data_5VU7 # _model_server_result.job_id aFVZYyb1hDykCCpAlJHzwg _model_server_result.datetime_utc '2025-01-10 22:00:33' _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 5vu7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":803}' # _entry.id 5VU7 # _exptl.entry_id 5VU7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 317.195 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL DIHYDROGEN 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 5VU7 _cell.length_a 66.55 _cell.length_b 112.61 _cell.length_c 145.46 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VU7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _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 _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 F _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 disulf ? disulf1 A SG CYS 428 A CYS 428 1_555 A SG CYS 442 A CYS 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 506 A CYS 506 1_555 A SG CYS 509 A CYS 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 C O3' DG 11 P DG 11 1_555 C P 9O4 12 P 9O4 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? hydrog WATSON-CRICK hydrog1 B N3 DC 6 T DC 6 1_555 C N1 DG 11 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 6 T DC 6 1_555 C O6 DG 11 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 6 T DC 6 1_555 C N2 DG 11 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 7 T DG 7 1_555 C N3 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 7 T DG 7 1_555 C O2 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 7 T DG 7 1_555 C N4 DC 10 P DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DC 8 T DC 8 1_555 C N1 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N4 DC 8 T DC 8 1_555 C O6 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O2 DC 8 T DC 8 1_555 C N2 DG 9 P DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 9 T DA 9 1_555 C N3 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 9 T DA 9 1_555 C O4 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DG 10 T DG 10 1_555 C N3 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 DG 10 T DG 10 1_555 C O2 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 DG 10 T DG 10 1_555 C N4 DC 7 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N3 DT 11 T DT 11 1_555 C N1 DA 6 P DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O4 DT 11 T DT 11 1_555 C N6 DA 6 P DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DT 12 T DT 12 1_555 C N1 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O4 DT 12 T DT 12 1_555 C N6 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DC 13 T DC 13 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N4 DC 13 T DC 13 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O2 DC 13 T DC 13 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DG 14 T DG 14 1_555 C N3 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 DG 14 T DG 14 1_555 C O2 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 DG 14 T DG 14 1_555 C N4 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N3 DC 15 T DC 15 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N4 DC 15 T DC 15 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O2 DC 15 T DC 15 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H12 N5 O6 P' _chem_comp.formula_weight 317.195 _chem_comp.id FA2 _chem_comp.mon_nstd_flag n _chem_comp.name '5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL DIHYDROGEN PHOSPHATE' _chem_comp.type 'rna linking' _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 P OP1 FA2 doub 266 n n P OP2 FA2 sing 267 n n P O3' FA2 sing 268 n n P OP3 FA2 sing 269 n n OP2 HOP2 FA2 sing 270 n n O3' C3' FA2 sing 271 n n N9 C4 FA2 sing 272 n y N9 C8 FA2 sing 273 n y N9 C1' FA2 sing 274 n n C4 N3 FA2 sing 275 n y C4 C5 FA2 doub 276 n y N3 C2 FA2 doub 277 n y C2 N1 FA2 sing 278 n y C2 H2 FA2 sing 279 n n N1 C6 FA2 doub 280 n y C6 N6 FA2 sing 281 n n C6 C5 FA2 sing 282 n y N6 H6A FA2 sing 283 n n N6 H6B FA2 sing 284 n n C5 N7 FA2 sing 285 n y N7 C8 FA2 doub 286 n y C8 H8 FA2 sing 287 n n C2' C1' FA2 sing 288 n n C2' C3' FA2 sing 289 n n C2' O2' FA2 sing 290 n n C2' H2' FA2 sing 291 n n C4' O4' FA2 sing 292 n n C4' C3' FA2 sing 293 n n C4' "H4'1" FA2 sing 294 n n C4' "H4'2" FA2 sing 295 n n O4' C1' FA2 sing 296 n n C1' H1' FA2 sing 297 n n C3' H3' FA2 sing 298 n n O2' HO2' FA2 sing 299 n n OP3 HOP3 FA2 sing 300 n n # _atom_sites.entry_id 5VU7 _atom_sites.fract_transf_matrix[1][1] 0.015026 _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] 0.00888 _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] 0.006875 _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 MG A 1 801 1 MG MG . E 5 SO4 A 1 802 2 SO4 SO4 . F 6 FA2 A 1 803 3 FA2 FA2 . # 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 P P FA2 . . . F 6 12.524 10.396 313.249 0.48 81.71 ? P FA2 803 A 1 HETATM 2 O OP1 FA2 . . . F 6 11.979 11.506 314.064 0.48 75.01 ? OP1 FA2 803 A 1 HETATM 3 O OP2 FA2 . . . F 6 11.572 9.263 313.259 0.48 68.83 ? OP2 FA2 803 A 1 HETATM 4 O O3' FA2 . . . F 6 12.733 10.883 311.739 0.48 53.42 ? O3' FA2 803 A 1 HETATM 5 N N9 FA2 . . . F 6 15.592 13.457 310.561 0.48 36.97 ? N9 FA2 803 A 1 HETATM 6 C C4 FA2 . . . F 6 16.665 14.265 310.12 0.48 34.05 ? C4 FA2 803 A 1 HETATM 7 N N3 FA2 . . . F 6 17.958 14.276 309.372 0.48 35 ? N3 FA2 803 A 1 HETATM 8 C C2 FA2 . . . F 6 18.42 15.741 309.432 0.48 41.75 ? C2 FA2 803 A 1 HETATM 9 N N1 FA2 . . . F 6 17.732 16.709 310.038 0.48 35.62 ? N1 FA2 803 A 1 HETATM 10 C C6 FA2 . . . F 6 16.743 16.62 310.59 0.48 34.69 ? C6 FA2 803 A 1 HETATM 11 N N6 FA2 . . . F 6 16.148 17.807 311.193 0.48 39.37 ? N6 FA2 803 A 1 HETATM 12 C C5 FA2 . . . F 6 16.198 15.597 310.681 0.48 41.56 ? C5 FA2 803 A 1 HETATM 13 N N7 FA2 . . . F 6 14.957 15.221 311.315 0.48 52.02 ? N7 FA2 803 A 1 HETATM 14 C C8 FA2 . . . F 6 14.703 14.039 311.203 0.48 47.91 ? C8 FA2 803 A 1 HETATM 15 C C2' FA2 . . . F 6 14.965 11.406 311.477 0.48 35.08 ? C2' FA2 803 A 1 HETATM 16 C C4' FA2 . . . F 6 13.71 10.727 309.523 0.48 47.81 ? C4' FA2 803 A 1 HETATM 17 O O4' FA2 . . . F 6 14.691 11.808 309.11 0.48 46.4 ? O4' FA2 803 A 1 HETATM 18 C C1' FA2 . . . F 6 15.541 12.044 310.293 0.48 34.05 ? C1' FA2 803 A 1 HETATM 19 C C3' FA2 . . . F 6 13.922 10.537 311.024 0.48 37.93 ? C3' FA2 803 A 1 HETATM 20 O O2' FA2 . . . F 6 15.791 10.723 311.969 0.48 37.88 ? O2' FA2 803 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 518 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #