data_6FU2 # _model_server_result.job_id 03BL9N6KgobPcAqxEkL5og _model_server_result.datetime_utc '2025-07-30 12:02:13' _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 6fu2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 6FU2 # _exptl.entry_id 6FU2 _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 102.16 _cell.angle_gamma 90 _cell.entry_id 6FU2 _cell.length_a 102.72 _cell.length_b 146.2 _cell.length_c 94.51 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FU2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,O,P _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' 2_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -102.72 0 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 K 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 F O1A PRP . C PRP 301 1_555 I MG MG . C MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc2 F O1B PRP . C PRP 301 1_555 I MG MG . C MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc3 G O2B ATP . C ATP 302 1_555 I MG MG . C MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc4 G O2A ATP . C ATP 302 1_555 I MG MG . C MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc5 H MG MG . C MG 303 1_555 K O2A PRP . D PRP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc6 H MG MG . C MG 303 1_555 K O2B PRP . D PRP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc7 H MG MG . C MG 303 1_555 L O2B ATP . D ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc8 H MG MG . C MG 303 1_555 L O1A ATP . D ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? # _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 326 n n C1 O1 PRP sing 327 n n C1 O4 PRP sing 328 n n C1 H1 PRP sing 329 n n C2 C3 PRP sing 330 n n C2 O2 PRP sing 331 n n C2 H2 PRP sing 332 n n C3 C4 PRP sing 333 n n C3 O3 PRP sing 334 n n C3 H3 PRP sing 335 n n C4 C5 PRP sing 336 n n C4 O4 PRP sing 337 n n C4 H4 PRP sing 338 n n C5 O5 PRP sing 339 n n C5 H51 PRP sing 340 n n C5 H52 PRP sing 341 n n O1 PA PRP sing 342 n n O2 HO2 PRP sing 343 n n O3 HO3 PRP sing 344 n n O5 P PRP sing 345 n n P O1P PRP doub 346 n n P O2P PRP sing 347 n n P O3P PRP sing 348 n n O2P HOP2 PRP sing 349 n n O3P HOP3 PRP sing 350 n n PA O1A PRP doub 351 n n PA O2A PRP sing 352 n n PA O3A PRP sing 353 n n O2A HOA2 PRP sing 354 n n O3A PB PRP sing 355 n n PB O1B PRP doub 356 n n PB O2B PRP sing 357 n n PB O3B PRP sing 358 n n O2B HOB2 PRP sing 359 n n O3B HOB3 PRP sing 360 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 6FU2 _atom_sites.fract_transf_matrix[1][1] 0.009735 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002098 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00684 _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] 0.010824 _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 TRS B 1 401 3 TRS TRS . F 4 PRP C 1 301 400 PRP PRP . G 5 ATP C 1 302 500 ATP ATP . H 6 MG C 1 303 1 MG MG . I 6 MG C 1 304 2 MG MG . J 3 TRS C 1 305 1 TRS TRS . K 4 PRP D 1 301 400 PRP PRP . L 5 ATP D 1 302 500 ATP ATP . M 3 TRS D 1 303 2 TRS TRS . N 7 HOH A 1 401 9 HOH HOH . N 7 HOH A 2 402 11 HOH HOH . N 7 HOH A 3 403 10 HOH HOH . O 7 HOH B 1 501 8 HOH HOH . O 7 HOH B 2 502 7 HOH HOH . O 7 HOH B 3 503 6 HOH HOH . O 7 HOH B 4 504 2 HOH HOH . O 7 HOH B 5 505 1 HOH HOH . P 7 HOH D 1 401 4 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 C C1 PRP . . . F 4 -21.579 -9.98 31.93 1 80.9 ? C1 PRP 301 C 1 HETATM 2 C C2 PRP . . . F 4 -23.073 -9.738 31.797 1 78.28 ? C2 PRP 301 C 1 HETATM 3 C C3 PRP . . . F 4 -23.6 -10 33.196 1 76.97 ? C3 PRP 301 C 1 HETATM 4 C C4 PRP . . . F 4 -22.51 -10.798 33.911 1 76.1 ? C4 PRP 301 C 1 HETATM 5 C C5 PRP . . . F 4 -22.973 -12.207 34.281 1 76.92 ? C5 PRP 301 C 1 HETATM 6 O O1 PRP . . . F 4 -20.894 -8.768 32.22 1 85.97 ? O1 PRP 301 C 1 HETATM 7 O O2 PRP . . . F 4 -23.366 -8.422 31.302 1 80.3 ? O2 PRP 301 C 1 HETATM 8 O O3 PRP . . . F 4 -23.872 -8.784 33.896 1 74.04 ? O3 PRP 301 C 1 HETATM 9 O O4 PRP . . . F 4 -21.397 -10.878 33.024 1 77.36 ? O4 PRP 301 C 1 HETATM 10 O O5 PRP . . . F 4 -21.926 -12.959 34.899 1 75.03 ? O5 PRP 301 C 1 HETATM 11 P P PRP . . . F 4 -22.019 -13.514 36.415 1 73.83 ? P PRP 301 C 1 HETATM 12 O O1P PRP . . . F 4 -23.322 -14.272 36.484 1 71.78 ? O1P PRP 301 C 1 HETATM 13 O O2P PRP . . . F 4 -20.843 -14.454 36.535 1 70.2 ? O2P PRP 301 C 1 HETATM 14 O O3P PRP . . . F 4 -21.944 -12.258 37.249 1 66.19 ? O3P PRP 301 C 1 HETATM 15 P PA PRP . . . F 4 -19.345 -8.558 31.822 1 86.79 ? PA PRP 301 C 1 HETATM 16 O O1A PRP . . . F 4 -19.175 -8.555 30.319 1 82.48 ? O1A PRP 301 C 1 HETATM 17 O O2A PRP . . . F 4 -18.536 -9.539 32.628 1 86.23 ? O2A PRP 301 C 1 HETATM 18 O O3A PRP . . . F 4 -19.068 -7.084 32.415 1 90.99 ? O3A PRP 301 C 1 HETATM 19 P PB PRP . . . F 4 -19.943 -5.773 32.062 1 98.12 ? PB PRP 301 C 1 HETATM 20 O O1B PRP . . . F 4 -19.597 -5.469 30.622 1 100.68 ? O1B PRP 301 C 1 HETATM 21 O O2B PRP . . . F 4 -21.403 -6.128 32.283 1 91.62 ? O2B PRP 301 C 1 HETATM 22 O O3B PRP . . . F 4 -19.385 -4.773 33.046 1 95.83 ? O3B PRP 301 C 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 47 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 691 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #