data_8OG4 # _model_server_result.job_id 1UA5dmK-2MEVQYgoh6sZfg _model_server_result.datetime_utc '2024-10-19 21:28:00' _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 8og4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1001}' # _entry.id 8OG4 # _exptl.entry_id 8OG4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _entity.pdbx_number_of_molecules 2 _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 8OG4 _cell.length_a 121.617 _cell.length_b 121.617 _cell.length_c 259.537 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OG4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall 'P 32 2"' _symmetry.space_group_name_H-M 'P 32 2 1' # _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,K,L _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 ? 4 G N N ? 4 I 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 3 5 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 C NAG 1 C 1 NAG A 2001 NAG 2 n C NAG 2 C 2 NAG A 2002 NAG 3 n D NAG 1 D 1 NAG A 3001 NAG 3 n D NAG 2 D 2 NAG A 3002 NAG 3 n D BMA 3 D 3 BMA A 3003 BMA 3 n D MAN 4 D 4 MAN A 3005 MAN 3 n D MAN 5 D 5 MAN A 3004 MAN 2 n E NAG 1 E 1 NAG B 2001 NAG 2 n E NAG 2 E 2 NAG B 2002 NAG 3 n F NAG 1 F 1 NAG B 3001 NAG 3 n F NAG 2 F 2 NAG B 3002 NAG 3 n F BMA 3 F 3 BMA B 3003 BMA 3 n F MAN 4 F 4 MAN B 3005 MAN 3 n F MAN 5 F 5 MAN B 3004 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 149 A CYS 177 1_555 A SG CYS 154 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? disulf ? disulf2 A SG CYS 160 A CYS 188 1_555 A SG CYS 208 A CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? disulf ? disulf3 A SG CYS 372 A CYS 400 1_555 A SG CYS 387 A CYS 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 A SG CYS 765 A CYS 793 1_555 B SG CYS 887 B CYS 915 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf5 A SG CYS 803 A CYS 831 1_555 A SG CYS 851 A CYS 879 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf6 A SG CYS 887 A CYS 915 1_555 B SG CYS 765 B CYS 793 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf7 B SG CYS 149 B CYS 177 1_555 B SG CYS 154 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? disulf ? disulf8 B SG CYS 160 B CYS 188 1_555 B SG CYS 208 B CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? disulf ? disulf9 B SG CYS 372 B CYS 400 1_555 B SG CYS 387 B CYS 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf10 B SG CYS 803 B CYS 831 1_555 B SG CYS 851 B CYS 879 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? covale ? covale1 A ND2 ASN 564 A ASN 592 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A C ASN 577 A ASN 605 1_555 A N CSO 578 A CSO 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C CSO 578 A CSO 606 1_555 A N ALA 579 A ALA 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale4 A ND2 ASN 762 A ASN 790 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale5 B ND2 ASN 564 B ASN 592 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale6 B C ASN 577 B ASN 605 1_555 B N CSO 578 B CSO 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 B C CSO 578 B CSO 606 1_555 B N ALA 579 B ALA 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 B ND2 ASN 762 B ASN 790 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale12 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale13 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale14 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale15 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale16 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale17 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale18 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? metalc ? metalc1 A OD1 ASP 718 A ASP 746 1_555 G MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc2 A OD2 ASP 718 A ASP 746 1_555 G MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc3 G MN MN . A MN 1001 1_555 H O2A UDP . A UDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc4 G MN MN . A MN 1001 1_555 H O2B UDP . A UDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc5 B OD1 ASP 718 B ASP 746 1_555 I MN MN . B MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc6 B OD2 ASP 718 B ASP 746 1_555 I MN MN . B MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc7 I MN MN . B MN 1001 1_555 J O1A UDP . B UDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc8 I MN MN . B MN 1001 1_555 J O2B UDP . B UDP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 8OG4 _atom_sites.fract_transf_matrix[1][1] 0.008223 _atom_sites.fract_transf_matrix[1][2] 0.004747 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009495 _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] 0.003853 _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 MN A 1 1001 1001 MN MN . H 5 UDP A 1 1002 1002 UDP UDP . I 4 MN B 1 1001 1001 MN MN . J 5 UDP B 1 1002 1002 UDP UDP . K 6 HOH A 1 1101 3038 HOH HOH . K 6 HOH A 2 1102 3063 HOH HOH . K 6 HOH A 3 1103 3057 HOH HOH . K 6 HOH A 4 1104 3006 HOH HOH . K 6 HOH A 5 1105 3065 HOH HOH . K 6 HOH A 6 1106 3004 HOH HOH . K 6 HOH A 7 1107 3030 HOH HOH . K 6 HOH A 8 1108 3064 HOH HOH . K 6 HOH A 9 1109 3009 HOH HOH . K 6 HOH A 10 1110 3053 HOH HOH . K 6 HOH A 11 1111 3050 HOH HOH . K 6 HOH A 12 1112 3072 HOH HOH . K 6 HOH A 13 1113 3014 HOH HOH . K 6 HOH A 14 1114 3022 HOH HOH . K 6 HOH A 15 1115 3002 HOH HOH . K 6 HOH A 16 1116 3029 HOH HOH . K 6 HOH A 17 1117 3010 HOH HOH . K 6 HOH A 18 1118 3025 HOH HOH . K 6 HOH A 19 1119 3055 HOH HOH . K 6 HOH A 20 1120 3011 HOH HOH . K 6 HOH A 21 1121 3031 HOH HOH . K 6 HOH A 22 1122 3045 HOH HOH . K 6 HOH A 23 1123 3033 HOH HOH . K 6 HOH A 24 1124 3046 HOH HOH . K 6 HOH A 25 1125 3066 HOH HOH . K 6 HOH A 26 1126 3016 HOH HOH . K 6 HOH A 27 1127 3062 HOH HOH . K 6 HOH A 28 1128 3051 HOH HOH . K 6 HOH A 29 1129 3028 HOH HOH . K 6 HOH A 30 1130 3020 HOH HOH . K 6 HOH A 31 1131 3042 HOH HOH . K 6 HOH A 32 1132 3036 HOH HOH . K 6 HOH A 33 1133 3047 HOH HOH . L 6 HOH B 1 1101 3056 HOH HOH . L 6 HOH B 2 1102 3048 HOH HOH . L 6 HOH B 3 1103 3043 HOH HOH . L 6 HOH B 4 1104 3023 HOH HOH . L 6 HOH B 5 1105 3026 HOH HOH . L 6 HOH B 6 1106 3067 HOH HOH . L 6 HOH B 7 1107 3032 HOH HOH . L 6 HOH B 8 1108 3007 HOH HOH . L 6 HOH B 9 1109 3003 HOH HOH . L 6 HOH B 10 1110 3039 HOH HOH . L 6 HOH B 11 1111 3054 HOH HOH . L 6 HOH B 12 1112 3059 HOH HOH . L 6 HOH B 13 1113 3001 HOH HOH . L 6 HOH B 14 1114 3060 HOH HOH . L 6 HOH B 15 1115 3058 HOH HOH . L 6 HOH B 16 1116 3008 HOH HOH . L 6 HOH B 17 1117 3037 HOH HOH . L 6 HOH B 18 1118 3019 HOH HOH . L 6 HOH B 19 1119 3015 HOH HOH . L 6 HOH B 20 1120 3034 HOH HOH . L 6 HOH B 21 1121 3044 HOH HOH . L 6 HOH B 22 1122 3035 HOH HOH . L 6 HOH B 23 1123 3049 HOH HOH . L 6 HOH B 24 1124 3069 HOH HOH . L 6 HOH B 25 1125 3041 HOH HOH . L 6 HOH B 26 1126 3073 HOH HOH . L 6 HOH B 27 1127 3061 HOH HOH . L 6 HOH B 28 1128 3013 HOH HOH . L 6 HOH B 29 1129 3012 HOH HOH . L 6 HOH B 30 1130 3005 HOH HOH . L 6 HOH B 31 1131 3027 HOH HOH . L 6 HOH B 32 1132 3052 HOH HOH . L 6 HOH B 33 1133 3074 HOH HOH . L 6 HOH B 34 1134 3040 HOH HOH . L 6 HOH B 35 1135 3068 HOH HOH . L 6 HOH B 36 1136 3018 HOH HOH . L 6 HOH B 37 1137 3071 HOH HOH . L 6 HOH B 38 1138 3021 HOH HOH . L 6 HOH B 39 1139 3017 HOH HOH . L 6 HOH B 40 1140 3024 HOH HOH . L 6 HOH B 41 1141 3070 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MN _atom_site.label_atom_id MN _atom_site.label_comp_id MN _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 4 _atom_site.Cartn_x 23.603 _atom_site.Cartn_y -8.559 _atom_site.Cartn_z 38.384 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 94.56 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 1001 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 145 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 1 #