data_3IVT # _model_server_result.job_id WduT5O-EQvWjUVuE_kbwJQ _model_server_result.datetime_utc '2024-12-04 02:42:40' _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 3ivt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 3IVT # _exptl.entry_id 3IVT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 2 _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 3IVT _cell.length_a 133.731 _cell.length_b 133.731 _cell.length_c 125.904 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IVT _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 D N N ? 3 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 OE1 GLU 49 A GLU 44 1_555 C ZN ZN . A ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc2 A O ARG 219 A ARG 214 1_555 D NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? metalc ? metalc3 A NE2 HIS 229 A HIS 224 1_555 C ZN ZN . A ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc4 A NE2 HIS 231 A HIS 226 1_555 C ZN ZN . A ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc5 I O HOH . A HOH 419 1_555 C ZN ZN . A ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc6 C ZN ZN . A ZN 500 1_555 E O1 AKG . A AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc7 C ZN ZN . A ZN 500 1_555 E O5 AKG . A AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc8 B OE1 GLU 49 B GLU 44 1_555 F ZN ZN . B ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc9 B O ARG 219 B ARG 214 1_555 G NA NA . B NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? metalc ? metalc10 B O VAL 222 B VAL 217 1_555 G NA NA . B NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.938 ? metalc ? metalc11 B NE2 HIS 229 B HIS 224 1_555 F ZN ZN . B ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc12 B NE2 HIS 231 B HIS 226 1_555 F ZN ZN . B ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc13 J O HOH . B HOH 419 1_555 F ZN ZN . B ZN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc14 J O HOH . B HOH 488 1_555 G NA NA . B NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc15 F ZN ZN . B ZN 500 1_555 H O5 AKG . B AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc16 F ZN ZN . B ZN 500 1_555 H O1 AKG . B AKG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3IVT _atom_sites.fract_transf_matrix[1][1] 0.007478 _atom_sites.fract_transf_matrix[1][2] 0.004317 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008635 _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] 0.007943 _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 ZN A 1 500 500 ZN ZN . D 3 NA A 1 501 501 NA NA . E 4 AKG A 1 1000 1000 AKG AKG . F 2 ZN B 1 500 500 ZN ZN . G 3 NA B 1 501 501 NA NA . H 4 AKG B 1 1000 1000 AKG AKG . I 5 HOH A 1 419 2 HOH HOH . I 5 HOH A 2 420 5 HOH HOH . I 5 HOH A 3 421 8 HOH HOH . I 5 HOH A 4 422 9 HOH HOH . I 5 HOH A 5 423 10 HOH HOH . I 5 HOH A 6 424 15 HOH HOH . I 5 HOH A 7 425 16 HOH HOH . I 5 HOH A 8 426 17 HOH HOH . I 5 HOH A 9 427 18 HOH HOH . I 5 HOH A 10 428 19 HOH HOH . I 5 HOH A 11 429 20 HOH HOH . I 5 HOH A 12 430 26 HOH HOH . I 5 HOH A 13 431 31 HOH HOH . I 5 HOH A 14 432 32 HOH HOH . I 5 HOH A 15 433 34 HOH HOH . I 5 HOH A 16 434 39 HOH HOH . I 5 HOH A 17 435 40 HOH HOH . I 5 HOH A 18 436 42 HOH HOH . I 5 HOH A 19 437 46 HOH HOH . I 5 HOH A 20 438 53 HOH HOH . I 5 HOH A 21 439 57 HOH HOH . I 5 HOH A 22 440 61 HOH HOH . I 5 HOH A 23 441 64 HOH HOH . I 5 HOH A 24 442 65 HOH HOH . I 5 HOH A 25 443 66 HOH HOH . I 5 HOH A 26 444 71 HOH HOH . I 5 HOH A 27 445 73 HOH HOH . I 5 HOH A 28 446 75 HOH HOH . I 5 HOH A 29 447 81 HOH HOH . I 5 HOH A 30 448 84 HOH HOH . I 5 HOH A 31 449 86 HOH HOH . I 5 HOH A 32 450 88 HOH HOH . I 5 HOH A 33 451 91 HOH HOH . I 5 HOH A 34 452 92 HOH HOH . I 5 HOH A 35 453 97 HOH HOH . I 5 HOH A 36 454 99 HOH HOH . I 5 HOH A 37 455 103 HOH HOH . I 5 HOH A 38 456 105 HOH HOH . I 5 HOH A 39 457 108 HOH HOH . I 5 HOH A 40 458 111 HOH HOH . I 5 HOH A 41 459 112 HOH HOH . I 5 HOH A 42 460 113 HOH HOH . I 5 HOH A 43 461 117 HOH HOH . I 5 HOH A 44 462 120 HOH HOH . I 5 HOH A 45 463 124 HOH HOH . I 5 HOH A 46 464 126 HOH HOH . I 5 HOH A 47 465 130 HOH HOH . I 5 HOH A 48 466 133 HOH HOH . I 5 HOH A 49 467 141 HOH HOH . I 5 HOH A 50 468 155 HOH HOH . I 5 HOH A 51 469 157 HOH HOH . I 5 HOH A 52 470 158 HOH HOH . I 5 HOH A 53 471 159 HOH HOH . I 5 HOH A 54 472 160 HOH HOH . I 5 HOH A 55 473 161 HOH HOH . I 5 HOH A 56 474 162 HOH HOH . I 5 HOH A 57 475 163 HOH HOH . I 5 HOH A 58 476 168 HOH HOH . I 5 HOH A 59 477 169 HOH HOH . I 5 HOH A 60 478 173 HOH HOH . I 5 HOH A 61 479 174 HOH HOH . I 5 HOH A 62 480 185 HOH HOH . I 5 HOH A 63 481 187 HOH HOH . I 5 HOH A 64 482 188 HOH HOH . I 5 HOH A 65 483 189 HOH HOH . I 5 HOH A 66 484 191 HOH HOH . I 5 HOH A 67 485 193 HOH HOH . I 5 HOH A 68 486 212 HOH HOH . I 5 HOH A 69 487 229 HOH HOH . I 5 HOH A 70 488 233 HOH HOH . I 5 HOH A 71 489 238 HOH HOH . I 5 HOH A 72 490 249 HOH HOH . I 5 HOH A 73 491 250 HOH HOH . I 5 HOH A 74 492 258 HOH HOH . I 5 HOH A 75 493 259 HOH HOH . I 5 HOH A 76 494 263 HOH HOH . I 5 HOH A 77 495 266 HOH HOH . J 5 HOH B 1 419 1 HOH HOH . J 5 HOH B 2 420 3 HOH HOH . J 5 HOH B 3 421 7 HOH HOH . J 5 HOH B 4 422 14 HOH HOH . J 5 HOH B 5 423 23 HOH HOH . J 5 HOH B 6 424 24 HOH HOH . J 5 HOH B 7 425 25 HOH HOH . J 5 HOH B 8 426 28 HOH HOH . J 5 HOH B 9 427 30 HOH HOH . J 5 HOH B 10 428 36 HOH HOH . J 5 HOH B 11 429 44 HOH HOH . J 5 HOH B 12 430 45 HOH HOH . J 5 HOH B 13 431 48 HOH HOH . J 5 HOH B 14 432 49 HOH HOH . J 5 HOH B 15 433 50 HOH HOH . J 5 HOH B 16 434 52 HOH HOH . J 5 HOH B 17 435 54 HOH HOH . J 5 HOH B 18 436 55 HOH HOH . J 5 HOH B 19 437 56 HOH HOH . J 5 HOH B 20 438 60 HOH HOH . J 5 HOH B 21 439 67 HOH HOH . J 5 HOH B 22 440 69 HOH HOH . J 5 HOH B 23 441 70 HOH HOH . J 5 HOH B 24 442 77 HOH HOH . J 5 HOH B 25 443 79 HOH HOH . J 5 HOH B 26 444 80 HOH HOH . J 5 HOH B 27 445 82 HOH HOH . J 5 HOH B 28 446 85 HOH HOH . J 5 HOH B 29 447 87 HOH HOH . J 5 HOH B 30 448 89 HOH HOH . J 5 HOH B 31 449 90 HOH HOH . J 5 HOH B 32 450 95 HOH HOH . J 5 HOH B 33 451 96 HOH HOH . J 5 HOH B 34 452 102 HOH HOH . J 5 HOH B 35 453 106 HOH HOH . J 5 HOH B 36 454 107 HOH HOH . J 5 HOH B 37 455 109 HOH HOH . J 5 HOH B 38 456 110 HOH HOH . J 5 HOH B 39 457 115 HOH HOH . J 5 HOH B 40 458 116 HOH HOH . J 5 HOH B 41 459 127 HOH HOH . J 5 HOH B 42 460 128 HOH HOH . J 5 HOH B 43 461 129 HOH HOH . J 5 HOH B 44 462 132 HOH HOH . J 5 HOH B 45 463 135 HOH HOH . J 5 HOH B 46 464 136 HOH HOH . J 5 HOH B 47 465 137 HOH HOH . J 5 HOH B 48 466 144 HOH HOH . J 5 HOH B 49 467 147 HOH HOH . J 5 HOH B 50 468 151 HOH HOH . J 5 HOH B 51 469 152 HOH HOH . J 5 HOH B 52 470 154 HOH HOH . J 5 HOH B 53 471 164 HOH HOH . J 5 HOH B 54 472 176 HOH HOH . J 5 HOH B 55 473 178 HOH HOH . J 5 HOH B 56 474 181 HOH HOH . J 5 HOH B 57 475 195 HOH HOH . J 5 HOH B 58 476 208 HOH HOH . J 5 HOH B 59 477 209 HOH HOH . J 5 HOH B 60 478 210 HOH HOH . J 5 HOH B 61 479 214 HOH HOH . J 5 HOH B 62 480 221 HOH HOH . J 5 HOH B 63 481 222 HOH HOH . J 5 HOH B 64 482 225 HOH HOH . J 5 HOH B 65 483 226 HOH HOH . J 5 HOH B 66 484 230 HOH HOH . J 5 HOH B 67 485 234 HOH HOH . J 5 HOH B 68 486 236 HOH HOH . J 5 HOH B 69 487 237 HOH HOH . J 5 HOH B 70 488 244 HOH HOH . J 5 HOH B 71 489 245 HOH HOH . J 5 HOH B 72 490 253 HOH HOH . J 5 HOH B 73 491 256 HOH HOH . J 5 HOH B 74 492 257 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _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 3 _atom_site.Cartn_x -33.437 _atom_site.Cartn_y 57.918 _atom_site.Cartn_z 18.873 _atom_site.occupancy 0.5 _atom_site.B_iso_or_equiv 33.19 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 501 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #