data_7LIU # _model_server_result.job_id Xw8LXgYvmXwgWayo_S6ZhA _model_server_result.datetime_utc '2024-11-22 22:15:52' _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 7liu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":902}' # _entry.id 7LIU # _exptl.entry_id 7LIU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 492.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium' _entity.pdbx_number_of_molecules 2 _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 7LIU _cell.length_a 114.476 _cell.length_b 114.476 _cell.length_c 281.793 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LIU _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N 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 E MG MG . A MG 901 1_555 F O2B 08T . A 08T 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc2 E MG MG . A MG 901 1_555 I O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc3 E MG MG . A MG 901 1_555 I O HOH . A HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc4 E MG MG . A MG 901 1_555 I O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc5 E MG MG . A MG 901 1_555 I O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc6 G MG MG . B MG 901 1_555 H O1B 08T . B 08T 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc7 G MG MG . B MG 901 1_555 J O HOH . B HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc8 G MG MG . B MG 901 1_555 J O HOH . B HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc9 G MG MG . B MG 901 1_555 J O HOH . B HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc10 G MG MG . B MG 901 1_555 J O HOH . B HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? hydrog WATSON-CRICK hydrog1 C N1 G 5 X G 705 1_555 D N3 DC 14 Y DC 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N2 G 5 X G 705 1_555 D O2 DC 14 Y DC 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C O6 G 5 X G 705 1_555 D N4 DC 14 Y DC 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N1 G 6 X G 706 1_555 D N3 DC 13 Y DC 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N2 G 6 X G 706 1_555 D O2 DC 13 Y DC 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C O6 G 6 X G 706 1_555 D N4 DC 13 Y DC 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N1 G 7 X G 707 1_555 D N3 DC 12 Y DC 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N2 G 7 X G 707 1_555 D O2 DC 12 Y DC 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C O6 G 7 X G 707 1_555 D N4 DC 12 Y DC 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N3 DC 8 X DC 708 1_555 D N1 DG 11 Y DG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N4 DC 8 X DC 708 1_555 D O6 DG 11 Y DG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O2 DC 8 X DC 708 1_555 D N2 DG 11 Y DG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N3 DC 9 X DC 709 1_555 D N1 DG 11 Y DG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N4 DC 9 X DC 709 1_555 D O6 DG 11 Y DG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O2 DC 9 X DC 709 1_555 D N2 DG 11 Y DG 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N1 DG 11 X DG 711 1_555 D N3 DC 8 Y DC 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C N2 DG 11 X DG 711 1_555 D O2 DC 8 Y DC 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C O6 DG 11 X DG 711 1_555 D N4 DC 8 Y DC 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N3 DC 12 X DC 712 1_555 D N1 G 7 Y G 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N4 DC 12 X DC 712 1_555 D O6 G 7 Y G 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C O2 DC 12 X DC 712 1_555 D N2 G 7 Y G 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C N3 DC 13 X DC 713 1_555 D N1 G 6 Y G 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N4 DC 13 X DC 713 1_555 D O6 G 6 Y G 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C O2 DC 13 X DC 713 1_555 D N2 G 6 Y G 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C N3 DC 14 X DC 714 1_555 D N1 G 5 Y G 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N4 DC 14 X DC 714 1_555 D O6 G 5 Y G 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C O2 DC 14 X DC 714 1_555 D N2 G 5 Y G 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H14 Be F3 N5 O10 P2' _chem_comp.formula_weight 492.201 _chem_comp.id 08T _chem_comp.mon_nstd_flag . _chem_comp.name '[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium' _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 O3' C3' 08T sing 1 n n O2' C2' 08T sing 2 n n C3' C4' 08T sing 3 n n C3' C2' 08T sing 4 n n C4' C5' 08T sing 5 n n C4' O4' 08T sing 6 n n C2' C1' 08T sing 7 n n C5' O5' 08T sing 8 n n O4' C1' 08T sing 9 n n C1' N9 08T sing 10 n n N3 C2 08T doub 11 n y N3 C4 08T sing 12 n y O2A PA 08T doub 13 n n C2 N1 08T sing 14 n y O5' PA 08T sing 15 n n C4 N9 08T sing 16 n y C4 C5 08T doub 17 n y N9 C8 08T sing 18 n y PA O1A 08T sing 19 n n PA O3A 08T sing 20 n n N1 C6 08T doub 21 n y C5 C6 08T sing 22 n y C5 N7 08T sing 23 n y O3A PB 08T sing 24 n n C8 N7 08T doub 25 n y C6 N6 08T sing 26 n n O1B PB 08T doub 27 n n PB O3B 08T sing 28 n n PB O2B 08T sing 29 n n F1 BE 08T sing 30 n n BE F3 08T sing 31 n n O3B BE 08T sing 32 n n BE F2 08T sing 33 n n C5' H1 08T sing 34 n n C5' H2 08T sing 35 n n C4' H3 08T sing 36 n n C3' H4 08T sing 37 n n O3' H5 08T sing 38 n n C2' H6 08T sing 39 n n O2' H7 08T sing 40 n n C1' H8 08T sing 41 n n O1A H9 08T sing 42 n n C2 H10 08T sing 43 n n O2B H11 08T sing 44 n n N6 H12 08T sing 45 n n N6 H13 08T sing 46 n n C8 H14 08T sing 47 n n # _atom_sites.entry_id 7LIU _atom_sites.fract_transf_matrix[1][1] 0.008735 _atom_sites.fract_transf_matrix[1][2] 0.005043 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010087 _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] 0.003549 _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 E 3 MG A 1 901 901 MG MG . F 4 08T A 1 902 2001 08T 08T . G 3 MG B 1 901 901 MG MG . H 4 08T B 1 902 2001 08T 08T . I 5 HOH A 1 1001 1 HOH HOH . I 5 HOH A 2 1002 2 HOH HOH . I 5 HOH A 3 1003 4 HOH HOH . I 5 HOH A 4 1004 3 HOH HOH . J 5 HOH B 1 1001 6 HOH HOH . J 5 HOH B 2 1002 5 HOH HOH . J 5 HOH B 3 1003 8 HOH HOH . J 5 HOH B 4 1004 7 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 P PA 08T . . . F 4 -70.856 36.909 43.231 1 69.04 ? PA 08T 902 A 1 HETATM 2 P PB 08T . . . F 4 -70.72 39.49 42.158 1 68.15 ? PB 08T 902 A 1 HETATM 3 BE BE 08T . . . F 4 -71.618 41.962 43.461 1 69.26 ? BE 08T 902 A 1 HETATM 4 C C5' 08T . . . F 4 -71.662 34.562 43.335 1 82.23 ? C5' 08T 902 A 1 HETATM 5 O O5' 08T . . . F 4 -71.959 35.836 42.817 1 79.38 ? O5' 08T 902 A 1 HETATM 6 C C4' 08T . . . F 4 -72.916 33.752 43.532 1 79.59 ? C4' 08T 902 A 1 HETATM 7 O O4' 08T . . . F 4 -73.249 33.161 42.281 1 83.92 ? O4' 08T 902 A 1 HETATM 8 C C3' 08T . . . F 4 -72.496 32.642 44.466 1 87.85 ? C3' 08T 902 A 1 HETATM 9 O O3' 08T . . . F 4 -73.629 32.149 45.176 1 91.48 ? O3' 08T 902 A 1 HETATM 10 C C2' 08T . . . F 4 -71.968 31.601 43.517 1 89.81 ? C2' 08T 902 A 1 HETATM 11 O O2' 08T . . . F 4 -72.08 30.294 44.083 1 96.28 ? O2' 08T 902 A 1 HETATM 12 C C1' 08T . . . F 4 -72.811 31.793 42.263 1 95.42 ? C1' 08T 902 A 1 HETATM 13 N N1 08T . . . F 4 -72.374 29.168 37.672 1 110.52 ? N1 08T 902 A 1 HETATM 14 O O1A 08T . . . F 4 -70.789 36.871 44.747 1 67.57 ? O1A 08T 902 A 1 HETATM 15 O O1B 08T . . . F 4 -70.571 39.254 40.676 1 69.38 ? O1B 08T 902 A 1 HETATM 16 F F1 08T . . . F 4 -70.757 41.444 44.589 1 67 ? F1 08T 902 A 1 HETATM 17 C C2 08T . . . F 4 -73.326 29.096 38.623 1 108.83 ? C2 08T 902 A 1 HETATM 18 O O2A 08T . . . F 4 -69.619 36.529 42.476 1 77.67 ? O2A 08T 902 A 1 HETATM 19 O O2B 08T . . . F 4 -69.522 39.562 43.074 1 72.97 ? O2B 08T 902 A 1 HETATM 20 F F2 08T . . . F 4 -73.089 42.114 43.81 1 72.72 ? F2 08T 902 A 1 HETATM 21 N N3 08T . . . F 4 -73.317 29.823 39.76 1 103.79 ? N3 08T 902 A 1 HETATM 22 O O3A 08T . . . F 4 -71.574 38.234 42.657 1 66.29 ? O3A 08T 902 A 1 HETATM 23 O O3B 08T . . . F 4 -71.618 40.837 42.293 1 65.57 ? O3B 08T 902 A 1 HETATM 24 F F3 08T . . . F 4 -71.033 43.186 42.791 1 80.19 ? F3 08T 902 A 1 HETATM 25 C C4 08T . . . F 4 -72.317 30.702 40.027 1 104.55 ? C4 08T 902 A 1 HETATM 26 C C5 08T . . . F 4 -71.239 30.837 39.033 1 106.87 ? C5 08T 902 A 1 HETATM 27 C C6 08T . . . F 4 -71.32 30.003 37.804 1 107.42 ? C6 08T 902 A 1 HETATM 28 N N6 08T . . . F 4 -70.369 30.073 36.843 1 103.38 ? N6 08T 902 A 1 HETATM 29 N N7 08T . . . F 4 -70.389 31.757 39.524 1 104.55 ? N7 08T 902 A 1 HETATM 30 C C8 08T . . . F 4 -70.87 32.178 40.72 1 99.44 ? C8 08T 902 A 1 HETATM 31 N N9 08T . . . F 4 -72.02 31.551 41.025 1 99.78 ? N9 08T 902 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #