data_4XYD # _model_server_result.job_id NBQrKH6p0Nbk1nqOHSOAyg _model_server_result.datetime_utc '2024-11-21 14:14:57' _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 4xyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":503}' # _entry.id 4XYD # _exptl.entry_id 4XYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _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 4XYD _cell.length_a 86.22 _cell.length_b 98.83 _cell.length_c 126.78 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 covale ? covale1 B SG CYS 62 B CYS 62 1_555 H CAB HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.664 ? covale ? covale2 B SG CYS 65 B CYS 65 1_555 H CAC HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.719 ? metalc ? metalc1 A NE2 HIS 53 A HIS 53 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc2 A OE1 GLU 122 A GLU 122 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc3 A OE2 GLU 122 A GLU 122 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? metalc ? metalc4 A ND1 HIS 194 A HIS 194 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? metalc ? metalc5 A OE1 GLU 198 A GLU 198 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc6 A OE2 GLU 198 A GLU 198 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc7 A NE2 HIS 245 A HIS 245 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? metalc ? metalc8 A NE2 HIS 246 A HIS 246 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc9 A NE2 HIS 334 A HIS 334 1_555 F FE HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc10 A NE2 HIS 336 A HIS 336 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? metalc ? metalc11 C O1D HEM . A HEM 501 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc12 D O2 UNL . A UNL 502 1_555 F FE HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc13 D O2 UNL . A UNL 502 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc14 D O1 UNL . A UNL 502 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc15 E CA CA . A CA 503 1_555 F O1A HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc16 E CA CA . A CA 503 1_555 F O2A HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.141 ? metalc ? metalc17 E CA CA . A CA 503 1_555 B O GLY 72 B GLY 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc18 E CA CA . A CA 503 1_555 B OH TYR 74 B TYR 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc19 B OE1 GLU 49 B GLU 49 1_555 I CU CU . B CU 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc20 B ND1 HIS 52 B HIS 52 1_555 I CU CU . B CU 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc21 B NE2 HIS 66 B HIS 66 1_555 H FE HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? metalc ? metalc22 B SD MET 116 B MET 116 1_555 H FE HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc23 B OE1 GLU 124 B GLU 124 1_555 I CU CU . B CU 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc24 I CU CU . B CU 202 1_555 K O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? # _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 4XYD _atom_sites.fract_transf_matrix[1][1] 0.011598 _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] 0.010118 _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] 0.007888 _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 C 3 HEM A 1 501 500 HEM HEM . D 4 UNL A 1 502 1 UNL UNL . E 5 CA A 1 503 700 CA CA . F 3 HEM A 1 504 600 HEM HEM . G 6 FE A 1 505 601 FE FE . H 7 HEC B 1 201 500 HEC HEC . I 8 CU B 1 202 600 CU CU . J 9 HOH A 1 601 13 HOH HOH . J 9 HOH A 2 602 17 HOH HOH . J 9 HOH A 3 603 11 HOH HOH . J 9 HOH A 4 604 15 HOH HOH . J 9 HOH A 5 605 2 HOH HOH . J 9 HOH A 6 606 12 HOH HOH . J 9 HOH A 7 607 8 HOH HOH . J 9 HOH A 8 608 5 HOH HOH . J 9 HOH A 9 609 4 HOH HOH . J 9 HOH A 10 610 14 HOH HOH . J 9 HOH A 11 611 1 HOH HOH . J 9 HOH A 12 612 3 HOH HOH . K 9 HOH B 1 301 10 HOH HOH . K 9 HOH B 2 302 7 HOH HOH . K 9 HOH B 3 303 9 HOH HOH . K 9 HOH B 4 304 6 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 5 _atom_site.Cartn_x 21.484 _atom_site.Cartn_y -9.239 _atom_site.Cartn_z -37.489 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 61.63 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 503 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 1126 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 1 #