data_8K8S # _model_server_result.job_id ra0zB1sozB8dIp-2TsjgYw _model_server_result.datetime_utc '2025-01-06 22:37:10' _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 8k8s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1102}' # _entry.id 8K8S # _exptl.entry_id 8K8S _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 483.156 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _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 7 _struct_asym.id G _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 metalc ? metalc1 A OD1 ASP 549 A ASP 549 1_555 F MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc2 A O TYR 550 A TYR 550 1_555 F MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc3 A OD2 ASP 753 A ASP 753 1_555 F MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? metalc ? metalc4 F MG MG . A MG 1101 1_555 G O1G HF4 . A HF4 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc5 F MG MG . A MG 1101 1_555 G O1B HF4 . A HF4 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc6 F MG MG . A MG 1101 1_555 G O1A HF4 . A HF4 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? hydrog WATSON-CRICK hydrog1 D N1 DA 1 E DA 14 1_555 E N3 DT 16 F DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N6 DA 1 E DA 14 1_555 E O4 DT 16 F DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N3 DT 2 E DT 15 1_555 E N1 DA 15 F DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D O4 DT 2 E DT 15 1_555 E N6 DA 15 F DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D N3 DC 3 E DC 16 1_555 E N1 DG 14 F DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N4 DC 3 E DC 16 1_555 E O6 DG 14 F DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D O2 DC 3 E DC 16 1_555 E N2 DG 14 F DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D N3 DC 4 E DC 17 1_555 E N1 DG 13 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N4 DC 4 E DC 17 1_555 E O6 DG 13 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D O2 DC 4 E DC 17 1_555 E N2 DG 13 F DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 D N3 DT 5 E DT 18 1_555 E N1 DA 12 F DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 D O4 DT 5 E DT 18 1_555 E N6 DA 12 F DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D N3 DC 6 E DC 19 1_555 E N1 DG 11 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D N4 DC 6 E DC 19 1_555 E O6 DG 11 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D O2 DC 6 E DC 19 1_555 E N2 DG 11 F DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D N3 DC 7 E DC 20 1_555 E N1 DG 10 F DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 D N4 DC 7 E DC 20 1_555 E O6 DG 10 F DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 D O2 DC 7 E DC 20 1_555 E N2 DG 10 F DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 D N3 DC 8 E DC 21 1_555 E N1 DG 9 F DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 D N4 DC 8 E DC 21 1_555 E O6 DG 9 F DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 D O2 DC 8 E DC 21 1_555 E N2 DG 9 F DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 D N3 DC 9 E DC 22 1_555 E N1 DG 8 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 D N4 DC 9 E DC 22 1_555 E O6 DG 8 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 D O2 DC 9 E DC 22 1_555 E N2 DG 8 F DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 D N3 DT 10 E DT 23 1_555 E N1 DA 7 F DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D O4 DT 10 E DT 23 1_555 E N6 DA 7 F DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 D N1 DA 11 E DA 24 1_555 E N3 DT 6 F DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 D N6 DA 11 E DA 24 1_555 E O4 DT 6 F DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 D N3 DC 12 E DC 25 1_555 E N1 DG 5 F DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 D N4 DC 12 E DC 25 1_555 E O6 DG 5 F DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 D O2 DC 12 E DC 25 1_555 E N2 DG 5 F DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id HF4 _chem_comp.mon_nstd_flag . _chem_comp.name 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Cytarabine-TRIPHOSPHATE # 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 O3G PG HF4 doub 278 n n O2G PG HF4 sing 279 n n PG O1G HF4 sing 280 n n PG O3B HF4 sing 281 n n O2B PB HF4 doub 282 n n O3B PB HF4 sing 283 n n PB O3A HF4 sing 284 n n PB O1B HF4 sing 285 n n O2' C2' HF4 sing 286 n n C3' O3' HF4 sing 287 n n C3' C2' HF4 sing 288 n n C3' C4' HF4 sing 289 n n O3A PA HF4 sing 290 n n C5' C4' HF4 sing 291 n n C5' O5' HF4 sing 292 n n C2' C1' HF4 sing 293 n n C4' O4' HF4 sing 294 n n O5' PA HF4 sing 295 n n O2A PA HF4 doub 296 n n PA O1A HF4 sing 297 n n C1' O4' HF4 sing 298 n n C1' N1 HF4 sing 299 n n C6 N1 HF4 sing 300 n n C6 C5 HF4 doub 301 n n N1 C2 HF4 sing 302 n n C5 C4 HF4 sing 303 n n C2 O2 HF4 doub 304 n n C2 N3 HF4 sing 305 n n C4 N3 HF4 doub 306 n n C4 N4 HF4 sing 307 n n C6 H1 HF4 sing 308 n n N4 H2 HF4 sing 309 n n N4 H3 HF4 sing 310 n n C5 H4 HF4 sing 311 n n O1G H5 HF4 sing 312 n n O2G H6 HF4 sing 313 n n O1B H7 HF4 sing 314 n n O1A H8 HF4 sing 315 n n C5' H9 HF4 sing 316 n n C5' H10 HF4 sing 317 n n C4' H11 HF4 sing 318 n n C3' H12 HF4 sing 319 n n O3' H13 HF4 sing 320 n n C2' H14 HF4 sing 321 n n O2' H15 HF4 sing 322 n n C1' H16 HF4 sing 323 n n # _atom_sites.entry_id 8K8S _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 6 MG A 1 1101 1 MG MG . G 7 HF4 A 1 1102 1 HF4 LIG . H 8 HOH A 1 1201 1 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 C C6 HF4 . . . G 7 142.034 156.467 136.741 1 13.23 ? C6 HF4 1102 A 1 HETATM 2 N N4 HF4 . . . G 7 142.246 153.311 134.458 1 18.83 ? N4 HF4 1102 A 1 HETATM 3 C C5 HF4 . . . G 7 141.909 155.593 135.537 1 10.37 ? C5 HF4 1102 A 1 HETATM 4 C C2 HF4 . . . G 7 143.036 154.505 138.021 1 17.55 ? C2 HF4 1102 A 1 HETATM 5 O O3G HF4 . . . G 7 143.815 163.327 132.519 1 28.73 ? O3G HF4 1102 A 1 HETATM 6 P PG HF4 . . . G 7 144.952 163.445 133.502 1 14.66 ? PG HF4 1102 A 1 HETATM 7 O O1G HF4 . . . G 7 144.558 164.398 134.601 1 16.76 ? O1G HF4 1102 A 1 HETATM 8 O O2G HF4 . . . G 7 146.188 163.956 132.809 1 20.01 ? O2G HF4 1102 A 1 HETATM 9 O O3B HF4 . . . G 7 145.283 161.955 134.11 1 2.1 ? O3B HF4 1102 A 1 HETATM 10 P PB HF4 . . . G 7 144.823 161.43 135.597 1 15.38 ? PB HF4 1102 A 1 HETATM 11 O O1B HF4 . . . G 7 144.579 162.586 136.533 1 6.6 ? O1B HF4 1102 A 1 HETATM 12 O O2B HF4 . . . G 7 145.938 160.573 136.133 1 25.71 ? O2B HF4 1102 A 1 HETATM 13 O O3A HF4 . . . G 7 143.503 160.46 135.466 1 26.11 ? O3A HF4 1102 A 1 HETATM 14 P PA HF4 . . . G 7 142.007 160.771 136.068 1 5.37 ? PA HF4 1102 A 1 HETATM 15 O O1A HF4 . . . G 7 141.912 162.172 136.612 1 15.49 ? O1A HF4 1102 A 1 HETATM 16 O O2A HF4 . . . G 7 140.962 160.581 135.002 1 6.74 ? O2A HF4 1102 A 1 HETATM 17 O O5' HF4 . . . G 7 141.759 159.719 137.301 1 12.26 ? O5' HF4 1102 A 1 HETATM 18 C C5' HF4 . . . G 7 142.19 160.145 138.556 1 15.31 ? C5' HF4 1102 A 1 HETATM 19 C C4' HF4 . . . G 7 142.825 159.039 139.303 1 5.99 ? C4' HF4 1102 A 1 HETATM 20 C C3' HF4 . . . G 7 143.991 158.732 138.713 1 10.98 ? C3' HF4 1102 A 1 HETATM 21 O O3' HF4 . . . G 7 145.093 159.575 139.216 1 25.44 ? O3' HF4 1102 A 1 HETATM 22 C C2' HF4 . . . G 7 144.208 157.322 139.17 1 13.96 ? C2' HF4 1102 A 1 HETATM 23 O O2' HF4 . . . G 7 145.023 156.716 138.282 1 33.4 ? O2' HF4 1102 A 1 HETATM 24 O O4' HF4 . . . G 7 141.928 157.724 139.137 1 5.97 ? O4' HF4 1102 A 1 HETATM 25 C C1' HF4 . . . G 7 142.751 156.711 139.164 1 6.01 ? C1' HF4 1102 A 1 HETATM 26 N N1 HF4 . . . G 7 142.593 155.914 137.968 1 3.59 ? N1 HF4 1102 A 1 HETATM 27 C C4 HF4 . . . G 7 142.357 154.18 135.61 1 11.1 ? C4 HF4 1102 A 1 HETATM 28 N N3 HF4 . . . G 7 142.907 153.654 136.827 1 17.42 ? N3 HF4 1102 A 1 HETATM 29 O O2 HF4 . . . G 7 143.49 154.074 139.021 1 22.53 ? O2 HF4 1102 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 29 #