data_1D6N # _model_server_result.job_id AQo94njFJ5D2G3FwEekWXA _model_server_result.datetime_utc '2025-03-05 22:22:38' _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 1d6n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":314}' # _entry.id 1D6N # _exptl.entry_id 1D6N _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 90 _cell.angle_gamma 90 _cell.entry_id 1D6N _cell.length_a 129.56 _cell.length_b 65.85 _cell.length_c 51.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D6N _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 2 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' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 129.56 65.85 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 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 A OE2 GLU 130 A GLU 133 1_555 C MG MG . A MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? metalc ? metalc2 A OD2 ASP 131 A ASP 134 1_555 C MG MG . A MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? metalc ? metalc3 E O2 PRP . A PRP 312 1_555 C MG MG . A MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc4 E O3 PRP . A PRP 312 1_555 C MG MG . A MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc5 E O1B PRP . A PRP 312 1_555 C MG MG . A MG 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc6 C MG MG . A MG 313 1_555 I O HOH . A HOH 989 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc7 C MG MG . A MG 313 1_555 I O HOH . A HOH 990 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc8 B OE2 GLU 130 B GLU 133 1_555 F MG MG . B MG 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc9 B OD2 ASP 131 B ASP 134 1_555 F MG MG . B MG 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc10 H O2 PRP . B PRP 314 1_555 F MG MG . B MG 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? metalc ? metalc11 H O3 PRP . B PRP 314 1_555 F MG MG . B MG 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc12 F MG MG . B MG 315 1_555 J O HOH . B HOH 991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc13 F MG MG . B MG 315 1_555 J O HOH . B HOH 992 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? # _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 1D6N _atom_sites.fract_transf_matrix[1][1] 0.007718 _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] 0.015186 _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] 0.019433 _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 1 313 313 MG MO2 . D 3 PPO A 1 300 300 PPO PPO . E 4 PRP A 1 312 312 PRP PRP . F 2 MG B 1 315 315 MG MO2 . G 3 PPO B 1 301 301 PPO PPO . H 4 PRP B 1 314 314 PRP PRP . I 5 HOH A 1 904 904 HOH HOH . I 5 HOH A 2 909 909 HOH HOH . I 5 HOH A 3 914 914 HOH HOH . I 5 HOH A 4 915 915 HOH HOH . I 5 HOH A 5 916 916 HOH HOH . I 5 HOH A 6 917 917 HOH HOH . I 5 HOH A 7 921 921 HOH HOH . I 5 HOH A 8 924 924 HOH HOH . I 5 HOH A 9 925 925 HOH HOH . I 5 HOH A 10 926 926 HOH HOH . I 5 HOH A 11 934 934 HOH HOH . I 5 HOH A 12 938 938 HOH HOH . I 5 HOH A 13 939 939 HOH HOH . I 5 HOH A 14 952 952 HOH HOH . I 5 HOH A 15 953 953 HOH HOH . I 5 HOH A 16 957 957 HOH HOH . I 5 HOH A 17 965 965 HOH HOH . I 5 HOH A 18 976 976 HOH HOH . I 5 HOH A 19 977 977 HOH HOH . I 5 HOH A 20 979 979 HOH HOH . I 5 HOH A 21 985 985 HOH HOH . I 5 HOH A 22 986 986 HOH HOH . I 5 HOH A 23 989 313 HOH MO2 . I 5 HOH A 24 990 313 HOH MO2 . J 5 HOH B 1 901 901 HOH HOH . J 5 HOH B 2 902 902 HOH HOH . J 5 HOH B 3 903 903 HOH HOH . J 5 HOH B 4 905 905 HOH HOH . J 5 HOH B 5 907 907 HOH HOH . J 5 HOH B 6 908 908 HOH HOH . J 5 HOH B 7 910 910 HOH HOH . J 5 HOH B 8 911 911 HOH HOH . J 5 HOH B 9 912 912 HOH HOH . J 5 HOH B 10 920 920 HOH HOH . J 5 HOH B 11 922 922 HOH HOH . J 5 HOH B 12 923 923 HOH HOH . J 5 HOH B 13 927 927 HOH HOH . J 5 HOH B 14 929 929 HOH HOH . J 5 HOH B 15 931 931 HOH HOH . J 5 HOH B 16 935 935 HOH HOH . J 5 HOH B 17 940 940 HOH HOH . J 5 HOH B 18 942 942 HOH HOH . J 5 HOH B 19 945 945 HOH HOH . J 5 HOH B 20 946 946 HOH HOH . J 5 HOH B 21 949 949 HOH HOH . J 5 HOH B 22 958 958 HOH HOH . J 5 HOH B 23 960 960 HOH HOH . J 5 HOH B 24 978 978 HOH HOH . J 5 HOH B 25 987 987 HOH HOH . J 5 HOH B 26 988 988 HOH HOH . J 5 HOH B 27 991 315 HOH MO2 . J 5 HOH B 28 992 315 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 . . . H 4 42.678 16.133 13.017 1 2 ? C1 PRP 314 B 1 HETATM 2 C C2 PRP . . . H 4 42.741 16.95 11.753 1 2 ? C2 PRP 314 B 1 HETATM 3 C C3 PRP . . . H 4 41.756 16.342 10.844 1 2 ? C3 PRP 314 B 1 HETATM 4 C C4 PRP . . . H 4 41.116 15.241 11.546 1 2 ? C4 PRP 314 B 1 HETATM 5 C C5 PRP . . . H 4 41.37 14.146 10.761 1 2 ? C5 PRP 314 B 1 HETATM 6 O O1 PRP . . . H 4 42.374 16.897 14.24 1 2 ? O1 PRP 314 B 1 HETATM 7 O O2 PRP . . . H 4 42.49 18.38 11.87 1 2 ? O2 PRP 314 B 1 HETATM 8 O O3 PRP . . . H 4 40.724 17.176 10.324 1 2 ? O3 PRP 314 B 1 HETATM 9 O O4 PRP . . . H 4 41.681 15.111 12.877 1 2 ? O4 PRP 314 B 1 HETATM 10 O O5 PRP . . . H 4 40.871 12.974 11.16 1 2 ? O5 PRP 314 B 1 HETATM 11 P P PRP . . . H 4 40.326 11.82 10.094 1 7.68 ? P PRP 314 B 1 HETATM 12 O O1P PRP . . . H 4 41.03 10.58 10.291 1 6.89 ? O1P PRP 314 B 1 HETATM 13 O O2P PRP . . . H 4 40.495 12.223 8.705 1 3.16 ? O2P PRP 314 B 1 HETATM 14 O O3P PRP . . . H 4 38.886 11.688 10.499 1 13.95 ? O3P PRP 314 B 1 HETATM 15 P PA PRP . . . H 4 42.732 18.191 15.083 1 3.99 ? PA PRP 314 B 1 HETATM 16 O O1A PRP . . . H 4 41.249 17.964 15.587 1 2 ? O1A PRP 314 B 1 HETATM 17 O O2A PRP . . . H 4 43.766 17.323 15.707 1 5.74 ? O2A PRP 314 B 1 HETATM 18 O O3A PRP . . . H 4 43.543 19.24 15.484 1 4.37 ? O3A PRP 314 B 1 HETATM 19 P PB PRP . . . H 4 44.996 19.497 15.898 1 4.07 ? PB PRP 314 B 1 HETATM 20 O O1B PRP . . . H 4 46.303 20.083 16.596 1 2 ? O1B PRP 314 B 1 HETATM 21 O O2B PRP . . . H 4 45.333 19.675 14.473 1 2.76 ? O2B PRP 314 B 1 HETATM 22 O O3B PRP . . . H 4 45.21 18.455 16.806 1 2.03 ? O3B PRP 314 B 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 217 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #