data_4MML # _model_server_result.job_id 7p7CmBGNOBlU8jutyyLDMQ _model_server_result.datetime_utc '2025-01-25 07:41:36' _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 4mml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":103}' # _entry.id 4MML # _exptl.entry_id 4MML _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 _cell.angle_gamma 120 _cell.entry_id 4MML _cell.length_a 65.79 _cell.length_b 65.79 _cell.length_c 28.13 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4MML _symmetry.cell_setting ? _symmetry.Int_Tables_number 168 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 6' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 y,-x+y,z 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 6_555 x-y,x,z 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-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 N1 C2 U5P sing 321 n n N1 C6 U5P sing 322 n n N1 C1' U5P sing 323 n n C2 N3 U5P sing 324 n n C2 O2 U5P doub 325 n n N3 C4 U5P sing 326 n n N3 HN3 U5P sing 327 n n C4 C5 U5P sing 328 n n C4 O4 U5P doub 329 n n C5 C6 U5P doub 330 n n C5 H5 U5P sing 331 n n C6 H6 U5P sing 332 n n C1' C2' U5P sing 333 n n C1' O4' U5P sing 334 n n C1' H1' U5P sing 335 n n C2' O2' U5P sing 336 n n C2' C3' U5P sing 337 n n C2' H2' U5P sing 338 n n O2' HO2' U5P sing 339 n n C3' C4' U5P sing 340 n n C3' O3' U5P sing 341 n n C3' H3' U5P sing 342 n n C4' O4' U5P sing 343 n n C4' C5' U5P sing 344 n n C4' H4' U5P sing 345 n n O3' HO3' U5P sing 346 n n C5' O5' U5P sing 347 n n C5' "H5'1" U5P sing 348 n n C5' "H5'2" U5P sing 349 n n O5' P U5P sing 350 n n P O1P U5P doub 351 n n P O2P U5P sing 352 n n P O3P U5P sing 353 n n O2P HOP2 U5P sing 354 n n O3P HOP3 U5P sing 355 n n # _atom_sites.entry_id 4MML _atom_sites.fract_transf_matrix[1][1] 0.0152 _atom_sites.fract_transf_matrix[1][2] 0.008776 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017551 _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] 0.035549 _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 B 2 SO4 A 1 101 1 SO4 SO4 . C 3 MG A 1 102 2 MG MG . D 4 U5P A 1 103 1 U5P U . E 5 HOH A 1 201 1 HOH HOH . E 5 HOH A 2 202 2 HOH HOH . E 5 HOH A 3 203 3 HOH HOH . E 5 HOH A 4 204 4 HOH HOH . E 5 HOH A 5 205 5 HOH HOH . E 5 HOH A 6 206 6 HOH HOH . E 5 HOH A 7 207 7 HOH HOH . E 5 HOH A 8 208 8 HOH HOH . E 5 HOH A 9 209 9 HOH HOH . E 5 HOH A 10 210 10 HOH HOH . E 5 HOH A 11 211 11 HOH HOH . E 5 HOH A 12 212 12 HOH HOH . E 5 HOH A 13 213 13 HOH HOH . E 5 HOH A 14 214 14 HOH HOH . E 5 HOH A 15 215 15 HOH HOH . E 5 HOH A 16 216 16 HOH HOH . E 5 HOH A 17 217 17 HOH HOH . E 5 HOH A 18 218 18 HOH HOH . E 5 HOH A 19 219 19 HOH HOH . E 5 HOH A 20 220 20 HOH HOH . E 5 HOH A 21 221 22 HOH HOH . E 5 HOH A 22 222 23 HOH HOH . E 5 HOH A 23 223 24 HOH HOH . E 5 HOH A 24 224 25 HOH HOH . E 5 HOH A 25 225 26 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 N1 U5P . . . D 4 -8.57 1.66 -6.936 1 27.35 ? N1 U5P 103 A 1 HETATM 2 C C2 U5P . . . D 4 -9.824 1.485 -7.478 1 24.56 ? C2 U5P 103 A 1 HETATM 3 N N3 U5P . . . D 4 -9.882 1.579 -8.844 1 27.65 ? N3 U5P 103 A 1 HETATM 4 C C4 U5P . . . D 4 -8.833 1.824 -9.704 1 26.49 ? C4 U5P 103 A 1 HETATM 5 C C5 U5P . . . D 4 -7.567 2.001 -9.055 1 25.71 ? C5 U5P 103 A 1 HETATM 6 C C6 U5P . . . D 4 -7.474 1.916 -7.725 1 24.76 ? C6 U5P 103 A 1 HETATM 7 O O2 U5P . . . D 4 -10.813 1.264 -6.803 1 24.93 ? O2 U5P 103 A 1 HETATM 8 O O4 U5P . . . D 4 -9.056 1.88 -10.916 1 26.88 ? O4 U5P 103 A 1 HETATM 9 C C1' U5P . . . D 4 -8.479 1.574 -5.461 1 28.07 ? C1' U5P 103 A 1 HETATM 10 C C2' U5P . . . D 4 -7.962 0.219 -4.967 1 28.44 ? C2' U5P 103 A 1 HETATM 11 O O2' U5P . . . D 4 -8.704 -0.159 -3.817 1 27.98 ? O2' U5P 103 A 1 HETATM 12 C C3' U5P . . . D 4 -6.529 0.549 -4.573 1 33.67 ? C3' U5P 103 A 1 HETATM 13 C C4' U5P . . . D 4 -6.642 1.988 -4.09 1 30.72 ? C4' U5P 103 A 1 HETATM 14 O O3' U5P . . . D 4 -6.035 -0.329 -3.576 1 29.59 ? O3' U5P 103 A 1 HETATM 15 O O4' U5P . . . D 4 -7.602 2.575 -4.99 1 29.29 ? O4' U5P 103 A 1 HETATM 16 C C5' U5P . . . D 4 -5.386 2.828 -4.049 1 32.11 ? C5' U5P 103 A 1 HETATM 17 O O5' U5P . . . D 4 -4.508 2.565 -5.13 1 36.74 ? O5' U5P 103 A 1 HETATM 18 P P U5P . . . D 4 -2.937 2.599 -4.898 1 43.6 ? P U5P 103 A 1 HETATM 19 O O1P U5P . . . D 4 -2.725 2.489 -3.427 1 38.3 ? O1P U5P 103 A 1 HETATM 20 O O2P U5P . . . D 4 -2.272 1.629 -5.812 1 51.6 ? O2P U5P 103 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 648 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #