data_1WVB # _model_server_result.job_id YYL78yeZP4QyaLyroMdTCg _model_server_result.datetime_utc '2024-11-18 20:41:05' _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 1wvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1315}' # _entry.id 1WVB # _exptl.entry_id 1WVB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 2 _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 1WVB _cell.length_a 90.272 _cell.length_b 90.272 _cell.length_c 69.305 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WVB _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1,2,3 B,F,G,H,J 2 1,4,5 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 90.272 0 0 5 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 45.136 78.177845 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 F N N ? 2 G N N # 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 metalc ? metalc1 A ND1 HIS 101 A HIS 101 1_555 C MN MN . A MN 1314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 A OD2 ASP 124 A ASP 124 1_555 C MN MN . A MN 1314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc3 A OD1 ASP 124 A ASP 124 1_555 D MN MN . A MN 1315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc4 A ND1 HIS 126 A HIS 126 1_555 D MN MN . A MN 1315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc5 A OD2 ASP 128 A ASP 128 1_555 C MN MN . A MN 1314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc6 A OD2 ASP 232 A ASP 232 1_555 C MN MN . A MN 1314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc7 A OD2 ASP 232 A ASP 232 1_555 D MN MN . A MN 1315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc8 A OD2 ASP 234 A ASP 234 1_555 D MN MN . A MN 1315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc9 A OD1 ASP 234 A ASP 234 1_555 D MN MN . A MN 1315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc10 C MN MN . A MN 1314 1_555 E B S2C . A S2C 1316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc11 C MN MN . A MN 1314 1_555 E O1 S2C . A S2C 1316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc12 C MN MN . A MN 1314 1_555 E O3 S2C . A S2C 1316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc13 D MN MN . A MN 1315 1_555 E O2 S2C . A S2C 1316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc14 D MN MN . A MN 1315 1_555 E O3 S2C . A S2C 1316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc15 B ND1 HIS 101 B HIS 101 1_555 F MN MN . B MN 2314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc16 B OD2 ASP 124 B ASP 124 1_555 F MN MN . B MN 2314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc17 B OD1 ASP 124 B ASP 124 1_555 G MN MN . B MN 2315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc18 B ND1 HIS 126 B HIS 126 1_555 G MN MN . B MN 2315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc19 B OD2 ASP 128 B ASP 128 1_555 F MN MN . B MN 2314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc20 B OD2 ASP 232 B ASP 232 1_555 F MN MN . B MN 2314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc21 B OD2 ASP 232 B ASP 232 1_555 G MN MN . B MN 2315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc22 B OD1 ASP 234 B ASP 234 1_555 G MN MN . B MN 2315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc23 B OD2 ASP 234 B ASP 234 1_555 G MN MN . B MN 2315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc24 H O1 S2C . B S2C 1317 1_555 F MN MN . B MN 2314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc25 H O3 S2C . B S2C 1317 1_555 F MN MN . B MN 2314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc26 H O2 S2C . B S2C 1317 1_555 G MN MN . B MN 2315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc27 H O3 S2C . B S2C 1317 1_555 G MN MN . B MN 2315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? # _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 1WVB _atom_sites.fract_transf_matrix[1][1] 0.011078 _atom_sites.fract_transf_matrix[1][2] 0.006396 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012791 _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] 0.014429 _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 2 MN A 1 1314 1314 MN MN . D 2 MN A 1 1315 1315 MN MN . E 3 S2C A 1 1316 1316 S2C S2C . F 2 MN B 1 2314 2314 MN MN . G 2 MN B 1 2315 2315 MN MN . H 3 S2C B 1 1317 1317 S2C S2C . I 4 HOH A 1 1317 5 HOH HOH . I 4 HOH A 2 1318 6 HOH HOH . I 4 HOH A 3 1319 7 HOH HOH . I 4 HOH A 4 1320 9 HOH HOH . I 4 HOH A 5 1321 10 HOH HOH . I 4 HOH A 6 1322 11 HOH HOH . I 4 HOH A 7 1323 13 HOH HOH . I 4 HOH A 8 1324 16 HOH HOH . I 4 HOH A 9 1325 18 HOH HOH . I 4 HOH A 10 1326 20 HOH HOH . I 4 HOH A 11 1327 23 HOH HOH . I 4 HOH A 12 1328 24 HOH HOH . I 4 HOH A 13 1329 25 HOH HOH . I 4 HOH A 14 1330 29 HOH HOH . I 4 HOH A 15 1331 30 HOH HOH . I 4 HOH A 16 1332 32 HOH HOH . I 4 HOH A 17 1333 34 HOH HOH . I 4 HOH A 18 1334 37 HOH HOH . I 4 HOH A 19 1335 39 HOH HOH . I 4 HOH A 20 1336 40 HOH HOH . I 4 HOH A 21 1337 41 HOH HOH . I 4 HOH A 22 1338 45 HOH HOH . I 4 HOH A 23 1339 46 HOH HOH . I 4 HOH A 24 1340 47 HOH HOH . I 4 HOH A 25 1341 48 HOH HOH . I 4 HOH A 26 1342 51 HOH HOH . I 4 HOH A 27 1343 52 HOH HOH . I 4 HOH A 28 1344 53 HOH HOH . I 4 HOH A 29 1345 54 HOH HOH . I 4 HOH A 30 1346 56 HOH HOH . I 4 HOH A 31 1347 57 HOH HOH . I 4 HOH A 32 1348 58 HOH HOH . I 4 HOH A 33 1349 60 HOH HOH . I 4 HOH A 34 1350 61 HOH HOH . I 4 HOH A 35 1351 62 HOH HOH . I 4 HOH A 36 1352 63 HOH HOH . I 4 HOH A 37 1353 68 HOH HOH . I 4 HOH A 38 1354 70 HOH HOH . I 4 HOH A 39 1355 74 HOH HOH . I 4 HOH A 40 1356 85 HOH HOH . I 4 HOH A 41 1357 86 HOH HOH . I 4 HOH A 42 1358 87 HOH HOH . I 4 HOH A 43 1359 88 HOH HOH . I 4 HOH A 44 1360 89 HOH HOH . I 4 HOH A 45 1361 90 HOH HOH . I 4 HOH A 46 1362 94 HOH HOH . I 4 HOH A 47 1363 98 HOH HOH . J 4 HOH B 1 2316 1 HOH HOH . J 4 HOH B 2 2317 2 HOH HOH . J 4 HOH B 3 2318 3 HOH HOH . J 4 HOH B 4 2319 4 HOH HOH . J 4 HOH B 5 2320 8 HOH HOH . J 4 HOH B 6 2321 12 HOH HOH . J 4 HOH B 7 2322 14 HOH HOH . J 4 HOH B 8 2323 15 HOH HOH . J 4 HOH B 9 2324 17 HOH HOH . J 4 HOH B 10 2325 19 HOH HOH . J 4 HOH B 11 2326 21 HOH HOH . J 4 HOH B 12 2327 22 HOH HOH . J 4 HOH B 13 2328 26 HOH HOH . J 4 HOH B 14 2329 27 HOH HOH . J 4 HOH B 15 2330 28 HOH HOH . J 4 HOH B 16 2331 31 HOH HOH . J 4 HOH B 17 2332 33 HOH HOH . J 4 HOH B 18 2333 35 HOH HOH . J 4 HOH B 19 2334 36 HOH HOH . J 4 HOH B 20 2335 38 HOH HOH . J 4 HOH B 21 2336 42 HOH HOH . J 4 HOH B 22 2337 44 HOH HOH . J 4 HOH B 23 2338 49 HOH HOH . J 4 HOH B 24 2339 50 HOH HOH . J 4 HOH B 25 2340 55 HOH HOH . J 4 HOH B 26 2341 59 HOH HOH . J 4 HOH B 27 2342 64 HOH HOH . J 4 HOH B 28 2343 65 HOH HOH . J 4 HOH B 29 2344 66 HOH HOH . J 4 HOH B 30 2345 67 HOH HOH . J 4 HOH B 31 2346 69 HOH HOH . J 4 HOH B 32 2347 71 HOH HOH . J 4 HOH B 33 2348 72 HOH HOH . J 4 HOH B 34 2349 73 HOH HOH . J 4 HOH B 35 2350 91 HOH HOH . J 4 HOH B 36 2351 92 HOH HOH . J 4 HOH B 37 2352 93 HOH HOH . J 4 HOH B 38 2353 95 HOH HOH . J 4 HOH B 39 2354 96 HOH HOH . J 4 HOH B 40 2355 97 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 D _atom_site.label_entity_id 2 _atom_site.Cartn_x 14.931 _atom_site.Cartn_y 13.691 _atom_site.Cartn_z -3.992 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 27.61 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 1315 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #