data_7VTF # _model_server_result.job_id Iy8ZTssEic88A2qqOLs-fA _model_server_result.datetime_utc '2024-12-26 17:09:04' _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 7vtf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 7VTF # _exptl.entry_id 7VTF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 243.217 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _entity.pdbx_number_of_molecules 4 _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 7VTF _cell.length_a 185.999 _cell.length_b 185.999 _cell.length_c 50.96 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VTF _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall 'P 3' _symmetry.space_group_name_H-M 'P 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I,J 1 1 C,D,G,H,K,L 2 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 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C9 H13 N3 O5' _chem_comp.formula_weight 243.217 _chem_comp.id CTN _chem_comp.mon_nstd_flag . _chem_comp.name 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CYTIDINE # 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 O5' C5' CTN sing 70 n n O5' H5' CTN sing 71 n n C5' C4' CTN sing 72 n n C5' "H5'1" CTN sing 73 n n C5' "H5'2" CTN sing 74 n n C4' O4' CTN sing 75 n n C4' C3' CTN sing 76 n n C4' H4' CTN sing 77 n n O4' C1' CTN sing 78 n n C1' N1 CTN sing 79 n n C1' C2' CTN sing 80 n n C1' H1' CTN sing 81 n n N1 C6 CTN sing 82 n y N1 C2 CTN sing 83 n y C6 C5 CTN doub 84 n y C6 H6 CTN sing 85 n n C5 C4 CTN sing 86 n y C5 H5 CTN sing 87 n n C4 N3 CTN doub 88 n y C4 N4 CTN sing 89 n n N3 C2 CTN sing 90 n y C2 O2 CTN doub 91 n n N4 HN41 CTN sing 92 n n N4 HN42 CTN sing 93 n n C2' O2' CTN sing 94 n n C2' C3' CTN sing 95 n n C2' H2' CTN sing 96 n n O2' H1 CTN sing 97 n n C3' O3' CTN sing 98 n n C3' H3' CTN sing 99 n n O3' H2 CTN sing 100 n n # _atom_sites.entry_id 7VTF _atom_sites.fract_transf_matrix[1][1] 0.005376 _atom_sites.fract_transf_matrix[1][2] 0.003104 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006208 _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] 0.019623 _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 2 CTN A 1 401 401 CTN CTN . F 2 CTN B 1 401 401 CTN CTN . G 2 CTN C 1 401 402 CTN CTN . H 2 CTN D 1 401 401 CTN CTN . I 3 HOH A 1 501 25 HOH HOH . I 3 HOH A 2 502 23 HOH HOH . I 3 HOH A 3 503 27 HOH HOH . I 3 HOH A 4 504 11 HOH HOH . I 3 HOH A 5 505 8 HOH HOH . I 3 HOH A 6 506 4 HOH HOH . I 3 HOH A 7 507 22 HOH HOH . I 3 HOH A 8 508 31 HOH HOH . J 3 HOH B 1 501 28 HOH HOH . J 3 HOH B 2 502 26 HOH HOH . J 3 HOH B 3 503 29 HOH HOH . J 3 HOH B 4 504 6 HOH HOH . J 3 HOH B 5 505 16 HOH HOH . J 3 HOH B 6 506 3 HOH HOH . J 3 HOH B 7 507 9 HOH HOH . J 3 HOH B 8 508 5 HOH HOH . K 3 HOH C 1 501 12 HOH HOH . K 3 HOH C 2 502 13 HOH HOH . K 3 HOH C 3 503 10 HOH HOH . K 3 HOH C 4 504 15 HOH HOH . K 3 HOH C 5 505 17 HOH HOH . K 3 HOH C 6 506 21 HOH HOH . K 3 HOH C 7 507 7 HOH HOH . K 3 HOH C 8 508 2 HOH HOH . L 3 HOH D 1 501 24 HOH HOH . L 3 HOH D 2 502 19 HOH HOH . L 3 HOH D 3 503 32 HOH HOH . L 3 HOH D 4 504 30 HOH HOH . L 3 HOH D 5 505 14 HOH HOH . L 3 HOH D 6 506 20 HOH HOH . L 3 HOH D 7 507 1 HOH HOH . L 3 HOH D 8 508 18 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 O O5' CTN . . . E 2 78.689 -24.588 -6.89 1 114.8 ? O5' CTN 401 A 1 HETATM 2 C C5' CTN . . . E 2 80.038 -24.628 -6.436 1 113.32 ? C5' CTN 401 A 1 HETATM 3 C C4' CTN . . . E 2 80.265 -23.683 -5.282 1 104.53 ? C4' CTN 401 A 1 HETATM 4 O O4' CTN . . . E 2 79.266 -23.925 -4.277 1 106.23 ? O4' CTN 401 A 1 HETATM 5 C C1' CTN . . . E 2 79.779 -23.542 -3.031 1 107.11 ? C1' CTN 401 A 1 HETATM 6 N N1 CTN . . . E 2 79.037 -24.281 -2 1 125.06 ? N1 CTN 401 A 1 HETATM 7 C C6 CTN . . . E 2 79.209 -25.606 -1.882 1 129.85 ? C6 CTN 401 A 1 HETATM 8 C C5 CTN . . . E 2 78.521 -26.303 -0.933 1 127.6 ? C5 CTN 401 A 1 HETATM 9 C C4 CTN . . . E 2 77.653 -25.65 -0.11 1 119.54 ? C4 CTN 401 A 1 HETATM 10 N N3 CTN . . . E 2 77.48 -24.327 -0.232 1 123.18 ? N3 CTN 401 A 1 HETATM 11 C C2 CTN . . . E 2 78.167 -23.63 -1.178 1 120.42 ? C2 CTN 401 A 1 HETATM 12 O O2 CTN . . . E 2 78.007 -22.431 -1.285 1 113.17 ? O2 CTN 401 A 1 HETATM 13 N N4 CTN . . . E 2 76.935 -26.37 0.879 1 109.35 ? N4 CTN 401 A 1 HETATM 14 C C2' CTN . . . E 2 81.274 -23.869 -3.074 1 95.77 ? C2' CTN 401 A 1 HETATM 15 O O2' CTN . . . E 2 82.022 -22.978 -2.272 1 70.48 ? O2' CTN 401 A 1 HETATM 16 C C3' CTN . . . E 2 81.617 -23.819 -4.578 1 94.55 ? C3' CTN 401 A 1 HETATM 17 O O3' CTN . . . E 2 82.411 -22.664 -4.85 1 77.91 ? O3' CTN 401 A 1 # _model_server_stats.io_time_ms 170 _model_server_stats.parse_time_ms 53 _model_server_stats.create_model_time_ms 67 _model_server_stats.query_time_ms 641 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 17 #