data_1VH3 # _model_server_result.job_id s39HDKaS8FdLTRUckv1g6Q _model_server_result.datetime_utc '2024-10-10 22:32:23' _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 1vh3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":263}' # _entry.id 1VH3 # _exptl.entry_id 1VH3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 543.373 _entity.id 2 _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 1VH3 _cell.length_a 177.48 _cell.length_b 48.281 _cell.length_c 96.488 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VH3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,F 1 1 B,E,G 2 1 C,H 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E 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 PRO 28 A PRO 28 1_555 A N MSE 29 A MSE 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale2 A C MSE 29 A MSE 29 1_555 A N ILE 30 A ILE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale3 A C CYS 66 A CYS 66 1_555 A N MSE 67 A MSE 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale4 A C MSE 67 A MSE 67 1_555 A N THR 68 A THR 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale5 A C ASN 122 A ASN 122 1_555 A N MSE 123 A MSE 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 A C MSE 123 A MSE 123 1_555 A N ALA 124 A ALA 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 A C PHE 167 A PHE 167 1_555 A N MSE 168 A MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C MSE 168 A MSE 168 1_555 A N ASN 169 A ASN 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale9 B C PRO 28 B PRO 28 1_555 B N MSE 29 B MSE 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 B C MSE 29 B MSE 29 1_555 B N ILE 30 B ILE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale11 B C CYS 66 B CYS 66 1_555 B N MSE 67 B MSE 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale12 B C MSE 67 B MSE 67 1_555 B N THR 68 B THR 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 B C ASN 122 B ASN 122 1_555 B N MSE 123 B MSE 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale14 B C MSE 123 B MSE 123 1_555 B N ALA 124 B ALA 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale15 B C PHE 167 B PHE 167 1_555 B N MSE 168 B MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale16 B C MSE 168 B MSE 168 1_555 B N ASN 169 B ASN 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale17 C C PRO 28 C PRO 28 1_555 C N MSE 29 C MSE 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale18 C C MSE 29 C MSE 29 1_555 C N ILE 30 C ILE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale19 C C CYS 66 C CYS 66 1_555 C N MSE 67 C MSE 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale20 C C MSE 67 C MSE 67 1_555 C N THR 68 C THR 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale21 C C ASN 122 C ASN 122 1_555 C N MSE 123 C MSE 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale22 C C MSE 123 C MSE 123 1_555 C N ALA 124 C ALA 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? # _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 70 n y N1C C6C CMK sing 71 n y N1C C1' CMK sing 72 n n C2C N3C CMK sing 73 n y C2C O2C CMK doub 74 n n N3C C4C CMK doub 75 n y C4C C5C CMK sing 76 n y C4C N4C CMK sing 77 n n C5C C6C CMK doub 78 n y C5C H5C CMK sing 79 n n C6C H6C CMK sing 80 n n N4C H4C1 CMK sing 81 n n N4C H4C2 CMK sing 82 n n C1' C2' CMK sing 83 n n C1' O4' CMK sing 84 n n C1' H1' CMK sing 85 n n C2' O2' CMK sing 86 n n C2' C3' CMK sing 87 n n C2' H2' CMK sing 88 n n O2' HA CMK sing 89 n n C3' C4' CMK sing 90 n n C3' O3' CMK sing 91 n n C3' H3' CMK sing 92 n n C4' O4' CMK sing 93 n n C4' C5' CMK sing 94 n n C4' H4' CMK sing 95 n n O3' HB CMK sing 96 n n C5' O5' CMK sing 97 n n C5' "H5'1" CMK sing 98 n n C5' "H5'2" CMK sing 99 n n O5' PA CMK sing 100 n n PA O1A CMK sing 101 n n PA O2A CMK doub 102 n n PA O2 CMK sing 103 n n O1A HO1A CMK sing 104 n n O6 C2 CMK sing 105 n n O6 C6 CMK sing 106 n n C2 O2 CMK sing 107 n n C2 C3 CMK sing 108 n n C2 C1 CMK sing 109 n n C3 C4 CMK sing 110 n n C3 H3C1 CMK sing 111 n n C3 H3C2 CMK sing 112 n n C4 O4 CMK sing 113 n n C4 C5 CMK sing 114 n n C4 H4 CMK sing 115 n n O4 HC CMK sing 116 n n C5 C6 CMK sing 117 n n C5 O5 CMK sing 118 n n C5 H5 CMK sing 119 n n C6 C7 CMK sing 120 n n C6 H6 CMK sing 121 n n C7 C8 CMK sing 122 n n C7 O7 CMK sing 123 n n C7 H7 CMK sing 124 n n C1 O1X CMK sing 125 n n C1 O1Y CMK doub 126 n n O1X H1X CMK sing 127 n n O5 HD CMK sing 128 n n C8 O8 CMK sing 129 n n C8 H8C1 CMK sing 130 n n C8 H8C2 CMK sing 131 n n O8 H8 CMK sing 132 n n O7 HE CMK sing 133 n n # _atom_sites.entry_id 1VH3 _atom_sites.fract_transf_matrix[1][1] 0.005634 _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] 0.020712 _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] 0.010364 _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 D 2 CMK A 1 263 1 CMK CPO . E 2 CMK B 1 263 2 CMK CPO . F 3 HOH A 1 264 5 HOH HOH . F 3 HOH A 2 265 12 HOH HOH . F 3 HOH A 3 266 15 HOH HOH . F 3 HOH A 4 267 16 HOH HOH . F 3 HOH A 5 268 17 HOH HOH . F 3 HOH A 6 269 18 HOH HOH . F 3 HOH A 7 270 21 HOH HOH . F 3 HOH A 8 271 22 HOH HOH . F 3 HOH A 9 272 24 HOH HOH . F 3 HOH A 10 273 26 HOH HOH . F 3 HOH A 11 274 29 HOH HOH . F 3 HOH A 12 275 31 HOH HOH . F 3 HOH A 13 276 35 HOH HOH . F 3 HOH A 14 277 39 HOH HOH . F 3 HOH A 15 278 41 HOH HOH . F 3 HOH A 16 279 43 HOH HOH . F 3 HOH A 17 280 45 HOH HOH . F 3 HOH A 18 281 50 HOH HOH . F 3 HOH A 19 282 51 HOH HOH . F 3 HOH A 20 283 55 HOH HOH . F 3 HOH A 21 284 56 HOH HOH . F 3 HOH A 22 285 57 HOH HOH . F 3 HOH A 23 286 59 HOH HOH . F 3 HOH A 24 287 60 HOH HOH . F 3 HOH A 25 288 61 HOH HOH . F 3 HOH A 26 289 65 HOH HOH . F 3 HOH A 27 290 66 HOH HOH . F 3 HOH A 28 291 67 HOH HOH . F 3 HOH A 29 292 72 HOH HOH . F 3 HOH A 30 293 73 HOH HOH . F 3 HOH A 31 294 74 HOH HOH . F 3 HOH A 32 295 76 HOH HOH . F 3 HOH A 33 296 78 HOH HOH . F 3 HOH A 34 297 80 HOH HOH . F 3 HOH A 35 298 81 HOH HOH . F 3 HOH A 36 299 82 HOH HOH . F 3 HOH A 37 300 84 HOH HOH . F 3 HOH A 38 301 85 HOH HOH . F 3 HOH A 39 302 88 HOH HOH . F 3 HOH A 40 303 89 HOH HOH . F 3 HOH A 41 304 90 HOH HOH . F 3 HOH A 42 305 91 HOH HOH . F 3 HOH A 43 306 92 HOH HOH . F 3 HOH A 44 307 94 HOH HOH . F 3 HOH A 45 308 95 HOH HOH . G 3 HOH B 1 264 3 HOH HOH . G 3 HOH B 2 265 6 HOH HOH . G 3 HOH B 3 266 7 HOH HOH . G 3 HOH B 4 267 8 HOH HOH . G 3 HOH B 5 268 9 HOH HOH . G 3 HOH B 6 269 10 HOH HOH . G 3 HOH B 7 270 11 HOH HOH . G 3 HOH B 8 271 13 HOH HOH . G 3 HOH B 9 272 23 HOH HOH . G 3 HOH B 10 273 27 HOH HOH . G 3 HOH B 11 274 28 HOH HOH . G 3 HOH B 12 275 33 HOH HOH . G 3 HOH B 13 276 36 HOH HOH . G 3 HOH B 14 277 37 HOH HOH . G 3 HOH B 15 278 38 HOH HOH . G 3 HOH B 16 279 44 HOH HOH . G 3 HOH B 17 280 52 HOH HOH . G 3 HOH B 18 281 53 HOH HOH . G 3 HOH B 19 282 54 HOH HOH . G 3 HOH B 20 283 62 HOH HOH . G 3 HOH B 21 284 63 HOH HOH . G 3 HOH B 22 285 64 HOH HOH . G 3 HOH B 23 286 68 HOH HOH . G 3 HOH B 24 287 69 HOH HOH . G 3 HOH B 25 288 70 HOH HOH . G 3 HOH B 26 289 71 HOH HOH . G 3 HOH B 27 290 79 HOH HOH . G 3 HOH B 28 291 83 HOH HOH . G 3 HOH B 29 292 93 HOH HOH . H 3 HOH C 1 263 4 HOH HOH . H 3 HOH C 2 264 14 HOH HOH . H 3 HOH C 3 265 19 HOH HOH . H 3 HOH C 4 266 20 HOH HOH . H 3 HOH C 5 267 25 HOH HOH . H 3 HOH C 6 268 30 HOH HOH . H 3 HOH C 7 269 32 HOH HOH . H 3 HOH C 8 270 34 HOH HOH . H 3 HOH C 9 271 40 HOH HOH . H 3 HOH C 10 272 42 HOH HOH . H 3 HOH C 11 273 46 HOH HOH . H 3 HOH C 12 274 47 HOH HOH . H 3 HOH C 13 275 48 HOH HOH . H 3 HOH C 14 276 49 HOH HOH . H 3 HOH C 15 277 58 HOH HOH . H 3 HOH C 16 278 75 HOH HOH . H 3 HOH C 17 279 77 HOH HOH . H 3 HOH C 18 280 86 HOH HOH . H 3 HOH C 19 281 87 HOH HOH . H 3 HOH C 20 282 96 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 . . . D 2 45.289 38.318 18.151 1 43 ? N1C CMK 263 A 1 HETATM 2 C C2C CMK . . . D 2 45.747 39.297 18.984 1 42.68 ? C2C CMK 263 A 1 HETATM 3 N N3C CMK . . . D 2 46.825 40.023 18.75 1 42.44 ? N3C CMK 263 A 1 HETATM 4 C C4C CMK . . . D 2 47.523 39.828 17.627 1 42.37 ? C4C CMK 263 A 1 HETATM 5 C C5C CMK . . . D 2 47.116 38.862 16.718 1 42.06 ? C5C CMK 263 A 1 HETATM 6 C C6C CMK . . . D 2 45.977 38.132 17.029 1 42.46 ? C6C CMK 263 A 1 HETATM 7 O O2C CMK . . . D 2 45.145 39.543 20.041 1 42.94 ? O2C CMK 263 A 1 HETATM 8 N N4C CMK . . . D 2 48.586 40.612 17.447 1 42.19 ? N4C CMK 263 A 1 HETATM 9 C C1' CMK . . . D 2 44.039 37.626 18.582 1 44.07 ? C1' CMK 263 A 1 HETATM 10 C C2' CMK . . . D 2 43.08 38.145 17.621 1 44.78 ? C2' CMK 263 A 1 HETATM 11 O O2' CMK . . . D 2 42.233 39.104 18.145 1 46.84 ? O2' CMK 263 A 1 HETATM 12 C C3' CMK . . . D 2 42.417 36.932 17.049 1 44.89 ? C3' CMK 263 A 1 HETATM 13 C C4' CMK . . . D 2 43.418 35.81 17.287 1 44.55 ? C4' CMK 263 A 1 HETATM 14 O O4' CMK . . . D 2 44.484 36.399 18.07 1 44.76 ? O4' CMK 263 A 1 HETATM 15 O O3' CMK . . . D 2 41.243 36.59 17.768 1 44.66 ? O3' CMK 263 A 1 HETATM 16 C C5' CMK . . . D 2 43.965 35.503 15.904 1 45.36 ? C5' CMK 263 A 1 HETATM 17 O O5' CMK . . . D 2 43.724 34.165 15.541 1 45.89 ? O5' CMK 263 A 1 HETATM 18 P PA CMK . . . D 2 44.357 33.866 14.257 1 46.92 ? PA CMK 263 A 1 HETATM 19 O O1A CMK . . . D 2 45.018 35.145 13.706 1 45.43 ? O1A CMK 263 A 1 HETATM 20 O O2A CMK . . . D 2 43.152 33.43 13.408 1 46.63 ? O2A CMK 263 A 1 HETATM 21 O O6 CMK . . . D 2 45.572 30.743 14.866 1 41.2 ? O6 CMK 263 A 1 HETATM 22 C C2 CMK . . . D 2 46.069 31.884 14.18 1 42.12 ? C2 CMK 263 A 1 HETATM 23 O O2 CMK . . . D 2 45.311 32.74 14.502 1 44.39 ? O2 CMK 263 A 1 HETATM 24 C C3 CMK . . . D 2 47.47 32.277 14.639 1 40.07 ? C3 CMK 263 A 1 HETATM 25 C C4 CMK . . . D 2 48.359 31.298 15.33 1 39.48 ? C4 CMK 263 A 1 HETATM 26 O O4 CMK . . . D 2 49.064 31.899 16.401 1 39.29 ? O4 CMK 263 A 1 HETATM 27 C C5 CMK . . . D 2 47.742 30.066 15.745 1 39.33 ? C5 CMK 263 A 1 HETATM 28 C C6 CMK . . . D 2 46.549 29.644 14.803 1 39.81 ? C6 CMK 263 A 1 HETATM 29 C C7 CMK . . . D 2 45.87 28.332 15.185 1 39.75 ? C7 CMK 263 A 1 HETATM 30 C C1 CMK . . . D 2 46.08 31.588 12.704 1 42.05 ? C1 CMK 263 A 1 HETATM 31 O O1X CMK . . . D 2 44.926 31.501 12.152 1 42.72 ? O1X CMK 263 A 1 HETATM 32 O O1Y CMK . . . D 2 47.175 31.553 12.077 1 42.73 ? O1Y CMK 263 A 1 HETATM 33 O O5 CMK . . . D 2 47.279 30.209 17.073 1 38.72 ? O5 CMK 263 A 1 HETATM 34 C C8 CMK . . . D 2 44.445 28.135 14.7 1 40.08 ? C8 CMK 263 A 1 HETATM 35 O O8 CMK . . . D 2 44.516 27.783 13.307 1 41.58 ? O8 CMK 263 A 1 HETATM 36 O O7 CMK . . . D 2 46.672 27.214 14.842 1 38.82 ? O7 CMK 263 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #