data_5EJI # _model_server_result.job_id y7hxlc9L7tM1YtG5rjxZNg _model_server_result.datetime_utc '2024-11-15 02:04:04' _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 5eji # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5EJI # _exptl.entry_id 5EJI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 175.959 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYROPHOSPHATE 2-' _entity.pdbx_number_of_molecules 1 _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 5EJI _cell.length_a 63.466 _cell.length_b 74.389 _cell.length_c 119.012 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EJI _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 63.466 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 63.466 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B O1A NAP . A NAP 301 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc2 B O3X NAP . A NAP 301 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc3 C MN MN . A MN 302 1_555 D O4 POP . A POP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc4 C MN MN . A MN 302 1_555 D O POP . A POP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? # _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 360 n n P1 O2 POP sing 361 n n P1 O3 POP sing 362 n n P1 O POP sing 363 n n O2 HO2 POP sing 364 n n O P2 POP sing 365 n n P2 O4 POP doub 366 n n P2 O5 POP sing 367 n n P2 O6 POP sing 368 n n O5 HO5 POP sing 369 n n # _atom_sites.entry_id 5EJI _atom_sites.fract_transf_matrix[1][1] 0.015756 _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] 0.013443 _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] 0.008402 _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 B 2 NAP A 1 301 1 NAP NAP . C 3 MN A 1 302 1 MN MN . D 4 POP A 1 303 1 POP POP . E 5 CIT A 1 304 1 CIT CIT . F 6 HOH A 1 401 21 HOH HOH . F 6 HOH A 2 402 29 HOH HOH . F 6 HOH A 3 403 8 HOH HOH . F 6 HOH A 4 404 7 HOH HOH . F 6 HOH A 5 405 20 HOH HOH . F 6 HOH A 6 406 5 HOH HOH . F 6 HOH A 7 407 16 HOH HOH . F 6 HOH A 8 408 12 HOH HOH . F 6 HOH A 9 409 13 HOH HOH . F 6 HOH A 10 410 26 HOH HOH . F 6 HOH A 11 411 28 HOH HOH . F 6 HOH A 12 412 27 HOH HOH . F 6 HOH A 13 413 30 HOH HOH . F 6 HOH A 14 414 6 HOH HOH . F 6 HOH A 15 415 23 HOH HOH . F 6 HOH A 16 416 3 HOH HOH . F 6 HOH A 17 417 10 HOH HOH . F 6 HOH A 18 418 15 HOH HOH . F 6 HOH A 19 419 9 HOH HOH . F 6 HOH A 20 420 17 HOH HOH . F 6 HOH A 21 421 14 HOH HOH . F 6 HOH A 22 422 4 HOH HOH . F 6 HOH A 23 423 11 HOH HOH . F 6 HOH A 24 424 24 HOH HOH . F 6 HOH A 25 425 2 HOH HOH . F 6 HOH A 26 426 33 HOH HOH . F 6 HOH A 27 427 31 HOH HOH . F 6 HOH A 28 428 1 HOH HOH . F 6 HOH A 29 429 19 HOH HOH . F 6 HOH A 30 430 32 HOH HOH . F 6 HOH A 31 431 22 HOH HOH . F 6 HOH A 32 432 34 HOH HOH . F 6 HOH A 33 433 18 HOH HOH . F 6 HOH A 34 434 25 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 . . . D 4 12.886 10.107 18.9 0.5 64.09 ? P1 POP 303 A 1 HETATM 2 O O1 POP . . . D 4 13.34 11.459 18.416 0.5 59.01 ? O1 POP 303 A 1 HETATM 3 O O2 POP . . . D 4 13.303 9.936 20.341 0.5 71.31 ? O2 POP 303 A 1 HETATM 4 O O3 POP . . . D 4 11.384 9.994 18.792 0.5 67.72 ? O3 POP 303 A 1 HETATM 5 O O POP . . . D 4 13.581 8.967 18.007 0.5 61.25 ? O POP 303 A 1 HETATM 6 P P2 POP . . . D 4 13.028 7.455 18.064 0.5 81.83 ? P2 POP 303 A 1 HETATM 7 O O4 POP . . . D 4 13.92 6.539 17.263 0.5 80.75 ? O4 POP 303 A 1 HETATM 8 O O5 POP . . . D 4 13 6.975 19.494 0.5 80.03 ? O5 POP 303 A 1 HETATM 9 O O6 POP . . . D 4 11.638 7.449 17.465 0.5 83.76 ? O6 POP 303 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 9 #