data_8CSB # _model_server_result.job_id KtC-K5sscanoGWk_qIK1yA _model_server_result.datetime_utc '2024-11-16 16:30:37' _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":"I","auth_seq_id":502}' # _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 . I 4 14.446 74.892 35.307 0.7 58.32 ? N1C CMK 502 B 1 HETATM 2 C C2C CMK . A . I 4 13.756 75.892 35.909 0.7 58.81 ? C2C CMK 502 B 1 HETATM 3 N N3C CMK . A . I 4 12.491 75.714 36.322 0.7 58.86 ? N3C CMK 502 B 1 HETATM 4 C C4C CMK . A . I 4 11.89 74.551 36.104 0.7 58.87 ? C4C CMK 502 B 1 HETATM 5 C C5C CMK . A . I 4 12.564 73.538 35.491 0.7 60.49 ? C5C CMK 502 B 1 HETATM 6 C C6C CMK . A . I 4 13.859 73.721 35.072 0.7 58.94 ? C6C CMK 502 B 1 HETATM 7 O O2C CMK . A . I 4 14.277 76.937 36.096 0.7 59.46 ? O2C CMK 502 B 1 HETATM 8 N N4C CMK . A . I 4 10.508 74.376 36.554 0.7 59.05 ? N4C CMK 502 B 1 HETATM 9 C C1' CMK . A . I 4 15.708 75.157 34.916 0.7 58.89 ? C1' CMK 502 B 1 HETATM 10 C C2' CMK . A . I 4 16.976 74.703 35.667 0.7 59.18 ? C2' CMK 502 B 1 HETATM 11 O O2' CMK . A . I 4 17.861 75.891 35.353 0.7 58.56 ? O2' CMK 502 B 1 HETATM 12 C C3' CMK . A . I 4 17.37 73.55 35.125 0.7 59.8 ? C3' CMK 502 B 1 HETATM 13 C C4' CMK . A . I 4 16.89 73.616 33.559 0.7 60.47 ? C4' CMK 502 B 1 HETATM 14 O O4' CMK . A . I 4 15.838 74.41 33.517 0.7 59.51 ? O4' CMK 502 B 1 HETATM 15 O O3' CMK . A . I 4 18.776 73.277 35.381 0.7 59.76 ? O3' CMK 502 B 1 HETATM 16 C C5' CMK . A . I 4 16.698 72.108 33.237 0.7 62.01 ? C5' CMK 502 B 1 HETATM 17 O O5' CMK . A . I 4 15.769 71.43 34.146 0.7 61.5 ? O5' CMK 502 B 1 HETATM 18 P PA CMK . A . I 4 14.984 70.054 33.551 0.7 60.31 ? PA CMK 502 B 1 HETATM 19 O O1A CMK . A . I 4 15.856 68.908 33.965 0.7 61.42 -1 O1A CMK 502 B 1 HETATM 20 O O2A CMK . A . I 4 13.622 69.896 34.132 0.7 59.92 ? O2A CMK 502 B 1 HETATM 21 O O6 CMK . A . I 4 15.53 68.157 31.078 0.7 74.5 ? O6 CMK 502 B 1 HETATM 22 C C2 CMK . A . I 4 14.459 69.213 30.992 0.7 72.05 ? C2 CMK 502 B 1 HETATM 23 O O2 CMK . A . I 4 14.739 70.281 31.893 0.7 68.41 ? O2 CMK 502 B 1 HETATM 24 C C3 CMK . A . I 4 14.32 69.895 29.62 0.7 75.09 ? C3 CMK 502 B 1 HETATM 25 C C4 CMK . A . I 4 15.571 69.853 28.85 0.7 81.94 ? C4 CMK 502 B 1 HETATM 26 O O4 CMK . A . I 4 16.548 70.603 29.615 0.7 74.43 ? O4 CMK 502 B 1 HETATM 27 C C5 CMK . A . I 4 16.151 68.49 28.656 0.7 89.21 ? C5 CMK 502 B 1 HETATM 28 C C6 CMK . A . I 4 15.874 67.512 29.799 0.7 82.51 ? C6 CMK 502 B 1 HETATM 29 C C7 CMK . A . I 4 17.056 66.6 30.014 0.7 84.2 ? C7 CMK 502 B 1 HETATM 30 C C1 CMK . A . I 4 13.182 68.546 31.358 0.7 69.11 ? C1 CMK 502 B 1 HETATM 31 O O1X CMK . A . I 4 13.223 67.349 31.819 0.7 68.12 ? O1X CMK 502 B 1 HETATM 32 O O1Y CMK . A . I 4 12.105 69.184 31.208 0.7 64.58 ? O1Y CMK 502 B 1 HETATM 33 O O5 CMK . A . I 4 17.567 68.678 28.438 0.7 90.04 ? O5 CMK 502 B 1 HETATM 34 C C8 CMK . A . I 4 16.768 65.259 29.297 0.7 83.97 ? C8 CMK 502 B 1 HETATM 35 O O8 CMK . A . I 4 17.969 64.681 28.841 0.7 79.86 ? O8 CMK 502 B 1 HETATM 36 O O7 CMK . A . I 4 18.233 67.22 29.514 0.7 88.03 ? O7 CMK 502 B 1 HETATM 37 H H5C CMK . A . I 4 12.144 72.719 35.357 0.7 73.16 ? H5C CMK 502 B 1 HETATM 38 H H6C CMK . A . I 4 14.315 73.041 34.632 0.7 71.3 ? H6C CMK 502 B 1 HETATM 39 H H4C1 CMK . A . I 4 10.129 73.613 36.461 0.7 71.43 ? H4C1 CMK 502 B 1 HETATM 40 H H4C2 CMK . A . I 4 10.087 75.026 36.929 0.7 71.43 ? H4C2 CMK 502 B 1 HETATM 41 H H1' CMK . A . I 4 15.799 76.119 34.998 0.7 71.24 ? H1' CMK 502 B 1 HETATM 42 H H2' CMK . A . I 4 16.895 74.48 36.608 0.7 71.6 ? H2' CMK 502 B 1 HETATM 43 H HA CMK . A . I 4 18.165 76.229 36.075 0.7 70.84 ? HA CMK 502 B 1 HETATM 44 H H3' CMK . A . I 4 16.903 72.793 35.512 0.7 72.34 ? H3' CMK 502 B 1 HETATM 45 H H4' CMK . A . I 4 17.474 74.043 32.913 0.7 73.14 ? H4' CMK 502 B 1 HETATM 46 H HB CMK . A . I 4 18.944 73.371 36.218 0.7 72.28 ? HB CMK 502 B 1 HETATM 47 H "H5'1" CMK . A . I 4 16.356 72.028 32.333 0.7 74.99 ? "H5'1" CMK 502 B 1 HETATM 48 H "H5'2" CMK . A . I 4 17.561 71.669 33.297 0.7 74.99 ? "H5'2" CMK 502 B 1 HETATM 49 H H3C1 CMK . A . I 4 14.067 70.821 29.755 0.7 90.68 ? H3C1 CMK 502 B 1 HETATM 50 H H3C2 CMK . A . I 4 13.627 69.443 29.115 0.7 90.68 ? H3C2 CMK 502 B 1 HETATM 51 H H4 CMK . A . I 4 15.389 70.226 27.974 0.7 98.9 ? H4 CMK 502 B 1 HETATM 52 H HC CMK . A . I 4 16.781 71.305 29.191 0.7 89.89 ? HC CMK 502 B 1 HETATM 53 H H5 CMK . A . I 4 15.752 68.069 27.879 0.7 107.63 ? H5 CMK 502 B 1 HETATM 54 H H6 CMK . A . I 4 15.114 66.979 29.517 0.7 99.59 ? H6 CMK 502 B 1 HETATM 55 H H7 CMK . A . I 4 17.198 66.429 30.958 0.7 101.61 ? H7 CMK 502 B 1 HETATM 56 H HD CMK . A . I 4 17.93 69.02 29.128 0.7 108.62 ? HD CMK 502 B 1 HETATM 57 H H8C1 CMK . A . I 4 16.182 65.42 28.54 0.7 101.34 ? H8C1 CMK 502 B 1 HETATM 58 H H8C2 CMK . A . I 4 16.335 64.651 29.917 0.7 101.34 ? H8C2 CMK 502 B 1 HETATM 59 H H8 CMK . A . I 4 18.455 64.502 29.514 0.7 96.41 ? H8 CMK 502 B 1 HETATM 60 H HE CMK . A . I 4 18.858 67.134 30.085 0.7 106.21 ? HE CMK 502 B 1 # _model_server_stats.io_time_ms 115 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 60 #