data_5CYB
#
_model_server_result.job_id            gV0GneyMsDphHq4LFuwweQ 
_model_server_result.datetime_utc      '2025-07-30 23:56:38' 
_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          5cyb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":205}' 
#
_entry.id    5CYB 
#
_exptl.entry_id    5CYB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              40.078 
_entity.id                          4 
_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         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            5CYB 
_cell.length_a            107.485 
_cell.length_b            107.485 
_cell.length_c            63.87 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5CYB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 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,G,H 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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' 10_666 -y+1,-x+1,-z+7/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 53.7425 93.084741 74.515 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 E N N 
? 4 F N N 
? 4 G 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 81 A ASP 81 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc2 A OD2 ASP 81 A ASP 81 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? 
metalc ? metalc3 A OE1 GLU 100 A GLU 100 1_555 E CA CA . A CA 204 1_555 ? B ? ? ? ? ? ? ? ? ? ? 3.045 ? 
metalc ? metalc4 A OE2 GLU 100 A GLU 100 1_555 E CA CA . A CA 204 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.938 ? 
metalc ? metalc5 A OD2 ASP 102 A ASP 102 1_555 E CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
metalc ? metalc6 A OD2 ASP 104 A ASP 104 1_555 E CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc7 A OD2 ASP 141 A ASP 141 1_555 F CA CA . A CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
metalc ? metalc8 C OXT ACT . A ACT 202 1_555 G CA CA . A CA 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.019 ? 
metalc ? metalc9 D CA CA . A CA 203 1_555 H O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc10 E CA CA . A CA 204 1_555 H O HOH . A HOH 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc11 F CA CA . A CA 205 1_555 H O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? 
#
_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                     5CYB 
_atom_sites.fract_transf_matrix[1][1]    0.009304 
_atom_sites.fract_transf_matrix[1][2]    0.005371 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010743 
_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]    0.015657 
_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 GOL A 1 201 1 GOL GOL . 
C 3 ACT A 1 202 1 ACT ACT . 
D 4 CA A 1 203 1 CA CA . 
E 4 CA A 1 204 2 CA CA . 
F 4 CA A 1 205 3 CA CA . 
G 4 CA A 1 206 4 CA CA . 
H 5 HOH A 1 301 54 HOH HOH . 
H 5 HOH A 2 302 48 HOH HOH . 
H 5 HOH A 3 303 64 HOH HOH . 
H 5 HOH A 4 304 78 HOH HOH . 
H 5 HOH A 5 305 7 HOH HOH . 
H 5 HOH A 6 306 24 HOH HOH . 
H 5 HOH A 7 307 30 HOH HOH . 
H 5 HOH A 8 308 31 HOH HOH . 
H 5 HOH A 9 309 19 HOH HOH . 
H 5 HOH A 10 310 8 HOH HOH . 
H 5 HOH A 11 311 22 HOH HOH . 
H 5 HOH A 12 312 66 HOH HOH . 
H 5 HOH A 13 313 1 HOH HOH . 
H 5 HOH A 14 314 4 HOH HOH . 
H 5 HOH A 15 315 12 HOH HOH . 
H 5 HOH A 16 316 39 HOH HOH . 
H 5 HOH A 17 317 29 HOH HOH . 
H 5 HOH A 18 318 13 HOH HOH . 
H 5 HOH A 19 319 25 HOH HOH . 
H 5 HOH A 20 320 5 HOH HOH . 
H 5 HOH A 21 321 2 HOH HOH . 
H 5 HOH A 22 322 9 HOH HOH . 
H 5 HOH A 23 323 18 HOH HOH . 
H 5 HOH A 24 324 43 HOH HOH . 
H 5 HOH A 25 325 41 HOH HOH . 
H 5 HOH A 26 326 20 HOH HOH . 
H 5 HOH A 27 327 67 HOH HOH . 
H 5 HOH A 28 328 16 HOH HOH . 
H 5 HOH A 29 329 15 HOH HOH . 
H 5 HOH A 30 330 50 HOH HOH . 
H 5 HOH A 31 331 52 HOH HOH . 
H 5 HOH A 32 332 23 HOH HOH . 
H 5 HOH A 33 333 6 HOH HOH . 
H 5 HOH A 34 334 17 HOH HOH . 
H 5 HOH A 35 335 72 HOH HOH . 
H 5 HOH A 36 336 47 HOH HOH . 
H 5 HOH A 37 337 60 HOH HOH . 
H 5 HOH A 38 338 40 HOH HOH . 
H 5 HOH A 39 339 11 HOH HOH . 
H 5 HOH A 40 340 35 HOH HOH . 
H 5 HOH A 41 341 61 HOH HOH . 
H 5 HOH A 42 342 27 HOH HOH . 
H 5 HOH A 43 343 26 HOH HOH . 
H 5 HOH A 44 344 79 HOH HOH . 
H 5 HOH A 45 345 37 HOH HOH . 
H 5 HOH A 46 346 44 HOH HOH . 
H 5 HOH A 47 347 21 HOH HOH . 
H 5 HOH A 48 348 59 HOH HOH . 
H 5 HOH A 49 349 45 HOH HOH . 
H 5 HOH A 50 350 34 HOH HOH . 
H 5 HOH A 51 351 38 HOH HOH . 
H 5 HOH A 52 352 51 HOH HOH . 
H 5 HOH A 53 353 71 HOH HOH . 
H 5 HOH A 54 354 53 HOH HOH . 
H 5 HOH A 55 355 75 HOH HOH . 
H 5 HOH A 56 356 14 HOH HOH . 
H 5 HOH A 57 357 68 HOH HOH . 
H 5 HOH A 58 358 49 HOH HOH . 
H 5 HOH A 59 359 77 HOH HOH . 
H 5 HOH A 60 360 10 HOH HOH . 
H 5 HOH A 61 361 28 HOH HOH . 
H 5 HOH A 62 362 73 HOH HOH . 
H 5 HOH A 63 363 33 HOH HOH . 
H 5 HOH A 64 364 42 HOH HOH . 
H 5 HOH A 65 365 36 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         F 
_atom_site.label_entity_id       4 
_atom_site.Cartn_x               10.64 
_atom_site.Cartn_y               27.835 
_atom_site.Cartn_z               33.345 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        115.97 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CA 
_atom_site.auth_comp_id          CA 
_atom_site.auth_seq_id           205 
_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           84 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           1404 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#