data_6WMV # _model_server_result.job_id AmqWS-RbGg_4E41nga89gw _model_server_result.datetime_utc '2024-11-27 22:22:23' _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 6wmv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":301}' # _entry.id 6WMV # _exptl.entry_id 6WMV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 9 _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 90.74 _cell.angle_gamma 90 _cell.entry_id 6WMV _cell.length_a 78.089 _cell.length_b 60.857 _cell.length_c 85.417 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WMV _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 9 _struct_asym.id Q _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 metalc ? metalc1 A OD1 ASP 169 A ASP 31 1_555 D NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc2 A OD2 ASP 169 A ASP 31 1_555 D NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.125 ? metalc ? metalc3 A OG1 THR 172 A THR 34 1_555 E NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc4 A O ASP 206 A ASP 68 1_555 E NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc5 A OD1 ASP 206 A ASP 68 1_555 E NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc6 A OD1 ASP 206 A ASP 68 1_555 F NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc7 A OD2 ASP 206 A ASP 68 1_555 F NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc8 A OD1 ASP 209 A ASP 71 1_555 E NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc9 A OD2 ASP 209 A ASP 71 1_555 E NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc10 A OG1 THR 220 A THR 82 1_555 D NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc11 A OD1 ASP 227 A ASP 89 1_555 E NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc12 A O ASP 227 A ASP 89 1_555 F NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc13 A OD1 ASP 227 A ASP 89 1_555 F NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc14 A OD1 ASP 231 A ASP 93 1_555 F NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc15 D NA NA . A NA 302 1_555 G O16 TCE . A TCE 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? metalc ? metalc16 B OD1 ASP 206 C ASP 68 1_555 S NA NA . C NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc17 B OD2 ASP 206 C ASP 68 1_555 S NA NA . C NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc18 B OD1 ASP 227 C ASP 89 1_555 S NA NA . C NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc19 B OD1 ASP 231 C ASP 93 1_555 S NA NA . C NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? # _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 162 n n O3P HOP3 C5P sing 163 n n P O1P C5P doub 164 n n P O2P C5P sing 165 n n P O5' C5P sing 166 n n O2P HOP2 C5P sing 167 n n O5' C5' C5P sing 168 n n C5' C4' C5P sing 169 n n C5' "H5'1" C5P sing 170 n n C5' "H5'2" C5P sing 171 n n C4' O4' C5P sing 172 n n C4' C3' C5P sing 173 n n C4' H4' C5P sing 174 n n O4' C1' C5P sing 175 n n C3' O3' C5P sing 176 n n C3' C2' C5P sing 177 n n C3' H3' C5P sing 178 n n O3' HO3' C5P sing 179 n n C2' O2' C5P sing 180 n n C2' C1' C5P sing 181 n n C2' "H2'1" C5P sing 182 n n O2' HO2' C5P sing 183 n n C1' N1 C5P sing 184 n n C1' H1' C5P sing 185 n n N1 C2 C5P sing 186 n n N1 C6 C5P sing 187 n n C2 N3 C5P sing 188 n n C2 O2 C5P doub 189 n n N3 C4 C5P doub 190 n n C4 C5 C5P sing 191 n n C4 N4 C5P sing 192 n n C5 C6 C5P doub 193 n n C5 H5 C5P sing 194 n n C6 H6 C5P sing 195 n n N4 HN41 C5P sing 196 n n N4 HN42 C5P sing 197 n n # _atom_sites.entry_id 6WMV _atom_sites.fract_transf_matrix[1][1] 0.012806 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000165 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016432 _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] 0.011708 _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 LIP A 1 301 301 LIP LIP . D 3 NA A 1 302 302 NA NA . E 3 NA A 1 303 303 NA NA . F 3 NA A 1 304 304 NA NA . G 4 TCE A 1 305 305 TCE TCE . H 5 1PE A 1 306 306 1PE 1PE . I 6 OLC A 1 307 307 OLC OLC . J 6 OLC A 1 308 308 OLC OLC . K 6 OLC A 1 309 309 OLC OLC . L 7 8K6 A 1 310 310 8K6 8K6 . M 7 8K6 A 1 311 311 8K6 8K6 . N 7 8K6 A 1 312 312 8K6 8K6 . O 7 8K6 A 1 313 313 8K6 8K6 . P 8 GOL A 1 314 314 GOL GOL . Q 9 C5P C 1 301 301 C5P C5P . R 10 FLC C 1 302 302 FLC FLC . S 3 NA C 1 303 303 NA NA . T 5 1PE C 1 304 304 1PE 1PE . U 6 OLC C 1 305 305 OLC OLC . V 6 OLC C 1 306 306 OLC OLC . W 6 OLC C 1 307 307 OLC OLC . X 6 OLC C 1 308 308 OLC OLC . Y 7 8K6 C 1 309 309 8K6 8K6 . Z 7 8K6 C 1 310 310 8K6 8K6 . AA 8 GOL C 1 311 311 GOL GOL . BA 8 GOL C 1 312 312 GOL GOL . CA 11 HOH A 1 401 316 HOH HOH . CA 11 HOH A 2 402 315 HOH HOH . CA 11 HOH A 3 403 325 HOH HOH . CA 11 HOH A 4 404 322 HOH HOH . CA 11 HOH A 5 405 316 HOH HOH . CA 11 HOH A 6 406 319 HOH HOH . CA 11 HOH A 7 407 328 HOH HOH . CA 11 HOH A 8 408 315 HOH HOH . CA 11 HOH A 9 409 326 HOH HOH . CA 11 HOH A 10 410 324 HOH HOH . CA 11 HOH A 11 411 324 HOH HOH . CA 11 HOH A 12 412 323 HOH HOH . CA 11 HOH A 13 413 318 HOH HOH . CA 11 HOH A 14 414 317 HOH HOH . CA 11 HOH A 15 415 321 HOH HOH . CA 11 HOH A 16 416 320 HOH HOH . DA 11 HOH C 1 401 313 HOH HOH . DA 11 HOH C 2 402 321 HOH HOH . DA 11 HOH C 3 403 323 HOH HOH . DA 11 HOH C 4 404 317 HOH HOH . DA 11 HOH C 5 405 319 HOH HOH . DA 11 HOH C 6 406 314 HOH HOH . DA 11 HOH C 7 407 320 HOH HOH . DA 11 HOH C 8 408 327 HOH HOH . DA 11 HOH C 9 409 326 HOH HOH . DA 11 HOH C 10 410 318 HOH HOH . DA 11 HOH C 11 411 322 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 . . . Q 9 36.943 6.98 26.068 1 76.98 ? O3P C5P 301 C 1 HETATM 2 P P C5P . . . Q 9 37.035 8.276 25.317 1 94.72 ? P C5P 301 C 1 HETATM 3 O O1P C5P . . . Q 9 35.81 9.12 25.515 1 93.61 ? O1P C5P 301 C 1 HETATM 4 O O2P C5P . . . Q 9 38.311 9.014 25.592 1 73.01 ? O2P C5P 301 C 1 HETATM 5 O O5' C5P . . . Q 9 37.04 7.91 23.758 1 80.9 ? O5' C5P 301 C 1 HETATM 6 C C5' C5P . . . Q 9 35.82 7.387 23.202 1 81.46 ? C5' C5P 301 C 1 HETATM 7 C C4' C5P . . . Q 9 36.057 6.553 21.967 1 76 ? C4' C5P 301 C 1 HETATM 8 O O4' C5P . . . Q 9 37.255 5.749 22.092 1 70.07 ? O4' C5P 301 C 1 HETATM 9 C C3' C5P . . . Q 9 34.964 5.517 21.683 1 74.85 ? C3' C5P 301 C 1 HETATM 10 O O3' C5P . . . Q 9 33.772 6.101 21.169 1 78.88 ? O3' C5P 301 C 1 HETATM 11 C C2' C5P . . . Q 9 35.7 4.551 20.752 1 65.51 ? C2' C5P 301 C 1 HETATM 12 O O2' C5P . . . Q 9 35.856 5.007 19.429 1 62.14 ? O2' C5P 301 C 1 HETATM 13 C C1' C5P . . . Q 9 37.076 4.522 21.416 1 67.27 ? C1' C5P 301 C 1 HETATM 14 N N1 C5P . . . Q 9 37.255 3.356 22.322 1 61.75 ? N1 C5P 301 C 1 HETATM 15 C C2 C5P . . . Q 9 36.969 3.443 23.688 1 66.25 ? C2 C5P 301 C 1 HETATM 16 N N3 C5P . . . Q 9 37.137 2.353 24.464 1 66.68 ? N3 C5P 301 C 1 HETATM 17 C C4 C5P . . . Q 9 37.564 1.202 23.948 1 62.27 ? C4 C5P 301 C 1 HETATM 18 C C5 C5P . . . Q 9 37.867 1.085 22.568 1 49.98 ? C5 C5P 301 C 1 HETATM 19 C C6 C5P . . . Q 9 37.691 2.173 21.805 1 56.09 ? C6 C5P 301 C 1 HETATM 20 O O2 C5P . . . Q 9 36.552 4.501 24.171 1 74.92 ? O2 C5P 301 C 1 HETATM 21 N N4 C5P . . . Q 9 37.702 0.185 24.778 1 56.39 ? N4 C5P 301 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #