data_2XR7 # _model_server_result.job_id QD9G8d770Hxa06_h06XhMA _model_server_result.datetime_utc '2024-11-08 07:05:31' _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 2xr7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 2XR7 # _exptl.entry_id 2XR7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 853.58 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MALONYL-COENZYME A' _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 2XR7 _cell.length_a 98.079 _cell.length_b 98.079 _cell.length_c 151.84 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XR7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 42 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 _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' 7_555 y,x,-z 0 1 0 1 0 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 # 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 ARG 36 A ARG 36 1_555 A N MSE 37 A MSE 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale2 A C MSE 37 A MSE 37 1_555 A N ARG 38 A ARG 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C ASP 106 A ASP 106 1_555 A N MSE 107 A MSE 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 A C MSE 107 A MSE 107 1_555 A N ASP 108 A ASP 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C GLY 213 A GLY 213 1_555 A N MSE 214 A MSE 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale6 A C MSE 214 A MSE 214 1_555 A N SER 215 A SER 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C GLU 219 A GLU 219 1_555 A N MSE 220 A MSE 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 A C MSE 220 A MSE 220 1_555 A N LYS 221 A LYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale9 A C HIS 225 A HIS 225 1_555 A N MSE 226 A MSE 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale10 A C MSE 226 A MSE 226 1_555 A N MSE 227 A MSE 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale11 A C MSE 227 A MSE 227 1_555 A N LYS 228 A LYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale12 A C LYS 228 A LYS 228 1_555 A N MSE 229 A MSE 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 A C MSE 229 A MSE 229 1_555 A N SER 230 A SER 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 A C GLY 296 A GLY 296 1_555 A N MSE 297 A MSE 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 A C MSE 297 A MSE 297 1_555 A N GLU 298 A GLU 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale16 A C ARG 355 A ARG 355 1_555 A N MSE 356 A MSE 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale17 A C MSE 356 A MSE 356 1_555 A N LYS 357 A LYS 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale18 A C SER 415 A SER 415 1_555 A N MSE 416 A MSE 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale19 A C MSE 416 A MSE 416 1_555 A N SER 417 A SER 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale20 A C ARG 438 A ARG 438 1_555 A N MSE 439 A MSE 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale21 A C MSE 439 A MSE 439 1_555 A N ASN 440 A ASN 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale22 A C ALA 444 A ALA 444 1_555 A N MSE 445 A MSE 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale23 A C MSE 445 A MSE 445 1_555 A N PHE 446 A PHE 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C24 H38 N7 O19 P3 S' _chem_comp.formula_weight 853.58 _chem_comp.id MLC _chem_comp.mon_nstd_flag . _chem_comp.name 'MALONYL-COENZYME A' _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 C8 N9 MLC sing 216 n y C8 N7 MLC doub 217 n y C8 H8 MLC sing 218 n n N9 C4 MLC sing 219 n y N9 C1' MLC sing 220 n n C4 C5 MLC sing 221 n y C4 N3 MLC doub 222 n y C5 N7 MLC sing 223 n y C5 C6 MLC doub 224 n y N3 C2 MLC sing 225 n y C2 N1 MLC doub 226 n y C2 H2 MLC sing 227 n n N1 C6 MLC sing 228 n y C6 N6 MLC sing 229 n n N6 HN61 MLC sing 230 n n N6 HN62 MLC sing 231 n n C1' C2' MLC sing 232 n n C1' O4' MLC sing 233 n n C1' H1' MLC sing 234 n n C2' O2' MLC sing 235 n n C2' C3' MLC sing 236 n n C2' H2' MLC sing 237 n n O2' HO2 MLC sing 238 n n C3' O3' MLC sing 239 n n C3' C4' MLC sing 240 n n C3' H3' MLC sing 241 n n O3' P3 MLC sing 242 n n C4' O4' MLC sing 243 n n C4' C5' MLC sing 244 n n C4' H4' MLC sing 245 n n C5' O5' MLC sing 246 n n C5' "H5'1" MLC sing 247 n n C5' "H5'2" MLC sing 248 n n O5' P1 MLC sing 249 n n P1 O11 MLC doub 250 n n P1 O12 MLC sing 251 n n P1 O6 MLC sing 252 n n O12 H12 MLC sing 253 n n O6 P2 MLC sing 254 n n P2 O21 MLC doub 255 n n P2 O22 MLC sing 256 n n P2 O7 MLC sing 257 n n O22 H22 MLC sing 258 n n O7 CPB MLC sing 259 n n CPB CPA MLC sing 260 n n CPB HPB1 MLC sing 261 n n CPB HPB2 MLC sing 262 n n CPA CP7 MLC sing 263 n n CPA CP9 MLC sing 264 n n CPA CP8 MLC sing 265 n n CP7 OP3 MLC sing 266 n n CP7 CP6 MLC sing 267 n n CP7 HP7 MLC sing 268 n n CP9 HP91 MLC sing 269 n n CP9 HP92 MLC sing 270 n n CP9 HP93 MLC sing 271 n n CP8 HP81 MLC sing 272 n n CP8 HP82 MLC sing 273 n n CP8 HP83 MLC sing 274 n n OP3 HP3 MLC sing 275 n n CP6 OP2 MLC doub 276 n n CP6 NP2 MLC sing 277 n n NP2 CP5 MLC sing 278 n n NP2 HP2 MLC sing 279 n n CP5 CP4 MLC sing 280 n n CP5 HP51 MLC sing 281 n n CP5 HP52 MLC sing 282 n n CP4 CP3 MLC sing 283 n n CP4 HP41 MLC sing 284 n n CP4 HP42 MLC sing 285 n n CP3 OP1 MLC doub 286 n n CP3 NP1 MLC sing 287 n n NP1 CP2 MLC sing 288 n n NP1 HP1 MLC sing 289 n n CP2 CP1 MLC sing 290 n n CP2 HP21 MLC sing 291 n n CP2 HP22 MLC sing 292 n n CP1 S MLC sing 293 n n CP1 HP11 MLC sing 294 n n CP1 HP12 MLC sing 295 n n S CM1 MLC sing 296 n n P3 O31 MLC sing 297 n n P3 O32 MLC sing 298 n n P3 O33 MLC doub 299 n n O31 H31 MLC sing 300 n n O32 H32 MLC sing 301 n n CM1 CM2 MLC sing 302 n n CM1 OM2 MLC doub 303 n n CM2 CM3 MLC sing 304 n n CM2 HM21 MLC sing 305 n n CM2 HM22 MLC sing 306 n n CM3 OM3 MLC sing 307 n n CM3 OM4 MLC doub 308 n n OM3 HO3 MLC sing 309 n n # _atom_sites.entry_id 2XR7 _atom_sites.fract_transf_matrix[1][1] 0.010196 _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] 0.010196 _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] 0.006586 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id MLC _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1001 _pdbx_nonpoly_scheme.auth_seq_num 1001 _pdbx_nonpoly_scheme.pdb_mon_id MLC _pdbx_nonpoly_scheme.auth_mon_id MLC _pdbx_nonpoly_scheme.pdb_ins_code . # 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 C C1' MLC . . . B 2 -3.978 -1.1 24.429 0.5 41.96 ? C1' MLC 1001 A 1 HETATM 2 C C2' MLC . . . B 2 -4.066 -0.071 23.286 0.5 42.48 ? C2' MLC 1001 A 1 HETATM 3 O O2' MLC . . . B 2 -2.798 0.573 23.14 0.5 40.63 ? O2' MLC 1001 A 1 HETATM 4 C C3' MLC . . . B 2 -4.413 -0.928 22.038 0.5 41.1 ? C3' MLC 1001 A 1 HETATM 5 O O3' MLC . . . B 2 -3.316 -1.125 21.128 0.5 36.01 ? O3' MLC 1001 A 1 HETATM 6 C C4' MLC . . . B 2 -4.763 -2.277 22.662 0.5 41.64 ? C4' MLC 1001 A 1 HETATM 7 O O4' MLC . . . B 2 -3.799 -2.371 23.723 0.5 39.79 ? O4' MLC 1001 A 1 HETATM 8 C C5' MLC . . . B 2 -6.24 -2.253 23.186 0.5 42.63 ? C5' MLC 1001 A 1 HETATM 9 O O5' MLC . . . B 2 -6.68 -0.967 23.731 0.5 39.62 ? O5' MLC 1001 A 1 HETATM 10 P P1 MLC . . . B 2 -8.131 -0.924 24.527 0.5 42.21 ? P1 MLC 1001 A 1 HETATM 11 O O11 MLC . . . B 2 -8.164 -2.057 25.497 0.5 39.88 ? O11 MLC 1001 A 1 HETATM 12 O O12 MLC . . . B 2 -8.398 0.465 24.984 0.5 42.23 ? O12 MLC 1001 A 1 HETATM 13 O O6 MLC . . . B 2 -9.194 -1.258 23.367 0.5 36.93 ? O6 MLC 1001 A 1 HETATM 14 P P2 MLC . . . B 2 -9.247 -2.729 22.722 0.5 38.14 ? P2 MLC 1001 A 1 HETATM 15 O O21 MLC . . . B 2 -9.735 -2.426 21.373 0.5 39.62 ? O21 MLC 1001 A 1 HETATM 16 O O22 MLC . . . B 2 -8.001 -3.533 22.915 0.5 36.68 ? O22 MLC 1001 A 1 HETATM 17 O O7 MLC . . . B 2 -10.433 -3.482 23.519 0.5 38.25 ? O7 MLC 1001 A 1 HETATM 18 C CPB MLC . . . B 2 -11.134 -2.84 24.59 0.5 37.87 ? CPB MLC 1001 A 1 HETATM 19 C CPA MLC . . . B 2 -11.851 -3.876 25.462 0.5 36.83 ? CPA MLC 1001 A 1 HETATM 20 C CP7 MLC . . . B 2 -10.834 -4.581 26.336 0.5 40.08 ? CP7 MLC 1001 A 1 HETATM 21 C CP9 MLC . . . B 2 -12.545 -4.93 24.595 0.5 29.85 ? CP9 MLC 1001 A 1 HETATM 22 C CP8 MLC . . . B 2 -12.857 -3.166 26.354 0.5 38.1 ? CP8 MLC 1001 A 1 HETATM 23 O OP3 MLC . . . B 2 -9.551 -4.582 25.678 0.5 42.69 ? OP3 MLC 1001 A 1 HETATM 24 C CP6 MLC . . . B 2 -11.365 -6.012 26.556 0.5 42.78 ? CP6 MLC 1001 A 1 HETATM 25 O OP2 MLC . . . B 2 -12 -6.285 27.582 0.5 42.78 ? OP2 MLC 1001 A 1 HETATM 26 N NP2 MLC . . . B 2 -11.125 -6.885 25.565 0.5 40.4 ? NP2 MLC 1001 A 1 HETATM 27 P P3 MLC . . . B 2 -3.367 -2.446 20.148 0.5 36.6 ? P3 MLC 1001 A 1 HETATM 28 O O31 MLC . . . B 2 -3.826 -1.895 18.709 0.5 32.75 ? O31 MLC 1001 A 1 HETATM 29 O O32 MLC . . . B 2 -1.853 -3 19.896 0.5 37.73 ? O32 MLC 1001 A 1 HETATM 30 O O33 MLC . . . B 2 -4.239 -3.52 20.666 0.5 36.38 ? O33 MLC 1001 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #