data_5DPN # _model_server_result.job_id BAleIOacR0iluwJWMhU37w _model_server_result.datetime_utc '2024-11-05 10:59:17' _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 5dpn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5DPN # loop_ _exptl.entry_id _exptl.method 5DPN 'X-RAY DIFFRACTION' 5DPN 'NEUTRON 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 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 5DPN _cell.length_a 72.977 _cell.length_b 49.856 _cell.length_c 45.091 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DPN _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 BGC BGC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 2 4 3 BGC BGC C1 O1 . O4 HO4 . sing 4 ? 2 5 4 XYS BGC C1 O1 . O6 HO6 . sing 5 ? 2 6 3 XYS BGC C1 O1 . O6 HO6 . sing 6 ? 2 7 2 XYS BGC C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B BGC 1 B 1 BGC B 1169 BGC 2 n B BGC 2 B 2 BGC B 1170 BGC 2 n B BGC 3 B 3 BGC B 1171 BGC 2 n B BGC 4 B 4 BGC B 1172 BGC 2 n B XYS 5 B 5 XYS B 1175 XYS 2 n B XYS 6 B 6 XYS B 1174 XYS 2 n B XYS 7 B 7 XYS B 1173 XYS # 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 O4 BGC . B BGC 1 1_555 B C1 BGC . B BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? covale ? covale2 B O4 BGC . B BGC 2 1_555 B C1 BGC . B BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale3 B O6 BGC . B BGC 2 1_555 B C1 XYS . B XYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale4 B O4 BGC . B BGC 3 1_555 B C1 BGC . B BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale5 B O6 BGC . B BGC 3 1_555 B C1 XYS . B XYS 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 ? covale ? covale6 B O6 BGC . B BGC 4 1_555 B C1 XYS . B XYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? metalc ? metalc1 A O GLY 9 A GLY 9 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc2 A OE2 GLU 11 A GLU 11 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc3 A O GLU 52 A GLU 52 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc4 A OE2 GLU 52 A GLU 52 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc5 A O LYS 55 A LYS 55 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc6 A OD1 ASP 160 A ASP 160 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc7 A OD2 ASP 160 A ASP 160 1_555 C CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? # _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 5DPN _atom_sites.fract_transf_matrix[1][1] 0.013703 _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] 0.020058 _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] 0.022177 _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 A 1 201 1167 CA CA . D 4 DOD A 1 301 35 DOD DOD . D 4 DOD A 2 302 45 DOD DOD . D 4 HOH A 3 303 53 HOH HOH . D 4 DOD A 4 304 50 DOD DOD . D 4 DOD A 5 305 25 DOD DOD . D 4 HOH A 6 306 60 HOH HOH . D 4 DOD A 7 307 42 DOD DOD . D 4 DOD A 8 308 12 DOD DOD . D 4 DOD A 9 309 48 DOD DOD . D 4 DOD A 10 310 32 DOD DOD . D 4 DOD A 11 311 34 DOD DOD . D 4 DOD A 12 312 30 DOD DOD . D 4 DOD A 13 313 52 DOD DOD . D 4 DOD A 14 314 22 DOD DOD . D 4 DOD A 15 315 1 DOD DOD . D 4 DOD A 16 316 6 DOD DOD . D 4 DOD A 17 317 51 DOD DOD . D 4 DOD A 18 318 14 DOD DOD . D 4 DOD A 19 319 5 DOD DOD . D 4 DOD A 20 320 10 DOD DOD . D 4 DOD A 21 321 28 DOD DOD . D 4 DOD A 22 322 39 DOD DOD . D 4 HOH A 23 323 59 HOH HOH . D 4 DOD A 24 324 13 DOD DOD . D 4 HOH A 25 325 55 HOH HOH . D 4 DOD A 26 326 2 DOD DOD . D 4 DOD A 27 327 36 DOD DOD . D 4 DOD A 28 328 27 DOD DOD . D 4 DOD A 29 329 44 DOD DOD . D 4 DOD A 30 330 38 DOD DOD . D 4 DOD A 31 331 17 DOD DOD . D 4 DOD A 32 332 24 DOD DOD . D 4 DOD A 33 333 37 DOD DOD . D 4 DOD A 34 334 41 DOD DOD . D 4 DOD A 35 335 49 DOD DOD . D 4 DOD A 36 336 18 DOD DOD . D 4 DOD A 37 337 21 DOD DOD . D 4 DOD A 38 338 40 DOD DOD . D 4 DOD A 39 339 26 DOD DOD . D 4 DOD A 40 340 23 DOD DOD . D 4 DOD A 41 341 31 DOD DOD . D 4 DOD A 42 342 4 DOD DOD . D 4 DOD A 43 343 11 DOD DOD . D 4 DOD A 44 344 7 DOD DOD . D 4 DOD A 45 345 15 DOD DOD . D 4 DOD A 46 346 16 DOD DOD . D 4 DOD A 47 347 29 DOD DOD . D 4 DOD A 48 348 3 DOD DOD . D 4 DOD A 49 349 33 DOD DOD . D 4 DOD A 50 350 43 DOD DOD . D 4 HOH A 51 351 57 HOH HOH . D 4 DOD A 52 352 20 DOD DOD . D 4 DOD A 53 353 9 DOD DOD . D 4 DOD A 54 354 19 DOD DOD . D 4 HOH A 55 355 58 HOH HOH . D 4 DOD A 56 356 47 DOD DOD . D 4 DOD A 57 357 8 DOD DOD . D 4 HOH A 58 358 56 HOH HOH . D 4 DOD A 59 359 46 DOD DOD . D 4 HOH A 60 360 54 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 C _atom_site.label_entity_id 3 _atom_site.Cartn_x -16.848 _atom_site.Cartn_y -18.353 _atom_site.Cartn_z 23.328 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 14.71 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 201 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #