data_4PD8 # _model_server_result.job_id 0YUk6p_-u5NEbkk5aXsDhw _model_server_result.datetime_utc '2024-11-27 10:53:59' _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 4pd8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4PD8 # _exptl.entry_id 4PD8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 281.265 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-methyl-3-(beta-D-ribofuranosyl)-3,7-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one _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 4PD8 _cell.length_a 119.636 _cell.length_b 119.636 _cell.length_c 83.064 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PD8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # 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_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 119.636 207.21563 0 3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -119.636 207.21563 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 metalc ? metalc1 A O ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc2 A OD1 ASN 155 A ASN 149 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc3 A O VAL 158 A VAL 152 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc4 A OG SER 189 A SER 183 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc5 A O ILE 190 A ILE 184 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc6 C NA NA . A NA 502 1_555 E O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? # _chem_comp.formula 'C12 H15 N3 O5' _chem_comp.formula_weight 281.265 _chem_comp.id P0C _chem_comp.mon_nstd_flag . _chem_comp.name 6-methyl-3-(beta-D-ribofuranosyl)-3,7-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '6-Methyl-3-(beta-D-2-ribofuranosyl)pyrrolo[2,3-d] pyrimidin-2-one' # 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 O20 C11 P0C doub 292 n n C11 N12 P0C sing 293 n n C11 N10 P0C sing 294 n n N12 C13 P0C doub 295 n n O09 C08 P0C sing 296 n n C08 C07 P0C sing 297 n n C08 C02 P0C sing 298 n n C13 N18 P0C sing 299 n n C13 C14 P0C sing 300 n n N10 C07 P0C sing 301 n n N10 C19 P0C sing 302 n n C07 O06 P0C sing 303 n n N18 C16 P0C sing 304 n n O06 C03 P0C sing 305 n n C19 C14 P0C doub 306 n n C14 C15 P0C sing 307 n n C02 O01 P0C sing 308 n n C02 C03 P0C sing 309 n n C16 C15 P0C doub 310 n n C16 C17 P0C sing 311 n n C03 C04 P0C sing 312 n n C04 O05 P0C sing 313 n n C17 H1 P0C sing 314 n n C17 H2 P0C sing 315 n n C17 H3 P0C sing 316 n n O01 H4 P0C sing 317 n n C02 H5 P0C sing 318 n n C03 H6 P0C sing 319 n n C04 H7 P0C sing 320 n n C04 H8 P0C sing 321 n n O05 H9 P0C sing 322 n n C07 H10 P0C sing 323 n n C08 H11 P0C sing 324 n n O09 H12 P0C sing 325 n n C15 H14 P0C sing 326 n n N18 H15 P0C sing 327 n n C19 H16 P0C sing 328 n n # _atom_sites.entry_id 4PD8 _atom_sites.fract_transf_matrix[1][1] 0.008359 _atom_sites.fract_transf_matrix[1][2] 0.004826 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009652 _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] 0.012039 _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 P0C A 1 501 1 P0C P06 . C 3 NA A 1 502 1 NA NA . D 4 DMU A 1 503 503 DMU DMU . E 5 HOH A 1 601 1 HOH HOH . E 5 HOH A 2 602 2 HOH HOH . E 5 HOH A 3 603 3 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 C C14 P0C . . . B 2 -16.211 135.903 -7.062 1 48.43 ? C14 P0C 501 A 1 HETATM 2 C C16 P0C . . . B 2 -15.782 133.715 -6.618 1 48.43 ? C16 P0C 501 A 1 HETATM 3 C C17 P0C . . . B 2 -15.459 132.42 -5.887 1 48.43 ? C17 P0C 501 A 1 HETATM 4 O O01 P0C . . . B 2 -19.859 140.862 -6.732 1 48.43 ? O01 P0C 501 A 1 HETATM 5 C C02 P0C . . . B 2 -18.779 139.944 -6.842 1 48.43 ? C02 P0C 501 A 1 HETATM 6 C C03 P0C . . . B 2 -17.476 140.494 -6.283 1 48.43 ? C03 P0C 501 A 1 HETATM 7 C C04 P0C . . . B 2 -17.264 140.232 -4.813 1 48.43 ? C04 P0C 501 A 1 HETATM 8 O O05 P0C . . . B 2 -17.67 138.945 -4.313 1 48.43 ? O05 P0C 501 A 1 HETATM 9 O O06 P0C . . . B 2 -16.406 139.923 -7.093 1 48.43 ? O06 P0C 501 A 1 HETATM 10 C C07 P0C . . . B 2 -16.96 139.312 -8.25 1 48.43 ? C07 P0C 501 A 1 HETATM 11 C C08 P0C . . . B 2 -18.437 139.694 -8.296 1 48.43 ? C08 P0C 501 A 1 HETATM 12 O O09 P0C . . . B 2 -18.689 140.86 -9.051 1 48.43 ? O09 P0C 501 A 1 HETATM 13 N N10 P0C . . . B 2 -16.717 137.861 -8.255 1 48.43 ? N10 P0C 501 A 1 HETATM 14 C C11 P0C . . . B 2 -16.78 137.123 -9.44 1 48.43 ? C11 P0C 501 A 1 HETATM 15 N N12 P0C . . . B 2 -16.558 135.788 -9.419 1 48.43 ? N12 P0C 501 A 1 HETATM 16 C C13 P0C . . . B 2 -16.276 135.163 -8.273 1 48.43 ? C13 P0C 501 A 1 HETATM 17 C C15 P0C . . . B 2 -15.901 134.988 -6.036 1 48.43 ? C15 P0C 501 A 1 HETATM 18 N N18 P0C . . . B 2 -16.01 133.851 -7.967 1 48.43 ? N18 P0C 501 A 1 HETATM 19 C C19 P0C . . . B 2 -16.431 137.224 -7.076 1 48.43 ? C19 P0C 501 A 1 HETATM 20 O O20 P0C . . . B 2 -17.039 137.675 -10.519 1 48.43 ? O20 P0C 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #