data_5KDF # _model_server_result.job_id FqO_BKbuDvpUNV1fRfsH1A _model_server_result.datetime_utc '2024-10-10 01:15:29' _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 5kdf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":204}' # _entry.id 5KDF # _exptl.entry_id 5KDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _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 120 _cell.entry_id 5KDF _cell.length_a 98.972 _cell.length_b 98.972 _cell.length_c 97.571 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KDF _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 98.972 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 49.486 85.712266 0 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 49.486 85.712266 48.7855 5 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 98.972 0 48.7855 6 'crystal symmetry operation' 12_555 x,x-y,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 48.7855 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E 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 OE2 GLU 27 A GLU 18 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.104 ? metalc ? metalc2 A O LYS 136 A LYS 127 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.004 ? metalc ? metalc3 A O GLU 139 A GLU 130 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? metalc ? metalc4 A O LYS 142 A LYS 133 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? metalc ? metalc5 E CA CA . A CA 204 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc6 E CA CA . A CA 204 1_555 G O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc7 E CA CA . A CA 204 1_555 G O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? # _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 5KDF _atom_sites.fract_transf_matrix[1][1] 0.010104 _atom_sites.fract_transf_matrix[1][2] 0.005833 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011667 _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] 0.010249 _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 6RU A 1 201 1 6RU 007 . C 3 CA A 1 202 204 CA CA . D 3 CA A 1 203 205 CA CA . E 3 CA A 1 204 206 CA CA . F 4 POP A 1 205 201 POP POP . G 5 HOH A 1 301 32 HOH HOH . G 5 HOH A 2 302 12 HOH HOH . G 5 HOH A 3 303 23 HOH HOH . G 5 HOH A 4 304 26 HOH HOH . G 5 HOH A 5 305 25 HOH HOH . G 5 HOH A 6 306 1 HOH HOH . G 5 HOH A 7 307 33 HOH HOH . G 5 HOH A 8 308 11 HOH HOH . G 5 HOH A 9 309 14 HOH HOH . G 5 HOH A 10 310 6 HOH HOH . G 5 HOH A 11 311 18 HOH HOH . G 5 HOH A 12 312 27 HOH HOH . G 5 HOH A 13 313 4 HOH HOH . G 5 HOH A 14 314 16 HOH HOH . G 5 HOH A 15 315 19 HOH HOH . G 5 HOH A 16 316 24 HOH HOH . G 5 HOH A 17 317 10 HOH HOH . G 5 HOH A 18 318 15 HOH HOH . G 5 HOH A 19 319 9 HOH HOH . G 5 HOH A 20 320 30 HOH HOH . G 5 HOH A 21 321 31 HOH HOH . G 5 HOH A 22 322 17 HOH HOH . G 5 HOH A 23 323 13 HOH HOH . G 5 HOH A 24 324 3 HOH HOH . G 5 HOH A 25 325 20 HOH HOH . G 5 HOH A 26 326 22 HOH HOH . G 5 HOH A 27 327 21 HOH HOH . # _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 3 _atom_site.Cartn_x 34.612 _atom_site.Cartn_y 36.209 _atom_site.Cartn_z 5.857 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 78.68 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 204 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #