data_5M0D # _model_server_result.job_id AcIzxhLqR5fmYtwGVaJd6A _model_server_result.datetime_utc '2024-11-15 10:44:05' _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 5m0d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":915}' # _entry.id 5M0D # _exptl.entry_id 5M0D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 126.904 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'IODIDE ION' _entity.pdbx_number_of_molecules 9 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.1 _cell.angle_gamma 90 _cell.entry_id 5M0D _cell.length_a 62.927 _cell.length_b 88.012 _cell.length_c 77.356 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M0D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J N N ? 3 K N 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 2 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 2 7 4 MAN MAN C1 O1 . O6 HO6 . sing 7 ? 2 8 3 MAN BMA C1 O1 . O3 HO3 . 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 NAG 1 B 1 NAG A 860 NAG 2 n B NAG 2 B 2 NAG A 861 NAG 2 n B BMA 3 B 3 BMA A 862 BMA 2 n B MAN 4 B 4 MAN A 864 MAN 2 n B MAN 5 B 5 MAN A 865 MAN 2 n B MAN 6 B 6 MAN A 866 MAN 2 n B MAN 7 B 7 MAN A 867 MAN 2 n B MAN 8 B 8 MAN A 863 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 23 A CYS 58 1_555 A SG CYS 40 A CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 27 A CYS 62 1_555 A SG CYS 58 A CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 38 A CYS 73 1_555 A SG CYS 51 A CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 44 A CYS 79 1_555 A SG CYS 50 A CYS 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 A SG CYS 67 A CYS 102 1_555 A SG CYS 84 A CYS 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf6 A SG CYS 72 A CYS 107 1_555 A SG CYS 102 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf7 A SG CYS 82 A CYS 117 1_555 A SG CYS 95 A CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf8 A SG CYS 88 A CYS 123 1_555 A SG CYS 94 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 A SG CYS 113 A CYS 148 1_555 A SG CYS 159 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 A SG CYS 121 A CYS 156 1_555 A SG CYS 315 A CYS 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? disulf ? disulf11 A SG CYS 378 A CYS 413 1_555 A SG CYS 770 A CYS 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 A SG CYS 531 A CYS 566 1_555 A SG CYS 631 A CYS 666 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 A SG CYS 533 A CYS 568 1_555 A SG CYS 616 A CYS 651 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf14 A SG CYS 739 A CYS 774 1_555 A SG CYS 749 A CYS 784 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 489 A ASN 524 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale3 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale4 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale6 B O3 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 B O6 MAN . B MAN 4 1_555 B C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 B O2 MAN . B MAN 5 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? metalc ? metalc1 A OD1 ASP 136 A ASP 171 1_555 M ZN ZN . A ZN 919 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc2 A OG1 THR 174 A THR 209 1_555 M ZN ZN . A ZN 919 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.795 ? metalc ? metalc3 A OD2 ASP 276 A ASP 311 1_555 L ZN ZN . A ZN 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc4 A NE2 HIS 280 A HIS 315 1_555 L ZN ZN . A ZN 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc5 A OD2 ASP 323 A ASP 358 1_555 M ZN ZN . A ZN 919 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc6 A NE2 HIS 324 A HIS 359 1_555 M ZN ZN . A ZN 919 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc7 A NE2 HIS 439 A HIS 474 1_555 L ZN ZN . A ZN 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc8 A O TYR 634 A TYR 669 1_555 P NA NA . A NA 922 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.937 ? metalc ? metalc9 A O ASP 637 A ASP 672 1_555 P NA NA . A NA 922 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc10 A O MET 640 A MET 675 1_555 P NA NA . A NA 922 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc11 A OD1 ASP 704 A ASP 739 1_555 N CA CA . A CA 920 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc12 A OD1 ASN 706 A ASN 741 1_555 N CA CA . A CA 920 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc13 A OD1 ASP 708 A ASP 743 1_555 N CA CA . A CA 920 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc14 A O LEU 710 A LEU 745 1_555 N CA CA . A CA 920 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc15 A OD1 ASP 712 A ASP 747 1_555 N CA CA . A CA 920 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc16 P NA NA . A NA 922 1_555 X O HOH . A HOH 1018 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? # _chem_comp.formula 'I -1' _chem_comp.formula_weight 126.904 _chem_comp.id IOD _chem_comp.mon_nstd_flag . _chem_comp.name 'IODIDE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5M0D _atom_sites.fract_transf_matrix[1][1] 0.015891 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003697 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011362 _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] 0.013273 _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 IOD A 1 909 913 IOD IOD . D 3 IOD A 1 910 914 IOD IOD . E 3 IOD A 1 911 915 IOD IOD . F 3 IOD A 1 912 916 IOD IOD . G 3 IOD A 1 913 917 IOD IOD . H 3 IOD A 1 914 918 IOD IOD . I 3 IOD A 1 915 919 IOD IOD . J 3 IOD A 1 916 920 IOD IOD . K 3 IOD A 1 917 921 IOD IOD . L 4 ZN A 1 918 910 ZN ZN . M 4 ZN A 1 919 911 ZN ZN . N 5 CA A 1 920 912 CA CA . O 6 7C8 A 1 921 1000 7C8 UNL . P 7 NA A 1 922 908 NA NA . Q 8 SCN A 1 923 1 SCN SCN . R 8 SCN A 1 924 2 SCN SCN . S 8 SCN A 1 925 3 SCN SCN . T 8 SCN A 1 926 4 SCN SCN . U 9 GOL A 1 927 1 GOL GOL . V 9 GOL A 1 928 2 GOL GOL . W 9 GOL A 1 929 3 GOL GOL . X 10 HOH A 1 1001 16 HOH HOH . X 10 HOH A 2 1002 5 HOH HOH . X 10 HOH A 3 1003 13 HOH HOH . X 10 HOH A 4 1004 2 HOH HOH . X 10 HOH A 5 1005 4 HOH HOH . X 10 HOH A 6 1006 14 HOH HOH . X 10 HOH A 7 1007 23 HOH HOH . X 10 HOH A 8 1008 18 HOH HOH . X 10 HOH A 9 1009 9 HOH HOH . X 10 HOH A 10 1010 10 HOH HOH . X 10 HOH A 11 1011 3 HOH HOH . X 10 HOH A 12 1012 21 HOH HOH . X 10 HOH A 13 1013 11 HOH HOH . X 10 HOH A 14 1014 1 HOH HOH . X 10 HOH A 15 1015 22 HOH HOH . X 10 HOH A 16 1016 8 HOH HOH . X 10 HOH A 17 1017 20 HOH HOH . X 10 HOH A 18 1018 6 HOH HOH . X 10 HOH A 19 1019 7 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol I _atom_site.label_atom_id I _atom_site.label_comp_id IOD _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id I _atom_site.label_entity_id 3 _atom_site.Cartn_x 7.758 _atom_site.Cartn_y -10.98 _atom_site.Cartn_z -23.359 _atom_site.occupancy 0.47 _atom_site.B_iso_or_equiv 84.29 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id I _atom_site.auth_comp_id IOD _atom_site.auth_seq_id 915 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 49 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 1222 _model_server_stats.encode_time_ms 47 _model_server_stats.element_count 1 #