data_8J8J # _model_server_result.job_id CV-Bxo3Tfjju2N9hq-UQIw _model_server_result.datetime_utc '2024-11-15 00:05:25' _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 8j8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 8J8J # _exptl.entry_id 8J8J _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 390.07 _entity.id 2 _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 3 _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 8J8J _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8J8J _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 _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 ? _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 ? 2 D N N ? 2 G N N ? 2 J 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 ASN 73 D ASN 73 1_555 E MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.993 ? metalc ? metalc2 A OD2 ASP 77 D ASP 77 1_555 E MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc3 D O1A PRP . D PRP 401 1_555 E MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc4 D O3B PRP . D PRP 401 1_555 E MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? metalc ? metalc5 B OD1 ASN 73 A ASN 73 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.993 ? metalc ? metalc6 B OD2 ASP 77 A ASP 77 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc7 G O1A PRP . A PRP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc8 G O3B PRP . A PRP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.717 ? metalc ? metalc9 C OD1 ASN 73 B ASN 73 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? metalc ? metalc10 C OD2 ASP 77 B ASP 77 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc11 J O1A PRP . B PRP 401 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc12 J O3B PRP . B PRP 401 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? # _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 402 n n C1 O1 PRP sing 403 n n C1 O4 PRP sing 404 n n C1 H1 PRP sing 405 n n C2 C3 PRP sing 406 n n C2 O2 PRP sing 407 n n C2 H2 PRP sing 408 n n C3 C4 PRP sing 409 n n C3 O3 PRP sing 410 n n C3 H3 PRP sing 411 n n C4 C5 PRP sing 412 n n C4 O4 PRP sing 413 n n C4 H4 PRP sing 414 n n C5 O5 PRP sing 415 n n C5 H51 PRP sing 416 n n C5 H52 PRP sing 417 n n O1 PA PRP sing 418 n n O2 HO2 PRP sing 419 n n O3 HO3 PRP sing 420 n n O5 P PRP sing 421 n n P O1P PRP doub 422 n n P O2P PRP sing 423 n n P O3P PRP sing 424 n n O2P HOP2 PRP sing 425 n n O3P HOP3 PRP sing 426 n n PA O1A PRP doub 427 n n PA O2A PRP sing 428 n n PA O3A PRP sing 429 n n O2A HOA2 PRP sing 430 n n O3A PB PRP sing 431 n n PB O1B PRP doub 432 n n PB O2B PRP sing 433 n n PB O3B PRP sing 434 n n O2B HOB2 PRP sing 435 n n O3B HOB3 PRP sing 436 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 8J8J _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 2 PRP D 1 401 1 PRP PRP . E 3 MG D 1 402 4 MG MG . F 4 PGW D 1 403 5 PGW LIG . G 2 PRP A 1 401 2 PRP PRP . H 3 MG A 1 402 5 MG MG . I 4 PGW A 1 403 4 PGW LIG . J 2 PRP B 1 401 3 PRP PRP . K 3 MG B 1 402 6 MG MG . L 4 PGW B 1 403 3 PGW LIG . # 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 . . . J 2 122.693 138.454 134.496 1 58.56 ? C1 PRP 401 B 1 HETATM 2 C C2 PRP . . . J 2 121.615 137.997 135.447 1 58.56 ? C2 PRP 401 B 1 HETATM 3 C C3 PRP . . . J 2 121.761 138.848 136.669 1 58.56 ? C3 PRP 401 B 1 HETATM 4 C C4 PRP . . . J 2 123.121 139.481 136.572 1 58.56 ? C4 PRP 401 B 1 HETATM 5 C C5 PRP . . . J 2 124.039 138.929 137.64 1 58.56 ? C5 PRP 401 B 1 HETATM 6 O O1 PRP . . . J 2 122.178 139.338 133.497 1 58.56 ? O1 PRP 401 B 1 HETATM 7 O O2 PRP . . . J 2 120.327 138.223 134.917 1 58.56 ? O2 PRP 401 B 1 HETATM 8 O O3 PRP . . . J 2 120.762 139.853 136.667 1 58.56 ? O3 PRP 401 B 1 HETATM 9 O O4 PRP . . . J 2 123.64 139.134 135.306 1 58.56 ? O4 PRP 401 B 1 HETATM 10 O O5 PRP . . . J 2 123.638 137.582 137.862 1 58.56 ? O5 PRP 401 B 1 HETATM 11 P P PRP . . . J 2 124.056 136.759 139.147 1 58.56 ? P PRP 401 B 1 HETATM 12 O O1P PRP . . . J 2 124.087 135.349 138.688 1 58.56 ? O1P PRP 401 B 1 HETATM 13 O O2P PRP . . . J 2 123.006 137.163 140.143 1 58.56 ? O2P PRP 401 B 1 HETATM 14 O O3P PRP . . . J 2 125.416 137.344 139.318 1 58.56 ? O3P PRP 401 B 1 HETATM 15 P PA PRP . . . J 2 122.707 139.369 131.982 1 58.56 ? PA PRP 401 B 1 HETATM 16 O O1A PRP . . . J 2 121.594 139.667 131.058 1 58.56 ? O1A PRP 401 B 1 HETATM 17 O O2A PRP . . . J 2 123.908 140.228 131.963 1 58.56 ? O2A PRP 401 B 1 HETATM 18 O O3A PRP . . . J 2 123.098 137.855 131.709 1 58.56 ? O3A PRP 401 B 1 HETATM 19 P PB PRP . . . J 2 122.478 136.987 130.54 1 58.56 ? PB PRP 401 B 1 HETATM 20 O O1B PRP . . . J 2 123.286 137.361 129.363 1 58.56 ? O1B PRP 401 B 1 HETATM 21 O O2B PRP . . . J 2 122.755 135.598 130.943 1 58.56 ? O2B PRP 401 B 1 HETATM 22 O O3B PRP . . . J 2 121.042 137.364 130.464 1 58.56 ? O3B PRP 401 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 109 _model_server_stats.query_time_ms 511 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 22 #