data_5EJZ # _model_server_result.job_id NSeJxr4b8ksXUW23vbCFJw _model_server_result.datetime_utc '2024-11-13 05:32:23' _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 5ejz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":921}' # _entry.id 5EJZ # _exptl.entry_id 5EJZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 5EJZ _cell.length_a 67.269 _cell.length_b 216.838 _cell.length_c 221.117 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EJZ _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 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,J,K,L,M,N _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 BGC BGC C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 4 4 3 BGC BGC C1 O1 . O4 HO4 . sing 4 ? 4 5 4 BGC BGC C1 O1 . O4 HO4 . sing 5 ? 4 6 5 BGC BGC C1 O1 . O4 HO4 . sing 6 ? 4 7 6 BGC BGC C1 O1 . O4 HO4 . sing 7 ? 4 8 7 BGC BGC C1 O1 . O4 HO4 . sing 8 ? 4 9 8 BGC BGC C1 O1 . O4 HO4 . sing 9 ? 4 10 9 BGC BGC C1 O1 . O4 HO4 . sing 10 ? 4 11 10 BGC BGC C1 O1 . O4 HO4 . sing 11 ? 4 12 11 BGC BGC C1 O1 . O4 HO4 . sing 12 ? 4 13 12 BGC BGC C1 O1 . O4 HO4 . sing 13 ? 4 14 13 BGC BGC C1 O1 . O4 HO4 . sing 14 ? 4 15 14 BGC BGC C1 O1 . O4 HO4 . sing 15 ? 4 16 15 BGC BGC C1 O1 . O4 HO4 . sing 16 ? 4 17 16 BGC BGC C1 O1 . O4 HO4 . sing 17 ? 4 18 17 SHG BGC C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D BGC 1 C 1 BGC A 901 BGC 4 n D BGC 2 C 2 BGC A 902 BGC 4 n D BGC 3 C 3 BGC A 903 BGC 4 n D BGC 4 C 4 BGC A 904 BGC 4 n D BGC 5 C 5 BGC A 905 BGC 4 n D BGC 6 C 6 BGC A 906 BGC 4 n D BGC 7 C 7 BGC A 907 BGC 4 n D BGC 8 C 8 BGC A 908 BGC 4 n D BGC 9 C 9 BGC A 909 BGC 4 n D BGC 10 C 10 BGC A 910 BGC 4 n D BGC 11 C 11 BGC A 911 BGC 4 n D BGC 12 C 12 BGC A 912 BGC 4 n D BGC 13 C 13 BGC A 913 BGC 4 n D BGC 14 C 14 BGC A 914 BGC 4 n D BGC 15 C 15 BGC A 915 BGC 4 n D BGC 16 C 16 BGC A 916 BGC 4 n D BGC 17 C 17 BGC A 917 BGC 4 n D SHG 18 C 18 SHG A 918 BGC # 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 disulf ? disulf1 B SG CYS 163 B CYS 163 1_555 B SG CYS 430 B CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 C C UNK 1 D UNK 169 1_555 C N UNK 2 D UNK 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 C C UNK 2 D UNK 170 1_555 C N UNK 3 D UNK 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 C C UNK 3 D UNK 171 1_555 C N UNK 4 D UNK 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 C C UNK 4 D UNK 172 1_555 C N UNK 5 D UNK 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 C C UNK 5 D UNK 173 1_555 C N UNK 6 D UNK 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 C C UNK 6 D UNK 174 1_555 C N UNK 7 D UNK 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 C C UNK 7 D UNK 175 1_555 C N UNK 8 D UNK 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 C C UNK 8 D UNK 176 1_555 C N UNK 9 D UNK 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 D O4 BGC . C BGC 1 1_555 D C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 D O4 BGC . C BGC 2 1_555 D C1 BGC . C BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 D O4 BGC . C BGC 3 1_555 D C1 BGC . C BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 D O4 BGC . C BGC 4 1_555 D C1 BGC . C BGC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale13 D O4 BGC . C BGC 5 1_555 D C1 BGC . C BGC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale14 D O4 BGC . C BGC 6 1_555 D C1 BGC . C BGC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale15 D O4 BGC . C BGC 7 1_555 D C1 BGC . C BGC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale16 D O4 BGC . C BGC 8 1_555 D C1 BGC . C BGC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale17 D O4 BGC . C BGC 9 1_555 D C1 BGC . C BGC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale18 D O4 BGC . C BGC 10 1_555 D C1 BGC . C BGC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale19 D O4 BGC . C BGC 11 1_555 D C1 BGC . C BGC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale20 D O4 BGC . C BGC 12 1_555 D C1 BGC . C BGC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale21 D O4 BGC . C BGC 13 1_555 D C1 BGC . C BGC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale22 D O4 BGC . C BGC 14 1_555 D C1 BGC . C BGC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale23 D O4 BGC . C BGC 15 1_555 D C1 BGC . C BGC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.545 ? covale ? covale24 D O4 BGC . C BGC 16 1_555 D C1 BGC . C BGC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale25 D O4 BGC . C BGC 17 1_555 D C1 SHG . C SHG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? metalc ? metalc1 G O1B UDP . A UDP 921 1_555 H MG MG . A MG 922 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.89 ? metalc ? metalc2 B O GLY 231 B GLY 231 1_555 K MG MG . B MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc3 B O LEU 234 B LEU 234 1_555 K MG MG . B MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc4 B O GLU 237 B GLU 237 1_555 K MG MG . B MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc5 B O ALA 487 B ALA 487 1_555 K MG MG . B MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.76 ? # _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 ? # 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 UDP sing 717 n n N1 C6 UDP sing 718 n n N1 C1' UDP sing 719 n n C2 N3 UDP sing 720 n n C2 O2 UDP doub 721 n n N3 C4 UDP sing 722 n n N3 HN3 UDP sing 723 n n C4 C5 UDP sing 724 n n C4 O4 UDP doub 725 n n C5 C6 UDP doub 726 n n C5 H5 UDP sing 727 n n C6 H6 UDP sing 728 n n C1' C2' UDP sing 729 n n C1' O4' UDP sing 730 n n C1' H1' UDP sing 731 n n C2' O2' UDP sing 732 n n C2' C3' UDP sing 733 n n C2' H2' UDP sing 734 n n O2' HO2' UDP sing 735 n n C3' C4' UDP sing 736 n n C3' O3' UDP sing 737 n n C3' H3' UDP sing 738 n n C4' O4' UDP sing 739 n n C4' C5' UDP sing 740 n n C4' H4' UDP sing 741 n n O3' HO3' UDP sing 742 n n C5' O5' UDP sing 743 n n C5' "H5'1" UDP sing 744 n n C5' "H5'2" UDP sing 745 n n O5' PA UDP sing 746 n n PA O1A UDP doub 747 n n PA O2A UDP sing 748 n n PA O3A UDP sing 749 n n O2A HOA2 UDP sing 750 n n O3A PB UDP sing 751 n n PB O1B UDP doub 752 n n PB O2B UDP sing 753 n n PB O3B UDP sing 754 n n O2B HOB2 UDP sing 755 n n O3B HOB3 UDP sing 756 n n # _atom_sites.entry_id 5EJZ _atom_sites.fract_transf_matrix[1][1] 0.014866 _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] 0.004612 _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] 0.004522 _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 E 5 C2E A 1 919 919 C2E C2E . F 5 C2E A 1 920 920 C2E C2E . G 6 UDP A 1 921 1 UDP UDP . H 7 MG A 1 922 1 MG MG . I 8 PLC A 1 923 1 PLC PLC . J 9 3PE A 1 924 1 3PE 3PE . K 7 MG B 1 801 1 MG MG . L 10 UND B 1 802 1 UND LDA . M 8 PLC B 1 803 1 PLC PLC . N 8 PLC B 1 804 1 PLC PLC . # 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 . . . G 6 -4.355 7.305 -102.282 1 102.84 ? N1 UDP 921 A 1 HETATM 2 C C2 UDP . . . G 6 -4.609 7.041 -103.615 1 105.88 ? C2 UDP 921 A 1 HETATM 3 N N3 UDP . . . G 6 -5.687 6.25 -103.96 1 109.36 ? N3 UDP 921 A 1 HETATM 4 C C4 UDP . . . G 6 -6.499 5.744 -102.962 1 111.32 ? C4 UDP 921 A 1 HETATM 5 C C5 UDP . . . G 6 -6.233 6.022 -101.629 1 107.73 ? C5 UDP 921 A 1 HETATM 6 C C6 UDP . . . G 6 -5.044 6.653 -101.306 1 106.52 ? C6 UDP 921 A 1 HETATM 7 O O2 UDP . . . G 6 -3.873 7.501 -104.489 1 105.82 ? O2 UDP 921 A 1 HETATM 8 O O4 UDP . . . G 6 -7.461 5.042 -103.25 1 116.18 ? O4 UDP 921 A 1 HETATM 9 C C1' UDP . . . G 6 -3.217 8.151 -101.892 1 92.79 ? C1' UDP 921 A 1 HETATM 10 C C2' UDP . . . G 6 -3.742 9.327 -101.103 1 93.57 ? C2' UDP 921 A 1 HETATM 11 O O2' UDP . . . G 6 -3.825 10.428 -101.963 1 106.77 ? O2' UDP 921 A 1 HETATM 12 C C3' UDP . . . G 6 -2.711 9.556 -100.019 1 91.6 ? C3' UDP 921 A 1 HETATM 13 C C4' UDP . . . G 6 -1.886 8.279 -99.99 1 91.24 ? C4' UDP 921 A 1 HETATM 14 O O4' UDP . . . G 6 -2.297 7.463 -101.067 1 80.07 ? O4' UDP 921 A 1 HETATM 15 O O3' UDP . . . G 6 -1.909 10.673 -100.337 1 77.13 ? O3' UDP 921 A 1 HETATM 16 C C5' UDP . . . G 6 -2.162 7.565 -98.68 1 92.84 ? C5' UDP 921 A 1 HETATM 17 O O5' UDP . . . G 6 -3.504 7.821 -98.327 1 89.66 ? O5' UDP 921 A 1 HETATM 18 P PA UDP . . . G 6 -3.976 7.867 -96.788 1 94.67 ? PA UDP 921 A 1 HETATM 19 O O1A UDP . . . G 6 -5.31 7.24 -96.6 1 116.52 ? O1A UDP 921 A 1 HETATM 20 O O2A UDP . . . G 6 -4.012 9.263 -96.328 1 80.36 ? O2A UDP 921 A 1 HETATM 21 O O3A UDP . . . G 6 -2.776 7.147 -95.977 1 116.52 ? O3A UDP 921 A 1 HETATM 22 P PB UDP . . . G 6 -2.213 7.698 -94.552 1 102.78 ? PB UDP 921 A 1 HETATM 23 O O1B UDP . . . G 6 -1.666 9.07 -94.627 1 107.85 ? O1B UDP 921 A 1 HETATM 24 O O2B UDP . . . G 6 -3.339 7.8 -93.612 1 103.83 ? O2B UDP 921 A 1 HETATM 25 O O3B UDP . . . G 6 -1.243 6.742 -93.985 1 103.12 ? O3B UDP 921 A 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #