data_2GDE # _model_server_result.job_id 7G5esASdRWRBjUaknwMcvQ _model_server_result.datetime_utc '2025-07-04 18:39:52' _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 2gde # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 2GDE # _exptl.entry_id 2GDE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM 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 99.06 _cell.angle_gamma 90 _cell.entry_id 2GDE _cell.length_a 70.084 _cell.length_b 72.169 _cell.length_c 70.357 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GDE _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 disulf ? disulf1 A SG CYS 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 C C GLU 8 D GLU 362 1_555 C N TYS 9 D TYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 C C TYS 9 D TYS 363 1_555 C N LEU 10 D LEU 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? metalc ? metalc1 D NA NA . H NA 402 1_555 G O HOH . H HOH 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? # _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 2GDE _atom_sites.fract_transf_matrix[1][1] 0.01427 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00228 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01386 _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] 0.01439 _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 NA H 1 402 402 NA NA . E 5 SN3 H 1 401 401 SN3 SN3 . F 6 HOH L 1 18 12 HOH HOH . F 6 HOH L 2 19 35 HOH HOH . F 6 HOH L 3 20 51 HOH HOH . F 6 HOH L 4 21 64 HOH HOH . F 6 HOH L 5 22 78 HOH HOH . F 6 HOH L 6 23 79 HOH HOH . G 6 HOH H 1 403 1 HOH HOH . G 6 HOH H 2 404 2 HOH HOH . G 6 HOH H 3 405 3 HOH HOH . G 6 HOH H 4 406 4 HOH HOH . G 6 HOH H 5 407 5 HOH HOH . G 6 HOH H 6 408 6 HOH HOH . G 6 HOH H 7 409 7 HOH HOH . G 6 HOH H 8 410 8 HOH HOH . G 6 HOH H 9 411 9 HOH HOH . G 6 HOH H 10 412 10 HOH HOH . G 6 HOH H 11 413 11 HOH HOH . G 6 HOH H 12 414 13 HOH HOH . G 6 HOH H 13 415 14 HOH HOH . G 6 HOH H 14 416 15 HOH HOH . G 6 HOH H 15 417 16 HOH HOH . G 6 HOH H 16 418 17 HOH HOH . G 6 HOH H 17 419 18 HOH HOH . G 6 HOH H 18 420 19 HOH HOH . G 6 HOH H 19 421 20 HOH HOH . G 6 HOH H 20 422 21 HOH HOH . G 6 HOH H 21 423 22 HOH HOH . G 6 HOH H 22 424 23 HOH HOH . G 6 HOH H 23 425 24 HOH HOH . G 6 HOH H 24 426 25 HOH HOH . G 6 HOH H 25 427 26 HOH HOH . G 6 HOH H 26 428 27 HOH HOH . G 6 HOH H 27 429 28 HOH HOH . G 6 HOH H 28 430 29 HOH HOH . G 6 HOH H 29 431 30 HOH HOH . G 6 HOH H 30 432 31 HOH HOH . G 6 HOH H 31 433 32 HOH HOH . G 6 HOH H 32 434 33 HOH HOH . G 6 HOH H 33 435 34 HOH HOH . G 6 HOH H 34 436 36 HOH HOH . G 6 HOH H 35 437 37 HOH HOH . G 6 HOH H 36 438 38 HOH HOH . G 6 HOH H 37 439 39 HOH HOH . G 6 HOH H 38 440 40 HOH HOH . G 6 HOH H 39 441 41 HOH HOH . G 6 HOH H 40 442 42 HOH HOH . G 6 HOH H 41 443 43 HOH HOH . G 6 HOH H 42 444 44 HOH HOH . G 6 HOH H 43 445 45 HOH HOH . G 6 HOH H 44 446 46 HOH HOH . G 6 HOH H 45 447 47 HOH HOH . G 6 HOH H 46 448 48 HOH HOH . G 6 HOH H 47 449 49 HOH HOH . G 6 HOH H 48 450 50 HOH HOH . G 6 HOH H 49 451 52 HOH HOH . G 6 HOH H 50 452 53 HOH HOH . G 6 HOH H 51 453 54 HOH HOH . G 6 HOH H 52 454 55 HOH HOH . G 6 HOH H 53 455 56 HOH HOH . G 6 HOH H 54 456 57 HOH HOH . G 6 HOH H 55 457 58 HOH HOH . G 6 HOH H 56 458 59 HOH HOH . G 6 HOH H 57 459 60 HOH HOH . G 6 HOH H 58 460 61 HOH HOH . G 6 HOH H 59 461 62 HOH HOH . G 6 HOH H 60 462 63 HOH HOH . G 6 HOH H 61 463 65 HOH HOH . G 6 HOH H 62 464 66 HOH HOH . G 6 HOH H 63 465 67 HOH HOH . G 6 HOH H 64 466 68 HOH HOH . G 6 HOH H 65 467 69 HOH HOH . G 6 HOH H 66 468 70 HOH HOH . G 6 HOH H 67 469 71 HOH HOH . G 6 HOH H 68 470 72 HOH HOH . G 6 HOH H 69 471 73 HOH HOH . G 6 HOH H 70 472 74 HOH HOH . G 6 HOH H 71 473 75 HOH HOH . G 6 HOH H 72 474 76 HOH HOH . G 6 HOH H 73 475 77 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 4 _atom_site.Cartn_x 7.194 _atom_site.Cartn_y -11.862 _atom_site.Cartn_z 29.075 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 61.33 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 402 _atom_site.auth_asym_id H _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #