data_8KA5 # _model_server_result.job_id RLmOCXI-_BFbt3MgV4QOCw _model_server_result.datetime_utc '2024-11-25 13:29:28' _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 8ka5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":101}' # _entry.id 8KA5 # _exptl.entry_id 8KA5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 198.111 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE" _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 120 _cell.entry_id 8KA5 _cell.length_a 72.093 _cell.length_b 72.093 _cell.length_c 188.189 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KA5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall 'P 32 2"' _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 3 _struct_asym.id E _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 P DC 11 B DC 12 1_555 E O3' 3DR . B 3DR 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.62 ? hydrog WATSON-CRICK hydrog1 B N3 DC 11 B DC 12 1_555 D N1 DG 32 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 11 B DC 12 1_555 D O6 DG 32 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 11 B DC 12 1_555 D N2 DG 32 D DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 12 B DG 13 1_555 D N3 DC 31 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 12 B DG 13 1_555 D O2 DC 31 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 12 B DG 13 1_555 D N4 DC 31 D DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 DA 13 B DA 14 1_555 D N3 DT 30 D DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N6 DA 13 B DA 14 1_555 D O4 DT 30 D DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DC 14 B DC 15 1_555 D N1 DG 29 D DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 DC 14 B DC 15 1_555 D O6 DG 29 D DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 DC 14 B DC 15 1_555 D N2 DG 29 D DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DG 15 B DG 16 1_555 D N3 DC 28 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 DG 15 B DG 16 1_555 D O2 DC 28 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 DG 15 B DG 16 1_555 D N4 DC 28 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 DG 16 B DG 17 1_555 D N3 DC 27 D DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N2 DG 16 B DG 17 1_555 D O2 DC 27 D DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O6 DG 16 B DG 17 1_555 D N4 DC 27 D DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N1 DA 17 B DA 18 1_555 D N3 DT 26 D DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N6 DA 17 B DA 18 1_555 D O4 DT 26 D DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N3 DT 18 B DT 19 1_555 D N1 DA 25 D DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O4 DT 18 B DT 19 1_555 D N6 DA 25 D DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N3 DC 19 B DC 20 1_555 D N1 DG 24 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N4 DC 19 B DC 20 1_555 D O6 DG 24 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O2 DC 19 B DC 20 1_555 D N2 DG 24 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C N1 DG 1 C DG 1 1_555 D N3 DC 43 D DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N2 DG 1 C DG 1 1_555 D O2 DC 43 D DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C O6 DG 1 C DG 1 1_555 D N4 DC 43 D DC 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C N3 DC 2 C DC 2 1_555 D N1 DG 42 D DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C N4 DC 2 C DC 2 1_555 D O6 DG 42 D DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C O2 DC 2 C DC 2 1_555 D N2 DG 42 D DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C N3 DT 3 C DT 3 1_555 D N1 DA 41 D DA 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C O4 DT 3 C DT 3 1_555 D N6 DA 41 D DA 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N1 DG 4 C DG 4 1_555 D N3 DC 40 D DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C N2 DG 4 C DG 4 1_555 D O2 DC 40 D DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C O6 DG 4 C DG 4 1_555 D N4 DC 40 D DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C N1 DA 5 C DA 5 1_555 D N3 DT 39 D DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C N6 DA 5 C DA 5 1_555 D O4 DT 39 D DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C N3 DT 6 C DT 6 1_555 D N1 DA 38 D DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C O4 DT 6 C DT 6 1_555 D N6 DA 38 D DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C N1 DG 7 C DG 7 1_555 D N3 DC 37 D DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C N2 DG 7 C DG 7 1_555 D O2 DC 37 D DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 C O6 DG 7 C DG 7 1_555 D N4 DC 37 D DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 C N3 DC 8 C DC 8 1_555 D N1 DG 36 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 C N4 DC 8 C DC 8 1_555 D O6 DG 36 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 C O2 DC 8 C DC 8 1_555 D N2 DG 36 D DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 C N1 DG 9 C DG 9 1_555 D N3 DC 35 D DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 C N2 DG 9 C DG 9 1_555 D O2 DC 35 D DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog48 C O6 DG 9 C DG 9 1_555 D N4 DC 35 D DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog49 C N3 DC 10 C DC 10 1_555 D N1 DG 34 D DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog50 C N4 DC 10 C DC 10 1_555 D O6 DG 34 D DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog51 C O2 DC 10 C DC 10 1_555 D N2 DG 34 D DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C5 H11 O6 P' _chem_comp.formula_weight 198.111 _chem_comp.id 3DR _chem_comp.mon_nstd_flag . _chem_comp.name "1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms 'ABASIC DIDEOXYRIBOSE' # 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' P 3DR sing 1 n n O5' C5' 3DR sing 2 n n P OP1 3DR doub 3 n n P OP2 3DR sing 4 n n P OP3 3DR sing 5 n n OP2 HOP2 3DR sing 6 n n OP3 HOP3 3DR sing 7 n n C2' C1' 3DR sing 8 n n C2' C3' 3DR sing 9 n n C2' H2' 3DR sing 10 n n C2' "H2''" 3DR sing 11 n n C5' C4' 3DR sing 12 n n C5' H5' 3DR sing 13 n n C5' "H5''" 3DR sing 14 n n C4' O4' 3DR sing 15 n n C4' C3' 3DR sing 16 n n C4' "H4'1" 3DR sing 17 n n O4' C1' 3DR sing 18 n n C1' "H1'1" 3DR sing 19 n n C1' "H1'2" 3DR sing 20 n n C3' O3' 3DR sing 21 n n C3' H3' 3DR sing 22 n n O3' HO3' 3DR sing 23 n n # _atom_sites.entry_id 8KA5 _atom_sites.fract_transf_matrix[1][1] 0.013871 _atom_sites.fract_transf_matrix[1][2] 0.008008 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016017 _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] 0.005314 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id E _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id 3DR _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 11 _pdbx_nonpoly_scheme.pdb_mon_id 3DR _pdbx_nonpoly_scheme.auth_mon_id 3DR _pdbx_nonpoly_scheme.pdb_ins_code . # 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' 3DR . . . E 3 23.197 -20.898 -10.706 1 60.95 ? O5' 3DR 101 B 1 HETATM 2 P P 3DR . . . E 3 21.723 -20.443 -10.291 1 62.01 ? P 3DR 101 B 1 HETATM 3 O OP1 3DR . . . E 3 21.862 -19.577 -9.074 1 70.49 ? OP1 3DR 101 B 1 HETATM 4 O OP2 3DR . . . E 3 21.078 -21.767 -10.027 1 66.51 -1 OP2 3DR 101 B 1 HETATM 5 O OP3 3DR . . . E 3 21.244 -19.702 -11.495 1 66.65 ? OP3 3DR 101 B 1 HETATM 6 C C2' 3DR . . . E 3 25.184 -19.146 -14.188 1 68.27 ? C2' 3DR 101 B 1 HETATM 7 C C5' 3DR . . . E 3 24.016 -19.996 -11.455 1 63.09 ? C5' 3DR 101 B 1 HETATM 8 C C4' 3DR . . . E 3 24.973 -20.699 -12.406 1 68.58 ? C4' 3DR 101 B 1 HETATM 9 O O4' 3DR . . . E 3 24.201 -21.205 -13.501 1 71.98 ? O4' 3DR 101 B 1 HETATM 10 C C1' 3DR . . . E 3 24.383 -20.361 -14.649 1 65.51 ? C1' 3DR 101 B 1 HETATM 11 C C3' 3DR . . . E 3 25.934 -19.673 -12.982 1 69.42 ? C3' 3DR 101 B 1 HETATM 12 O O3' 3DR . . . E 3 27.13 -20.283 -13.504 1 76.83 ? O3' 3DR 101 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 12 #