data_8JBM # _model_server_result.job_id '_vFVUQy928W0QFMqpwax7w' _model_server_result.datetime_utc '2024-11-24 10:38:01' _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 8jbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":1101}' # _entry.id 8JBM # _exptl.entry_id 8JBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.333 _cell.angle_gamma 90 _cell.entry_id 8JBM _cell.length_a 196.984 _cell.length_b 74.426 _cell.length_c 162.976 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,B,C,G,H,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,OA 1 1 D,E,F,I,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,PA,QA 2 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 ? 7 J N N ? 7 K N N ? 7 L N N ? 7 Z N N ? 7 AA N N ? 7 BA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide 6 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 4 5 4 MAN MAN C1 O1 . O6 HO6 . sing 5 ? 4 6 3 MAN BMA C1 O1 . O3 HO3 . sing 6 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 8 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 9 ? 5 5 3 MAN BMA C1 O1 . O6 HO6 . sing 10 ? 6 2 1 NAG 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 4 n G NAG 1 F 1 NAG B 421 NAG 4 n G NAG 2 F 2 NAG B 422 NAG 4 n G BMA 3 F 3 BMA B 423 BMA 4 n G MAN 4 F 4 MAN B 425 MAN 4 n G MAN 5 F 5 MAN B 426 MAN 4 n G MAN 6 F 6 MAN B 424 MAN 5 n H NAG 1 H 1 NAG B 431 NAG 5 n H NAG 2 H 2 NAG B 432 NAG 5 n H BMA 3 H 3 BMA B 433 BMA 5 n H MAN 4 H 4 MAN B 434 MAN 5 n H MAN 5 H 5 MAN B 435 MAN 6 n I NAG 1 I 1 NAG D 421 NAG 6 n I NAG 2 I 2 NAG D 422 NAG # 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 B SG CYS 126 B CYS 126 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 B SG CYS 159 B CYS 159 1_555 B SG CYS 175 B CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 B SG CYS 213 B CYS 213 1_555 B SG CYS 276 B CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 E SG CYS 126 D CYS 126 1_555 E SG CYS 149 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 E SG CYS 159 D CYS 159 1_555 E SG CYS 175 D CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 E SG CYS 213 D CYS 213 1_555 E SG CYS 276 D CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 B ND2 ASN 158 B ASN 158 1_555 G C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 B ND2 ASN 265 B ASN 265 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 E ND2 ASN 158 D ASN 158 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale4 E ND2 ASN 265 D ASN 265 1_555 LA C1 NAG . D NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale5 G O4 NAG . F NAG 1 1_555 G C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 G O4 NAG . F NAG 2 1_555 G C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 G O6 BMA . F BMA 3 1_555 G C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale8 G O3 BMA . F BMA 3 1_555 G C1 MAN . F MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 G O6 MAN . F MAN 4 1_555 G C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale11 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.487 ? covale ? covale12 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale13 H O6 BMA . H BMA 3 1_555 H C1 MAN . H MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale14 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? metalc ? metalc1 A OD1 ASP 715 A ASP 710 1_555 J MN MN . A MN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc2 A OD2 ASP 745 A ASP 740 1_555 L MN MN . A MN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc3 A OG SER 780 A SER 775 1_555 K MN MN . A MN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc4 A OE2 GLU 784 A GLU 779 1_555 K MN MN . A MN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc5 A OD1 ASP 809 A ASP 804 1_555 K MN MN . A MN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc6 J MN MN . A MN 1101 1_555 OA O HOH . A HOH 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc7 K MN MN . A MN 1102 1_555 OA O HOH . A HOH 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc8 L MN MN . A MN 1103 1_555 OA O HOH . A HOH 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc9 D OD1 ASP 715 C ASP 710 1_555 Z MN MN . C MN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc10 D OD1 ASP 745 C ASP 740 1_555 BA MN MN . C MN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc11 D OG SER 780 C SER 775 1_555 AA MN MN . C MN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc12 D OE2 GLU 784 C GLU 779 1_555 AA MN MN . C MN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc13 D OD1 ASP 809 C ASP 804 1_555 AA MN MN . C MN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc14 Z MN MN . C MN 1101 1_555 PA O HOH . C HOH 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc15 Z MN MN . C MN 1101 1_555 PA O HOH . C HOH 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc16 AA MN MN . C MN 1102 1_555 PA O HOH . C HOH 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc17 BA MN MN . C MN 1103 1_555 PA O HOH . C HOH 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc18 BA MN MN . C MN 1103 1_555 PA O HOH . C HOH 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? # _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 8JBM _atom_sites.fract_transf_matrix[1][1] 0.005077 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002513 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013436 _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] 0.006846 _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 J 7 MN A 1 1101 2003 MN MN . K 7 MN A 1 1102 2005 MN MN . L 7 MN A 1 1103 2008 MN MN . M 8 CLR A 1 1104 2009 CLR CLR . N 9 PC1 A 1 1105 2011 PC1 PC1 . O 10 PCW A 1 1106 2012 PCW PCW . P 9 PC1 A 1 1107 2013 PC1 PC1 . Q 10 PCW A 1 1108 2014 PCW PCW . R 8 CLR A 1 1109 2015 CLR CLR . S 9 PC1 A 1 1110 2016 PC1 PC1 . T 10 PCW A 1 1111 2017 PCW PCW . U 10 PCW A 1 1112 2018 PCW PCW . V 10 PCW A 1 1113 2021 PCW PCW . W 10 PCW A 1 1114 2022 PCW PCW . X 10 PCW B 1 401 2020 PCW PCW . Y 8 CLR G 1 101 2010 CLR CLR . Z 7 MN C 1 1101 2003 MN MN . AA 7 MN C 1 1102 2005 MN MN . BA 7 MN C 1 1103 2008 MN MN . CA 8 CLR C 1 1104 2009 CLR CLR . DA 10 PCW C 1 1105 2011 PCW PCW . EA 10 PCW C 1 1106 2012 PCW PCW . FA 10 PCW C 1 1107 2016 PCW PCW . GA 10 PCW C 1 1108 2017 PCW PCW . HA 10 PCW C 1 1109 2018 PCW PCW . IA 10 PCW C 1 1110 2019 PCW PCW . JA 10 PCW C 1 1111 2023 PCW PCW . KA 8 CLR D 1 401 2015 CLR CLR . LA 11 NAG D 1 402 431 NAG NAG . MA 8 CLR E 1 101 2010 CLR CLR . NA 12 DMU E 1 102 2051 DMU DMU . OA 13 HOH A 1 1201 2113 HOH HOH . OA 13 HOH A 2 1202 2132 HOH HOH . OA 13 HOH A 3 1203 2101 HOH HOH . OA 13 HOH A 4 1204 2102 HOH HOH . OA 13 HOH A 5 1205 2126 HOH HOH . OA 13 HOH A 6 1206 2131 HOH HOH . OA 13 HOH A 7 1207 2106 HOH HOH . OA 13 HOH A 8 1208 2107 HOH HOH . OA 13 HOH A 9 1209 2104 HOH HOH . OA 13 HOH A 10 1210 2141 HOH HOH . OA 13 HOH A 11 1211 2116 HOH HOH . OA 13 HOH A 12 1212 2143 HOH HOH . OA 13 HOH A 13 1213 2139 HOH HOH . OA 13 HOH A 14 1214 2128 HOH HOH . OA 13 HOH A 15 1215 2134 HOH HOH . OA 13 HOH A 16 1216 2142 HOH HOH . OA 13 HOH A 17 1217 2133 HOH HOH . OA 13 HOH A 18 1218 2125 HOH HOH . OA 13 HOH A 19 1219 2135 HOH HOH . PA 13 HOH C 1 1201 2113 HOH HOH . PA 13 HOH C 2 1202 2106 HOH HOH . PA 13 HOH C 3 1203 2134 HOH HOH . PA 13 HOH C 4 1204 2131 HOH HOH . PA 13 HOH C 5 1205 2104 HOH HOH . PA 13 HOH C 6 1206 2101 HOH HOH . PA 13 HOH C 7 1207 2132 HOH HOH . PA 13 HOH C 8 1208 2138 HOH HOH . PA 13 HOH C 9 1209 2103 HOH HOH . PA 13 HOH C 10 1210 2102 HOH HOH . PA 13 HOH C 11 1211 2142 HOH HOH . PA 13 HOH C 12 1212 2136 HOH HOH . QA 13 HOH D 1 501 502 HOH HOH . QA 13 HOH D 2 502 503 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 Z _atom_site.label_entity_id 7 _atom_site.Cartn_x 34.214 _atom_site.Cartn_y 4.076 _atom_site.Cartn_z 11.827 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 80.25 _atom_site.pdbx_formal_charge 2 _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 1101 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #