data_6EQL # _model_server_result.job_id xa7Wj582eqaDFhjAu3qhKQ _model_server_result.datetime_utc '2024-12-21 14:37:42' _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 6eql # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6EQL # _exptl.entry_id 6EQL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 6EQL _cell.length_a 66.17 _cell.length_b 81.05 _cell.length_c 111.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EQL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 OD2 ASP 103 A ASP 102 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc2 A OD1 ASP 105 A ASP 104 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc3 A OD2 ASP 105 A ASP 104 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? covale ? covale1 A C ILE 195 A ILE 194 1_555 A N PHI 196 A PHI 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C PHI 196 A PHI 195 1_555 A N SER 197 A SER 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc4 A NE2 HIS 213 A HIS 212 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc5 B OD2 ASP 103 B ASP 102 1_555 F MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc6 B OD1 ASP 105 B ASP 104 1_555 F MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc7 B OD2 ASP 105 B ASP 104 1_555 F MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc8 B NE2 HIS 213 B HIS 212 1_555 F MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc9 C O2A UDP . A UDP 301 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc10 C O2B UDP . A UDP 301 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc11 E O1A UDP . B UDP 301 1_555 F MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc12 E O1B UDP . B UDP 301 1_555 F MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6EQL _atom_sites.fract_transf_matrix[1][1] 0.015113 _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] 0.012338 _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] 0.008993 _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 C 2 UDP A 1 301 1 UDP UDP . D 3 MN A 1 302 1 MN MN . E 2 UDP B 1 301 2 UDP UDP . F 3 MN B 1 302 2 MN MN . G 4 2PE B 1 303 1 2PE 2PE . H 5 EDO B 1 304 1 EDO EDO . I 6 HOH A 1 401 16 HOH HOH . I 6 HOH A 2 402 18 HOH HOH . I 6 HOH A 3 403 47 HOH HOH . I 6 HOH A 4 404 40 HOH HOH . I 6 HOH A 5 405 8 HOH HOH . I 6 HOH A 6 406 3 HOH HOH . I 6 HOH A 7 407 43 HOH HOH . I 6 HOH A 8 408 14 HOH HOH . I 6 HOH A 9 409 4 HOH HOH . I 6 HOH A 10 410 5 HOH HOH . I 6 HOH A 11 411 2 HOH HOH . I 6 HOH A 12 412 7 HOH HOH . I 6 HOH A 13 413 15 HOH HOH . I 6 HOH A 14 414 17 HOH HOH . I 6 HOH A 15 415 42 HOH HOH . I 6 HOH A 16 416 39 HOH HOH . I 6 HOH A 17 417 22 HOH HOH . I 6 HOH A 18 418 12 HOH HOH . I 6 HOH A 19 419 41 HOH HOH . I 6 HOH A 20 420 11 HOH HOH . I 6 HOH A 21 421 55 HOH HOH . I 6 HOH A 22 422 13 HOH HOH . I 6 HOH A 23 423 44 HOH HOH . J 6 HOH B 1 401 9 HOH HOH . J 6 HOH B 2 402 37 HOH HOH . J 6 HOH B 3 403 23 HOH HOH . J 6 HOH B 4 404 50 HOH HOH . J 6 HOH B 5 405 30 HOH HOH . J 6 HOH B 6 406 54 HOH HOH . J 6 HOH B 7 407 31 HOH HOH . J 6 HOH B 8 408 32 HOH HOH . J 6 HOH B 9 409 25 HOH HOH . J 6 HOH B 10 410 29 HOH HOH . J 6 HOH B 11 411 24 HOH HOH . J 6 HOH B 12 412 53 HOH HOH . J 6 HOH B 13 413 26 HOH HOH . J 6 HOH B 14 414 36 HOH HOH . J 6 HOH B 15 415 35 HOH HOH . J 6 HOH B 16 416 28 HOH HOH . J 6 HOH B 17 417 19 HOH HOH . J 6 HOH B 18 418 52 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 UDP . . . E 2 -18.962 -15.042 19.082 1 53.6 ? N1 UDP 301 B 1 HETATM 2 C C2 UDP . . . E 2 -19.412 -15.974 19.996 1 48.78 ? C2 UDP 301 B 1 HETATM 3 N N3 UDP . . . E 2 -19.676 -15.478 21.25 1 50.32 ? N3 UDP 301 B 1 HETATM 4 C C4 UDP . . . E 2 -19.536 -14.169 21.669 1 53.27 ? C4 UDP 301 B 1 HETATM 5 C C5 UDP . . . E 2 -19.066 -13.265 20.665 1 44.78 ? C5 UDP 301 B 1 HETATM 6 C C6 UDP . . . E 2 -18.799 -13.72 19.429 1 51.75 ? C6 UDP 301 B 1 HETATM 7 O O2 UDP . . . E 2 -19.566 -17.155 19.719 1 44.91 ? O2 UDP 301 B 1 HETATM 8 O O4 UDP . . . E 2 -19.815 -13.866 22.84 1 50.06 ? O4 UDP 301 B 1 HETATM 9 C C1' UDP . . . E 2 -18.659 -15.513 17.72 1 48.83 ? C1' UDP 301 B 1 HETATM 10 C C2' UDP . . . E 2 -19.884 -15.574 16.808 1 49.98 ? C2' UDP 301 B 1 HETATM 11 O O2' UDP . . . E 2 -19.668 -16.494 15.745 1 47.53 ? O2' UDP 301 B 1 HETATM 12 C C3' UDP . . . E 2 -19.934 -14.138 16.294 1 53.7 ? C3' UDP 301 B 1 HETATM 13 C C4' UDP . . . E 2 -18.454 -13.802 16.13 1 50.72 ? C4' UDP 301 B 1 HETATM 14 O O4' UDP . . . E 2 -17.762 -14.597 17.121 1 52.08 ? O4' UDP 301 B 1 HETATM 15 O O3' UDP . . . E 2 -20.627 -14.038 15.056 1 43.5 ? O3' UDP 301 B 1 HETATM 16 C C5' UDP . . . E 2 -18.106 -12.347 16.318 1 47.3 ? C5' UDP 301 B 1 HETATM 17 O O5' UDP . . . E 2 -19.127 -11.549 15.685 1 47.3 ? O5' UDP 301 B 1 HETATM 18 P PA UDP . . . E 2 -20.187 -10.743 16.535 1 46.5 ? PA UDP 301 B 1 HETATM 19 O O1A UDP . . . E 2 -21.463 -10.786 15.783 1 53.91 ? O1A UDP 301 B 1 HETATM 20 O O2A UDP . . . E 2 -20.219 -11.228 17.979 1 50.75 ? O2A UDP 301 B 1 HETATM 21 O O3A UDP . . . E 2 -19.626 -9.264 16.576 1 45.08 ? O3A UDP 301 B 1 HETATM 22 P PB UDP . . . E 2 -19.816 -8.253 15.373 1 45.04 ? PB UDP 301 B 1 HETATM 23 O O1B UDP . . . E 2 -19.837 -9.176 14.152 1 55.89 ? O1B UDP 301 B 1 HETATM 24 O O2B UDP . . . E 2 -21.213 -7.671 15.631 1 37.45 ? O2B UDP 301 B 1 HETATM 25 O O3B UDP . . . E 2 -18.736 -7.224 15.325 1 49.98 ? O3B UDP 301 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #