data_4GDK # _model_server_result.job_id onuyzIGYWoTwTDARoZdt7w _model_server_result.datetime_utc '2024-11-04 23:09:26' _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 4gdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 4GDK # _exptl.entry_id 4GDK _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 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 90 _cell.entry_id 4GDK _cell.length_a 43.757 _cell.length_b 113.153 _cell.length_c 210.685 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GDK _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,H,I,J,K,L,M,N _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 ? 4 G N N ? 4 H 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 E O ALA 95 E ALA 95 1_555 H NA NA . E NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc2 E OD1 ASN 99 E ASN 99 1_555 H NA NA . E NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc3 B OD1 ASN 99 B ASN 99 1_555 G NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc4 G NA NA . B NA 301 1_555 J O HOH . B HOH 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc5 B O PRO 97 B PRO 97 1_555 G NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc6 H NA NA . E NA 301 1_555 M O HOH . E HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc7 G NA NA . B NA 301 1_555 J O HOH . B HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc8 G NA NA . B NA 301 1_555 J O HOH . B HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc9 B O ALA 95 B ALA 95 1_555 G NA NA . B NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc10 H NA NA . E NA 301 1_555 M O HOH . E HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc11 E O PRO 97 E PRO 97 1_555 H NA NA . E NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? covale ? covale1 A C GLY 91 A GLY 140 1_555 B NZ LYS 130 B LYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 D C GLY 91 D GLY 140 1_555 E NZ LYS 130 E LYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _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 4GDK _atom_sites.fract_transf_matrix[1][1] 0.022853 _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] 0.008838 _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] 0.004746 _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 4 NA B 1 301 1 NA NA . H 4 NA E 1 301 1 NA NA . I 5 HOH A 1 201 35 HOH HOH . I 5 HOH A 2 202 45 HOH HOH . I 5 HOH A 3 203 49 HOH HOH . J 5 HOH B 1 401 2 HOH HOH . J 5 HOH B 2 402 3 HOH HOH . J 5 HOH B 3 403 5 HOH HOH . J 5 HOH B 4 404 6 HOH HOH . J 5 HOH B 5 405 8 HOH HOH . J 5 HOH B 6 406 9 HOH HOH . J 5 HOH B 7 407 10 HOH HOH . J 5 HOH B 8 408 11 HOH HOH . J 5 HOH B 9 409 12 HOH HOH . J 5 HOH B 10 410 13 HOH HOH . J 5 HOH B 11 411 15 HOH HOH . J 5 HOH B 12 412 20 HOH HOH . J 5 HOH B 13 413 21 HOH HOH . J 5 HOH B 14 414 22 HOH HOH . J 5 HOH B 15 415 24 HOH HOH . J 5 HOH B 16 416 26 HOH HOH . J 5 HOH B 17 417 27 HOH HOH . J 5 HOH B 18 418 28 HOH HOH . J 5 HOH B 19 419 31 HOH HOH . J 5 HOH B 20 420 32 HOH HOH . J 5 HOH B 21 421 34 HOH HOH . J 5 HOH B 22 422 36 HOH HOH . J 5 HOH B 23 423 38 HOH HOH . J 5 HOH B 24 424 39 HOH HOH . J 5 HOH B 25 425 40 HOH HOH . J 5 HOH B 26 426 41 HOH HOH . J 5 HOH B 27 427 46 HOH HOH . J 5 HOH B 28 428 50 HOH HOH . J 5 HOH B 29 429 51 HOH HOH . J 5 HOH B 30 430 52 HOH HOH . J 5 HOH B 31 431 53 HOH HOH . J 5 HOH B 32 432 57 HOH HOH . J 5 HOH B 33 433 58 HOH HOH . J 5 HOH B 34 434 60 HOH HOH . J 5 HOH B 35 435 61 HOH HOH . J 5 HOH B 36 436 62 HOH HOH . J 5 HOH B 37 437 63 HOH HOH . J 5 HOH B 38 438 64 HOH HOH . J 5 HOH B 39 439 65 HOH HOH . J 5 HOH B 40 440 68 HOH HOH . J 5 HOH B 41 441 72 HOH HOH . J 5 HOH B 42 442 73 HOH HOH . J 5 HOH B 43 443 74 HOH HOH . J 5 HOH B 44 444 75 HOH HOH . K 5 HOH C 1 101 14 HOH HOH . K 5 HOH C 2 102 18 HOH HOH . K 5 HOH C 3 103 33 HOH HOH . K 5 HOH C 4 104 37 HOH HOH . K 5 HOH C 5 105 43 HOH HOH . K 5 HOH C 6 106 56 HOH HOH . K 5 HOH C 7 107 66 HOH HOH . L 5 HOH D 1 201 16 HOH HOH . M 5 HOH E 1 401 1 HOH HOH . M 5 HOH E 2 402 4 HOH HOH . M 5 HOH E 3 403 7 HOH HOH . M 5 HOH E 4 404 19 HOH HOH . M 5 HOH E 5 405 25 HOH HOH . M 5 HOH E 6 406 29 HOH HOH . M 5 HOH E 7 407 44 HOH HOH . M 5 HOH E 8 408 47 HOH HOH . M 5 HOH E 9 409 48 HOH HOH . M 5 HOH E 10 410 67 HOH HOH . M 5 HOH E 11 411 69 HOH HOH . M 5 HOH E 12 412 70 HOH HOH . M 5 HOH E 13 413 76 HOH HOH . N 5 HOH F 1 101 17 HOH HOH . N 5 HOH F 2 102 23 HOH HOH . N 5 HOH F 3 103 30 HOH HOH . N 5 HOH F 4 104 42 HOH HOH . N 5 HOH F 5 105 54 HOH HOH . N 5 HOH F 6 106 55 HOH HOH . N 5 HOH F 7 107 59 HOH HOH . N 5 HOH F 8 108 71 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 G _atom_site.label_entity_id 4 _atom_site.Cartn_x -4.395 _atom_site.Cartn_y -1.794 _atom_site.Cartn_z 60.445 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 52.2 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 301 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #