data_7LL3 # _model_server_result.job_id PA3a6S2TeooAt09sXLvmSw _model_server_result.datetime_utc '2024-11-22 18:22:43' _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 7ll3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":704}' # _entry.id 7LL3 # _exptl.entry_id 7LL3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine" _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 7LL3 _cell.length_a 123.655 _cell.length_b 123.655 _cell.length_c 289.409 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LL3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _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,K,L,M,N _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -61.8275 107.088371 48.234833 # _struct_asym.details ? _struct_asym.entity_id 3 _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 metalc ? metalc1 G O1B PPK . A PPK 705 1_555 H MG MG . A MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc2 G O3G PPK . A PPK 705 1_555 I MG MG . A MG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.949 ? metalc ? metalc3 H MG MG . A MG 706 1_555 B OE2 GLU 43 B GLU 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? metalc ? metalc4 H MG MG . A MG 706 1_555 N O HOH . B HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc5 I MG MG . A MG 707 1_555 M O HOH . A HOH 832 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id UNP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine" _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 O2G PG UNP doub 385 n n PG O3G UNP sing 386 n n PG O1G UNP sing 387 n n PG N2B UNP sing 388 n n N2B PB UNP sing 389 n n PB O1B UNP sing 390 n n PB O3B UNP doub 391 n n PB O3A UNP sing 392 n n O3A PA UNP sing 393 n n PA O1A UNP sing 394 n n PA O2A UNP doub 395 n n PA O5' UNP sing 396 n n O5' C5' UNP sing 397 n n C5' C4' UNP sing 398 n n C4' C3' UNP sing 399 n n C4' O4' UNP sing 400 n n C3' O3' UNP sing 401 n n C3' C2' UNP sing 402 n n C2' O2' UNP sing 403 n n C2' C1' UNP sing 404 n n O4' C1' UNP sing 405 n n C1' N1 UNP sing 406 n n N1 C2 UNP sing 407 n n N1 C6 UNP sing 408 n n C2 O2 UNP doub 409 n n C2 N3 UNP sing 410 n n C6 C5 UNP doub 411 n n C5 C4 UNP sing 412 n n C4 N3 UNP sing 413 n n C4 O4 UNP doub 414 n n O3G HO3G UNP sing 415 n n O1G HO1G UNP sing 416 n n N2B HN2B UNP sing 417 n n O1B HO1B UNP sing 418 n n O1A HO1A UNP sing 419 n n C5' H5' UNP sing 420 n n C5' "H5'A" UNP sing 421 n n C4' H4' UNP sing 422 n n C3' H3' UNP sing 423 n n O3' HO3' UNP sing 424 n n C2' H2' UNP sing 425 n n O2' HO2' UNP sing 426 n n C1' H1' UNP sing 427 n n C6 H6 UNP sing 428 n n C5 H5 UNP sing 429 n n N3 HN3 UNP sing 430 n n # _atom_sites.entry_id 7LL3 _atom_sites.fract_transf_matrix[1][1] 0.008087 _atom_sites.fract_transf_matrix[1][2] 0.004669 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009338 _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] 0.003455 _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 C 2 EDO A 1 701 701 EDO EDO . D 2 EDO A 1 702 1201 EDO EDO . E 2 EDO A 1 703 1301 EDO EDO . F 3 UNP A 1 704 1401 UNP UNP . G 4 PPK A 1 705 1501 PPK PPK . H 5 MG A 1 706 1 MG MG . I 5 MG A 1 707 2 MG MG . J 2 EDO B 1 701 701 EDO EDO . K 2 EDO B 1 702 801 EDO EDO . L 4 PPK B 1 703 1001 PPK PPK . M 6 HOH A 1 801 129 HOH HOH . M 6 HOH A 2 802 145 HOH HOH . M 6 HOH A 3 803 71 HOH HOH . M 6 HOH A 4 804 138 HOH HOH . M 6 HOH A 5 805 62 HOH HOH . M 6 HOH A 6 806 67 HOH HOH . M 6 HOH A 7 807 37 HOH HOH . M 6 HOH A 8 808 23 HOH HOH . M 6 HOH A 9 809 4 HOH HOH . M 6 HOH A 10 810 45 HOH HOH . M 6 HOH A 11 811 72 HOH HOH . M 6 HOH A 12 812 50 HOH HOH . M 6 HOH A 13 813 81 HOH HOH . M 6 HOH A 14 814 36 HOH HOH . M 6 HOH A 15 815 6 HOH HOH . M 6 HOH A 16 816 87 HOH HOH . M 6 HOH A 17 817 17 HOH HOH . M 6 HOH A 18 818 92 HOH HOH . M 6 HOH A 19 819 58 HOH HOH . M 6 HOH A 20 820 30 HOH HOH . M 6 HOH A 21 821 24 HOH HOH . M 6 HOH A 22 822 131 HOH HOH . M 6 HOH A 23 823 13 HOH HOH . M 6 HOH A 24 824 20 HOH HOH . M 6 HOH A 25 825 9 HOH HOH . M 6 HOH A 26 826 80 HOH HOH . M 6 HOH A 27 827 33 HOH HOH . M 6 HOH A 28 828 76 HOH HOH . M 6 HOH A 29 829 147 HOH HOH . M 6 HOH A 30 830 68 HOH HOH . M 6 HOH A 31 831 5 HOH HOH . M 6 HOH A 32 832 39 HOH HOH . M 6 HOH A 33 833 1 HOH HOH . M 6 HOH A 34 834 40 HOH HOH . M 6 HOH A 35 835 123 HOH HOH . M 6 HOH A 36 836 66 HOH HOH . M 6 HOH A 37 837 35 HOH HOH . M 6 HOH A 38 838 82 HOH HOH . M 6 HOH A 39 839 47 HOH HOH . M 6 HOH A 40 840 38 HOH HOH . M 6 HOH A 41 841 85 HOH HOH . M 6 HOH A 42 842 7 HOH HOH . M 6 HOH A 43 843 79 HOH HOH . M 6 HOH A 44 844 48 HOH HOH . M 6 HOH A 45 845 83 HOH HOH . M 6 HOH A 46 846 16 HOH HOH . M 6 HOH A 47 847 55 HOH HOH . M 6 HOH A 48 848 84 HOH HOH . M 6 HOH A 49 849 114 HOH HOH . M 6 HOH A 50 850 27 HOH HOH . M 6 HOH A 51 851 125 HOH HOH . M 6 HOH A 52 852 57 HOH HOH . M 6 HOH A 53 853 56 HOH HOH . M 6 HOH A 54 854 133 HOH HOH . M 6 HOH A 55 855 12 HOH HOH . M 6 HOH A 56 856 73 HOH HOH . M 6 HOH A 57 857 19 HOH HOH . M 6 HOH A 58 858 144 HOH HOH . M 6 HOH A 59 859 139 HOH HOH . M 6 HOH A 60 860 103 HOH HOH . M 6 HOH A 61 861 120 HOH HOH . M 6 HOH A 62 862 146 HOH HOH . M 6 HOH A 63 863 69 HOH HOH . M 6 HOH A 64 864 150 HOH HOH . M 6 HOH A 65 865 136 HOH HOH . M 6 HOH A 66 866 108 HOH HOH . M 6 HOH A 67 867 126 HOH HOH . M 6 HOH A 68 868 135 HOH HOH . M 6 HOH A 69 869 112 HOH HOH . M 6 HOH A 70 870 26 HOH HOH . M 6 HOH A 71 871 53 HOH HOH . M 6 HOH A 72 872 107 HOH HOH . N 6 HOH B 1 801 99 HOH HOH . N 6 HOH B 2 802 116 HOH HOH . N 6 HOH B 3 803 127 HOH HOH . N 6 HOH B 4 804 111 HOH HOH . N 6 HOH B 5 805 64 HOH HOH . N 6 HOH B 6 806 32 HOH HOH . N 6 HOH B 7 807 118 HOH HOH . N 6 HOH B 8 808 14 HOH HOH . N 6 HOH B 9 809 41 HOH HOH . N 6 HOH B 10 810 65 HOH HOH . N 6 HOH B 11 811 95 HOH HOH . N 6 HOH B 12 812 137 HOH HOH . N 6 HOH B 13 813 105 HOH HOH . N 6 HOH B 14 814 54 HOH HOH . N 6 HOH B 15 815 121 HOH HOH . N 6 HOH B 16 816 59 HOH HOH . N 6 HOH B 17 817 18 HOH HOH . N 6 HOH B 18 818 49 HOH HOH . N 6 HOH B 19 819 10 HOH HOH . N 6 HOH B 20 820 31 HOH HOH . N 6 HOH B 21 821 115 HOH HOH . N 6 HOH B 22 822 3 HOH HOH . N 6 HOH B 23 823 42 HOH HOH . N 6 HOH B 24 824 86 HOH HOH . N 6 HOH B 25 825 8 HOH HOH . N 6 HOH B 26 826 25 HOH HOH . N 6 HOH B 27 827 2 HOH HOH . N 6 HOH B 28 828 22 HOH HOH . N 6 HOH B 29 829 44 HOH HOH . N 6 HOH B 30 830 60 HOH HOH . N 6 HOH B 31 831 34 HOH HOH . N 6 HOH B 32 832 78 HOH HOH . N 6 HOH B 33 833 63 HOH HOH . N 6 HOH B 34 834 134 HOH HOH . N 6 HOH B 35 835 94 HOH HOH . N 6 HOH B 36 836 91 HOH HOH . N 6 HOH B 37 837 11 HOH HOH . N 6 HOH B 38 838 43 HOH HOH . N 6 HOH B 39 839 141 HOH HOH . N 6 HOH B 40 840 117 HOH HOH . N 6 HOH B 41 841 101 HOH HOH . N 6 HOH B 42 842 132 HOH HOH . N 6 HOH B 43 843 140 HOH HOH . N 6 HOH B 44 844 51 HOH HOH . N 6 HOH B 45 845 15 HOH HOH . N 6 HOH B 46 846 124 HOH HOH . N 6 HOH B 47 847 70 HOH HOH . N 6 HOH B 48 848 90 HOH HOH . N 6 HOH B 49 849 75 HOH HOH . N 6 HOH B 50 850 102 HOH HOH . N 6 HOH B 51 851 152 HOH HOH . N 6 HOH B 52 852 104 HOH HOH . N 6 HOH B 53 853 52 HOH HOH . N 6 HOH B 54 854 46 HOH HOH . N 6 HOH B 55 855 93 HOH HOH . N 6 HOH B 56 856 143 HOH HOH . N 6 HOH B 57 857 130 HOH HOH . N 6 HOH B 58 858 109 HOH HOH . N 6 HOH B 59 859 128 HOH HOH . N 6 HOH B 60 860 97 HOH HOH . N 6 HOH B 61 861 113 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 O2G UNP . . . F 3 1.845 27.891 0.802 1 144.69 ? O2G UNP 704 A 1 HETATM 2 P PG UNP . . . F 3 2.08 26.884 1.925 1 147.82 ? PG UNP 704 A 1 HETATM 3 O O3G UNP . . . F 3 1.372 25.58 1.571 1 139.66 ? O3G UNP 704 A 1 HETATM 4 O O1G UNP . . . F 3 1.537 27.423 3.192 1 137.98 ? O1G UNP 704 A 1 HETATM 5 N N2B UNP . . . F 3 3.803 26.617 2.113 1 167.24 ? N2B UNP 704 A 1 HETATM 6 P PB UNP . . . F 3 4.4 25.51 3.285 1 182.83 ? PB UNP 704 A 1 HETATM 7 O O1B UNP . . . F 3 3.902 25.894 4.642 1 188.76 ? O1B UNP 704 A 1 HETATM 8 O O3B UNP . . . F 3 3.873 24.139 2.944 1 183.48 ? O3B UNP 704 A 1 HETATM 9 O O3A UNP . . . F 3 6.077 25.479 3.291 1 185.57 ? O3A UNP 704 A 1 HETATM 10 P PA UNP . . . F 3 7.1 26.772 3.465 1 174.57 ? PA UNP 704 A 1 HETATM 11 O O1A UNP . . . F 3 6.573 27.715 4.574 1 179.64 ? O1A UNP 704 A 1 HETATM 12 O O2A UNP . . . F 3 7.188 27.526 2.18 1 167.21 ? O2A UNP 704 A 1 HETATM 13 O O5' UNP . . . F 3 8.625 26.248 3.892 1 165.56 ? O5' UNP 704 A 1 HETATM 14 C C5' UNP . . . F 3 8.903 25.992 5.235 1 158.09 ? C5' UNP 704 A 1 HETATM 15 C C4' UNP . . . F 3 10.415 25.695 5.405 1 152.72 ? C4' UNP 704 A 1 HETATM 16 C C3' UNP . . . F 3 10.628 24.752 6.309 1 151.73 ? C3' UNP 704 A 1 HETATM 17 O O3' UNP . . . F 3 11.063 23.525 5.63 1 151.78 ? O3' UNP 704 A 1 HETATM 18 C C2' UNP . . . F 3 11.818 25.283 7.316 1 150.71 ? C2' UNP 704 A 1 HETATM 19 O O2' UNP . . . F 3 12.783 24.281 7.498 1 152.25 ? O2' UNP 704 A 1 HETATM 20 O O4' UNP . . . F 3 11.186 26.988 5.96 1 150.82 ? O4' UNP 704 A 1 HETATM 21 C C1' UNP . . . F 3 12.373 26.374 6.718 1 145.65 ? C1' UNP 704 A 1 HETATM 22 N N1 UNP . . . F 3 12.911 27.302 7.687 1 134.91 ? N1 UNP 704 A 1 HETATM 23 C C2 UNP . . . F 3 14.328 27.74 7.606 1 127.65 ? C2 UNP 704 A 1 HETATM 24 O O2 UNP . . . F 3 15.042 27.332 6.74 1 122.02 ? O2 UNP 704 A 1 HETATM 25 C C6 UNP . . . F 3 12.059 27.808 8.746 1 131.71 ? C6 UNP 704 A 1 HETATM 26 C C5 UNP . . . F 3 12.602 28.772 9.76 1 124.45 ? C5 UNP 704 A 1 HETATM 27 C C4 UNP . . . F 3 14.02 29.205 9.674 1 116.86 ? C4 UNP 704 A 1 HETATM 28 N N3 UNP . . . F 3 14.867 28.695 8.613 1 120.99 ? N3 UNP 704 A 1 HETATM 29 O O4 UNP . . . F 3 14.461 29.977 10.485 1 111.53 ? O4 UNP 704 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #