data_5C51 # _model_server_result.job_id IjtY20NqkAKEN4UlCJeNFw _model_server_result.datetime_utc '2025-08-04 03:16:49' _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 5c51 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":4003}' # _entry.id 5C51 # _exptl.entry_id 5C51 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 487.186 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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 90 _cell.entry_id 5C51 _cell.length_a 215.049 _cell.length_b 215.049 _cell.length_c 161.692 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C51 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 H _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 D C2 DA 2 P DA 4 1_555 E C2 DT 25 T DT 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale2 D C4 DA 2 P DA 4 1_555 E O2 DT 25 T DT 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale3 D O3' DA 21 P DA 23 1_555 D P DOC 22 P DOC 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 A OD1 ASP 856 A ASP 890 1_555 G MG MG . A MG 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc2 A OD1 ASP 1101 A ASP 1135 1_555 G MG MG . A MG 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc3 F MG MG . A MG 4001 1_555 H OAH 1RY . A 1RY 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc4 F MG MG . A MG 4001 1_555 H OAO 1RY . A 1RY 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? metalc ? metalc5 G MG MG . A MG 4002 1_555 H OAF 1RY . A 1RY 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc6 G MG MG . A MG 4002 1_555 H OAI 1RY . A 1RY 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? hydrog WATSON-CRICK hydrog1 D N1 DA 4 P DA 6 1_555 E N3 DT 22 T DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N6 DA 4 P DA 6 1_555 E O4 DT 22 T DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N3 DC 5 P DC 7 1_555 E N1 DG 21 T DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D N4 DC 5 P DC 7 1_555 E O6 DG 21 T DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D O2 DC 5 P DC 7 1_555 E N2 DG 21 T DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N1 DG 6 P DG 8 1_555 E N3 DC 20 T DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D N2 DG 6 P DG 8 1_555 E O2 DC 20 T DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D O6 DG 6 P DG 8 1_555 E N4 DC 20 T DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N1 DA 7 P DA 9 1_555 E N3 DT 19 T DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D N6 DA 7 P DA 9 1_555 E O4 DT 19 T DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog11 D N1 DG 8 P DG 10 1_555 E O2 DC 18 T DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog12 D N2 DG 8 P DG 10 1_555 E N3 DC 18 T DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D N1 DG 9 P DG 11 1_555 E N3 DC 17 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D N2 DG 9 P DG 11 1_555 E O2 DC 17 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D O6 DG 9 P DG 11 1_555 E N4 DC 17 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D N1 DG 10 P DG 12 1_555 E N3 DC 16 T DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 D N2 DG 10 P DG 12 1_555 E O2 DC 16 T DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 D O6 DG 10 P DG 12 1_555 E N4 DC 16 T DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog19 D N3 DC 11 P DC 13 1_555 E N2 DG 15 T DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog20 D O2 DC 12 P DC 14 1_555 E N2 DG 14 T DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 D N1 DA 13 P DA 15 1_555 E N3 DT 13 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 D N6 DA 13 P DA 15 1_555 E O4 DT 13 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 D N1 DG 14 P DG 16 1_555 E N3 DC 12 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 D N2 DG 14 P DG 16 1_555 E O2 DC 12 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 D O6 DG 14 P DG 16 1_555 E N4 DC 12 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D N3 DT 15 P DT 17 1_555 E N1 DA 11 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 D O4 DT 15 P DT 17 1_555 E N6 DA 11 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog28 D O6 DG 16 P DG 18 1_555 E N4 DC 10 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 D N3 DC 17 P DC 19 1_555 E N1 DG 9 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 D N4 DC 17 P DC 19 1_555 E O6 DG 9 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 D O2 DC 17 P DC 19 1_555 E N2 DG 9 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 D N3 DC 18 P DC 20 1_555 E N1 DG 8 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 D N4 DC 18 P DC 20 1_555 E O6 DG 8 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 D O2 DC 18 P DC 20 1_555 E N2 DG 8 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog35 D N3 DC 18 P DC 20 1_555 E N2 DG 9 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog36 D O2 DC 18 P DC 20 1_555 E N1 DG 9 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DT MISPAIR' hydrog37 D N2 DG 19 P DG 21 1_555 E O2 DT 7 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog38 D N3 DT 20 P DT 22 1_555 E N1 DA 6 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 D N1 DA 21 P DA 23 1_555 E N3 DT 5 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 D N6 DA 21 P DA 23 1_555 E O4 DT 5 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 D N3 DOC 22 P DOC 24 1_555 E N1 DG 4 T DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 D N4 DOC 22 P DOC 24 1_555 E O6 DG 4 T DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 D O2 DOC 22 P DOC 24 1_555 E N2 DG 4 T DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C8 H13 F N3 O12 P3 S' _chem_comp.formula_weight 487.186 _chem_comp.id 1RY _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' _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 OAG PAZ 1RY doub 1 n n FAJ CAU 1RY sing 2 n n OAF PAZ 1RY sing 3 n n OAH PBA 1RY doub 4 n n PAZ OAC 1RY sing 5 n n PAZ OAQ 1RY sing 6 n n NAA CAT 1RY sing 7 n n OAD PBA 1RY sing 8 n n CAU CAT 1RY sing 9 n n CAU CAK 1RY doub 10 n n PBA OAR 1RY sing 11 n n PBA OAO 1RY sing 12 n n OAR PBB 1RY sing 13 n n OAQ PBB 1RY sing 14 n n CAT NAN 1RY doub 15 n n CAK NAY 1RY sing 16 n n PBB OAE 1RY doub 17 n n PBB OAI 1RY sing 18 n n OAO CAL 1RY sing 19 n n NAN CAV 1RY sing 20 n n NAY CAV 1RY sing 21 n n NAY CAX 1RY sing 22 n n CAV OAB 1RY doub 23 n n SAS CAM 1RY sing 24 n n SAS CAW 1RY sing 25 n n CAL CAW 1RY sing 26 n n CAM CAX 1RY sing 27 n n CAX OAP 1RY sing 28 n n OAP CAW 1RY sing 29 n n OAC H1 1RY sing 30 n n OAF H2 1RY sing 31 n n OAI H3 1RY sing 32 n n OAD H4 1RY sing 33 n n CAL H5 1RY sing 34 n n CAL H6 1RY sing 35 n n CAW H7 1RY sing 36 n n CAM H8 1RY sing 37 n n CAM H9 1RY sing 38 n n CAX H10 1RY sing 39 n n CAK H11 1RY sing 40 n n NAA H12 1RY sing 41 n n NAA H13 1RY sing 42 n n # _atom_sites.entry_id 5C51 _atom_sites.fract_transf_matrix[1][1] 0.00465 _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] 0.00465 _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] 0.006185 _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 F 5 MG A 1 4001 4001 MG MG . G 5 MG A 1 4002 4002 MG MG . H 6 1RY A 1 4003 1 1RY FTC . # 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 OAC 1RY . . . H 6 57.159 -19.863 1.949 1 76.63 ? OAC 1RY 4003 A 1 HETATM 2 P PAZ 1RY . . . H 6 56.902 -20.574 0.637 1 78.66 ? PAZ 1RY 4003 A 1 HETATM 3 O OAF 1RY . . . H 6 57.944 -21.641 0.449 1 70.94 ? OAF 1RY 4003 A 1 HETATM 4 O OAG 1RY . . . H 6 56.97 -19.584 -0.487 1 78.76 ? OAG 1RY 4003 A 1 HETATM 5 O OAQ 1RY . . . H 6 55.414 -21.258 0.693 1 74.66 ? OAQ 1RY 4003 A 1 HETATM 6 P PBB 1RY . . . H 6 55.029 -22.391 1.715 1 70.48 ? PBB 1RY 4003 A 1 HETATM 7 O OAI 1RY . . . H 6 56.201 -23.247 1.956 1 77.37 ? OAI 1RY 4003 A 1 HETATM 8 O OAE 1RY . . . H 6 53.917 -23.215 1.159 1 79.54 ? OAE 1RY 4003 A 1 HETATM 9 O OAR 1RY . . . H 6 54.561 -21.708 3.063 1 73.44 ? OAR 1RY 4003 A 1 HETATM 10 P PBA 1RY . . . H 6 55.418 -21.597 4.381 1 71.76 ? PBA 1RY 4003 A 1 HETATM 11 O OAH 1RY . . . H 6 56.919 -21.768 4.078 1 71.88 ? OAH 1RY 4003 A 1 HETATM 12 O OAD 1RY . . . H 6 55.182 -20.201 5.015 1 74.46 ? OAD 1RY 4003 A 1 HETATM 13 O OAO 1RY . . . H 6 54.959 -22.71 5.403 1 63.47 ? OAO 1RY 4003 A 1 HETATM 14 C CAL 1RY . . . H 6 55.462 -23.995 5.233 1 63.81 ? CAL 1RY 4003 A 1 HETATM 15 C CAW 1RY . . . H 6 54.262 -25.042 5.346 1 64.87 ? CAW 1RY 4003 A 1 HETATM 16 O OAP 1RY . . . H 6 52.992 -24.37 4.98 1 65.53 ? OAP 1RY 4003 A 1 HETATM 17 S SAS 1RY . . . H 6 54.173 -25.553 6.812 1 64.21 ? SAS 1RY 4003 A 1 HETATM 18 C CAM 1RY . . . H 6 52.704 -25.069 7.355 1 64.49 ? CAM 1RY 4003 A 1 HETATM 19 C CAX 1RY . . . H 6 51.908 -24.788 6.129 1 65.63 ? CAX 1RY 4003 A 1 HETATM 20 N NAY 1RY . . . H 6 51.091 -23.837 6.352 1 65.59 ? NAY 1RY 4003 A 1 HETATM 21 C CAK 1RY . . . H 6 51.486 -22.571 6.168 1 64.85 ? CAK 1RY 4003 A 1 HETATM 22 C CAU 1RY . . . H 6 50.565 -21.545 6.421 1 64.87 ? CAU 1RY 4003 A 1 HETATM 23 F FAJ 1RY . . . H 6 50.901 -20.284 6.256 1 64.21 ? FAJ 1RY 4003 A 1 HETATM 24 C CAV 1RY . . . H 6 49.877 -24.115 6.762 1 66.31 ? CAV 1RY 4003 A 1 HETATM 25 O OAB 1RY . . . H 6 49.545 -25.315 6.924 1 67.04 ? OAB 1RY 4003 A 1 HETATM 26 N NAN 1RY . . . H 6 48.974 -23.17 7.014 1 66.39 ? NAN 1RY 4003 A 1 HETATM 27 C CAT 1RY . . . H 6 49.269 -21.88 6.859 1 65.7 ? CAT 1RY 4003 A 1 HETATM 28 N NAA 1RY . . . H 6 48.294 -20.863 7.13 1 65.82 ? NAA 1RY 4003 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #