data_4OHB # _model_server_result.job_id BCyYRgycYlbiFb-GwaOlFA _model_server_result.datetime_utc '2024-11-05 21:01:08' _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 4ohb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4OHB # _exptl.entry_id 4OHB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 353.223 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)" _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 4OHB _cell.length_a 45.426 _cell.length_b 101.808 _cell.length_c 81.744 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4OHB _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _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 ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 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,B,C 1 1 A,B,C 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' 4_555 x,-y,-z 1 0 0 0 -1 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 # _chem_comp.formula 'C10 H16 N3 O9 P' _chem_comp.formula_weight 353.223 _chem_comp.id 5HM _chem_comp.mon_nstd_flag n _chem_comp.name "5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms "5-hydroxymethylcytidine 5'-monophosphate" # 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 N4 C4 5HM sing 1 n n C4 N3 5HM doub 2 n n C4 C5 5HM sing 3 n n N3 C2 5HM sing 4 n n CM5 OM5 5HM sing 5 n n CM5 C5 5HM sing 6 n n C5 C6 5HM doub 7 n n C2 O2 5HM doub 8 n n C2 N1 5HM sing 9 n n C6 N1 5HM sing 10 n n N1 C1' 5HM sing 11 n n OP1 P 5HM doub 12 n n C1' O4' 5HM sing 13 n n C1' C2' 5HM sing 14 n n OP2 P 5HM sing 15 n n O4' C4' 5HM sing 16 n n C2' O2' 5HM sing 17 n n C2' C3' 5HM sing 18 n n P O5' 5HM sing 19 n n P OP3 5HM sing 20 n n O5' C5' 5HM sing 21 n n C5' C4' 5HM sing 22 n n C4' C3' 5HM sing 23 n n C3' O3' 5HM sing 24 n n OP3 H1 5HM sing 25 n n OP2 H2 5HM sing 26 n n C5' H3 5HM sing 27 n n C5' H4 5HM sing 28 n n C4' H5 5HM sing 29 n n C3' H6 5HM sing 30 n n O3' HO3' 5HM sing 31 n n C2' H8 5HM sing 32 n n O2' H9 5HM sing 33 n n C1' H10 5HM sing 34 n n C6 H11 5HM sing 35 n n CM5 H12 5HM sing 36 n n CM5 H13 5HM sing 37 n n OM5 H14 5HM sing 38 n n N4 H15 5HM sing 39 n n N4 H16 5HM sing 40 n n # _atom_sites.entry_id 4OHB _atom_sites.fract_transf_matrix[1][1] 0.022014 _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] 0.009822 _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] 0.012233 _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 5HM A 1 201 1 5HM 5HM . C 3 HOH A 1 301 1 HOH HOH . C 3 HOH A 2 302 2 HOH HOH . C 3 HOH A 3 303 3 HOH HOH . C 3 HOH A 4 304 4 HOH HOH . C 3 HOH A 5 305 5 HOH HOH . C 3 HOH A 6 306 8 HOH HOH . C 3 HOH A 7 307 9 HOH HOH . C 3 HOH A 8 308 10 HOH HOH . C 3 HOH A 9 309 11 HOH HOH . C 3 HOH A 10 310 12 HOH HOH . C 3 HOH A 11 311 13 HOH HOH . C 3 HOH A 12 312 14 HOH HOH . C 3 HOH A 13 313 15 HOH HOH . C 3 HOH A 14 314 16 HOH HOH . C 3 HOH A 15 315 17 HOH HOH . C 3 HOH A 16 316 19 HOH HOH . C 3 HOH A 17 317 20 HOH HOH . C 3 HOH A 18 318 21 HOH HOH . C 3 HOH A 19 319 22 HOH HOH . C 3 HOH A 20 320 24 HOH HOH . C 3 HOH A 21 321 26 HOH HOH . C 3 HOH A 22 322 27 HOH HOH . C 3 HOH A 23 323 28 HOH HOH . C 3 HOH A 24 324 31 HOH HOH . C 3 HOH A 25 325 32 HOH HOH . C 3 HOH A 26 326 33 HOH HOH . C 3 HOH A 27 327 34 HOH HOH . C 3 HOH A 28 328 37 HOH HOH . C 3 HOH A 29 329 39 HOH HOH . C 3 HOH A 30 330 40 HOH HOH . C 3 HOH A 31 331 41 HOH HOH . C 3 HOH A 32 332 42 HOH HOH . C 3 HOH A 33 333 43 HOH HOH . C 3 HOH A 34 334 44 HOH HOH . C 3 HOH A 35 335 45 HOH HOH . C 3 HOH A 36 336 46 HOH HOH . C 3 HOH A 37 337 48 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 OP3 5HM . . . B 2 3.773 -7.235 -3.234 1 30.14 ? OP3 5HM 201 A 1 HETATM 2 P P 5HM . . . B 2 2.904 -6.901 -4.454 1 34.98 ? P 5HM 201 A 1 HETATM 3 O OP1 5HM . . . B 2 3.12 -7.865 -5.629 1 30.88 ? OP1 5HM 201 A 1 HETATM 4 O OP2 5HM . . . B 2 2.791 -5.438 -4.819 1 33.66 ? OP2 5HM 201 A 1 HETATM 5 O O5' 5HM . . . B 2 1.413 -7.204 -3.967 1 29.37 ? O5' 5HM 201 A 1 HETATM 6 C C5' 5HM . . . B 2 1.126 -8.577 -3.73 1 33.72 ? C5' 5HM 201 A 1 HETATM 7 C C4' 5HM . . . B 2 -0.371 -8.722 -3.582 1 37.08 ? C4' 5HM 201 A 1 HETATM 8 O O4' 5HM . . . B 2 -1.043 -8.225 -4.754 1 36.38 ? O4' 5HM 201 A 1 HETATM 9 C C3' 5HM . . . B 2 -0.72 -10.182 -3.369 1 38.76 ? C3' 5HM 201 A 1 HETATM 10 O O3' 5HM . . . B 2 -1.304 -10.43 -2.073 1 38.65 ? O3' 5HM 201 A 1 HETATM 11 C C2' 5HM . . . B 2 -1.674 -10.496 -4.502 1 37.66 ? C2' 5HM 201 A 1 HETATM 12 O O2' 5HM . . . B 2 -2.961 -10.787 -3.971 1 38.19 ? O2' 5HM 201 A 1 HETATM 13 C C1' 5HM . . . B 2 -1.699 -9.304 -5.447 1 38.58 ? C1' 5HM 201 A 1 HETATM 14 N N1 5HM . . . B 2 -0.982 -9.669 -6.701 1 38.66 ? N1 5HM 201 A 1 HETATM 15 C C2 5HM . . . B 2 -1.56 -10.511 -7.562 1 33.84 ? C2 5HM 201 A 1 HETATM 16 O O2 5HM . . . B 2 -2.784 -11.01 -7.269 1 34.01 ? O2 5HM 201 A 1 HETATM 17 C C6 5HM . . . B 2 0.242 -9.138 -6.953 1 36.34 ? C6 5HM 201 A 1 HETATM 18 C C5 5HM . . . B 2 0.945 -9.462 -8.088 1 34.05 ? C5 5HM 201 A 1 HETATM 19 C CM5 5HM . . . B 2 2.286 -8.817 -8.298 1 37.69 ? CM5 5HM 201 A 1 HETATM 20 O OM5 5HM . . . B 2 2.116 -7.403 -8.093 1 40.65 ? OM5 5HM 201 A 1 HETATM 21 C C4 5HM . . . B 2 0.284 -10.413 -9.033 1 34.83 ? C4 5HM 201 A 1 HETATM 22 N N3 5HM . . . B 2 -0.944 -10.893 -8.7 1 32.89 ? N3 5HM 201 A 1 HETATM 23 N N4 5HM . . . B 2 0.837 -10.802 -10.214 1 35.78 ? N4 5HM 201 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 210 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 23 #