data_1RIT # _model_server_result.job_id 69zrC9xhnupAAgGK-plIaQ _model_server_result.datetime_utc '2024-12-21 12:04:49' _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 1rit # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":255}' # _entry.id 1RIT # _exptl.entry_id 1RIT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) 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 120 _cell.entry_id 1RIT _cell.length_a 94.9 _cell.length_b 94.9 _cell.length_c 144.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RIT _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA _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 ? 5 J N N ? 5 Q N N ? 5 U N N ? 5 Y N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GAL _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 E BGC 1 E 1 BGC C 240 LAT 2 n E GAL 2 E 2 GAL C 240 LAT 2 n F BGC 1 F 1 BGC D 240 LAT 2 n F GAL 2 F 2 GAL D 240 LAT # 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 E O4 BGC . E BGC 1 1_555 E C1 GAL . E GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 sing covale ? covale2 F O4 BGC . F BGC 1 1_555 F C1 GAL . F GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 sing metalc ? metalc1 A OD1 ASP 123 A ASP 123 1_555 I CA CA . A CA 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.029 ? metalc ? metalc2 A OD2 ASP 123 A ASP 123 1_555 I CA CA . A CA 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? metalc ? metalc3 A O TYR 125 A TYR 125 1_555 I CA CA . A CA 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc4 A OD1 ASN 127 A ASN 127 1_555 I CA CA . A CA 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc5 A OD2 ASP 132 A ASP 132 1_555 I CA CA . A CA 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc6 A NE2 HIS 137 A HIS 137 1_555 J MN MN . A MN 249 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc7 B OE2 GLU 121 B GLU 121 1_555 Q MN MN . B MN 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc8 B OD2 ASP 123 B ASP 123 1_555 P CA CA . B CA 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc9 B OD1 ASP 123 B ASP 123 1_555 P CA CA . B CA 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? metalc ? metalc10 B O TYR 125 B TYR 125 1_555 P CA CA . B CA 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? metalc ? metalc11 B OD1 ASN 127 B ASN 127 1_555 P CA CA . B CA 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc12 B NE2 HIS 137 B HIS 137 1_555 Q MN MN . B MN 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc13 C OE2 GLU 121 C GLU 121 1_555 U MN MN . C MN 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc14 C OD1 ASP 123 C ASP 123 1_555 T CA CA . C CA 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc15 C OD2 ASP 123 C ASP 123 1_555 T CA CA . C CA 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.09 ? metalc ? metalc16 C OD2 ASP 123 C ASP 123 1_555 U MN MN . C MN 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc17 C O TYR 125 C TYR 125 1_555 T CA CA . C CA 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc18 C OD1 ASN 127 C ASN 127 1_555 T CA CA . C CA 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc19 C OD2 ASP 132 C ASP 132 1_555 T CA CA . C CA 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.029 ? metalc ? metalc20 C OD1 ASP 132 C ASP 132 1_555 U MN MN . C MN 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc21 U MN MN . C MN 253 1_555 BA O HOH . C HOH 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc22 D OE2 GLU 121 D GLU 121 1_555 Y MN MN . D MN 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc23 D OD2 ASP 123 D ASP 123 1_555 X CA CA . D CA 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc24 D OD1 ASP 123 D ASP 123 1_555 X CA CA . D CA 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc25 D O TYR 125 D TYR 125 1_555 X CA CA . D CA 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc26 D OD1 ASN 127 D ASN 127 1_555 X CA CA . D CA 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc27 D OD2 ASP 132 D ASP 132 1_555 X CA CA . D CA 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc28 D OD1 ASP 132 D ASP 132 1_555 Y MN MN . D MN 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? # _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 1RIT _atom_sites.fract_transf_matrix[1][1] 0.010537 _atom_sites.fract_transf_matrix[1][2] 0.006084 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012168 _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] 0.00694 _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 3 SFP A 1 243 237 SFP POR . H 3 SFP A 1 244 238 SFP POR . I 4 CA A 1 248 233 CA CA . J 5 MN A 1 249 234 MN MN . K 3 SFP A 1 250 235 SFP POR . L 3 SFP A 1 251 236 SFP POR . M 3 SFP B 1 237 235 SFP POR . N 3 SFP B 1 238 236 SFP POR . O 3 SFP B 1 245 237 SFP POR . P 4 CA B 1 250 233 CA CA . Q 5 MN B 1 251 234 MN MN . R 3 SFP C 1 239 235 SFP POR . S 3 SFP C 1 240 236 SFP POR . T 4 CA C 1 252 233 CA CA . U 5 MN C 1 253 234 MN MN . V 3 SFP D 1 241 235 SFP POR . W 3 SFP D 1 242 236 SFP POR . X 4 CA D 1 254 233 CA CA . Y 5 MN D 1 255 234 MN MN . Z 6 HOH A 1 252 1 HOH TIP . Z 6 HOH A 2 253 3 HOH TIP . Z 6 HOH A 3 254 5 HOH TIP . Z 6 HOH A 4 255 6 HOH TIP . Z 6 HOH A 5 256 9 HOH TIP . Z 6 HOH A 6 257 10 HOH TIP . Z 6 HOH A 7 258 14 HOH TIP . Z 6 HOH A 8 259 15 HOH TIP . Z 6 HOH A 9 260 19 HOH TIP . Z 6 HOH A 10 261 20 HOH TIP . Z 6 HOH A 11 262 25 HOH TIP . Z 6 HOH A 12 263 28 HOH TIP . Z 6 HOH A 13 264 31 HOH TIP . Z 6 HOH A 14 265 32 HOH TIP . Z 6 HOH A 15 266 33 HOH TIP . Z 6 HOH A 16 267 38 HOH TIP . AA 6 HOH B 1 252 4 HOH TIP . AA 6 HOH B 2 253 8 HOH TIP . AA 6 HOH B 3 254 16 HOH TIP . AA 6 HOH B 4 255 18 HOH TIP . AA 6 HOH B 5 256 21 HOH TIP . AA 6 HOH B 6 257 30 HOH TIP . AA 6 HOH B 7 258 36 HOH TIP . BA 6 HOH C 1 254 2 HOH TIP . BA 6 HOH C 2 255 22 HOH TIP . BA 6 HOH C 3 256 23 HOH TIP . BA 6 HOH C 4 257 24 HOH TIP . BA 6 HOH C 5 258 26 HOH TIP . BA 6 HOH C 6 259 29 HOH TIP . BA 6 HOH C 7 260 34 HOH TIP . BA 6 HOH C 8 261 39 HOH TIP . BA 6 HOH C 9 262 40 HOH TIP . CA 6 HOH D 1 256 7 HOH TIP . CA 6 HOH D 2 257 11 HOH TIP . CA 6 HOH D 3 258 12 HOH TIP . CA 6 HOH D 4 259 13 HOH TIP . CA 6 HOH D 5 260 17 HOH TIP . CA 6 HOH D 6 261 27 HOH TIP . CA 6 HOH D 7 262 35 HOH TIP . CA 6 HOH D 8 263 37 HOH TIP . CA 6 HOH D 9 264 41 HOH TIP . CA 6 HOH D 10 265 42 HOH TIP . # _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 Y _atom_site.label_entity_id 5 _atom_site.Cartn_x -11.716 _atom_site.Cartn_y 18.01 _atom_site.Cartn_z 23.583 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 75.21 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 255 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #