data_8CSB # _model_server_result.job_id EQsmPnXpGBUAHpT4M9VeJw _model_server_result.datetime_utc '2025-07-14 06:27:54' _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 8csb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":505}' # _entry.id 8CSB # _exptl.entry_id 8CSB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 543.373 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID" _entity.pdbx_number_of_molecules 2 _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 8CSB _cell.length_a 92.71 _cell.length_b 157.44 _cell.length_c 120.06 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CSB _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_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,D,E,F,G,K 1 1,2 B,H,I,J,L 2 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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 60.03 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 I 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 covale ? covale1 A C HIS 28 A HIS 27 1_555 A N CSO 29 A CSO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C CSO 29 A CSO 28 1_555 A N ALA 30 A ALA 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 B C HIS 28 B HIS 27 1_555 B N CSO 29 B CSO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 B C CSO 29 B CSO 28 1_555 B N ALA 30 B ALA 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C17 H26 N3 O15 P' _chem_comp.formula_weight 543.373 _chem_comp.id CMK _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID' # 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 N1C C2C CMK sing 106 n y N1C C6C CMK sing 107 n y N1C C1' CMK sing 108 n n C2C N3C CMK sing 109 n y C2C O2C CMK doub 110 n n N3C C4C CMK doub 111 n y C4C C5C CMK sing 112 n y C4C N4C CMK sing 113 n n C5C C6C CMK doub 114 n y C5C H5C CMK sing 115 n n C6C H6C CMK sing 116 n n N4C H4C1 CMK sing 117 n n N4C H4C2 CMK sing 118 n n C1' C2' CMK sing 119 n n C1' O4' CMK sing 120 n n C1' H1' CMK sing 121 n n C2' O2' CMK sing 122 n n C2' C3' CMK sing 123 n n C2' H2' CMK sing 124 n n O2' HA CMK sing 125 n n C3' C4' CMK sing 126 n n C3' O3' CMK sing 127 n n C3' H3' CMK sing 128 n n C4' O4' CMK sing 129 n n C4' C5' CMK sing 130 n n C4' H4' CMK sing 131 n n O3' HB CMK sing 132 n n C5' O5' CMK sing 133 n n C5' "H5'1" CMK sing 134 n n C5' "H5'2" CMK sing 135 n n O5' PA CMK sing 136 n n PA O1A CMK sing 137 n n PA O2A CMK doub 138 n n PA O2 CMK sing 139 n n O1A HO1A CMK sing 140 n n O6 C2 CMK sing 141 n n O6 C6 CMK sing 142 n n C2 O2 CMK sing 143 n n C2 C3 CMK sing 144 n n C2 C1 CMK sing 145 n n C3 C4 CMK sing 146 n n C3 H3C1 CMK sing 147 n n C3 H3C2 CMK sing 148 n n C4 O4 CMK sing 149 n n C4 C5 CMK sing 150 n n C4 H4 CMK sing 151 n n O4 HC CMK sing 152 n n C5 C6 CMK sing 153 n n C5 O5 CMK sing 154 n n C5 H5 CMK sing 155 n n C6 C7 CMK sing 156 n n C6 H6 CMK sing 157 n n C7 C8 CMK sing 158 n n C7 O7 CMK sing 159 n n C7 H7 CMK sing 160 n n C1 O1X CMK sing 161 n n C1 O1Y CMK doub 162 n n O1X H1X CMK sing 163 n n O5 HD CMK sing 164 n n C8 O8 CMK sing 165 n n C8 H8C1 CMK sing 166 n n C8 H8C2 CMK sing 167 n n O8 H8 CMK sing 168 n n O7 HE CMK sing 169 n n # _atom_sites.entry_id 8CSB _atom_sites.fract_transf_matrix[1][1] 0.010786 _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] 0.006352 _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] 0.008329 _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 2 PO4 A 1 501 1 PO4 PO4 . D 2 PO4 A 1 502 3 PO4 PO4 . E 2 PO4 A 1 503 4 PO4 PO4 . F 3 C5P A 1 504 1 C5P C5P . G 4 CMK A 1 505 2 CMK CMK . H 2 PO4 B 1 501 2 PO4 PO4 . I 4 CMK B 1 502 1 CMK CMK . J 3 C5P B 1 503 2 C5P C5P . K 5 HOH A 1 601 82 HOH HOH . K 5 HOH A 2 602 34 HOH HOH . K 5 HOH A 3 603 37 HOH HOH . K 5 HOH A 4 604 78 HOH HOH . K 5 HOH A 5 605 76 HOH HOH . K 5 HOH A 6 606 33 HOH HOH . K 5 HOH A 7 607 55 HOH HOH . K 5 HOH A 8 608 74 HOH HOH . K 5 HOH A 9 609 69 HOH HOH . K 5 HOH A 10 610 36 HOH HOH . K 5 HOH A 11 611 39 HOH HOH . K 5 HOH A 12 612 62 HOH HOH . K 5 HOH A 13 613 79 HOH HOH . K 5 HOH A 14 614 51 HOH HOH . K 5 HOH A 15 615 21 HOH HOH . K 5 HOH A 16 616 9 HOH HOH . K 5 HOH A 17 617 68 HOH HOH . K 5 HOH A 18 618 44 HOH HOH . K 5 HOH A 19 619 27 HOH HOH . K 5 HOH A 20 620 3 HOH HOH . K 5 HOH A 21 621 30 HOH HOH . K 5 HOH A 22 622 8 HOH HOH . K 5 HOH A 23 623 6 HOH HOH . K 5 HOH A 24 624 73 HOH HOH . K 5 HOH A 25 625 53 HOH HOH . K 5 HOH A 26 626 10 HOH HOH . K 5 HOH A 27 627 49 HOH HOH . K 5 HOH A 28 628 28 HOH HOH . K 5 HOH A 29 629 59 HOH HOH . K 5 HOH A 30 630 20 HOH HOH . K 5 HOH A 31 631 18 HOH HOH . K 5 HOH A 32 632 81 HOH HOH . K 5 HOH A 33 633 56 HOH HOH . K 5 HOH A 34 634 43 HOH HOH . K 5 HOH A 35 635 50 HOH HOH . K 5 HOH A 36 636 66 HOH HOH . K 5 HOH A 37 637 19 HOH HOH . K 5 HOH A 38 638 31 HOH HOH . K 5 HOH A 39 639 58 HOH HOH . K 5 HOH A 40 640 54 HOH HOH . K 5 HOH A 41 641 67 HOH HOH . K 5 HOH A 42 642 83 HOH HOH . K 5 HOH A 43 643 64 HOH HOH . K 5 HOH A 44 644 71 HOH HOH . L 5 HOH B 1 601 75 HOH HOH . L 5 HOH B 2 602 80 HOH HOH . L 5 HOH B 3 603 48 HOH HOH . L 5 HOH B 4 604 13 HOH HOH . L 5 HOH B 5 605 1 HOH HOH . L 5 HOH B 6 606 63 HOH HOH . L 5 HOH B 7 607 57 HOH HOH . L 5 HOH B 8 608 23 HOH HOH . L 5 HOH B 9 609 46 HOH HOH . L 5 HOH B 10 610 61 HOH HOH . L 5 HOH B 11 611 16 HOH HOH . L 5 HOH B 12 612 35 HOH HOH . L 5 HOH B 13 613 25 HOH HOH . L 5 HOH B 14 614 32 HOH HOH . L 5 HOH B 15 615 5 HOH HOH . L 5 HOH B 16 616 17 HOH HOH . L 5 HOH B 17 617 12 HOH HOH . L 5 HOH B 18 618 2 HOH HOH . L 5 HOH B 19 619 14 HOH HOH . L 5 HOH B 20 620 41 HOH HOH . L 5 HOH B 21 621 4 HOH HOH . L 5 HOH B 22 622 38 HOH HOH . L 5 HOH B 23 623 26 HOH HOH . L 5 HOH B 24 624 52 HOH HOH . L 5 HOH B 25 625 72 HOH HOH . L 5 HOH B 26 626 7 HOH HOH . L 5 HOH B 27 627 45 HOH HOH . L 5 HOH B 28 628 85 HOH HOH . L 5 HOH B 29 629 70 HOH HOH . L 5 HOH B 30 630 40 HOH HOH . L 5 HOH B 31 631 47 HOH HOH . L 5 HOH B 32 632 84 HOH HOH . L 5 HOH B 33 633 22 HOH HOH . L 5 HOH B 34 634 11 HOH HOH . L 5 HOH B 35 635 60 HOH HOH . L 5 HOH B 36 636 15 HOH HOH . L 5 HOH B 37 637 24 HOH HOH . L 5 HOH B 38 638 77 HOH HOH . L 5 HOH B 39 639 42 HOH HOH . L 5 HOH B 40 640 65 HOH HOH . L 5 HOH B 41 641 29 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 N1C CMK . A . G 4 12.008 16.423 20.621 0.71 57.4 ? N1C CMK 505 A 1 HETATM 2 C C2C CMK . A . G 4 11.166 15.453 20.196 0.71 62.46 ? C2C CMK 505 A 1 HETATM 3 N N3C CMK . A . G 4 9.845 15.696 20.122 0.71 58.93 ? N3C CMK 505 A 1 HETATM 4 C C4C CMK . A . G 4 9.352 16.88 20.484 0.71 57.22 ? C4C CMK 505 A 1 HETATM 5 C C5C CMK . A . G 4 10.185 17.867 20.944 0.71 57.23 ? C5C CMK 505 A 1 HETATM 6 C C6C CMK . A . G 4 11.532 17.604 21.019 0.71 56.94 ? C6C CMK 505 A 1 HETATM 7 O O2C CMK . A . G 4 11.55 14.39 19.846 0.71 57.46 ? O2C CMK 505 A 1 HETATM 8 N N4C CMK . A . G 4 7.907 17.048 20.373 0.71 57.27 ? N4C CMK 505 A 1 HETATM 9 C C1' CMK . A . G 4 13.305 16.098 20.657 0.71 57.37 ? C1' CMK 505 A 1 HETATM 10 C C2' CMK . A . G 4 14.32 16.482 19.541 0.71 57.43 ? C2' CMK 505 A 1 HETATM 11 O O2' CMK . A . G 4 15.393 15.419 19.682 0.71 57.75 ? O2' CMK 505 A 1 HETATM 12 C C3' CMK . A . G 4 14.761 17.712 19.814 0.71 59.5 ? C3' CMK 505 A 1 HETATM 13 C C4' CMK . A . G 4 14.778 17.692 21.451 0.71 58.34 ? C4' CMK 505 A 1 HETATM 14 O O4' CMK . A . G 4 13.834 16.891 21.889 0.71 57.87 ? O4' CMK 505 A 1 HETATM 15 O O3' CMK . A . G 4 16.034 18.136 19.245 0.71 57.2 ? O3' CMK 505 A 1 HETATM 16 C C5' CMK . A . G 4 14.67 19.177 21.859 0.71 60.23 ? C5' CMK 505 A 1 HETATM 17 O O5' CMK . A . G 4 13.695 20.005 21.126 0.71 59.67 ? O5' CMK 505 A 1 HETATM 18 P PA CMK . A . G 4 13.075 21.363 21.96 0.71 58.47 ? PA CMK 505 A 1 HETATM 19 O O1A CMK . A . G 4 13.903 22.453 21.393 0.71 61.18 -1 O1A CMK 505 A 1 HETATM 20 O O2A CMK . A . G 4 11.623 21.4 21.582 0.71 57.84 ? O2A CMK 505 A 1 HETATM 21 O O6 CMK . A . G 4 14.421 23.476 24.072 0.71 71.4 ? O6 CMK 505 A 1 HETATM 22 C C2 CMK . A . G 4 13.373 22.483 24.477 0.71 69.22 ? C2 CMK 505 A 1 HETATM 23 O O2 CMK . A . G 4 13.355 21.33 23.618 0.71 72.43 ? O2 CMK 505 A 1 HETATM 24 C C3 CMK . A . G 4 13.656 21.924 25.881 0.71 71.64 ? C3 CMK 505 A 1 HETATM 25 C C4 CMK . A . G 4 15.09 21.622 26.039 0.71 73.44 ? C4 CMK 505 A 1 HETATM 26 O O4 CMK . A . G 4 15.538 20.854 24.911 0.71 67.27 ? O4 CMK 505 A 1 HETATM 27 C C5 CMK . A . G 4 15.872 22.885 26.034 0.71 77.41 ? C5 CMK 505 A 1 HETATM 28 C C6 CMK . A . G 4 15.245 23.984 25.19 0.71 76.39 ? C6 CMK 505 A 1 HETATM 29 C C7 CMK . A . G 4 16.302 24.874 24.574 0.71 77.3 ? C7 CMK 505 A 1 HETATM 30 C C1 CMK . A . G 4 12.027 23.125 24.458 0.71 66 ? C1 CMK 505 A 1 HETATM 31 O O1X CMK . A . G 4 11.825 24.256 23.848 0.71 61.89 ? O1X CMK 505 A 1 HETATM 32 O O1Y CMK . A . G 4 11.118 22.45 25.048 0.71 62.45 ? O1Y CMK 505 A 1 HETATM 33 O O5 CMK . A . G 4 17.147 22.57 25.475 0.71 78.35 ? O5 CMK 505 A 1 HETATM 34 C C8 CMK . A . G 4 16.593 26.019 25.567 0.71 79.44 ? C8 CMK 505 A 1 HETATM 35 O O8 CMK . A . G 4 17.829 26.614 25.253 0.71 76.14 ? O8 CMK 505 A 1 HETATM 36 O O7 CMK . A . G 4 17.446 24.079 24.273 0.71 78.45 ? O7 CMK 505 A 1 HETATM 37 H H5C CMK . A . G 4 9.846 18.694 21.2 0.71 69.25 ? H5C CMK 505 A 1 HETATM 38 H H6C CMK . A . G 4 12.113 18.251 21.348 0.71 68.9 ? H6C CMK 505 A 1 HETATM 39 H H4C1 CMK . A . G 4 7.543 17.745 20.708 0.71 69.3 ? H4C1 CMK 505 A 1 HETATM 40 H H4C2 CMK . A . G 4 7.43 16.468 19.951 0.71 69.3 ? H4C2 CMK 505 A 1 HETATM 41 H H1' CMK . A . G 4 13.342 15.13 20.614 0.71 69.41 ? H1' CMK 505 A 1 HETATM 42 H H2' CMK . A . G 4 13.945 16.543 18.649 0.71 69.49 ? H2' CMK 505 A 1 HETATM 43 H HA CMK . A . G 4 15.814 15.365 18.944 0.71 69.87 ? HA CMK 505 A 1 HETATM 44 H H3' CMK . A . G 4 14.142 18.35 19.424 0.71 71.97 ? H3' CMK 505 A 1 HETATM 45 H H4' CMK . A . G 4 15.569 17.279 21.831 0.71 70.59 ? H4' CMK 505 A 1 HETATM 46 H HB CMK . A . G 4 15.879 18.345 18.424 0.71 69.21 ? HB CMK 505 A 1 HETATM 47 H "H5'1" CMK . A . G 4 14.43 19.205 22.798 0.71 72.85 ? "H5'1" CMK 505 A 1 HETATM 48 H "H5'2" CMK . A . G 4 15.544 19.578 21.736 0.71 72.85 ? "H5'2" CMK 505 A 1 HETATM 49 H H3C1 CMK . A . G 4 13.393 22.581 26.546 0.71 86.54 ? H3C1 CMK 505 A 1 HETATM 50 H H3C2 CMK . A . G 4 13.142 21.112 26.012 0.71 86.54 ? H3C2 CMK 505 A 1 HETATM 51 H H4 CMK . A . G 4 15.227 21.115 26.854 0.71 88.7 ? H4 CMK 505 A 1 HETATM 52 H HC CMK . A . G 4 15.029 20.182 24.828 0.71 81.3 ? HC CMK 505 A 1 HETATM 53 H H5 CMK . A . G 4 15.947 23.216 26.943 0.71 93.47 ? H5 CMK 505 A 1 HETATM 54 H H6 CMK . A . G 4 14.699 24.497 25.805 0.71 92.24 ? H6 CMK 505 A 1 HETATM 55 H H7 CMK . A . G 4 16.012 25.275 23.74 0.71 93.33 ? H7 CMK 505 A 1 HETATM 56 H HD CMK . A . G 4 17.416 21.834 25.803 0.71 94.59 ? HD CMK 505 A 1 HETATM 57 H H8C1 CMK . A . G 4 15.89 26.685 25.507 0.71 95.91 ? H8C1 CMK 505 A 1 HETATM 58 H H8C2 CMK . A . G 4 16.626 25.664 26.469 0.71 95.91 ? H8C2 CMK 505 A 1 HETATM 59 H H8 CMK . A . G 4 18.331 26.028 24.898 0.71 91.94 ? H8 CMK 505 A 1 HETATM 60 H HE CMK . A . G 4 17.944 24.036 24.959 0.71 94.71 ? HE CMK 505 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 600 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 60 #