data_3BI3 # _model_server_result.job_id RV4lLtqU-LQEaX36bg9RFQ _model_server_result.datetime_utc '2024-11-13 19:08:05' _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 3bi3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 3BI3 # _exptl.entry_id 3BI3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.73 _cell.angle_gamma 90 _cell.entry_id 3BI3 _cell.length_a 41.407 _cell.length_b 75.629 _cell.length_c 50.972 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BI3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 117 A CYS 129 1_555 B S 2YR 10 B 2YR 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale2 B O3' DA 7 B DA 7 1_555 B P MA7 8 B MA7 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? covale ? covale3 B O3' MA7 8 B MA7 8 1_555 B P DA 9 B DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? covale ? covale4 B O3' DA 9 B DA 9 1_555 B P 2YR 10 B 2YR 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? covale ? covale5 B O3' 2YR 10 B 2YR 10 1_555 B P DC 11 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? metalc ? metalc1 A NE2 HIS 119 A HIS 131 1_555 D MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc2 A OD1 ASP 121 A ASP 133 1_555 D MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc3 A NE2 HIS 175 A HIS 187 1_555 D MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc4 D MN MN . A MN 301 1_555 E O2 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc5 D MN MN . A MN 301 1_555 E O5 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc6 D MN MN . A MN 301 1_555 F O HOH . A HOH 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? hydrog WATSON-CRICK hydrog1 B N1 DA 2 B DA 2 1_555 C N3 DT 13 C DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 2 B DA 2 1_555 C O4 DT 13 C DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog3 B N1 DG 3 B DG 3 1_555 C N3 DC 12 C DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 4 B DG 4 1_555 C N3 DC 11 C DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 4 B DG 4 1_555 C O2 DC 11 C DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 4 B DG 4 1_555 C N4 DC 11 C DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DT 5 B DT 5 1_555 C N1 DA 10 C DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O4 DT 5 B DT 5 1_555 C N6 DA 10 C DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 6 B DA 6 1_555 C N3 DT 9 C DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 6 B DA 6 1_555 C O4 DT 9 C DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DA 9 B DA 9 1_555 C N3 DT 6 C DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N6 DA 9 B DA 9 1_555 C O4 DT 6 C DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N3 DC 11 B DC 11 1_555 C N1 DG 4 C DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N4 DC 11 B DC 11 1_555 C O6 DG 4 C DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O2 DC 11 B DC 11 1_555 C N2 DG 4 C DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 12 B DG 12 1_555 C N3 DC 3 C DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 12 B DG 12 1_555 C O2 DC 3 C DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 12 B DG 12 1_555 C N4 DC 3 C DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DT 13 B DT 13 1_555 C N1 DA 2 C DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 DT 13 B DT 13 1_555 C N6 DA 2 C DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 3BI3 _atom_sites.fract_transf_matrix[1][1] 0.024151 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007721 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013222 _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] 0.020597 _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 D 4 MN A 1 301 214 MN MN . E 5 AKG A 1 302 216 AKG AKG . F 6 HOH A 1 401 2 HOH HOH . F 6 HOH A 2 402 3 HOH HOH . F 6 HOH A 3 403 4 HOH HOH . F 6 HOH A 4 404 5 HOH HOH . F 6 HOH A 5 405 8 HOH HOH . F 6 HOH A 6 406 9 HOH HOH . F 6 HOH A 7 407 10 HOH HOH . F 6 HOH A 8 408 11 HOH HOH . F 6 HOH A 9 409 12 HOH HOH . F 6 HOH A 10 410 13 HOH HOH . F 6 HOH A 11 411 14 HOH HOH . F 6 HOH A 12 412 15 HOH HOH . F 6 HOH A 13 413 16 HOH HOH . F 6 HOH A 14 414 17 HOH HOH . F 6 HOH A 15 415 18 HOH HOH . F 6 HOH A 16 416 19 HOH HOH . F 6 HOH A 17 417 21 HOH HOH . F 6 HOH A 18 418 22 HOH HOH . F 6 HOH A 19 419 23 HOH HOH . F 6 HOH A 20 420 25 HOH HOH . F 6 HOH A 21 421 26 HOH HOH . F 6 HOH A 22 422 27 HOH HOH . F 6 HOH A 23 423 28 HOH HOH . F 6 HOH A 24 424 30 HOH HOH . F 6 HOH A 25 425 32 HOH HOH . F 6 HOH A 26 426 33 HOH HOH . F 6 HOH A 27 427 34 HOH HOH . F 6 HOH A 28 428 35 HOH HOH . F 6 HOH A 29 429 36 HOH HOH . F 6 HOH A 30 430 37 HOH HOH . F 6 HOH A 31 431 38 HOH HOH . F 6 HOH A 32 432 39 HOH HOH . F 6 HOH A 33 433 40 HOH HOH . F 6 HOH A 34 434 41 HOH HOH . F 6 HOH A 35 435 42 HOH HOH . F 6 HOH A 36 436 43 HOH HOH . F 6 HOH A 37 437 45 HOH HOH . F 6 HOH A 38 438 46 HOH HOH . F 6 HOH A 39 439 49 HOH HOH . F 6 HOH A 40 440 50 HOH HOH . F 6 HOH A 41 441 52 HOH HOH . F 6 HOH A 42 442 53 HOH HOH . F 6 HOH A 43 443 54 HOH HOH . F 6 HOH A 44 444 56 HOH HOH . F 6 HOH A 45 445 59 HOH HOH . F 6 HOH A 46 446 60 HOH HOH . F 6 HOH A 47 447 61 HOH HOH . F 6 HOH A 48 448 62 HOH HOH . F 6 HOH A 49 449 64 HOH HOH . F 6 HOH A 50 450 66 HOH HOH . F 6 HOH A 51 451 67 HOH HOH . F 6 HOH A 52 452 68 HOH HOH . F 6 HOH A 53 453 69 HOH HOH . F 6 HOH A 54 454 70 HOH HOH . F 6 HOH A 55 455 71 HOH HOH . F 6 HOH A 56 456 73 HOH HOH . F 6 HOH A 57 457 74 HOH HOH . F 6 HOH A 58 458 77 HOH HOH . F 6 HOH A 59 459 78 HOH HOH . F 6 HOH A 60 460 79 HOH HOH . F 6 HOH A 61 461 80 HOH HOH . F 6 HOH A 62 462 81 HOH HOH . F 6 HOH A 63 463 83 HOH HOH . F 6 HOH A 64 464 84 HOH HOH . F 6 HOH A 65 465 85 HOH HOH . F 6 HOH A 66 466 86 HOH HOH . F 6 HOH A 67 467 87 HOH HOH . F 6 HOH A 68 468 88 HOH HOH . F 6 HOH A 69 469 89 HOH HOH . F 6 HOH A 70 470 90 HOH HOH . F 6 HOH A 71 471 91 HOH HOH . F 6 HOH A 72 472 92 HOH HOH . F 6 HOH A 73 473 93 HOH HOH . F 6 HOH A 74 474 94 HOH HOH . F 6 HOH A 75 475 97 HOH HOH . F 6 HOH A 76 476 98 HOH HOH . F 6 HOH A 77 477 99 HOH HOH . F 6 HOH A 78 478 102 HOH HOH . F 6 HOH A 79 479 103 HOH HOH . F 6 HOH A 80 480 104 HOH HOH . F 6 HOH A 81 481 105 HOH HOH . F 6 HOH A 82 482 107 HOH HOH . F 6 HOH A 83 483 108 HOH HOH . F 6 HOH A 84 484 109 HOH HOH . F 6 HOH A 85 485 110 HOH HOH . F 6 HOH A 86 486 113 HOH HOH . F 6 HOH A 87 487 114 HOH HOH . F 6 HOH A 88 488 117 HOH HOH . F 6 HOH A 89 489 118 HOH HOH . F 6 HOH A 90 490 120 HOH HOH . F 6 HOH A 91 491 121 HOH HOH . F 6 HOH A 92 492 122 HOH HOH . F 6 HOH A 93 493 124 HOH HOH . F 6 HOH A 94 494 126 HOH HOH . F 6 HOH A 95 495 127 HOH HOH . F 6 HOH A 96 496 128 HOH HOH . F 6 HOH A 97 497 129 HOH HOH . F 6 HOH A 98 498 130 HOH HOH . F 6 HOH A 99 499 131 HOH HOH . F 6 HOH A 100 500 132 HOH HOH . F 6 HOH A 101 501 133 HOH HOH . F 6 HOH A 102 502 134 HOH HOH . F 6 HOH A 103 503 135 HOH HOH . F 6 HOH A 104 504 136 HOH HOH . F 6 HOH A 105 505 137 HOH HOH . F 6 HOH A 106 506 138 HOH HOH . F 6 HOH A 107 507 139 HOH HOH . F 6 HOH A 108 508 140 HOH HOH . F 6 HOH A 109 509 141 HOH HOH . F 6 HOH A 110 510 142 HOH HOH . F 6 HOH A 111 511 143 HOH HOH . F 6 HOH A 112 512 144 HOH HOH . F 6 HOH A 113 513 145 HOH HOH . F 6 HOH A 114 514 146 HOH HOH . F 6 HOH A 115 515 147 HOH HOH . F 6 HOH A 116 516 148 HOH HOH . F 6 HOH A 117 517 149 HOH HOH . F 6 HOH A 118 518 150 HOH HOH . F 6 HOH A 119 519 151 HOH HOH . F 6 HOH A 120 520 152 HOH HOH . F 6 HOH A 121 521 153 HOH HOH . F 6 HOH A 122 522 155 HOH HOH . F 6 HOH A 123 523 157 HOH HOH . F 6 HOH A 124 524 158 HOH HOH . F 6 HOH A 125 525 159 HOH HOH . F 6 HOH A 126 526 160 HOH HOH . F 6 HOH A 127 527 161 HOH HOH . F 6 HOH A 128 528 162 HOH HOH . F 6 HOH A 129 529 163 HOH HOH . F 6 HOH A 130 530 167 HOH HOH . F 6 HOH A 131 531 168 HOH HOH . G 6 HOH B 1 101 1 HOH HOH . G 6 HOH B 2 102 6 HOH HOH . G 6 HOH B 3 103 29 HOH HOH . G 6 HOH B 4 104 31 HOH HOH . G 6 HOH B 5 105 44 HOH HOH . G 6 HOH B 6 106 47 HOH HOH . G 6 HOH B 7 107 48 HOH HOH . G 6 HOH B 8 108 55 HOH HOH . G 6 HOH B 9 109 57 HOH HOH . G 6 HOH B 10 110 58 HOH HOH . G 6 HOH B 11 111 63 HOH HOH . G 6 HOH B 12 112 75 HOH HOH . G 6 HOH B 13 113 82 HOH HOH . G 6 HOH B 14 114 95 HOH HOH . G 6 HOH B 15 115 96 HOH HOH . G 6 HOH B 16 116 101 HOH HOH . G 6 HOH B 17 117 106 HOH HOH . G 6 HOH B 18 118 119 HOH HOH . G 6 HOH B 19 119 123 HOH HOH . G 6 HOH B 20 120 125 HOH HOH . G 6 HOH B 21 121 165 HOH HOH . H 6 HOH C 1 101 7 HOH HOH . H 6 HOH C 2 102 20 HOH HOH . H 6 HOH C 3 103 24 HOH HOH . H 6 HOH C 4 104 51 HOH HOH . H 6 HOH C 5 105 65 HOH HOH . H 6 HOH C 6 106 72 HOH HOH . H 6 HOH C 7 107 76 HOH HOH . H 6 HOH C 8 108 100 HOH HOH . H 6 HOH C 9 109 111 HOH HOH . H 6 HOH C 10 110 112 HOH HOH . H 6 HOH C 11 111 115 HOH HOH . H 6 HOH C 12 112 116 HOH HOH . H 6 HOH C 13 113 154 HOH HOH . H 6 HOH C 14 114 156 HOH HOH . H 6 HOH C 15 115 164 HOH HOH . H 6 HOH C 16 116 166 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 4 _atom_site.Cartn_x -5.243 _atom_site.Cartn_y -0.908 _atom_site.Cartn_z -28.994 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 25.53 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 301 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #