data_1I0L # _model_server_result.job_id 9DZ-KOsYXGt-a6YgDfYQfg _model_server_result.datetime_utc '2024-11-26 16:11:27' _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 1i0l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 1I0L # _exptl.entry_id 1I0L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.07 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _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 93.94 _cell.angle_gamma 90 _cell.entry_id 1I0L _cell.length_a 39.57 _cell.length_b 103.5 _cell.length_c 52.15 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1I0L _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 E N N ? 4 I 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 A OD1 ASP 171 A ASP 171 1_555 C MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc2 E O2A PRP . A PRP 801 1_555 C MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc3 E O1B PRP . A PRP 801 1_555 C MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc4 C MG MG . A MG 902 1_555 J O HOH . A HOH 993 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc5 C MG MG . A MG 902 1_555 J O HOH . A HOH 994 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc6 C MG MG . A MG 902 1_555 J O HOH . A HOH 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc7 B OD1 ASP 171 B ASP 171 1_555 F MG MG . B MG 912 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc8 I O2 PRP . B PRP 811 1_555 G MG MG . B MG 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc9 I O3 PRP . B PRP 811 1_555 G MG MG . B MG 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc10 I O1 PRP . B PRP 811 1_555 G MG MG . B MG 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc11 I O3B PRP . B PRP 811 1_555 G MG MG . B MG 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc12 I O2A PRP . B PRP 811 1_555 F MG MG . B MG 912 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc13 I O1B PRP . B PRP 811 1_555 F MG MG . B MG 912 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc14 G MG MG . B MG 910 1_555 K O HOH . B HOH 977 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc15 G MG MG . B MG 910 1_555 K O HOH . B HOH 978 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc16 F MG MG . B MG 912 1_555 K O HOH . B HOH 974 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc17 F MG MG . B MG 912 1_555 K O HOH . B HOH 975 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc18 F MG MG . B MG 912 1_555 K O HOH . B HOH 976 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? # _chem_comp.formula 'C5 H13 O14 P3' _chem_comp.formula_weight 390.07 _chem_comp.id PRP _chem_comp.mon_nstd_flag n _chem_comp.name 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID;1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose;1-O-pyrophosphono-5-O-phosphono-D-ribose;1-O-pyrophosphono-5-O-phosphono-ribose' # 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 C1 C2 PRP sing 292 n n C1 O1 PRP sing 293 n n C1 O4 PRP sing 294 n n C1 H1 PRP sing 295 n n C2 C3 PRP sing 296 n n C2 O2 PRP sing 297 n n C2 H2 PRP sing 298 n n C3 C4 PRP sing 299 n n C3 O3 PRP sing 300 n n C3 H3 PRP sing 301 n n C4 C5 PRP sing 302 n n C4 O4 PRP sing 303 n n C4 H4 PRP sing 304 n n C5 O5 PRP sing 305 n n C5 H51 PRP sing 306 n n C5 H52 PRP sing 307 n n O1 PA PRP sing 308 n n O2 HO2 PRP sing 309 n n O3 HO3 PRP sing 310 n n O5 P PRP sing 311 n n P O1P PRP doub 312 n n P O2P PRP sing 313 n n P O3P PRP sing 314 n n O2P HOP2 PRP sing 315 n n O3P HOP3 PRP sing 316 n n PA O1A PRP doub 317 n n PA O2A PRP sing 318 n n PA O3A PRP sing 319 n n O2A HOA2 PRP sing 320 n n O3A PB PRP sing 321 n n PB O1B PRP doub 322 n n PB O2B PRP sing 323 n n PB O3B PRP sing 324 n n O2B HOB2 PRP sing 325 n n O3B HOB3 PRP sing 326 n n # _pdbx_chem_comp_identifier.comp_id PRP _pdbx_chem_comp_identifier.identifier a-D-Ribf1PO35PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 1I0L _atom_sites.fract_transf_matrix[1][1] 0.025272 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00174 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009662 _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] 0.019221 _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 MG A 1 902 902 MG MO3 . D 3 7HP A 1 800 800 7HP 7HP . E 4 PRP A 1 801 801 PRP PRP . F 2 MG B 1 912 912 MG MO3 . G 2 MG B 1 910 910 MG MO2 . H 3 7HP B 1 810 810 7HP 7HP . I 4 PRP B 1 811 811 PRP PRP . J 5 HOH A 1 903 1 HOH HOH . J 5 HOH A 2 904 3 HOH HOH . J 5 HOH A 3 905 4 HOH HOH . J 5 HOH A 4 906 5 HOH HOH . J 5 HOH A 5 907 7 HOH HOH . J 5 HOH A 6 908 8 HOH HOH . J 5 HOH A 7 909 9 HOH HOH . J 5 HOH A 8 910 10 HOH HOH . J 5 HOH A 9 911 11 HOH HOH . J 5 HOH A 10 912 14 HOH HOH . J 5 HOH A 11 913 15 HOH HOH . J 5 HOH A 12 914 16 HOH HOH . J 5 HOH A 13 915 19 HOH HOH . J 5 HOH A 14 916 20 HOH HOH . J 5 HOH A 15 917 21 HOH HOH . J 5 HOH A 16 918 22 HOH HOH . J 5 HOH A 17 919 23 HOH HOH . J 5 HOH A 18 920 25 HOH HOH . J 5 HOH A 19 921 26 HOH HOH . J 5 HOH A 20 922 27 HOH HOH . J 5 HOH A 21 923 28 HOH HOH . J 5 HOH A 22 924 29 HOH HOH . J 5 HOH A 23 925 30 HOH HOH . J 5 HOH A 24 926 31 HOH HOH . J 5 HOH A 25 927 32 HOH HOH . J 5 HOH A 26 928 33 HOH HOH . J 5 HOH A 27 929 34 HOH HOH . J 5 HOH A 28 930 35 HOH HOH . J 5 HOH A 29 931 40 HOH HOH . J 5 HOH A 30 932 41 HOH HOH . J 5 HOH A 31 933 43 HOH HOH . J 5 HOH A 32 934 44 HOH HOH . J 5 HOH A 33 935 49 HOH HOH . J 5 HOH A 34 936 50 HOH HOH . J 5 HOH A 35 937 51 HOH HOH . J 5 HOH A 36 938 52 HOH HOH . J 5 HOH A 37 939 53 HOH HOH . J 5 HOH A 38 940 54 HOH HOH . J 5 HOH A 39 941 55 HOH HOH . J 5 HOH A 40 942 56 HOH HOH . J 5 HOH A 41 943 57 HOH HOH . J 5 HOH A 42 944 58 HOH HOH . J 5 HOH A 43 945 91 HOH HOH . J 5 HOH A 44 946 92 HOH HOH . J 5 HOH A 45 947 94 HOH HOH . J 5 HOH A 46 948 97 HOH HOH . J 5 HOH A 47 949 98 HOH HOH . J 5 HOH A 48 950 99 HOH HOH . J 5 HOH A 49 951 100 HOH HOH . J 5 HOH A 50 952 101 HOH HOH . J 5 HOH A 51 953 102 HOH HOH . J 5 HOH A 52 954 105 HOH HOH . J 5 HOH A 53 955 107 HOH HOH . J 5 HOH A 54 956 108 HOH HOH . J 5 HOH A 55 957 109 HOH HOH . J 5 HOH A 56 958 110 HOH HOH . J 5 HOH A 57 959 111 HOH HOH . J 5 HOH A 58 960 112 HOH HOH . J 5 HOH A 59 961 113 HOH HOH . J 5 HOH A 60 962 114 HOH HOH . J 5 HOH A 61 963 115 HOH HOH . J 5 HOH A 62 964 116 HOH HOH . J 5 HOH A 63 965 117 HOH HOH . J 5 HOH A 64 966 118 HOH HOH . J 5 HOH A 65 967 125 HOH HOH . J 5 HOH A 66 968 126 HOH HOH . J 5 HOH A 67 969 127 HOH HOH . J 5 HOH A 68 970 128 HOH HOH . J 5 HOH A 69 971 129 HOH HOH . J 5 HOH A 70 972 130 HOH HOH . J 5 HOH A 71 973 140 HOH HOH . J 5 HOH A 72 974 141 HOH HOH . J 5 HOH A 73 975 142 HOH HOH . J 5 HOH A 74 976 143 HOH HOH . J 5 HOH A 75 977 145 HOH HOH . J 5 HOH A 76 978 146 HOH HOH . J 5 HOH A 77 979 148 HOH HOH . J 5 HOH A 78 980 149 HOH HOH . J 5 HOH A 79 981 152 HOH HOH . J 5 HOH A 80 982 153 HOH HOH . J 5 HOH A 81 983 166 HOH HOH . J 5 HOH A 82 984 167 HOH HOH . J 5 HOH A 83 985 168 HOH HOH . J 5 HOH A 84 986 169 HOH HOH . J 5 HOH A 85 987 170 HOH HOH . J 5 HOH A 86 988 171 HOH HOH . J 5 HOH A 87 989 172 HOH HOH . J 5 HOH A 88 990 173 HOH HOH . J 5 HOH A 89 991 174 HOH HOH . J 5 HOH A 90 992 180 HOH HOH . J 5 HOH A 91 993 902 HOH MO3 . J 5 HOH A 92 994 902 HOH MO3 . J 5 HOH A 93 995 902 HOH MO3 . K 5 HOH B 1 913 12 HOH HOH . K 5 HOH B 2 914 13 HOH HOH . K 5 HOH B 3 915 17 HOH HOH . K 5 HOH B 4 916 18 HOH HOH . K 5 HOH B 5 917 42 HOH HOH . K 5 HOH B 6 918 45 HOH HOH . K 5 HOH B 7 919 46 HOH HOH . K 5 HOH B 8 920 47 HOH HOH . K 5 HOH B 9 921 59 HOH HOH . K 5 HOH B 10 922 60 HOH HOH . K 5 HOH B 11 923 61 HOH HOH . K 5 HOH B 12 924 62 HOH HOH . K 5 HOH B 13 925 63 HOH HOH . K 5 HOH B 14 926 64 HOH HOH . K 5 HOH B 15 927 65 HOH HOH . K 5 HOH B 16 928 66 HOH HOH . K 5 HOH B 17 929 67 HOH HOH . K 5 HOH B 18 930 68 HOH HOH . K 5 HOH B 19 931 69 HOH HOH . K 5 HOH B 20 932 70 HOH HOH . K 5 HOH B 21 933 71 HOH HOH . K 5 HOH B 22 934 72 HOH HOH . K 5 HOH B 23 935 74 HOH HOH . K 5 HOH B 24 936 75 HOH HOH . K 5 HOH B 25 937 76 HOH HOH . K 5 HOH B 26 938 77 HOH HOH . K 5 HOH B 27 939 78 HOH HOH . K 5 HOH B 28 940 79 HOH HOH . K 5 HOH B 29 941 80 HOH HOH . K 5 HOH B 30 942 81 HOH HOH . K 5 HOH B 31 943 82 HOH HOH . K 5 HOH B 32 944 84 HOH HOH . K 5 HOH B 33 945 88 HOH HOH . K 5 HOH B 34 946 89 HOH HOH . K 5 HOH B 35 947 90 HOH HOH . K 5 HOH B 36 948 93 HOH HOH . K 5 HOH B 37 949 119 HOH HOH . K 5 HOH B 38 950 120 HOH HOH . K 5 HOH B 39 951 121 HOH HOH . K 5 HOH B 40 952 122 HOH HOH . K 5 HOH B 41 953 123 HOH HOH . K 5 HOH B 42 954 124 HOH HOH . K 5 HOH B 43 955 131 HOH HOH . K 5 HOH B 44 956 132 HOH HOH . K 5 HOH B 45 957 133 HOH HOH . K 5 HOH B 46 958 134 HOH HOH . K 5 HOH B 47 959 135 HOH HOH . K 5 HOH B 48 960 144 HOH HOH . K 5 HOH B 49 961 150 HOH HOH . K 5 HOH B 50 962 154 HOH HOH . K 5 HOH B 51 963 155 HOH HOH . K 5 HOH B 52 964 156 HOH HOH . K 5 HOH B 53 965 157 HOH HOH . K 5 HOH B 54 966 159 HOH HOH . K 5 HOH B 55 967 160 HOH HOH . K 5 HOH B 56 968 165 HOH HOH . K 5 HOH B 57 969 175 HOH HOH . K 5 HOH B 58 970 176 HOH HOH . K 5 HOH B 59 971 177 HOH HOH . K 5 HOH B 60 972 178 HOH HOH . K 5 HOH B 61 973 179 HOH HOH . K 5 HOH B 62 974 912 HOH MO3 . K 5 HOH B 63 975 912 HOH MO3 . K 5 HOH B 64 976 912 HOH MO3 . K 5 HOH B 65 977 910 HOH MO2 . K 5 HOH B 66 978 910 HOH MO2 . # 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 C1 PRP . . . E 4 41.085 61.753 30.633 1 32.44 ? C1 PRP 801 A 1 HETATM 2 C C2 PRP . . . E 4 40.273 60.94 29.777 1 36.09 ? C2 PRP 801 A 1 HETATM 3 C C3 PRP . . . E 4 41.318 60.332 28.849 1 36.61 ? C3 PRP 801 A 1 HETATM 4 C C4 PRP . . . E 4 42.449 61.365 28.883 1 33.93 ? C4 PRP 801 A 1 HETATM 5 C C5 PRP . . . E 4 42.597 61.947 27.499 1 32.79 ? C5 PRP 801 A 1 HETATM 6 O O1 PRP . . . E 4 41.753 60.983 31.686 1 28.42 ? O1 PRP 801 A 1 HETATM 7 O O2 PRP . . . E 4 39.595 60.152 30.737 1 43.62 ? O2 PRP 801 A 1 HETATM 8 O O3 PRP . . . E 4 41.669 59.048 29.291 1 37.43 ? O3 PRP 801 A 1 HETATM 9 O O4 PRP . . . E 4 41.894 62.416 29.736 1 30.7 ? O4 PRP 801 A 1 HETATM 10 O O5 PRP . . . E 4 42.088 63.284 27.275 1 29.15 ? O5 PRP 801 A 1 HETATM 11 P P PRP . . . E 4 42.033 63.895 25.73 1 27.31 ? P PRP 801 A 1 HETATM 12 O O1P PRP . . . E 4 42.409 62.697 24.917 1 21.89 ? O1P PRP 801 A 1 HETATM 13 O O2P PRP . . . E 4 42.975 65.02 25.797 1 28.59 ? O2P PRP 801 A 1 HETATM 14 O O3P PRP . . . E 4 40.65 64.418 25.544 1 24.41 ? O3P PRP 801 A 1 HETATM 15 P PA PRP . . . E 4 41.977 61.849 33.003 1 23.92 ? PA PRP 801 A 1 HETATM 16 O O1A PRP . . . E 4 43.221 62.569 32.825 1 24.37 ? O1A PRP 801 A 1 HETATM 17 O O2A PRP . . . E 4 40.857 62.774 33.064 1 22.75 ? O2A PRP 801 A 1 HETATM 18 O O3A PRP . . . E 4 42.033 60.797 34.065 1 25.12 ? O3A PRP 801 A 1 HETATM 19 P PB PRP . . . E 4 40.893 60.315 34.915 1 23.18 ? PB PRP 801 A 1 HETATM 20 O O1B PRP . . . E 4 39.841 61.348 34.976 1 19.24 ? O1B PRP 801 A 1 HETATM 21 O O2B PRP . . . E 4 41.414 60 36.286 1 21.54 ? O2B PRP 801 A 1 HETATM 22 O O3B PRP . . . E 4 40.377 59.011 34.427 1 19.34 ? O3B PRP 801 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #