 HN41 C5P sing 104 n n N4 HN42 C5P sing 105 n n # _atom_sites.entry_id 4BES _atom_sites.fract_transf_matrix[1][1] 0.011866 _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] 0.008176 _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] 0.018187 _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 B 2 C5P A 1 1000 1000 C5P C5P . C 3 PC A 1 2000 2000 PC PC . D 4 SO4 A 1 3000 3000 SO4 SO4 . E 4 SO4 A 1 3001 3001 SO4 SO4 . F 4 SO4 A 1 3002 3002 SO4 SO4 . G 5 HOH A 1 2001 2001 HOH HOH . G 5 HOH A 2 2002 2002 HOH HOH . G 5 HOH A 3 2003 2003 HOH HOH . G 5 HOH A 4 2004 2004 HOH HOH . G 5 HOH A 5 2005 2005 HOH HOH . G 5 HOH A 6 2006 2006 HOH HOH . G 5 HOH A 7 2007 2007 HOH HOH . G 5 HOH A 8 2008 2008 HOH HOH . G 5 HOH A 9 2009 2009 HOH HOH . G 5 HOH A 10 2010 2010 HOH HOH . G 5 HOH A 11 2011 2011 HOH HOH . G 5 HOH A 12 2012 2012 HOH HOH . G 5 HOH A 13 2013 2013 HOH HOH . G 5 HOH A 14 2014 2014 HOH HOH . G 5 HOH A 15 2015 2015 HOH HOH . G 5 HOH A 16 2016 2016 HOH HOH . G 5 HOH A 17 2017 2017 HOH HOH . G 5 HOH A 18 2018 2018 HOH HOH . G 5 HOH A 19 2019 2019 HOH HOH . G 5 HOH A 20 2020 2020 HOH HOH . G 5 HOH A 21 2021 2021 HOH HOH . G 5 HOH A 22 2022 2022 HOH HOH . G 5 HOH A 23 2023 2023 HOH HOH . G 5 HOH A 24 2024 2024 HOH HOH . G 5 HOH A 25 2025 2025 HOH HOH . G 5 HOH A 26 2026 2026 HOH HOH . G 5 HOH A 27 2027 2027 HOH HOH . G 5 HOH A 28 2028 2028 HOH HOH . G 5 HOH A 29 2029 2029 HOH HOH . G 5 HOH A 30 2030 2030 HOH HOH . G 5 HOH A 31 2031 2031 HOH HOH . G 5 HOH A 32 2032 2032 HOH HOH . G 5 HOH A 33 2033 2033 HOH HOH . G 5 HOH A 34 2034 2034 HOH HOH . G 5 HOH A 35 2035 2035 HOH HOH . G 5 HOH A 36 2036 2036 HOH HOH . G 5 HOH A 37 2037 2037 HOH HOH . G 5 HOH A 38 2038 2038 HOH HOH . G 5 HOH A 39 2039 2039 HOH HOH . G 5 HOH A 40 2040 2040 HOH HOH . G 5 HOH A 41 2041 2041 HOH HOH . G 5 HOH A 42 2042 2042 HOH HOH . G 5 HOH A 43 2043 2043 HOH HOH . G 5 HOH A 44 2044 2044 HOH HOH . G 5 HOH A 45 2045 2045 HOH HOH . G 5 HOH A 46 2046 2046 HOH HOH . G 5 HOH A 47 2047 2047 HOH HOH . G 5 HOH A 48 2048 2048 HOH HOH . G 5 HOH A 49 2049 2049 HOH HOH . G 5 HOH A 50 2050 2050 HOH HOH . G 5 HOH A 51 2051 2051 HOH HOH . G 5 HOH A 52 2052 2052 HOH HOH . G 5 HOH A 53 2053 2053 HOH HOH . G 5 HOH A 54 2054 2054 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 . . . B 2 -9.846 29.93 3.63 1 62.28 ? O3P C5P 1000 A 1 HETATM 2 P P C5P . . . B 2 -9.132 28.62 3.828 1 59.93 ? P C5P 1000 A 1 HETATM 3 O O1P C5P . . . B 2 -7.61 28.745 3.827 1 60.24 ? O1P C5P 1000 A 1 HETATM 4 O O2P C5P . . . B 2 -9.686 28.055 5.113 1 57.56 ? O2P C5P 1000 A 1 HETATM 5 O O5' C5P . . . B 2 -9.647 27.696 2.635 1 59.71 ? O5' C5P 1000 A 1 HETATM 6 C C5' C5P . . . B 2 -10.203 26.369 2.689 1 59.3 ? C5' C5P 1000 A 1 HETATM 7 C C4' C5P . . . B 2 -9.501 25.472 1.702 1 60.58 ? C4' C5P 1000 A 1 HETATM 8 O O4' C5P . . . B 2 -8.084 25.751 1.663 1 61.05 ? O4' C5P 1000 A 1 HETATM 9 C C3' C5P . . . B 2 -9.582 23.988 2.026 1 60.54 ? C3' C5P 1000 A 1 HETATM 10 O O3' C5P . . . B 2 -10.832 23.456 1.614 1 59.91 ? O3' C5P 1000 A 1 HETATM 11 C C2' C5P . . . B 2 -8.402 23.433 1.234 1 61.15 ? C2' C5P 1000 A 1 HETATM 12 O O2' C5P . . . B 2 -8.7 23.296 -0.147 1 63.32 ? O2' C5P 1000 A 1 HETATM 13 C C1' C5P . . . B 2 -7.368 24.551 1.409 1 60.61 ? C1' C5P 1000 A 1 HETATM 14 N N1 C5P . . . B 2 -6.42 24.295 2.52 1 60.45 ? N1 C5P 1000 A 1 HETATM 15 C C2 C5P . . . B 2 -5.419 23.332 2.318 1 60.95 ? C2 C5P 1000 A 1 HETATM 16 N N3 C5P . . . B 2 -4.542 23.076 3.328 1 60.59 ? N3 C5P 1000 A 1 HETATM 17 C C4 C5P . . . B 2 -4.631 23.733 4.497 1 60.11 ? C4 C5P 1000 A 1 HETATM 18 C C5 C5P . . . B 2 -5.644 24.714 4.727 1 59.28 ? C5 C5P 1000 A 1 HETATM 19 C C6 C5P . . . B 2 -6.511 24.961 3.73 1 59.04 ? C6 C5P 1000 A 1 HETATM 20 O O2 C5P . . . B 2 -5.368 22.736 1.24 1 61.82 ? O2 C5P 1000 A 1 HETATM 21 N N4 C5P . . . B 2 -3.749 23.44 5.452 1 60.07 ? N4 C5P 1000 A 1 HETATM 22 H HOP3 C5P . . . B 2 -9.773 30.563 2.871 1 62.45 ? HOP3 C5P 1000 A 1 HETATM 23 H HOP2 C5P . . . B 2 -9.855 28.623 5.908 1 57.32 ? HOP2 C5P 1000 A 1 HETATM 24 H "H5'1" C5P . . . B 2 -11.259 26.427 2.429 1 59.39 ? "H5'1" C5P 1000 A 1 HETATM 25 H "H5'2" C5P . . . B 2 -10.094 26.026 3.716 1 59.2 ? "H5'2" C5P 1000 A 1 HETATM 26 H H4' C5P . . . B 2 -9.853 25.669 0.691 1 60.77 ? H4' C5P 1000 A 1 HETATM 27 H H3' C5P . . . B 2 -9.458 23.798 3.092 1 60.63 ? H3' C5P 1000 A 1 HETATM 28 H HO3' C5P . . . B 2 -11.116 22.806 2.309 1 59.96 ? HO3' C5P 1000 A 1 HETATM 29 H "H2'1" C5P . . . B 2 -8.081 22.495 1.684 1 61.17 ? "H2'1" C5P 1000 A 1 HETATM 30 H HO2' C5P . . . B 2 -9.589 22.855 -0.177 1 63.5 ? HO2' C5P 1000 A 1 HETATM 31 H H1' C5P . . . B 2 -6.817 24.683 0.478 1 60.34 ? H1' C5P 1000 A 1 HETATM 32 H H5 C5P . . . B 2 -5.726 25.25 5.669 1 59.22 ? H5 C5P 1000 A 1 HETATM 33 H H6 C5P . . . B 2 -7.31 25.684 3.878 1 58.85 ? H6 C5P 1000 A 1 HETATM 34 H HN41 C5P . . . B 2 -3.016 22.749 5.327 1 60.1 ? HN41 C5P 1000 A 1 HETATM 35 H HN42 C5P . . . B 2 -3.775 23.9 6.357 1 60.12 ? HN42 C5P 1000 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #