data_5YDI # _model_server_result.job_id iMuypKjSGO1w5dPjAVpzmQ _model_server_result.datetime_utc '2025-09-03 21:54:25' _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 5ydi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":805}' # _entry.id 5YDI # _exptl.entry_id 5YDI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM 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 90 _cell.entry_id 5YDI _cell.length_a 127.44 _cell.length_b 235.91 _cell.length_c 167.27 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,H,I,J,K,R 1 1,2 B,C,D,E,F,L,M,N,O,P,Q,S,T 2 1 # 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 K N N ? 6 M N N ? 6 N N N ? 6 Q N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 5 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 6 ? 3 5 4 MAN MAN C1 O1 . O6 HO6 . sing 7 ? 3 6 3 MAN BMA 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 D NAG 1 D 1 NAG B 801 NAG 2 n D NAG 2 D 2 NAG B 802 NAG 2 n D BMA 3 D 3 BMA B 803 BMA 3 n E NAG 1 E 1 NAG B 804 NAG 3 n E NAG 2 E 2 NAG B 805 NAG 3 n E BMA 3 E 3 BMA B 806 BMA 3 n E MAN 4 E 4 MAN B 808 MAN 3 n E MAN 5 E 5 MAN B 809 MAN 3 n E MAN 6 E 6 MAN B 807 MAN 2 n F NAG 1 F 1 NAG C 801 NAG 2 n F NAG 2 F 2 NAG C 802 NAG 2 n F BMA 3 F 3 BMA C 803 BMA # 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 67 A CYS 228 1_555 A SG CYS 94 A CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 253 A CYS 414 1_555 A SG CYS 266 A CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 401 A CYS 562 1_555 A SG CYS 522 A CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 B SG CYS 67 B CYS 228 1_555 B SG CYS 94 B CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 253 B CYS 414 1_555 B SG CYS 266 B CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 B SG CYS 401 B CYS 562 1_555 B SG CYS 522 B CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf7 C SG CYS 67 C CYS 228 1_555 C SG CYS 94 C CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 C SG CYS 253 C CYS 414 1_555 C SG CYS 266 C CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf9 C SG CYS 401 C CYS 562 1_555 C SG CYS 522 C CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A ND2 ASN 59 A ASN 220 1_555 G C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale2 A ND2 ASN 509 A ASN 670 1_555 H C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 B ND2 ASN 59 B ASN 220 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 B ND2 ASN 509 B ASN 670 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 C ND2 ASN 59 C ASN 220 1_555 O C1 NAG . C NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 C ND2 ASN 509 C ASN 670 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale10 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale11 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale12 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale13 E O6 MAN . E MAN 4 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale14 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A OG SER 199 A SER 360 1_555 K NA NA . A NA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc2 J O1 GOL . A GOL 804 1_555 K NA NA . A NA 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc3 B OG SER 199 B SER 360 1_555 M NA NA . B NA 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc4 L O3 GOL . B GOL 810 1_555 N NA NA . B NA 812 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc5 M NA NA . B NA 811 1_555 S O HOH . B HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc6 C OG SER 199 C SER 360 1_555 Q NA NA . C NA 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc7 Q NA NA . C NA 806 1_555 T O HOH . C HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5YDI _atom_sites.fract_transf_matrix[1][1] 0.007847 _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] 0.004239 _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] 0.005978 _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 G 4 NAG A 1 801 801 NAG NAG . H 4 NAG A 1 802 802 NAG NAG . I 5 GOL A 1 803 803 GOL GOL . J 5 GOL A 1 804 804 GOL GOL . K 6 NA A 1 805 805 NA NA . L 5 GOL B 1 810 810 GOL GOL . M 6 NA B 1 811 811 NA NA . N 6 NA B 1 812 812 NA NA . O 4 NAG C 1 804 804 NAG NAG . P 5 GOL C 1 805 805 GOL GOL . Q 6 NA C 1 806 806 NA NA . R 7 HOH A 1 901 901 HOH HOH . R 7 HOH A 2 902 902 HOH HOH . R 7 HOH A 3 903 903 HOH HOH . S 7 HOH B 1 901 901 HOH HOH . T 7 HOH C 1 901 901 HOH HOH . T 7 HOH C 2 902 902 HOH HOH . T 7 HOH C 3 903 903 HOH HOH . T 7 HOH C 4 904 904 HOH HOH . T 7 HOH C 5 905 905 HOH HOH . T 7 HOH C 6 906 906 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id K _atom_site.label_entity_id 6 _atom_site.Cartn_x 13.878 _atom_site.Cartn_y -20.464 _atom_site.Cartn_z -19.556 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 22.68 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 805 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #