data_1YRU # _model_server_result.job_id g9NRZnO2ihBVXtkIWA2T3A _model_server_result.datetime_utc '2024-11-04 23:10:06' _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 1yru # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":801}' # _entry.id 1YRU # _exptl.entry_id 1YRU _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 2 _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 1YRU _cell.length_a 79.441 _cell.length_b 79.441 _cell.length_c 139.181 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YRU _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 ? 3 C N N ? 3 D 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 F O HOH . B HOH 42 1_555 D CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc2 B OD2 ASP 19 B ASP 93 1_555 D CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 B OD1 ASP 21 B ASP 95 1_555 D CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc4 B ND2 ASN 23 B ASN 97 1_555 D CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.335 ? metalc ? metalc5 B OD1 ASN 23 B ASN 97 1_555 D CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc6 B O TYR 25 B TYR 99 1_555 D CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc7 B OE1 GLU 30 B GLU 104 1_555 D CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc8 B OE2 GLU 30 B GLU 104 1_555 D CA CA . B CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc9 B OD2 ASP 55 B ASP 129 1_555 C CA CA . B CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc10 B OD1 ASP 57 B ASP 131 1_555 C CA CA . B CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc11 B OD1 ASP 59 B ASP 133 1_555 C CA CA . B CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc12 B O GLN 61 B GLN 135 1_555 C CA CA . B CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc13 B OE1 GLU 66 B GLU 140 1_555 C CA CA . B CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc14 B OE2 GLU 66 B GLU 140 1_555 C CA CA . B CA 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? # _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 1YRU _atom_sites.fract_transf_matrix[1][1] 0.012588 _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] 0.012588 _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] 0.007185 _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 CA B 1 800 800 CA CA2 . D 3 CA B 1 801 801 CA CA2 . E 4 HOH A 1 365 1 HOH TIP . E 4 HOH A 2 366 2 HOH TIP . E 4 HOH A 3 367 3 HOH TIP . E 4 HOH A 4 368 4 HOH TIP . E 4 HOH A 5 369 5 HOH TIP . E 4 HOH A 6 370 6 HOH TIP . E 4 HOH A 7 371 7 HOH TIP . E 4 HOH A 8 372 8 HOH TIP . E 4 HOH A 9 373 9 HOH TIP . E 4 HOH A 10 374 11 HOH TIP . E 4 HOH A 11 375 12 HOH TIP . E 4 HOH A 12 376 14 HOH TIP . E 4 HOH A 13 377 15 HOH TIP . E 4 HOH A 14 378 17 HOH TIP . E 4 HOH A 15 379 19 HOH TIP . E 4 HOH A 16 380 20 HOH TIP . E 4 HOH A 17 381 21 HOH TIP . E 4 HOH A 18 382 22 HOH TIP . E 4 HOH A 19 383 23 HOH TIP . E 4 HOH A 20 384 24 HOH TIP . E 4 HOH A 21 385 26 HOH TIP . E 4 HOH A 22 386 29 HOH TIP . E 4 HOH A 23 387 30 HOH TIP . E 4 HOH A 24 388 31 HOH TIP . E 4 HOH A 25 389 32 HOH TIP . E 4 HOH A 26 390 34 HOH TIP . E 4 HOH A 27 391 35 HOH TIP . E 4 HOH A 28 392 36 HOH TIP . E 4 HOH A 29 393 37 HOH TIP . E 4 HOH A 30 394 39 HOH TIP . E 4 HOH A 31 395 40 HOH TIP . E 4 HOH A 32 396 41 HOH TIP . E 4 HOH A 33 397 43 HOH TIP . E 4 HOH A 34 398 44 HOH TIP . E 4 HOH A 35 399 45 HOH TIP . E 4 HOH A 36 400 46 HOH TIP . E 4 HOH A 37 401 48 HOH TIP . E 4 HOH A 38 402 49 HOH TIP . E 4 HOH A 39 403 50 HOH TIP . E 4 HOH A 40 404 51 HOH TIP . E 4 HOH A 41 405 53 HOH TIP . E 4 HOH A 42 406 54 HOH TIP . E 4 HOH A 43 407 55 HOH TIP . E 4 HOH A 44 408 56 HOH TIP . E 4 HOH A 45 409 58 HOH TIP . E 4 HOH A 46 410 60 HOH TIP . E 4 HOH A 47 411 61 HOH TIP . E 4 HOH A 48 412 62 HOH TIP . E 4 HOH A 49 413 63 HOH TIP . E 4 HOH A 50 414 64 HOH TIP . E 4 HOH A 51 415 65 HOH TIP . E 4 HOH A 52 416 66 HOH TIP . E 4 HOH A 53 417 67 HOH TIP . E 4 HOH A 54 418 69 HOH TIP . E 4 HOH A 55 419 70 HOH TIP . E 4 HOH A 56 420 71 HOH TIP . F 4 HOH B 1 10 10 HOH TIP . F 4 HOH B 2 16 16 HOH TIP . F 4 HOH B 3 18 18 HOH TIP . F 4 HOH B 4 25 25 HOH TIP . F 4 HOH B 5 27 27 HOH TIP . F 4 HOH B 6 28 28 HOH TIP . F 4 HOH B 7 33 33 HOH TIP . F 4 HOH B 8 38 38 HOH TIP . F 4 HOH B 9 42 42 HOH TIP . F 4 HOH B 10 47 47 HOH TIP . F 4 HOH B 11 52 52 HOH TIP . F 4 HOH B 12 57 57 HOH TIP . F 4 HOH B 13 59 59 HOH TIP . F 4 HOH B 14 68 68 HOH TIP . # _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 D _atom_site.label_entity_id 3 _atom_site.Cartn_x 19.038 _atom_site.Cartn_y 17.665 _atom_site.Cartn_z 57.89 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 39.92 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 801 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #