data_5UBQ # _model_server_result.job_id SoOhRpCHYK7AxQ564KBAnQ _model_server_result.datetime_utc '2025-02-05 07:46:27' _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 5ubq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":502}' # _entry.id 5UBQ # _exptl.entry_id 5UBQ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 24.305 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 138-meric 138 'complete point assembly' 1 ? hexameric 6 'point asymmetric unit' 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 1 (1-23) A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 2 1 # 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 'point symmetry operation' ? ? 0.89536 0.445309 0.005537 -0.445318 0.895373 0.000316 -0.004817 -0.002749 0.999985 -128.22863 149.33164 11.96234 3 'point symmetry operation' ? ? 0.504323 0.863426 0.012415 -0.863466 0.504396 -0.003442 -0.009234 -0.008984 0.999917 -162.13827 391.75436 25.06058 4 'point symmetry operation' ? ? 0.039969 0.999087 0.015078 -0.999161 0.040098 -0.008329 -0.008926 -0.014732 0.999852 -88.04165 585.69333 36.46901 5 'point symmetry operation' ? ? -0.442742 0.896528 0.014701 -0.896644 -0.442626 -0.010605 -0.003 -0.017877 0.999836 74.19596 721.80373 45.07082 6 'point symmetry operation' ? ? -0.759639 0.65021 0.013246 -0.650345 -0.7595 -0.01456 0.000593 -0.019674 0.999806 239.90329 773.96693 54.53169 7 'point symmetry operation' ? ? -0.946647 0.322095 0.010681 -0.322242 -0.946493 -0.017654 0.004424 -0.020154 0.999787 404.26336 763.32751 63.37952 8 'point symmetry operation' ? ? -0.974071 -0.226203 0.004331 0.226081 -0.973915 -0.019426 0.008612 -0.017943 0.999802 595.73439 626.56489 71.25851 9 'point symmetry operation' ? ? -0.80472 -0.593654 0.000669 0.593547 -0.804596 -0.018078 0.01127 -0.01415 0.999836 685.10414 476.43352 78.67464 10 'point symmetry operation' ? ? -0.213532 -0.976908 -0.007406 0.976834 -0.213394 -0.016076 0.014124 -0.010667 0.999843 642.26121 181.46866 -37.47493 11 'point symmetry operation' ? ? 0.293975 -0.955777 -0.008301 0.95573 0.294052 -0.010602 0.012574 -0.004817 0.999909 502.05395 15.34221 -29.61384 12 'point symmetry operation' ? ? 0.603594 -0.797261 -0.007091 0.797234 0.603633 -0.006707 0.009628 -0.001604 0.999952 370.74388 -62.91315 -20.66762 13 'point symmetry operation' ? ? 0.80476 -0.593579 -0.005107 0.593565 0.804776 -0.004019 0.006495 0.000203 0.999979 247.39942 -98.84464 -11.32986 14 'point symmetry operation' ? ? -0.936221 -0.351413 -0.000252 0.351338 -0.936008 -0.021233 0.007226 -0.019968 0.999775 765.79668 606.34338 -17.40836 15 'point symmetry operation' ? ? -0.741668 -0.670758 -0.003394 0.670685 -0.741489 -0.019372 0.010477 -0.016644 0.999807 835.60787 459.50576 -9.96858 16 'point symmetry operation' ? ? -0.431379 -0.902148 -0.006396 0.902101 -0.431246 -0.015543 0.011264 -0.012475 0.999859 843.997 291.6244 -2.26127 17 'point symmetry operation' ? ? -0.05461 -0.998485 -0.006691 0.998446 -0.054531 -0.011476 0.011094 -0.007307 0.999912 786.49946 132.56874 5.24457 18 'point symmetry operation' ? ? 0.363722 -0.931486 -0.006385 0.931461 0.363764 -0.007512 0.00932 -0.003215 0.999951 657.3832 2.08337 13.57489 19 'point symmetry operation' ? ? 0.703824 -0.710363 -0.003908 0.710354 0.703835 -0.003683 0.005367 -0.000184 0.999986 494.12145 -64.15925 22.76502 20 'point symmetry operation' ? ? 0.902291 -0.431122 -0.002198 0.431122 0.902293 -0.000554 0.002222 -0.000448 0.999997 343.93716 -73.63623 32.71915 21 'point symmetry operation' ? ? 0.99949 0.031862 0.002003 -0.031865 0.999491 0.001356 -0.001959 -0.001419 0.999997 158.79385 11.78763 43.74659 22 'point symmetry operation' ? ? 0.912816 0.408336 0.005316 -0.408351 0.912823 0.002061 -0.004012 -0.004052 0.999984 44.30584 133.03231 54.29704 23 'point symmetry operation' ? ? 0.662649 0.748864 0.009918 -0.748908 0.662673 0.00106 -0.005779 -0.00813 0.99995 -14.41015 305.56142 65.35382 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 K N N ? 4 N 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 covale ? covale1 A N GLY 45 C GLY 45 1_555 F CG ASP 74 B ASP 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.203 ? covale ? covale2 A N GLY 45 C GLY 45 1_555 F OD2 ASP 74 B ASP 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale3 A CA GLY 45 C GLY 45 1_555 F CB ASP 74 B ASP 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? covale ? covale4 A CA GLY 45 C GLY 45 1_555 F OD1 ASP 74 B ASP 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale5 A CA GLY 45 C GLY 45 1_555 F OD2 ASP 74 B ASP 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? covale ? covale6 A C GLY 45 C GLY 45 1_555 F OD2 ASP 74 B ASP 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale7 A C GLN 256 C GLN 256 1_555 F CZ2 TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 ? covale ? covale8 A O GLN 256 C GLN 256 1_555 F CZ2 TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale9 A N THR 257 C THR 257 1_555 F CZ2 TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.512 ? covale ? covale10 A N THR 257 C THR 257 1_555 F CE2 TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.281 ? covale ? covale11 A CA THR 257 C THR 257 1_555 F CD1 TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? covale ? covale12 A CA THR 257 C THR 257 1_555 F CD2 TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale13 A C THR 257 C THR 257 1_555 F CD2 TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.518 ? covale ? covale14 A C THR 257 C THR 257 1_555 F CE2 TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.226 ? covale ? covale15 A CB THR 257 C THR 257 1_555 F CD1 TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale16 A OG1 THR 257 C THR 257 1_555 F CG TRP 397 B TRP 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale17 A CG PRO 261 C PRO 261 1_555 F CE2 PHE 394 B PHE 394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.501 ? covale ? covale18 A NZ LYS 336 C LYS 336 1_555 F O LYS 174 B LYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale19 A O TRP 346 C TRP 346 1_555 F CG MET 388 B MET 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? covale ? covale20 A CB TRP 346 C TRP 346 1_555 F CG ARG 391 B ARG 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale21 A CD1 TRP 346 C TRP 346 1_555 F CZ ARG 391 B ARG 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale22 A CD1 TRP 346 C TRP 346 1_555 F NH1 ARG 391 B ARG 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.594 ? covale ? covale23 A CZ3 TRP 346 C TRP 346 1_555 F CB ALA 393 B ALA 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.289 ? covale ? covale24 B CB ASP 74 D ASP 74 1_555 C CA GLY 45 E GLY 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.369 ? covale ? covale25 B CG ASP 74 D ASP 74 1_555 C N GLY 45 E GLY 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.214 ? covale ? covale26 B OD1 ASP 74 D ASP 74 1_555 C CA GLY 45 E GLY 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale27 B OD2 ASP 74 D ASP 74 1_555 C N GLY 45 E GLY 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale28 B OD2 ASP 74 D ASP 74 1_555 C CA GLY 45 E GLY 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale29 B OD2 ASP 74 D ASP 74 1_555 C C GLY 45 E GLY 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.488 ? covale ? covale30 B O LYS 174 D LYS 174 1_555 C NZ LYS 336 E LYS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale31 B CG MET 388 D MET 388 1_555 C O TRP 346 E TRP 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.279 ? covale ? covale32 B CG ARG 391 D ARG 391 1_555 C CB TRP 346 E TRP 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.575 ? covale ? covale33 B CZ ARG 391 D ARG 391 1_555 C CD1 TRP 346 E TRP 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale34 B CB ALA 393 D ALA 393 1_555 C CZ3 TRP 346 E TRP 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.279 ? covale ? covale35 B CE2 PHE 394 D PHE 394 1_555 C CG PRO 261 E PRO 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale36 B CZ2 TRP 397 D TRP 397 1_555 C C GLN 256 E GLN 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.293 ? covale ? covale37 B CZ2 TRP 397 D TRP 397 1_555 C O GLN 256 E GLN 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale38 B CG TRP 397 D TRP 397 1_555 C OG1 THR 257 E THR 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? covale ? covale39 B CD1 TRP 397 D TRP 397 1_555 C CA THR 257 E THR 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.617 ? covale ? covale40 B CD1 TRP 397 D TRP 397 1_555 C CB THR 257 E THR 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale41 B CD2 TRP 397 D TRP 397 1_555 C CA THR 257 E THR 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale42 B CD2 TRP 397 D TRP 397 1_555 C C THR 257 E THR 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale43 B CE2 TRP 397 D TRP 397 1_555 C N THR 257 E THR 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.308 ? covale ? covale44 B CE2 TRP 397 D TRP 397 1_555 C C THR 257 E THR 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.211 ? covale ? covale45 B CZ2 TRP 397 D TRP 397 1_555 C N THR 257 E THR 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.54 ? metalc ? metalc1 A OD1 ASP 69 C ASP 69 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc2 A OE1 GLU 71 C GLU 71 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc3 A OE2 GLU 71 C GLU 71 1_555 H MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc4 C OD1 ASP 69 E ASP 69 1_555 K MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc5 C OE1 GLU 71 E GLU 71 1_555 K MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc6 C OE2 GLU 71 E GLU 71 1_555 K MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc7 E OD1 ASP 69 A ASP 69 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc8 E OE1 GLU 71 A GLU 71 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc9 E OE2 GLU 71 A GLU 71 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5UBQ _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 GTP C 1 501 442 GTP GTP . H 4 MG C 1 502 443 MG MG2 . I 5 GDP D 1 501 430 GDP GDP . J 3 GTP E 1 501 442 GTP GTP . K 4 MG E 1 502 443 MG MG2 . L 5 GDP F 1 501 430 GDP GDP . M 3 GTP A 1 501 442 GTP GTP . N 4 MG A 1 502 443 MG MG2 . O 5 GDP B 1 501 430 GDP GDP . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id K _atom_site.label_entity_id 4 _atom_site.Cartn_x 333.233 _atom_site.Cartn_y 259.072 _atom_site.Cartn_z 364.729 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 10 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 502 _atom_site.auth_asym_id E _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #