data_8ERP # _model_server_result.job_id P5s3f3UrwOtm9QZYjPJzFw _model_server_result.datetime_utc '2025-04-18 08:11:39' _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 8erp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":507}' # _entry.id 8ERP # _exptl.entry_id 8ERP _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 488.324 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM" _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 8ERP _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ERP _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _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 ? _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 ? 4 G N N ? 4 V 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 OD1 ASP 111 B ASP 111 1_555 C MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc2 A OD1 ASP 111 B ASP 111 1_555 D MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc3 A OD1 ASP 132 B ASP 132 1_555 C MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc4 A OD2 ASP 132 B ASP 132 1_555 D MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc5 A OD1 ASP 136 B ASP 136 1_555 C MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc6 A OD2 ASP 136 B ASP 136 1_555 C MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc7 D MG MG . B MG 502 1_555 G O2A CDC . B CDC 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc8 D MG MG . B MG 502 1_555 G O3B CDC . B CDC 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc9 B OD1 ASP 111 A ASP 111 1_555 R MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc10 B OD1 ASP 111 A ASP 111 1_555 S MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc11 B OD1 ASP 132 A ASP 132 1_555 R MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc12 B OD2 ASP 132 A ASP 132 1_555 S MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc13 B OD1 ASP 136 A ASP 136 1_555 R MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc14 B OD2 ASP 136 A ASP 136 1_555 R MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc15 S MG MG . A MG 504 1_555 V O2A CDC . A CDC 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc16 S MG MG . A MG 504 1_555 V O3B CDC . A CDC 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? # _chem_comp.formula 'C14 H26 N4 O11 P2' _chem_comp.formula_weight 488.324 _chem_comp.id CDC _chem_comp.mon_nstd_flag . _chem_comp.name "[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM" _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 CDC sing 70 n n N1 C6 CDC sing 71 n n N1 C1' CDC sing 72 n n C2 N3 CDC sing 73 n n C2 O2 CDC doub 74 n n N3 C4 CDC doub 75 n n C4 C5 CDC sing 76 n n C4 N4 CDC sing 77 n n C5 C6 CDC doub 78 n n C5 H5 CDC sing 79 n n C6 H6 CDC sing 80 n n N4 H41 CDC sing 81 n n N4 H42 CDC sing 82 n n C1' C2' CDC sing 83 n n C1' O4' CDC sing 84 n n C1' H1' CDC sing 85 n n C2' O2' CDC sing 86 n n C2' C3' CDC sing 87 n n C2' H2' CDC sing 88 n n O2' "HO'2" CDC sing 89 n n C3' C4' CDC sing 90 n n C3' O3' CDC sing 91 n n C3' H3' CDC sing 92 n n C4' O4' CDC sing 93 n n C4' C5' CDC sing 94 n n C4' H4' CDC sing 95 n n O3' H3T CDC sing 96 n n C5' O5' CDC sing 97 n n C5' "H5'1" CDC sing 98 n n C5' "H5'2" CDC sing 99 n n O5' PA CDC sing 100 n n PA O1A CDC doub 101 n n PA O2A CDC sing 102 n n PA O3A CDC sing 103 n n O2A HO2A CDC sing 104 n n O3A PB CDC sing 105 n n PB O1B CDC sing 106 n n PB O2B CDC sing 107 n n PB O3B CDC doub 108 n n O1B C14 CDC sing 109 n n C14 C15 CDC sing 110 n n C14 H141 CDC sing 111 n n C14 H142 CDC sing 112 n n C15 N11 CDC sing 113 n n C15 H151 CDC sing 114 n n C15 H152 CDC sing 115 n n N11 C16 CDC sing 116 n n N11 C17 CDC sing 117 n n N11 C18 CDC sing 118 n n C16 H161 CDC sing 119 n n C16 H162 CDC sing 120 n n C16 H163 CDC sing 121 n n C17 H171 CDC sing 122 n n C17 H172 CDC sing 123 n n C17 H173 CDC sing 124 n n C18 H181 CDC sing 125 n n C18 H182 CDC sing 126 n n C18 H183 CDC sing 127 n n # _atom_sites.entry_id 8ERP _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 MG B 1 501 401 MG MG . D 2 MG B 1 502 402 MG MG . E 3 LBN B 1 503 702 LBN XXX . F 3 LBN B 1 504 704 LBN XXX . G 4 CDC B 1 505 709 CDC CDC . H 3 LBN B 1 506 710 LBN LBN . I 3 LBN B 1 507 711 LBN XXX . J 3 LBN B 1 508 721 LBN XXX . K 3 LBN B 1 509 723 LBN XXX . L 3 LBN B 1 510 724 LBN XXX . M 3 LBN B 1 511 725 LBN XXX . N 3 LBN B 1 512 712 LBN XXX . O 3 LBN B 1 513 722 LBN XXX . P 3 LBN A 1 501 712 LBN XXX . Q 3 LBN A 1 502 722 LBN XXX . R 2 MG A 1 503 401 MG MG . S 2 MG A 1 504 402 MG MG . T 3 LBN A 1 505 702 LBN XXX . U 3 LBN A 1 506 704 LBN XXX . V 4 CDC A 1 507 709 CDC CDC . W 3 LBN A 1 508 710 LBN LBN . X 3 LBN A 1 509 711 LBN XXX . Y 3 LBN A 1 510 721 LBN XXX . Z 3 LBN A 1 511 723 LBN XXX . AA 3 LBN A 1 512 724 LBN XXX . BA 3 LBN A 1 513 725 LBN XXX . # 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 CDC . . . V 4 124.167 139.937 88.306 1 50.05 ? N1 CDC 507 A 1 HETATM 2 C C2 CDC . . . V 4 125.426 139.669 87.762 1 50.05 ? C2 CDC 507 A 1 HETATM 3 N N3 CDC . . . V 4 126.482 139.509 88.604 1 50.05 ? N3 CDC 507 A 1 HETATM 4 C C4 CDC . . . V 4 126.315 139.606 89.933 1 50.05 ? C4 CDC 507 A 1 HETATM 5 C C5 CDC . . . V 4 125.039 139.878 90.506 1 50.05 ? C5 CDC 507 A 1 HETATM 6 C C6 CDC . . . V 4 124.003 140.035 89.666 1 50.05 ? C6 CDC 507 A 1 HETATM 7 O O2 CDC . . . V 4 125.54 139.586 86.538 1 50.05 ? O2 CDC 507 A 1 HETATM 8 N N4 CDC . . . V 4 127.384 139.439 90.713 1 50.05 ? N4 CDC 507 A 1 HETATM 9 C C1' CDC . . . V 4 123.031 140.11 87.386 1 50.05 ? C1' CDC 507 A 1 HETATM 10 C C2' CDC . . . V 4 121.733 139.44 87.869 1 50.05 ? C2' CDC 507 A 1 HETATM 11 O O2' CDC . . . V 4 121.115 138.725 86.806 1 50.05 ? O2' CDC 507 A 1 HETATM 12 C C3' CDC . . . V 4 120.882 140.632 88.319 1 50.05 ? C3' CDC 507 A 1 HETATM 13 C C4' CDC . . . V 4 121.364 141.744 87.4 1 50.05 ? C4' CDC 507 A 1 HETATM 14 O O4' CDC . . . V 4 122.775 141.497 87.247 1 50.05 ? O4' CDC 507 A 1 HETATM 15 O O3' CDC . . . V 4 119.493 140.385 88.133 1 50.05 ? O3' CDC 507 A 1 HETATM 16 C C5' CDC . . . V 4 121.151 143.145 87.918 1 50.05 ? C5' CDC 507 A 1 HETATM 17 O O5' CDC . . . V 4 120.302 143.093 89.084 1 50.05 ? O5' CDC 507 A 1 HETATM 18 P PA CDC . . . V 4 120.347 144.069 90.36 1 50.05 ? PA CDC 507 A 1 HETATM 19 O O1A CDC . . . V 4 120.56 145.471 89.953 1 50.05 -1 O1A CDC 507 A 1 HETATM 20 O O2A CDC . . . V 4 121.409 143.508 91.302 1 50.05 ? O2A CDC 507 A 1 HETATM 21 O O3A CDC . . . V 4 118.946 143.887 91.094 1 50.05 ? O3A CDC 507 A 1 HETATM 22 P PB CDC . . . V 4 118.578 143.45 92.588 1 50.05 ? PB CDC 507 A 1 HETATM 23 O O1B CDC . . . V 4 117.952 144.798 93.169 1 50.05 ? O1B CDC 507 A 1 HETATM 24 O O2B CDC . . . V 4 117.502 142.439 92.546 1 50.05 -1 O2B CDC 507 A 1 HETATM 25 O O3B CDC . . . V 4 119.834 143.141 93.312 1 50.05 ? O3B CDC 507 A 1 HETATM 26 C C14 CDC . . . V 4 117.673 144.915 94.586 1 50.05 ? C14 CDC 507 A 1 HETATM 27 C C15 CDC . . . V 4 118.115 146.279 95.059 1 50.05 ? C15 CDC 507 A 1 HETATM 28 N N11 CDC . . . V 4 117.278 147.453 94.597 1 50.05 ? N11 CDC 507 A 1 HETATM 29 C C16 CDC . . . V 4 117.813 147.992 93.307 1 50.05 ? C16 CDC 507 A 1 HETATM 30 C C17 CDC . . . V 4 117.326 148.534 95.632 1 50.05 ? C17 CDC 507 A 1 HETATM 31 C C18 CDC . . . V 4 115.855 147.035 94.398 1 50.05 ? C18 CDC 507 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #