data_8V7F # _model_server_result.job_id ITd9kSRfnkpCstC8Dg3Aiw _model_server_result.datetime_utc '2024-11-14 10:43:32' _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 8v7f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 8V7F # _exptl.entry_id 8V7F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 490.197 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine" _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 8V7F _cell.length_a 98.7 _cell.length_b 98.7 _cell.length_c 82.324 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8V7F _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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 _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 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 covale ? covale1 C O3' DA 7 P DA 8 1_555 C P CAR 8 P CAR 9 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.611 ? covale ? covale2 C O3' DA 7 P DA 8 1_555 C P CAR 8 P CAR 9 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.608 ? metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc3 A O MET 17 A MET 14 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc4 A OD2 ASP 118 A ASP 115 1_555 D MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc5 A OD1 ASP 118 A ASP 115 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc6 A OE1 GLU 119 A GLU 116 1_555 E MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc7 D MN MN . A MN 501 1_555 F O1A DZ4 . A DZ4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.196 ? metalc ? metalc8 D MN MN . A MN 501 1_555 F O2G DZ4 . A DZ4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.231 ? metalc ? metalc9 D MN MN . A MN 501 1_555 F O1B DZ4 . A DZ4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.269 ? metalc ? metalc10 E MN MN . A MN 502 1_555 F O1A DZ4 . A DZ4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.341 ? metalc ? metalc11 E MN MN . A MN 502 1_555 G O HOH . A HOH 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc12 E MN MN . A MN 502 1_555 C O3' CAR 8 P CAR 9 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.579 ? hydrog WATSON-CRICK hydrog1 B N1 DG 5 T DG 6 1_555 C N3 CAR 8 P CAR 9 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N1 DG 5 T DG 6 1_555 C N3 CAR 8 P CAR 9 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N2 DG 5 T DG 6 1_555 C O2 CAR 8 P CAR 9 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 5 T DG 6 1_555 C O2 CAR 8 P CAR 9 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 5 T DG 6 1_555 C N4 CAR 8 P CAR 9 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 5 T DG 6 1_555 C N4 CAR 8 P CAR 9 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DT 6 T DT 7 1_555 C N1 DA 7 P DA 8 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DT 6 T DT 7 1_555 C N1 DA 7 P DA 8 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O4 DT 6 T DT 7 1_555 C N6 DA 7 P DA 8 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O4 DT 6 T DT 7 1_555 C N6 DA 7 P DA 8 1_555 ? ? ? ? B ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DG 7 T DG 8 1_555 C N3 DC 6 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N2 DG 7 T DG 8 1_555 C O2 DC 6 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 DG 7 T DG 8 1_555 C N4 DC 6 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 8 T DA 9 1_555 C N3 DT 5 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 8 T DA 9 1_555 C O4 DT 5 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 9 T DC 10 1_555 C N1 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 9 T DC 10 1_555 C O6 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 9 T DC 10 1_555 C N2 DG 4 P DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DG 10 T DG 11 1_555 C N3 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N2 DG 10 T DG 11 1_555 C O2 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O6 DG 10 T DG 11 1_555 C N4 DC 3 P DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N3 DC 11 T DC 12 1_555 C N1 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N4 DC 11 T DC 12 1_555 C O6 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O2 DC 11 T DC 12 1_555 C N2 DG 2 P DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N3 DT 12 T DT 13 1_555 C N1 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O4 DT 12 T DT 13 1_555 C N6 DA 1 P DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H17 N6 O11 P3' _chem_comp.formula_weight 490.197 _chem_comp.id DZ4 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine" _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 C2 N1 DZ4 doub 268 n y N1 C6 DZ4 sing 269 n y N3 C2 DZ4 sing 270 n y C2 H2 DZ4 sing 271 n n N3 C4 DZ4 doub 272 n y N9 C4 DZ4 sing 273 n y C4 C5 DZ4 sing 274 n y C5 N7 DZ4 sing 275 n y C5 C6 DZ4 doub 276 n y C6 N6 DZ4 sing 277 n n N6 HN6 DZ4 sing 278 n n N6 HN6A DZ4 sing 279 n n C8 N7 DZ4 doub 280 n y N9 C8 DZ4 sing 281 n y C8 H8 DZ4 sing 282 n n C1' N9 DZ4 sing 283 n n O5' PA DZ4 sing 284 n n O1A PA DZ4 doub 285 n n PA O2A DZ4 sing 286 n n PA N3A DZ4 sing 287 n n O1B PB DZ4 doub 288 n n N3A PB DZ4 sing 289 n n PB O2B DZ4 sing 290 n n PB O3B DZ4 sing 291 n n O1G PG DZ4 doub 292 n n PG O3B DZ4 sing 293 n n PG O2G DZ4 sing 294 n n PG O3G DZ4 sing 295 n n O4' C1' DZ4 sing 296 n n C1' C2' DZ4 sing 297 n n C1' H1' DZ4 sing 298 n n C3' C2' DZ4 sing 299 n n C2' H2' DZ4 sing 300 n n C2' "H2'A" DZ4 sing 301 n n O2A HO2A DZ4 sing 302 n n O2B HO2B DZ4 sing 303 n n O2G HO2G DZ4 sing 304 n n C4' C3' DZ4 sing 305 n n C3' O3' DZ4 sing 306 n n C3' H3' DZ4 sing 307 n n O3' HO3' DZ4 sing 308 n n N3A HN3A DZ4 sing 309 n n O3G HO3G DZ4 sing 310 n n O4' C4' DZ4 sing 311 n n C4' C5' DZ4 sing 312 n n C4' H4' DZ4 sing 313 n n C5' O5' DZ4 sing 314 n n C5' H5' DZ4 sing 315 n n C5' "H5'A" DZ4 sing 316 n n # _atom_sites.entry_id 8V7F _atom_sites.fract_transf_matrix[1][1] 0.010132 _atom_sites.fract_transf_matrix[1][2] 0.00585 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011699 _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] 0.012147 _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 MN A 1 501 502 MN MN . E 4 MN A 1 502 503 MN MN . F 5 DZ4 A 1 503 504 DZ4 DZ4 . G 6 HOH A 1 601 7 HOH HOH . G 6 HOH A 2 602 2 HOH HOH . G 6 HOH A 3 603 3 HOH HOH . G 6 HOH A 4 604 14 HOH HOH . G 6 HOH A 5 605 9 HOH HOH . G 6 HOH A 6 606 12 HOH HOH . G 6 HOH A 7 607 8 HOH HOH . G 6 HOH A 8 608 11 HOH HOH . G 6 HOH A 9 609 10 HOH HOH . G 6 HOH A 10 610 13 HOH HOH . G 6 HOH A 11 611 5 HOH HOH . G 6 HOH A 12 612 1 HOH HOH . G 6 HOH A 13 613 4 HOH HOH . G 6 HOH A 14 614 6 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 DZ4 . B . F 5 -23.98 50.101 6.465 1 28.74 ? N1 DZ4 503 A 1 HETATM 2 C C2 DZ4 . B . F 5 -22.857 50.311 5.772 1 25.63 ? C2 DZ4 503 A 1 HETATM 3 N N3 DZ4 . B . F 5 -22.008 49.381 5.389 1 30.83 ? N3 DZ4 503 A 1 HETATM 4 C C4 DZ4 . B . F 5 -22.297 48.096 5.719 1 29.92 ? C4 DZ4 503 A 1 HETATM 5 C C5 DZ4 . B . F 5 -23.458 47.807 6.444 1 24.12 ? C5 DZ4 503 A 1 HETATM 6 C C6 DZ4 . B . F 5 -24.306 48.838 6.813 1 31.74 ? C6 DZ4 503 A 1 HETATM 7 N N6 DZ4 . B . F 5 -25.433 48.614 7.509 1 29.25 ? N6 DZ4 503 A 1 HETATM 8 N N7 DZ4 . B . F 5 -23.488 46.476 6.641 1 28.62 ? N7 DZ4 503 A 1 HETATM 9 C C8 DZ4 . B . F 5 -22.399 45.931 6.051 1 29.05 ? C8 DZ4 503 A 1 HETATM 10 N N9 DZ4 . B . F 5 -21.675 46.916 5.497 1 35.89 ? N9 DZ4 503 A 1 HETATM 11 P PA DZ4 . B . F 5 -21.569 41.791 5.886 1 26.04 ? PA DZ4 503 A 1 HETATM 12 P PB DZ4 . B . F 5 -19.042 41.553 7.269 1 25.33 ? PB DZ4 503 A 1 HETATM 13 P PG DZ4 . B . F 5 -19.284 38.816 8.373 1 27.52 ? PG DZ4 503 A 1 HETATM 14 C C1' DZ4 . B . F 5 -20.393 46.709 4.769 1 25.84 ? C1' DZ4 503 A 1 HETATM 15 O O1A DZ4 . B . F 5 -21.246 40.556 5.184 1 27.61 ? O1A DZ4 503 A 1 HETATM 16 O O1B DZ4 . B . F 5 -18.512 41.146 5.964 1 23.06 ? O1B DZ4 503 A 1 HETATM 17 O O1G DZ4 . B . F 5 -20.214 38.614 9.516 1 25.53 ? O1G DZ4 503 A 1 HETATM 18 C C2' DZ4 . B . F 5 -19.238 46.407 5.703 1 27 ? C2' DZ4 503 A 1 HETATM 19 O O2A DZ4 . B . F 5 -23.054 41.767 6.342 1 26.37 -1 O2A DZ4 503 A 1 HETATM 20 O O2B DZ4 . B . F 5 -18.252 42.775 7.798 1 27.55 -1 O2B DZ4 503 A 1 HETATM 21 O O2G DZ4 . B . F 5 -19.949 38.452 7.041 1 19.98 -1 O2G DZ4 503 A 1 HETATM 22 C C3' DZ4 . B . F 5 -19.091 44.898 5.634 1 26.32 ? C3' DZ4 503 A 1 HETATM 23 O O3' DZ4 . B . F 5 -17.716 44.555 5.824 1 23.99 ? O3' DZ4 503 A 1 HETATM 24 N N3A DZ4 . B . F 5 -20.638 41.922 7.227 1 24.74 ? N3A DZ4 503 A 1 HETATM 25 O O3B DZ4 . B . F 5 -18.826 40.402 8.332 1 28.77 ? O3B DZ4 503 A 1 HETATM 26 O O3G DZ4 . B . F 5 -17.999 37.981 8.543 1 25.33 -1 O3G DZ4 503 A 1 HETATM 27 C C4' DZ4 . B . F 5 -19.547 44.585 4.209 1 27.25 ? C4' DZ4 503 A 1 HETATM 28 O O4' DZ4 . B . F 5 -20.518 45.616 3.856 1 25.19 ? O4' DZ4 503 A 1 HETATM 29 C C5' DZ4 . B . F 5 -20.191 43.172 4.103 1 24.1 ? C5' DZ4 503 A 1 HETATM 30 O O5' DZ4 . B . F 5 -21.359 43.077 4.908 1 24.41 ? O5' DZ4 503 A 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 30 #