data_8DB9 # _model_server_result.job_id 2Mw3wqyhYIwKYmkahHHosQ _model_server_result.datetime_utc '2025-04-10 17:18:19' _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 8db9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 8DB9 # _exptl.entry_id 8DB9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 65.466 _cell.angle_beta 80.791 _cell.angle_gamma 87.323 _cell.entry_id 8DB9 _cell.length_a 50.406 _cell.length_b 75.382 _cell.length_c 88.856 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DB9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,E,F,G,H,I 1 1 D,J,K 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' 1_655 x+1,y,z 1 0 0 0 1 0 0 0 1 50.406 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N ? 2 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 A OD1 ASP 8 A ASP 8 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc2 A OD2 ASP 8 A ASP 8 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.117 ? metalc ? metalc3 A OD1 ASP 13 A ASP 13 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc4 A OD2 ASP 13 A ASP 13 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.826 ? metalc ? metalc5 A O LEU 125 A LEU 125 1_555 E CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc6 B OD1 ASP 8 B ASP 8 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc7 B OD1 ASP 13 B ASP 13 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc8 B OD2 ASP 13 B ASP 13 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? metalc ? metalc9 B O LEU 125 B LEU 125 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? metalc ? metalc10 B OD2 ASP 239 B ASP 239 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc11 F O13 R1Y . B R1Y 401 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc12 F O14 R1Y . B R1Y 401 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc13 C OD1 ASP 8 C ASP 8 1_555 I CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc14 C OD1 ASP 13 C ASP 13 1_555 I CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? metalc ? metalc15 C O LEU 125 C LEU 125 1_555 I CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc16 H O13 R1Y . C R1Y 401 1_555 I CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? metalc ? metalc17 H O14 R1Y . C R1Y 401 1_555 I CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc18 D OD1 ASP 8 D ASP 8 1_555 K CA CA . D CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc19 D OD1 ASP 13 D ASP 13 1_555 K CA CA . D CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc20 D OD2 ASP 13 D ASP 13 1_555 K CA CA . D CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc21 D O LEU 125 D LEU 125 1_555 K CA CA . D CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc22 D OD2 ASP 239 D ASP 239 1_555 K CA CA . D CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc23 J O13 R1Y . D R1Y 401 1_555 K CA CA . D CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc24 J O14 R1Y . D R1Y 401 1_555 K CA CA . D CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 8DB9 _atom_sites.fract_transf_matrix[1][1] 0.019839 _atom_sites.fract_transf_matrix[1][2] -0.000928 _atom_sites.fract_transf_matrix[1][3] -0.003111 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01328 _atom_sites.fract_transf_matrix[2][3] -0.006032 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012522 _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 2 CA A 1 401 2 CA CA . F 3 R1Y B 1 401 401 R1Y VIR . G 2 CA B 1 402 1 CA CA . H 3 R1Y C 1 401 402 R1Y VIR . I 2 CA C 1 402 3 CA CA . J 3 R1Y D 1 401 403 R1Y VIR . K 2 CA D 1 402 4 CA CA . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id E _atom_site.label_entity_id 2 _atom_site.Cartn_x 0.603 _atom_site.Cartn_y -4.826 _atom_site.Cartn_z -7.06 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 45.92 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 401 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 532 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #