data_8UK4 # _model_server_result.job_id 7hw2qyx2-Nbzb_NWIQtyZQ _model_server_result.datetime_utc '2024-11-13 06:04:07' _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 8uk4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 8UK4 # _exptl.entry_id 8UK4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 481.184 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine" _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 8UK4 _cell.length_a 98.795 _cell.length_b 98.795 _cell.length_c 80.29 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UK4 _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,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 4 _struct_asym.id D _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 O3' DT 3 T DT 3 1_555 B P XB9 4 T XB9 4 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.61 ? covale ? covale2 B O3' XB9 4 T XB9 4 1_555 B P DA 5 T DA 5 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.605 ? metalc ? metalc1 A OD2 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc2 A O MET 17 A MET 14 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc3 A OD2 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? metalc ? metalc4 D O2A 1FZ . A 1FZ 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc5 D O1B 1FZ . A 1FZ 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc6 D O1G 1FZ . A 1FZ 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? hydrog WATSON-CRICK hydrog1 B N1 DA 5 T DA 5 1_555 C N3 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 5 T DA 5 1_555 C O4 DT 8 P DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N3 DT 6 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O4 DT 6 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DG 7 T DG 7 1_555 C N3 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N2 DG 7 T DG 7 1_555 C O2 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O6 DG 7 T DG 7 1_555 C N4 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 8 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 8 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DC 9 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N4 DC 9 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O2 DC 9 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 10 T DG 10 1_555 C N3 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 10 T DG 10 1_555 C O2 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 10 T DG 10 1_555 C N4 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DC 11 T DC 11 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 DC 11 T DC 11 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 DC 11 T DC 11 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 12 T DT 12 1_555 C N1 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 12 T DT 12 1_555 C N6 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H18 N3 O13 P3' _chem_comp.formula_weight 481.184 _chem_comp.id 1FZ _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine" _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 O3G PG 1FZ doub 1 n n O1G PG 1FZ sing 2 n n O2G PG 1FZ sing 3 n n PG O3B 1FZ sing 4 n n O1A PA 1FZ doub 5 n n O3B PB 1FZ sing 6 n n O2B PB 1FZ doub 7 n n PB N3A 1FZ sing 8 n n PB O1B 1FZ sing 9 n n PA N3A 1FZ sing 10 n n PA O2A 1FZ sing 11 n n PA O5' 1FZ sing 12 n n C5' O5' 1FZ sing 13 n n C5' C4' 1FZ sing 14 n n O3' C3' 1FZ sing 15 n n C4' C3' 1FZ sing 16 n n C4' O4' 1FZ sing 17 n n C3' C2' 1FZ sing 18 n n O4' C1' 1FZ sing 19 n n C5M C5 1FZ sing 20 n n C2' C1' 1FZ sing 21 n n C6 C5 1FZ doub 22 n n C6 N1 1FZ sing 23 n n C1' N1 1FZ sing 24 n n C5 C4 1FZ sing 25 n n N1 C2 1FZ sing 26 n n C4 O4 1FZ doub 27 n n C4 N3 1FZ sing 28 n n C2 N3 1FZ sing 29 n n C2 O2 1FZ doub 30 n n C6 H1 1FZ sing 31 n n C5M H2 1FZ sing 32 n n C5M H3 1FZ sing 33 n n C5M H4 1FZ sing 34 n n N3 H5 1FZ sing 35 n n C1' H6 1FZ sing 36 n n C2' H7 1FZ sing 37 n n C2' H8 1FZ sing 38 n n C3' H9 1FZ sing 39 n n O3' H10 1FZ sing 40 n n C4' H11 1FZ sing 41 n n C5' H12 1FZ sing 42 n n C5' H13 1FZ sing 43 n n O2A H14 1FZ sing 44 n n N3A H15 1FZ sing 45 n n O1B H16 1FZ sing 46 n n O1G H17 1FZ sing 47 n n O2G H18 1FZ sing 48 n n # _atom_sites.entry_id 8UK4 _atom_sites.fract_transf_matrix[1][1] 0.010122 _atom_sites.fract_transf_matrix[1][2] 0.005844 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011688 _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] 0.012455 _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 1FZ A 1 501 504 1FZ 1FZ . E 5 MG A 1 502 1 MG MG . F 6 HOH A 1 601 9 HOH HOH . F 6 HOH A 2 602 4 HOH HOH . F 6 HOH A 3 603 7 HOH HOH . F 6 HOH A 4 604 13 HOH HOH . F 6 HOH A 5 605 12 HOH HOH . F 6 HOH A 6 606 6 HOH HOH . F 6 HOH A 7 607 8 HOH HOH . G 6 HOH T 1 101 5 HOH HOH . G 6 HOH T 2 102 1 HOH HOH . G 6 HOH T 3 103 10 HOH HOH . G 6 HOH T 4 104 2 HOH HOH . G 6 HOH T 5 105 3 HOH HOH . H 6 HOH P 1 101 11 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 O O2 1FZ . . . D 4 17.305 -41.828 -2.904 1 84.3 ? O2 1FZ 501 A 1 HETATM 2 O O4 1FZ . . . D 4 20.445 -39.135 -5.029 1 85.11 ? O4 1FZ 501 A 1 HETATM 3 C C4 1FZ . . . D 4 20.143 -40.163 -4.491 1 89.13 ? C4 1FZ 501 A 1 HETATM 4 C C5 1FZ . . . D 4 21.167 -41.24 -4.327 1 83.87 ? C5 1FZ 501 A 1 HETATM 5 C C6 1FZ . . . D 4 20.796 -42.53 -3.644 1 82.08 ? C6 1FZ 501 A 1 HETATM 6 C C5M 1FZ . . . D 4 22.591 -41.02 -4.849 1 81.28 ? C5M 1FZ 501 A 1 HETATM 7 N N3 1FZ . . . D 4 18.783 -40.382 -3.993 1 91.74 ? N3 1FZ 501 A 1 HETATM 8 C C2 1FZ . . . D 4 18.411 -41.668 -3.315 1 88.42 ? C2 1FZ 501 A 1 HETATM 9 N N1 1FZ . . . D 4 19.435 -42.745 -3.144 1 89.34 ? N1 1FZ 501 A 1 HETATM 10 C C1' 1FZ . . . D 4 19.054 -44.069 -2.444 1 88.98 ? C1' 1FZ 501 A 1 HETATM 11 C C2' 1FZ . . . D 4 18.929 -45.009 -3.277 1 84.83 ? C2' 1FZ 501 A 1 HETATM 12 C C3' 1FZ . . . D 4 20.209 -46.002 -3.077 1 80.3 ? C3' 1FZ 501 A 1 HETATM 13 O O3' 1FZ . . . D 4 19.831 -47.386 -3.409 1 68.31 ? O3' 1FZ 501 A 1 HETATM 14 O O4' 1FZ . . . D 4 20.109 -44.53 -1.388 1 78.64 ? O4' 1FZ 501 A 1 HETATM 15 C C4' 1FZ . . . D 4 20.58 -45.91 -1.854 1 78.27 ? C4' 1FZ 501 A 1 HETATM 16 C C5' 1FZ . . . D 4 22.164 -45.93 -1.849 1 78.51 ? C5' 1FZ 501 A 1 HETATM 17 O O5' 1FZ . . . D 4 22.58 -45.128 -2.953 1 84.27 ? O5' 1FZ 501 A 1 HETATM 18 P PA 1FZ . . . D 4 24.044 -45.505 -3.681 1 84.47 ? PA 1FZ 501 A 1 HETATM 19 O O1A 1FZ . . . D 4 24.655 -44.27 -4.33 1 88.42 ? O1A 1FZ 501 A 1 HETATM 20 O O2A 1FZ . . . D 4 24.951 -46.14 -2.629 1 70.08 ? O2A 1FZ 501 A 1 HETATM 21 N N3A 1FZ . . . D 4 23.773 -46.556 -5.024 1 86.09 ? N3A 1FZ 501 A 1 HETATM 22 P PB 1FZ . . . D 4 23.219 -48.177 -4.875 1 79.43 ? PB 1FZ 501 A 1 HETATM 23 O O1B 1FZ . . . D 4 23.449 -48.74 -3.489 1 83.76 ? O1B 1FZ 501 A 1 HETATM 24 O O2B 1FZ . . . D 4 21.747 -48.221 -5.25 1 75.52 ? O2B 1FZ 501 A 1 HETATM 25 O O3B 1FZ . . . D 4 24.062 -49.039 -6.029 1 77.5 ? O3B 1FZ 501 A 1 HETATM 26 P PG 1FZ . . . D 4 25.673 -49.442 -5.912 1 77.26 ? PG 1FZ 501 A 1 HETATM 27 O O1G 1FZ . . . D 4 26.202 -49.18 -4.5 1 73.54 ? O1G 1FZ 501 A 1 HETATM 28 O O3G 1FZ . . . D 4 26.45 -48.632 -6.933 1 84.3 ? O3G 1FZ 501 A 1 HETATM 29 O O2G 1FZ . . . D 4 25.744 -50.928 -6.231 1 76.46 ? O2G 1FZ 501 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 29 #