data_3TIJ # _model_server_result.job_id iOJGkl05xN6m86FrMA2o0Q _model_server_result.datetime_utc '2024-11-27 17:07:33' _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 3tij # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":419}' # _entry.id 3TIJ # _exptl.entry_id 3TIJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE _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 3TIJ _cell.length_a 119.717 _cell.length_b 119.717 _cell.length_c 83.136 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TIJ _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,F,G,H,I _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_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 59.8585 -103.677963 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 119.717 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 metalc ? metalc1 A OD1 ASN 155 A ASN 149 1_555 D NA NA . A NA 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc2 A O ASN 155 A ASN 149 1_555 D NA NA . A NA 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc3 A O VAL 158 A VAL 152 1_555 D NA NA . A NA 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc4 A OG SER 189 A SER 183 1_555 D NA NA . A NA 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc5 A O ILE 190 A ILE 184 1_555 D NA NA . A NA 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc6 D NA NA . A NA 421 1_555 I O HOH . A HOH 467 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? # _chem_comp.formula 'C9 H12 N2 O6' _chem_comp.formula_weight 244.201 _chem_comp.id URI _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE _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 URI sing 413 n n N1 C6 URI sing 414 n n N1 C1' URI sing 415 n n C2 N3 URI sing 416 n n C2 O2 URI doub 417 n n N3 C4 URI sing 418 n n N3 H3 URI sing 419 n n C4 C5 URI sing 420 n n C4 O4 URI doub 421 n n C5 C6 URI doub 422 n n C5 H5 URI sing 423 n n C6 H6 URI sing 424 n n C1' C2' URI sing 425 n n C1' O4' URI sing 426 n n C1' H1' URI sing 427 n n C2' C3' URI sing 428 n n C2' O2' URI sing 429 n n C2' H2' URI sing 430 n n C3' C4' URI sing 431 n n C3' O3' URI sing 432 n n C3' H3' URI sing 433 n n C4' O4' URI sing 434 n n C4' C5' URI sing 435 n n C4' H4' URI sing 436 n n O2' HO2' URI sing 437 n n O3' HO3' URI sing 438 n n C5' O5' URI sing 439 n n C5' "H5'1" URI sing 440 n n C5' "H5'2" URI sing 441 n n O5' HO5' URI sing 442 n n # _atom_sites.entry_id 3TIJ _atom_sites.fract_transf_matrix[1][1] 0.008353 _atom_sites.fract_transf_matrix[1][2] 0.004823 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009645 _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] 0.012028 _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 URI A 1 419 1 URI URI . C 3 DMU A 1 420 1 DMU DMU . D 4 NA A 1 421 1 NA NA . E 3 DMU A 1 422 1 DMU LMT . F 3 DMU A 1 423 1 DMU LMT . G 3 DMU A 1 424 1 DMU LMT . H 3 DMU A 1 425 1 DMU LMT . I 5 HOH A 1 426 1 HOH HOH . I 5 HOH A 2 427 2 HOH HOH . I 5 HOH A 3 428 3 HOH HOH . I 5 HOH A 4 429 4 HOH HOH . I 5 HOH A 5 430 5 HOH HOH . I 5 HOH A 6 431 6 HOH HOH . I 5 HOH A 7 432 7 HOH HOH . I 5 HOH A 8 433 8 HOH HOH . I 5 HOH A 9 434 9 HOH HOH . I 5 HOH A 10 435 10 HOH HOH . I 5 HOH A 11 436 11 HOH HOH . I 5 HOH A 12 437 12 HOH HOH . I 5 HOH A 13 438 13 HOH HOH . I 5 HOH A 14 439 14 HOH HOH . I 5 HOH A 15 440 15 HOH HOH . I 5 HOH A 16 441 16 HOH HOH . I 5 HOH A 17 442 17 HOH HOH . I 5 HOH A 18 443 18 HOH HOH . I 5 HOH A 19 444 19 HOH HOH . I 5 HOH A 20 445 20 HOH HOH . I 5 HOH A 21 446 21 HOH HOH . I 5 HOH A 22 447 22 HOH HOH . I 5 HOH A 23 448 23 HOH HOH . I 5 HOH A 24 449 24 HOH HOH . I 5 HOH A 25 450 25 HOH HOH . I 5 HOH A 26 451 26 HOH HOH . I 5 HOH A 27 452 27 HOH HOH . I 5 HOH A 28 453 28 HOH HOH . I 5 HOH A 29 454 29 HOH HOH . I 5 HOH A 30 455 30 HOH HOH . I 5 HOH A 31 456 31 HOH HOH . I 5 HOH A 32 457 32 HOH HOH . I 5 HOH A 33 458 33 HOH HOH . I 5 HOH A 34 459 34 HOH HOH . I 5 HOH A 35 460 35 HOH HOH . I 5 HOH A 36 461 36 HOH HOH . I 5 HOH A 37 462 37 HOH HOH . I 5 HOH A 38 463 38 HOH HOH . I 5 HOH A 39 464 39 HOH HOH . I 5 HOH A 40 465 40 HOH HOH . I 5 HOH A 41 466 41 HOH HOH . I 5 HOH A 42 467 42 HOH HOH . I 5 HOH A 43 468 43 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 URI . . . B 2 51.195 -20.219 -8.998 1 43.69 ? N1 URI 419 A 1 HETATM 2 C C2 URI . . . B 2 50.543 -20.529 -10.183 1 45.88 ? C2 URI 419 A 1 HETATM 3 N N3 URI . . . B 2 49.478 -21.397 -10.073 1 41.3 ? N3 URI 419 A 1 HETATM 4 C C4 URI . . . B 2 49.015 -21.978 -8.905 1 41.94 ? C4 URI 419 A 1 HETATM 5 C C5 URI . . . B 2 49.735 -21.621 -7.716 1 38.55 ? C5 URI 419 A 1 HETATM 6 C C6 URI . . . B 2 50.784 -20.779 -7.8 1 42.11 ? C6 URI 419 A 1 HETATM 7 O O2 URI . . . B 2 50.867 -20.063 -11.26 1 45.46 ? O2 URI 419 A 1 HETATM 8 O O4 URI . . . B 2 48.05 -22.739 -8.968 1 48.17 ? O4 URI 419 A 1 HETATM 9 C C1' URI . . . B 2 52.357 -19.295 -9.108 1 47.75 ? C1' URI 419 A 1 HETATM 10 C C2' URI . . . B 2 51.926 -17.832 -9.257 1 46.53 ? C2' URI 419 A 1 HETATM 11 C C3' URI . . . B 2 51.976 -17.353 -7.809 1 46.5 ? C3' URI 419 A 1 HETATM 12 C C4' URI . . . B 2 53.178 -18.118 -7.25 1 46.97 ? C4' URI 419 A 1 HETATM 13 O O2' URI . . . B 2 52.899 -17.152 -10.041 1 47.86 ? O2' URI 419 A 1 HETATM 14 O O3' URI . . . B 2 52.098 -15.948 -7.679 1 49.9 ? O3' URI 419 A 1 HETATM 15 O O4' URI . . . B 2 53.139 -19.396 -7.93 1 40.59 ? O4' URI 419 A 1 HETATM 16 C C5' URI . . . B 2 53.187 -18.327 -5.752 1 45.02 ? C5' URI 419 A 1 HETATM 17 O O5' URI . . . B 2 51.913 -18.741 -5.271 1 43.15 ? O5' URI 419 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 358 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 17 #