data_7DFH # _model_server_result.job_id 1aHgCR0gRLGb_HtLXZ9eQA _model_server_result.datetime_utc '2024-11-21 09:20:43' _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 7dfh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1006}' # _entry.id 7DFH # _exptl.entry_id 7DFH _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 175.959 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYROPHOSPHATE 2-' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,M,N,O _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 ? 8 L N N ? 8 M 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 covale ? covale1 E O3' G 8 P G 20 1_555 N P RVP . P RVP 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? metalc ? metalc1 A OD1 ASN 210 A ASN 209 1_555 I MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc2 A ND1 HIS 296 A HIS 295 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc3 A SG CYS 302 A CYS 301 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc4 A SG CYS 307 A CYS 306 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc5 A SG CYS 311 A CYS 310 1_555 G ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc6 A SG CYS 488 A CYS 487 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc7 A SG CYS 646 A CYS 645 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc8 A SG CYS 647 A CYS 646 1_555 H ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc9 A OD2 ASP 761 A ASP 760 1_555 J MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc10 I MG MG . A MG 1003 1_555 L O6 POP . A POP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc11 I MG MG . A MG 1003 1_555 L O2 POP . A POP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? metalc ? metalc12 J MG MG . A MG 1004 1_555 N O2P RVP . P RVP 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? hydrog WATSON-CRICK hydrog1 E N1 G 1 P G 13 1_555 F N3 C 12 T C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 E N2 G 1 P G 13 1_555 F O2 C 12 T C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 E O6 G 1 P G 13 1_555 F N4 C 12 T C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 E N3 C 2 P C 14 1_555 F N1 G 11 T G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 E N4 C 2 P C 14 1_555 F O6 G 11 T G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 E O2 C 2 P C 14 1_555 F N2 G 11 T G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 E N3 U 3 P U 15 1_555 F N1 A 10 T A 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 E O4 U 3 P U 15 1_555 F N6 A 10 T A 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 E N1 A 4 P A 16 1_555 F N3 U 9 T U 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 E N6 A 4 P A 16 1_555 F O4 U 9 T U 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 E N3 U 5 P U 17 1_555 F N1 A 8 T A 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E O4 U 5 P U 17 1_555 F N6 A 8 T A 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 E N1 G 6 P G 18 1_555 F N3 C 7 T C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E N2 G 6 P G 18 1_555 F O2 C 7 T C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E O6 G 6 P G 18 1_555 F N4 C 7 T C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog16 E N3 U 7 P U 19 1_555 F N1 A 6 T A 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog17 E N1 G 8 P G 20 1_555 F N3 C 5 T C 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'H2 O7 P2 -2' _chem_comp.formula_weight 175.959 _chem_comp.id POP _chem_comp.mon_nstd_flag . _chem_comp.name 'PYROPHOSPHATE 2-' _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 P1 O1 POP doub 375 n n P1 O2 POP sing 376 n n P1 O3 POP sing 377 n n P1 O POP sing 378 n n O2 HO2 POP sing 379 n n O P2 POP sing 380 n n P2 O4 POP doub 381 n n P2 O5 POP sing 382 n n P2 O6 POP sing 383 n n O5 HO5 POP sing 384 n n # _atom_sites.entry_id 7DFH _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 G 6 ZN A 1 1001 1001 ZN ZN . H 6 ZN A 1 1002 1002 ZN ZN . I 7 MG A 1 1003 1003 MG MG . J 7 MG A 1 1004 1004 MG MG . K 7 MG A 1 1005 1005 MG MG . L 8 POP A 1 1006 1301 POP POP . M 8 POP A 1 1007 1302 POP POP . N 9 RVP P 1 1201 1201 RVP LIG . O 10 HOH A 1 1101 1105 HOH HOH . O 10 HOH A 2 1102 1104 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 P P1 POP . . . L 8 160.364 136.899 101.434 1 81.74 ? P1 POP 1006 A 1 HETATM 2 O O1 POP . . . L 8 160.584 137.647 100.146 1 81.74 ? O1 POP 1006 A 1 HETATM 3 O O2 POP . . . L 8 160.034 137.882 102.525 1 81.74 ? O2 POP 1006 A 1 HETATM 4 O O3 POP . . . L 8 161.633 136.177 101.804 1 81.74 ? O3 POP 1006 A 1 HETATM 5 O O POP . . . L 8 159.135 135.862 101.359 1 81.74 ? O POP 1006 A 1 HETATM 6 P P2 POP . . . L 8 157.792 136.06 100.488 1 81.74 ? P2 POP 1006 A 1 HETATM 7 O O4 POP . . . L 8 157.971 136.985 99.311 1 81.74 ? O4 POP 1006 A 1 HETATM 8 O O5 POP . . . L 8 157.386 134.709 99.954 1 81.74 ? O5 POP 1006 A 1 HETATM 9 O O6 POP . . . L 8 156.718 136.617 101.389 1 81.74 ? O6 POP 1006 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 9 #