data_1G9F # _model_server_result.job_id nODGJlN5eCOffPQ-x6vacg _model_server_result.datetime_utc '2025-09-04 14:57:15' _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 1g9f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":254}' # _entry.id 1G9F # _exptl.entry_id 1G9F _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 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 1G9F _cell.length_a 122.64 _cell.length_b 122.64 _cell.length_c 90.56 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1G9F _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 3_645 -y+1,x-1/2,z+1/4 0 -1 0 1 0 0 0 0 1 122.64 -61.32 22.64 3 'crystal symmetry operation' 6_556 x,-y+1/2,-z+5/4 1 0 0 0 -1 0 0 0 -1 0 61.32 113.2 4 'crystal symmetry operation' 8_666 -y+1,-x+1,-z+1 0 -1 0 -1 0 0 0 0 -1 122.64 122.64 90.56 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 GAL C1 O1 . O2 HO2 . sing 3 ? 3 3 2 GAL NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 1 NAG GAL C1 O1 . O3 HO3 . sing 5 ? 3 5 4 GAL NAG C1 O1 . O4 HO4 . 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 256 NAG 2 n B NAG 2 B 2 NAG A 258 NAG 3 n C GAL 1 C 1 GAL S 5 GAL 3 n C NAG 2 C 2 NAG S 3 NAG 3 n C GAL 3 C 3 GAL S 4 GAL 3 n C NAG 4 C 4 NAG S 1 NAG 3 n C GAL 5 C 5 GAL S 2 GAL # 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 A ND2 ASN 75 A ASN 75 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale3 C O2 GAL . C GAL 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale4 C O3 GAL . C GAL 1 1_555 C C1 NAG . C NAG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 GAL . C GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale6 C O4 NAG . C NAG 4 1_555 C C1 GAL . C GAL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? metalc ? metalc1 A OE2 GLU 124 A GLU 124 1_555 D MN MN . A MN 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc2 A OD2 ASP 126 A ASP 126 1_555 D MN MN . A MN 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc3 A OD1 ASP 126 A ASP 126 1_555 E CA CA . A CA 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc4 A OD2 ASP 126 A ASP 126 1_555 E CA CA . A CA 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc5 A O PHE 128 A PHE 128 1_555 E CA CA . A CA 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc6 A OD1 ASN 130 A ASN 130 1_555 E CA CA . A CA 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc7 A OD1 ASP 133 A ASP 133 1_555 D MN MN . A MN 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc8 A OD2 ASP 133 A ASP 133 1_555 E CA CA . A CA 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc9 A NE2 HIS 138 A HIS 138 1_555 D MN MN . A MN 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc10 D MN MN . A MN 254 1_555 F O HOH . A HOH 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc11 D MN MN . A MN 254 1_555 F O HOH . A HOH 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc12 E CA CA . A CA 255 1_555 F O HOH . A HOH 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc13 E CA CA . A CA 255 1_555 F O HOH . A HOH 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? # _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 1G9F _atom_sites.fract_transf_matrix[1][1] 0.008154 _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] 0.008154 _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] 0.011042 _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 D 4 MN A 1 254 254 MN MN . E 5 CA A 1 255 255 CA CA . F 6 HOH A 1 264 1 HOH WAT . F 6 HOH A 2 265 2 HOH WAT . F 6 HOH A 3 266 3 HOH WAT . F 6 HOH A 4 267 4 HOH WAT . F 6 HOH A 5 268 5 HOH WAT . F 6 HOH A 6 269 6 HOH WAT . F 6 HOH A 7 270 7 HOH WAT . F 6 HOH A 8 271 8 HOH WAT . F 6 HOH A 9 272 9 HOH WAT . # _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 D _atom_site.label_entity_id 4 _atom_site.Cartn_x 100.005 _atom_site.Cartn_y 20.594 _atom_site.Cartn_z 27.786 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 29.3 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 254 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #