data_8Y40 # _model_server_result.job_id FIDKZxzRwjIXJ6HFgbfmjg _model_server_result.datetime_utc '2025-03-05 03:31:56' _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 8y40 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":5103}' # _entry.id 8Y40 # _exptl.entry_id 8Y40 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 40.078 _entity.id 6 _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 ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 12-meric _pdbx_struct_assembly.oligomeric_count 12 _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,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA _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 x,y,z _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 ? 6 O N N ? 6 T N N ? 6 Y N N ? 6 DA 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 I OE1 GLU 3967 A GLU 3967 1_555 O CA CA . A CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc2 I OE2 GLU 3967 A GLU 3967 1_555 O CA CA . A CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.118 ? metalc ? metalc3 I SG CYS 4961 A CYS 4961 1_555 N ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc4 I ND1 HIS 4978 A HIS 4978 1_555 N ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc5 I O THR 5001 A THR 5001 1_555 O CA CA . A CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc6 J OE1 GLU 3967 B GLU 3967 1_555 T CA CA . B CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc7 J OE2 GLU 3967 B GLU 3967 1_555 T CA CA . B CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.113 ? metalc ? metalc8 J SG CYS 4961 B CYS 4961 1_555 S ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc9 J ND1 HIS 4978 B HIS 4978 1_555 S ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc10 J O THR 5001 B THR 5001 1_555 T CA CA . B CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc11 K OE1 GLU 3967 C GLU 3967 1_555 Y CA CA . C CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc12 K OE2 GLU 3967 C GLU 3967 1_555 Y CA CA . C CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? metalc ? metalc13 K SG CYS 4961 C CYS 4961 1_555 X ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc14 K ND1 HIS 4978 C HIS 4978 1_555 X ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc15 K O THR 5001 C THR 5001 1_555 Y CA CA . C CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc16 L OE1 GLU 3967 D GLU 3967 1_555 DA CA CA . D CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc17 L OE2 GLU 3967 D GLU 3967 1_555 DA CA CA . D CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.117 ? metalc ? metalc18 L SG CYS 4961 D CYS 4961 1_555 CA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc19 L ND1 HIS 4978 D HIS 4978 1_555 CA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc20 L O THR 5001 D THR 5001 1_555 DA CA CA . D CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? # _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 8Y40 _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 M 4 F0U A 1 5101 1 F0U CHL . N 5 ZN A 1 5102 1 ZN ZN . O 6 CA A 1 5103 1 CA CA . P 7 ATP A 1 5104 1 ATP ATP . Q 8 CFF A 1 5105 1 CFF CFF . R 4 F0U B 1 5101 2 F0U CHL . S 5 ZN B 1 5102 2 ZN ZN . T 6 CA B 1 5103 2 CA CA . U 7 ATP B 1 5104 2 ATP ATP . V 8 CFF B 1 5105 2 CFF CFF . W 4 F0U C 1 5101 3 F0U CHL . X 5 ZN C 1 5102 3 ZN ZN . Y 6 CA C 1 5103 3 CA CA . Z 7 ATP C 1 5104 3 ATP ATP . AA 8 CFF C 1 5105 3 CFF CFF . BA 4 F0U D 1 5101 4 F0U CHL . CA 5 ZN D 1 5102 4 ZN ZN . DA 6 CA D 1 5103 4 CA CA . EA 7 ATP D 1 5104 4 ATP ATP . FA 8 CFF D 1 5105 4 CFF CFF . # _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 Y _atom_site.label_entity_id 6 _atom_site.Cartn_x 313.013 _atom_site.Cartn_y 252.006 _atom_site.Cartn_z 290.831 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 42.96 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 5103 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 161 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #