data_8B67 # _model_server_result.job_id 2-bgUuGSuUTzbGtyn4c3Jg _model_server_result.datetime_utc '2024-10-11 07:14:34' _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 8b67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1304}' # _entry.id 8B67 # _exptl.entry_id 8B67 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-TRIPHOSPHATE" _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 111.48 _cell.angle_gamma 90 _cell.entry_id 8B67 _cell.length_a 162.061 _cell.length_b 67.36 _cell.length_c 152.129 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B67 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 5 _struct_asym.id G _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 covale ? covale1 B O3' DT 10 P DT 10 1_555 B P DOC 11 P DOC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? metalc ? metalc1 A OD1 ASP 295 A ASP 290 1_555 F CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc2 A OD2 ASP 295 A ASP 290 1_555 F CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc3 A OE1 GLU 297 A GLU 292 1_555 F CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc4 A OD2 ASP 482 A ASP 477 1_555 F CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc5 A OD1 ASP 645 A ASP 640 1_555 D CA CA . A CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc6 A OD2 ASP 645 A ASP 640 1_555 D CA CA . A CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.157 ? metalc ? metalc7 A OD2 ASP 645 A ASP 640 1_555 E CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc8 A O VAL 646 A VAL 641 1_555 D CA CA . A CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc9 A OD2 ASP 882 A ASP 877 1_555 D CA CA . A CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc10 A OE2 GLU 950 A GLU 945 1_555 E CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc11 D CA CA . A CA 1301 1_555 G O2B CTP . A CTP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc12 D CA CA . A CA 1301 1_555 G O3G CTP . A CTP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc13 D CA CA . A CA 1301 1_555 G O1A CTP . A CTP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc14 E CA CA . A CA 1302 1_555 G O3G CTP . A CTP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc15 E CA CA . A CA 1302 1_555 G O2G CTP . A CTP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc16 F CA CA . A CA 1303 1_555 H O ACT . A ACT 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc17 F CA CA . A CA 1303 1_555 H OXT ACT . A ACT 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? hydrog WATSON-CRICK hydrog1 B N3 DT 1 P DT 1 1_555 C N1 DA 16 T DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B O4 DT 1 P DT 1 1_555 C N6 DA 16 T DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DA 2 P DA 2 1_555 C N3 DT 15 T DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N6 DA 2 P DA 2 1_555 C O4 DT 15 T DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DA 3 P DA 3 1_555 C N3 DT 14 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N6 DA 3 P DA 3 1_555 C O4 DT 14 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DC 4 P DC 4 1_555 C N1 DG 13 T DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N4 DC 4 P DC 4 1_555 C O6 DG 13 T DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O2 DC 4 P DC 4 1_555 C N2 DG 13 T DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DC 5 P DC 5 1_555 C N1 DG 12 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N4 DC 5 P DC 5 1_555 C O6 DG 12 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O2 DC 5 P DC 5 1_555 C N2 DG 12 T DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 6 P DG 6 1_555 C N3 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 6 P DG 6 1_555 C O2 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 6 P DG 6 1_555 C N4 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 7 P DC 7 1_555 C N1 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 7 P DC 7 1_555 C O6 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 7 P DC 7 1_555 C N2 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DG 8 P DG 8 1_555 C N3 DC 9 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N2 DG 8 P DG 8 1_555 C O2 DC 9 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O6 DG 8 P DG 8 1_555 C N4 DC 9 T DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N3 DT 9 P DT 9 1_555 C N1 DA 8 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O4 DT 9 P DT 9 1_555 C N6 DA 8 T DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 DT 10 P DT 10 1_555 C N1 DA 7 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O4 DT 10 P DT 10 1_555 C N6 DA 7 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N3 DOC 11 P DOC 11 1_555 C N1 DG 6 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N4 DOC 11 P DOC 11 1_555 C O6 DG 6 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O2 DOC 11 P DOC 11 1_555 C N2 DG 6 T DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id CTP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-TRIPHOSPHATE" _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 CTP sing 76 n n N1 C6 CTP sing 77 n n N1 C1' CTP sing 78 n n C2 N3 CTP sing 79 n n C2 O2 CTP doub 80 n n N3 C4 CTP doub 81 n n C4 C5 CTP sing 82 n n C4 N4 CTP sing 83 n n C5 C6 CTP doub 84 n n C5 H5 CTP sing 85 n n C6 H6 CTP sing 86 n n N4 HN41 CTP sing 87 n n N4 HN42 CTP sing 88 n n C1' C2' CTP sing 89 n n C1' O4' CTP sing 90 n n C1' H1' CTP sing 91 n n C2' O2' CTP sing 92 n n C2' C3' CTP sing 93 n n C2' H2' CTP sing 94 n n O2' HO2' CTP sing 95 n n C3' C4' CTP sing 96 n n C3' O3' CTP sing 97 n n C3' H3' CTP sing 98 n n C4' O4' CTP sing 99 n n C4' C5' CTP sing 100 n n C4' H4' CTP sing 101 n n O3' HO3' CTP sing 102 n n C5' O5' CTP sing 103 n n C5' "H5'1" CTP sing 104 n n C5' "H5'2" CTP sing 105 n n O5' PA CTP sing 106 n n PA O1A CTP doub 107 n n PA O2A CTP sing 108 n n PA O3A CTP sing 109 n n O2A HOA2 CTP sing 110 n n O3A PB CTP sing 111 n n PB O1B CTP doub 112 n n PB O2B CTP sing 113 n n PB O3B CTP sing 114 n n O2B HOB2 CTP sing 115 n n O3B PG CTP sing 116 n n PG O1G CTP doub 117 n n PG O2G CTP sing 118 n n PG O3G CTP sing 119 n n O2G HOG2 CTP sing 120 n n O3G HOG3 CTP sing 121 n n # _atom_sites.entry_id 8B67 _atom_sites.fract_transf_matrix[1][1] 0.006171 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002428 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014846 _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] 0.007064 _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 D 4 CA A 1 1301 1301 CA CA . E 4 CA A 1 1302 1311 CA CA . F 4 CA A 1 1303 1321 CA CA . G 5 CTP A 1 1304 1401 CTP CTP . H 6 ACT A 1 1305 1402 ACT ACT . I 7 HOH A 1 1401 12 HOH HOH . I 7 HOH A 2 1402 8 HOH HOH . I 7 HOH A 3 1403 15 HOH HOH . I 7 HOH A 4 1404 19 HOH HOH . I 7 HOH A 5 1405 16 HOH HOH . I 7 HOH A 6 1406 23 HOH HOH . I 7 HOH A 7 1407 17 HOH HOH . I 7 HOH A 8 1408 22 HOH HOH . I 7 HOH A 9 1409 5 HOH HOH . J 7 HOH P 1 101 14 HOH HOH . K 7 HOH T 1 101 2 HOH HOH . K 7 HOH T 2 102 10 HOH HOH . K 7 HOH T 3 103 11 HOH HOH . K 7 HOH T 4 104 3 HOH HOH . K 7 HOH T 5 105 13 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 CTP . . . G 5 7.72 14.251 33.831 1 31.86 ? N1 CTP 1304 A 1 HETATM 2 C C2 CTP . . . G 5 6.64 13.378 33.954 1 25.94 ? C2 CTP 1304 A 1 HETATM 3 N N3 CTP . . . G 5 5.477 13.841 34.462 1 21.65 ? N3 CTP 1304 A 1 HETATM 4 C C4 CTP . . . G 5 5.366 15.122 34.829 1 23.65 ? C4 CTP 1304 A 1 HETATM 5 C C5 CTP . . . G 5 6.454 16.027 34.703 1 18.55 ? C5 CTP 1304 A 1 HETATM 6 C C6 CTP . . . G 5 7.603 15.556 34.199 1 24.12 ? C6 CTP 1304 A 1 HETATM 7 O O2 CTP . . . G 5 6.785 12.201 33.596 1 19.89 ? O2 CTP 1304 A 1 HETATM 8 N N4 CTP . . . G 5 4.205 15.521 35.322 1 28.19 ? N4 CTP 1304 A 1 HETATM 9 C C1' CTP . . . G 5 8.975 13.714 33.245 1 37.28 ? C1' CTP 1304 A 1 HETATM 10 C C2' CTP . . . G 5 8.946 13.735 31.712 1 37.81 ? C2' CTP 1304 A 1 HETATM 11 O O2' CTP . . . G 5 9.438 12.507 31.223 1 40.25 ? O2' CTP 1304 A 1 HETATM 12 C C3' CTP . . . G 5 9.848 14.93 31.388 1 30.57 ? C3' CTP 1304 A 1 HETATM 13 C C4' CTP . . . G 5 10.878 14.83 32.515 1 34.21 ? C4' CTP 1304 A 1 HETATM 14 O O4' CTP . . . G 5 10.062 14.509 33.665 1 32.19 ? O4' CTP 1304 A 1 HETATM 15 O O3' CTP . . . G 5 10.467 14.838 30.113 1 30.2 ? O3' CTP 1304 A 1 HETATM 16 C C5' CTP . . . G 5 11.682 16.074 32.787 1 33.81 ? C5' CTP 1304 A 1 HETATM 17 O O5' CTP . . . G 5 10.871 16.997 33.542 1 24.28 ? O5' CTP 1304 A 1 HETATM 18 P PA CTP . . . G 5 10.713 18.479 32.986 1 28.49 ? PA CTP 1304 A 1 HETATM 19 O O1A CTP . . . G 5 12.059 19.083 32.784 1 34.98 ? O1A CTP 1304 A 1 HETATM 20 O O2A CTP . . . G 5 9.72 19.214 33.813 1 34.28 ? O2A CTP 1304 A 1 HETATM 21 O O3A CTP . . . G 5 10.068 18.186 31.555 1 52.59 ? O3A CTP 1304 A 1 HETATM 22 P PB CTP . . . G 5 10.505 18.589 30.074 1 25.93 ? PB CTP 1304 A 1 HETATM 23 O O1B CTP . . . G 5 9.616 17.89 29.118 1 39.04 ? O1B CTP 1304 A 1 HETATM 24 O O2B CTP . . . G 5 11.977 18.439 29.96 1 34.68 ? O2B CTP 1304 A 1 HETATM 25 O O3B CTP . . . G 5 10.142 20.142 30.071 1 25.38 ? O3B CTP 1304 A 1 HETATM 26 P PG CTP . . . G 5 11.065 21.445 29.982 1 30.4 ? PG CTP 1304 A 1 HETATM 27 O O1G CTP . . . G 5 11.12 21.793 28.532 1 44.27 ? O1G CTP 1304 A 1 HETATM 28 O O2G CTP . . . G 5 10.397 22.498 30.804 1 26.06 ? O2G CTP 1304 A 1 HETATM 29 O O3G CTP . . . G 5 12.401 21.03 30.531 1 38.68 ? O3G CTP 1304 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #