data_5YN3 # _model_server_result.job_id JlleNoLCd7RrkPF3DSJplg _model_server_result.datetime_utc '2024-11-09 23:20:28' _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 5yn3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":502}' # _entry.id 5YN3 # _exptl.entry_id 5YN3 _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 8 _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 5YN3 _cell.length_a 79.472 _cell.length_b 126.417 _cell.length_c 171.181 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YN3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_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 _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 ? 2 E N N ? 2 F N N ? 2 I N N ? 2 J N N ? 2 L N N ? 2 M N N ? 2 O N N ? 2 P 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 OE2 GLU 245 A GLU 233 1_555 E MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc2 A OE2 GLU 281 A GLU 269 1_555 E MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc3 A OE1 GLU 281 A GLU 269 1_555 F MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc4 A OD2 ASP 309 A ASP 297 1_555 E MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc5 A OD2 ASP 320 A ASP 308 1_555 F MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.853 ? metalc ? metalc6 A OD1 ASP 322 A ASP 310 1_555 F MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? metalc ? metalc7 A OD2 ASP 352 A ASP 340 1_555 E MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc8 E MN MN . A MN 501 1_555 G O1 GOL . A GOL 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc9 E MN MN . A MN 501 1_555 G O2 GOL . A GOL 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc10 B OE2 GLU 245 B GLU 233 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc11 B OE1 GLU 281 B GLU 269 1_555 I MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc12 B OE2 GLU 281 B GLU 269 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc13 B OD2 ASP 309 B ASP 297 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc14 B OD1 ASP 320 B ASP 308 1_555 I MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc15 B OD2 ASP 320 B ASP 308 1_555 I MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc16 B OD1 ASP 322 B ASP 310 1_555 I MN MN . B MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc17 B OD2 ASP 352 B ASP 340 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc18 J MN MN . B MN 502 1_555 K O1 GOL . B GOL 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc19 C OE1 GLU 245 C GLU 233 1_555 L MN MN . C MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc20 C OE2 GLU 281 C GLU 269 1_555 L MN MN . C MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc21 C OE1 GLU 281 C GLU 269 1_555 M MN MN . C MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc22 C OD2 ASP 309 C ASP 297 1_555 L MN MN . C MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc23 C OD2 ASP 320 C ASP 308 1_555 M MN MN . C MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc24 C OD1 ASP 322 C ASP 310 1_555 M MN MN . C MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc25 L MN MN . C MN 501 1_555 N O3 GOL . C GOL 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc26 M MN MN . C MN 502 1_555 T O HOH . C HOH 632 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc27 D OE2 GLU 245 D GLU 233 1_555 O MN MN . D MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc28 D OE2 GLU 281 D GLU 269 1_555 O MN MN . D MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc29 D OE1 GLU 281 D GLU 269 1_555 P MN MN . D MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc30 D OD2 ASP 309 D ASP 297 1_555 O MN MN . D MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc31 D OD2 ASP 320 D ASP 308 1_555 P MN MN . D MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? metalc ? metalc32 D OD2 ASP 352 D ASP 340 1_555 O MN MN . D MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc33 O MN MN . D MN 501 1_555 Q O3 GOL . D GOL 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? # _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 5YN3 _atom_sites.fract_transf_matrix[1][1] 0.012583 _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] 0.00791 _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] 0.005842 _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 E 2 MN A 1 501 6 MN MN . F 2 MN A 1 502 7 MN MN . G 3 GOL A 1 503 1 GOL GOL . H 3 GOL A 1 504 2 GOL GOL . I 2 MN B 1 501 1 MN MN . J 2 MN B 1 502 8 MN MN . K 3 GOL B 1 503 3 GOL GOL . L 2 MN C 1 501 4 MN MN . M 2 MN C 1 502 5 MN MN . N 3 GOL C 1 503 4 GOL GOL . O 2 MN D 1 501 2 MN MN . P 2 MN D 1 502 3 MN MN . Q 3 GOL D 1 503 5 GOL GOL . R 4 HOH A 1 601 173 HOH HOH . R 4 HOH A 2 602 128 HOH HOH . R 4 HOH A 3 603 132 HOH HOH . R 4 HOH A 4 604 198 HOH HOH . R 4 HOH A 5 605 84 HOH HOH . R 4 HOH A 6 606 32 HOH HOH . R 4 HOH A 7 607 197 HOH HOH . R 4 HOH A 8 608 51 HOH HOH . R 4 HOH A 9 609 196 HOH HOH . R 4 HOH A 10 610 6 HOH HOH . R 4 HOH A 11 611 199 HOH HOH . R 4 HOH A 12 612 11 HOH HOH . R 4 HOH A 13 613 164 HOH HOH . R 4 HOH A 14 614 203 HOH HOH . R 4 HOH A 15 615 97 HOH HOH . R 4 HOH A 16 616 39 HOH HOH . R 4 HOH A 17 617 35 HOH HOH . R 4 HOH A 18 618 130 HOH HOH . R 4 HOH A 19 619 111 HOH HOH . R 4 HOH A 20 620 45 HOH HOH . R 4 HOH A 21 621 47 HOH HOH . R 4 HOH A 22 622 42 HOH HOH . R 4 HOH A 23 623 29 HOH HOH . R 4 HOH A 24 624 18 HOH HOH . R 4 HOH A 25 625 142 HOH HOH . R 4 HOH A 26 626 185 HOH HOH . R 4 HOH A 27 627 99 HOH HOH . R 4 HOH A 28 628 115 HOH HOH . R 4 HOH A 29 629 150 HOH HOH . R 4 HOH A 30 630 78 HOH HOH . R 4 HOH A 31 631 17 HOH HOH . R 4 HOH A 32 632 119 HOH HOH . R 4 HOH A 33 633 92 HOH HOH . R 4 HOH A 34 634 120 HOH HOH . R 4 HOH A 35 635 88 HOH HOH . R 4 HOH A 36 636 134 HOH HOH . R 4 HOH A 37 637 135 HOH HOH . R 4 HOH A 38 638 175 HOH HOH . R 4 HOH A 39 639 37 HOH HOH . R 4 HOH A 40 640 30 HOH HOH . R 4 HOH A 41 641 169 HOH HOH . R 4 HOH A 42 642 183 HOH HOH . R 4 HOH A 43 643 77 HOH HOH . R 4 HOH A 44 644 28 HOH HOH . R 4 HOH A 45 645 44 HOH HOH . R 4 HOH A 46 646 100 HOH HOH . R 4 HOH A 47 647 194 HOH HOH . R 4 HOH A 48 648 36 HOH HOH . R 4 HOH A 49 649 180 HOH HOH . R 4 HOH A 50 650 137 HOH HOH . R 4 HOH A 51 651 174 HOH HOH . R 4 HOH A 52 652 170 HOH HOH . R 4 HOH A 53 653 186 HOH HOH . S 4 HOH B 1 601 154 HOH HOH . S 4 HOH B 2 602 103 HOH HOH . S 4 HOH B 3 603 129 HOH HOH . S 4 HOH B 4 604 131 HOH HOH . S 4 HOH B 5 605 85 HOH HOH . S 4 HOH B 6 606 140 HOH HOH . S 4 HOH B 7 607 87 HOH HOH . S 4 HOH B 8 608 138 HOH HOH . S 4 HOH B 9 609 79 HOH HOH . S 4 HOH B 10 610 5 HOH HOH . S 4 HOH B 11 611 200 HOH HOH . S 4 HOH B 12 612 53 HOH HOH . S 4 HOH B 13 613 80 HOH HOH . S 4 HOH B 14 614 201 HOH HOH . S 4 HOH B 15 615 25 HOH HOH . S 4 HOH B 16 616 93 HOH HOH . S 4 HOH B 17 617 3 HOH HOH . S 4 HOH B 18 618 33 HOH HOH . S 4 HOH B 19 619 144 HOH HOH . S 4 HOH B 20 620 66 HOH HOH . S 4 HOH B 21 621 151 HOH HOH . S 4 HOH B 22 622 95 HOH HOH . S 4 HOH B 23 623 163 HOH HOH . S 4 HOH B 24 624 114 HOH HOH . S 4 HOH B 25 625 70 HOH HOH . S 4 HOH B 26 626 20 HOH HOH . S 4 HOH B 27 627 27 HOH HOH . S 4 HOH B 28 628 63 HOH HOH . S 4 HOH B 29 629 68 HOH HOH . S 4 HOH B 30 630 171 HOH HOH . S 4 HOH B 31 631 12 HOH HOH . S 4 HOH B 32 632 145 HOH HOH . S 4 HOH B 33 633 40 HOH HOH . S 4 HOH B 34 634 2 HOH HOH . S 4 HOH B 35 635 146 HOH HOH . S 4 HOH B 36 636 165 HOH HOH . S 4 HOH B 37 637 38 HOH HOH . S 4 HOH B 38 638 202 HOH HOH . S 4 HOH B 39 639 181 HOH HOH . S 4 HOH B 40 640 193 HOH HOH . S 4 HOH B 41 641 192 HOH HOH . S 4 HOH B 42 642 107 HOH HOH . T 4 HOH C 1 601 161 HOH HOH . T 4 HOH C 2 602 41 HOH HOH . T 4 HOH C 3 603 162 HOH HOH . T 4 HOH C 4 604 118 HOH HOH . T 4 HOH C 5 605 117 HOH HOH . T 4 HOH C 6 606 124 HOH HOH . T 4 HOH C 7 607 147 HOH HOH . T 4 HOH C 8 608 123 HOH HOH . T 4 HOH C 9 609 22 HOH HOH . T 4 HOH C 10 610 105 HOH HOH . T 4 HOH C 11 611 110 HOH HOH . T 4 HOH C 12 612 126 HOH HOH . T 4 HOH C 13 613 195 HOH HOH . T 4 HOH C 14 614 167 HOH HOH . T 4 HOH C 15 615 15 HOH HOH . T 4 HOH C 16 616 125 HOH HOH . T 4 HOH C 17 617 9 HOH HOH . T 4 HOH C 18 618 141 HOH HOH . T 4 HOH C 19 619 72 HOH HOH . T 4 HOH C 20 620 24 HOH HOH . T 4 HOH C 21 621 113 HOH HOH . T 4 HOH C 22 622 61 HOH HOH . T 4 HOH C 23 623 64 HOH HOH . T 4 HOH C 24 624 139 HOH HOH . T 4 HOH C 25 625 155 HOH HOH . T 4 HOH C 26 626 58 HOH HOH . T 4 HOH C 27 627 76 HOH HOH . T 4 HOH C 28 628 52 HOH HOH . T 4 HOH C 29 629 86 HOH HOH . T 4 HOH C 30 630 46 HOH HOH . T 4 HOH C 31 631 14 HOH HOH . T 4 HOH C 32 632 179 HOH HOH . T 4 HOH C 33 633 182 HOH HOH . T 4 HOH C 34 634 94 HOH HOH . T 4 HOH C 35 635 4 HOH HOH . T 4 HOH C 36 636 60 HOH HOH . T 4 HOH C 37 637 8 HOH HOH . T 4 HOH C 38 638 191 HOH HOH . T 4 HOH C 39 639 54 HOH HOH . T 4 HOH C 40 640 168 HOH HOH . T 4 HOH C 41 641 172 HOH HOH . U 4 HOH D 1 601 43 HOH HOH . U 4 HOH D 2 602 90 HOH HOH . U 4 HOH D 3 603 159 HOH HOH . U 4 HOH D 4 604 1 HOH HOH . U 4 HOH D 5 605 112 HOH HOH . U 4 HOH D 6 606 101 HOH HOH . U 4 HOH D 7 607 7 HOH HOH . U 4 HOH D 8 608 67 HOH HOH . U 4 HOH D 9 609 96 HOH HOH . U 4 HOH D 10 610 69 HOH HOH . U 4 HOH D 11 611 127 HOH HOH . U 4 HOH D 12 612 34 HOH HOH . U 4 HOH D 13 613 26 HOH HOH . U 4 HOH D 14 614 109 HOH HOH . U 4 HOH D 15 615 143 HOH HOH . U 4 HOH D 16 616 184 HOH HOH . U 4 HOH D 17 617 188 HOH HOH . U 4 HOH D 18 618 81 HOH HOH . U 4 HOH D 19 619 98 HOH HOH . U 4 HOH D 20 620 56 HOH HOH . U 4 HOH D 21 621 189 HOH HOH . U 4 HOH D 22 622 91 HOH HOH . U 4 HOH D 23 623 50 HOH HOH . U 4 HOH D 24 624 16 HOH HOH . U 4 HOH D 25 625 13 HOH HOH . U 4 HOH D 26 626 102 HOH HOH . U 4 HOH D 27 627 74 HOH HOH . U 4 HOH D 28 628 48 HOH HOH . U 4 HOH D 29 629 166 HOH HOH . U 4 HOH D 30 630 108 HOH HOH . U 4 HOH D 31 631 65 HOH HOH . U 4 HOH D 32 632 23 HOH HOH . U 4 HOH D 33 633 187 HOH HOH . U 4 HOH D 34 634 133 HOH HOH . U 4 HOH D 35 635 153 HOH HOH . U 4 HOH D 36 636 122 HOH HOH . U 4 HOH D 37 637 55 HOH HOH . U 4 HOH D 38 638 83 HOH HOH . U 4 HOH D 39 639 75 HOH HOH . U 4 HOH D 40 640 73 HOH HOH . U 4 HOH D 41 641 116 HOH HOH . U 4 HOH D 42 642 10 HOH HOH . U 4 HOH D 43 643 148 HOH HOH . U 4 HOH D 44 644 59 HOH HOH . U 4 HOH D 45 645 104 HOH HOH . U 4 HOH D 46 646 21 HOH HOH . U 4 HOH D 47 647 89 HOH HOH . U 4 HOH D 48 648 121 HOH HOH . U 4 HOH D 49 649 82 HOH HOH . U 4 HOH D 50 650 31 HOH HOH . U 4 HOH D 51 651 71 HOH HOH . U 4 HOH D 52 652 106 HOH HOH . U 4 HOH D 53 653 19 HOH HOH . U 4 HOH D 54 654 156 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 P _atom_site.label_entity_id 2 _atom_site.Cartn_x -13.379 _atom_site.Cartn_y -8.352 _atom_site.Cartn_z -5.239 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 37.47 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 502 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 85 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #