data_5K8D # _model_server_result.job_id dejAgjD88EIzCdlG63E-2w _model_server_result.datetime_utc '2025-04-13 13:16:32' _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 5k8d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":806}' # _entry.id 5K8D # _exptl.entry_id 5K8D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 6 _entity.src_method man _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 90 _cell.entry_id 5K8D _cell.length_a 136.295 _cell.length_b 136.295 _cell.length_c 365.098 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K8D _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,G,H,I,J _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 ? 6 F N N ? 6 G N N ? 6 H N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide 5 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 5 4 3 BMA BMA C1 O1 . O3 HO3 . sing 8 ? 5 5 4 MAN BMA C1 O1 . O2 HO2 . sing 9 ? 5 6 3 MAN BMA C1 O1 . O6 HO6 . sing 10 ? 5 7 6 MAN MAN 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 3 n C NAG 1 C 1 NAG A 2410 NAG 3 n C NAG 2 C 2 NAG A 2411 NAG 3 n C BMA 3 C 3 BMA A 2412 BMA 3 n C MAN 4 C 4 MAN A 2413 MAN 4 n D NAG 1 D 1 NAG B 2420 NAG 4 n D NAG 2 D 2 NAG B 2421 NAG 5 n E NAG 1 E 1 NAG B 2430 NAG 5 n E NAG 2 E 2 NAG B 2431 NAG 5 n E BMA 3 E 3 BMA B 2432 BMA 5 n E BMA 4 E 4 BMA B 2435 BMA 5 n E MAN 5 E 5 MAN B 2436 MAN 5 n E MAN 6 E 6 MAN B 2433 MAN 5 n E MAN 7 E 7 MAN B 2434 MAN # 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 disulf ? disulf1 A SG CYS 248 A CYS 248 1_555 A SG CYS 329 A CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 528 A CYS 528 1_555 A SG CYS 554 A CYS 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? disulf ? disulf3 A SG CYS 630 A CYS 630 1_555 A SG CYS 711 A CYS 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? disulf ? disulf4 B SG CYS 139 B CYS 1832 1_555 B SG CYS 165 B CYS 1858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 B SG CYS 481 B CYS 2174 1_555 B SG CYS 633 B CYS 2326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? covale ? covale1 A ND2 ASN 239 A ASN 239 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A CD1 ILE 617 A ILE 617 1_555 A O ALA 704 A ALA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.519 ? covale ? covale3 B ND2 ASN 117 B ASN 1810 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 B ND2 ASN 425 B ASN 2118 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale7 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale10 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 E O3 BMA . E BMA 3 1_555 E C1 BMA . E BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale12 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale13 E O2 BMA . E BMA 4 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale14 E O6 MAN . E MAN 6 1_555 E C1 MAN . E MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? metalc ? metalc1 A O LYS 107 A LYS 107 1_555 H CA CA . A CA 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc2 A O ALA 108 A ALA 108 1_555 H CA CA . A CA 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? metalc ? metalc3 A OD2 ASP 116 A ASP 116 1_555 F CA CA . A CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc4 A O GLU 122 A GLU 122 1_555 F CA CA . A CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.129 ? metalc ? metalc5 A OD2 ASP 126 A ASP 126 1_555 F CA CA . A CA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc6 A OD1 ASP 126 A ASP 126 1_555 H CA CA . A CA 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc7 A ND1 HIS 267 A HIS 267 1_555 I CU CU . A CU 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc8 A SG CYS 310 A CYS 310 1_555 I CU CU . A CU 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc9 A ND1 HIS 315 A HIS 315 1_555 I CU CU . A CU 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.853 ? metalc ? metalc10 A O SER 535 A SER 535 1_555 G CA CA . A CA 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc11 A OD1 ASN 538 A ASN 538 1_555 G CA CA . A CA 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.138 ? metalc ? metalc12 A OD1 ASP 542 A ASP 542 1_555 G CA CA . A CA 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.015 ? metalc ? metalc13 B ND1 HIS 261 B HIS 1954 1_555 J CU CU . B CU 2610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc14 B SG CYS 307 B CYS 2000 1_555 J CU CU . B CU 2610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? # _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 5K8D _atom_sites.fract_transf_matrix[1][1] 0.007337 _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] 0.007337 _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] 0.002739 _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 F 6 CA A 1 805 2400 CA CA . G 6 CA A 1 806 2402 CA CA . H 6 CA A 1 807 2401 CA CA . I 7 CU A 1 808 2403 CU CU . J 7 CU B 1 2610 2404 CU CU . # _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 G _atom_site.label_entity_id 6 _atom_site.Cartn_x -2.342 _atom_site.Cartn_y 27.235 _atom_site.Cartn_z 13.883 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 236.24 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 806 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #