data_5I38 # _model_server_result.job_id bFc5bwlNEIGYkGRfQaj3pA _model_server_result.datetime_utc '2024-11-24 05:33:54' _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 5i38 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":303}' # _entry.id 5I38 # _exptl.entry_id 5I38 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 142.109 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE _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 5I38 _cell.length_a 70.24 _cell.length_b 74.97 _cell.length_c 121.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5I38 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 E N N ? 3 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 A NE2 HIS 39 A HIS 42 1_555 D CU CU . A CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc2 A NE2 HIS 57 A HIS 60 1_555 D CU CU . A CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc3 A NE2 HIS 66 A HIS 69 1_555 D CU CU . A CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc4 A NE2 HIS 201 A HIS 204 1_555 C CU CU . A CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc5 A NE2 HIS 205 A HIS 208 1_555 C CU CU . A CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc6 A NE2 HIS 228 A HIS 231 1_555 C CU CU . A CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc7 C CU CU . A CU 301 1_555 I O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc8 D CU CU . A CU 302 1_555 I O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc9 B NE2 HIS 39 B HIS 42 1_555 F CU CU . B CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc10 B NE2 HIS 57 B HIS 60 1_555 F CU CU . B CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc11 B NE2 HIS 66 B HIS 69 1_555 F CU CU . B CU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc12 B NE2 HIS 201 B HIS 204 1_555 G CU CU . B CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc13 B NE2 HIS 205 B HIS 208 1_555 G CU CU . B CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc14 B NE2 HIS 228 B HIS 231 1_555 G CU CU . B CU 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc15 F CU CU . B CU 301 1_555 J O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc16 G CU CU . B CU 302 1_555 J O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? # _chem_comp.formula 'C6 H6 O4' _chem_comp.formula_weight 142.109 _chem_comp.id KOJ _chem_comp.mon_nstd_flag . _chem_comp.name 5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 KOJ doub 160 n y C1 O5 KOJ sing 161 n y C1 H1 KOJ sing 162 n n C2 C3 KOJ sing 163 n y C2 O2 KOJ sing 164 n n C3 C4 KOJ sing 165 n y C3 O3 KOJ doub 166 n n C4 C5 KOJ doub 167 n y C4 H4 KOJ sing 168 n n C5 C6 KOJ sing 169 n n C5 O5 KOJ sing 170 n y C6 O6 KOJ sing 171 n n C6 H6C1 KOJ sing 172 n n C6 H6C2 KOJ sing 173 n n O2 H2 KOJ sing 174 n n O6 H6 KOJ sing 175 n n # _atom_sites.entry_id 5I38 _atom_sites.fract_transf_matrix[1][1] 0.014237 _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] 0.013339 _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] 0.008217 _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 CU A 1 301 1 CU CU . D 2 CU A 1 302 2 CU CU . E 3 KOJ A 1 303 4735 KOJ KOJ . F 2 CU B 1 301 3 CU CU . G 2 CU B 1 302 4 CU CU . H 3 KOJ B 1 303 4736 KOJ KOJ . I 4 HOH A 1 401 1 HOH HOH . I 4 HOH A 2 402 11 HOH HOH . I 4 HOH A 3 403 10 HOH HOH . I 4 HOH A 4 404 15 HOH HOH . I 4 HOH A 5 405 42 HOH HOH . I 4 HOH A 6 406 77 HOH HOH . I 4 HOH A 7 407 47 HOH HOH . I 4 HOH A 8 408 14 HOH HOH . I 4 HOH A 9 409 91 HOH HOH . I 4 HOH A 10 410 12 HOH HOH . I 4 HOH A 11 411 40 HOH HOH . I 4 HOH A 12 412 25 HOH HOH . I 4 HOH A 13 413 26 HOH HOH . I 4 HOH A 14 414 87 HOH HOH . I 4 HOH A 15 415 18 HOH HOH . I 4 HOH A 16 416 13 HOH HOH . I 4 HOH A 17 417 57 HOH HOH . I 4 HOH A 18 418 5 HOH HOH . I 4 HOH A 19 419 41 HOH HOH . I 4 HOH A 20 420 52 HOH HOH . I 4 HOH A 21 421 39 HOH HOH . I 4 HOH A 22 422 54 HOH HOH . I 4 HOH A 23 423 92 HOH HOH . I 4 HOH A 24 424 49 HOH HOH . I 4 HOH A 25 425 30 HOH HOH . I 4 HOH A 26 426 74 HOH HOH . I 4 HOH A 27 427 36 HOH HOH . I 4 HOH A 28 428 96 HOH HOH . I 4 HOH A 29 429 50 HOH HOH . I 4 HOH A 30 430 28 HOH HOH . I 4 HOH A 31 431 61 HOH HOH . I 4 HOH A 32 432 35 HOH HOH . I 4 HOH A 33 433 17 HOH HOH . I 4 HOH A 34 434 32 HOH HOH . I 4 HOH A 35 435 85 HOH HOH . I 4 HOH A 36 436 9 HOH HOH . I 4 HOH A 37 437 29 HOH HOH . I 4 HOH A 38 438 56 HOH HOH . I 4 HOH A 39 439 21 HOH HOH . I 4 HOH A 40 440 19 HOH HOH . I 4 HOH A 41 441 60 HOH HOH . I 4 HOH A 42 442 93 HOH HOH . I 4 HOH A 43 443 84 HOH HOH . I 4 HOH A 44 444 58 HOH HOH . I 4 HOH A 45 445 31 HOH HOH . I 4 HOH A 46 446 23 HOH HOH . J 4 HOH B 1 401 2 HOH HOH . J 4 HOH B 2 402 34 HOH HOH . J 4 HOH B 3 403 8 HOH HOH . J 4 HOH B 4 404 82 HOH HOH . J 4 HOH B 5 405 27 HOH HOH . J 4 HOH B 6 406 6 HOH HOH . J 4 HOH B 7 407 94 HOH HOH . J 4 HOH B 8 408 4 HOH HOH . J 4 HOH B 9 409 44 HOH HOH . J 4 HOH B 10 410 63 HOH HOH . J 4 HOH B 11 411 22 HOH HOH . J 4 HOH B 12 412 16 HOH HOH . J 4 HOH B 13 413 80 HOH HOH . J 4 HOH B 14 414 67 HOH HOH . J 4 HOH B 15 415 69 HOH HOH . J 4 HOH B 16 416 64 HOH HOH . J 4 HOH B 17 417 62 HOH HOH . J 4 HOH B 18 418 53 HOH HOH . J 4 HOH B 19 419 76 HOH HOH . J 4 HOH B 20 420 79 HOH HOH . J 4 HOH B 21 421 59 HOH HOH . J 4 HOH B 22 422 38 HOH HOH . J 4 HOH B 23 423 51 HOH HOH . J 4 HOH B 24 424 68 HOH HOH . J 4 HOH B 25 425 45 HOH HOH . J 4 HOH B 26 426 46 HOH HOH . J 4 HOH B 27 427 89 HOH HOH . J 4 HOH B 28 428 86 HOH HOH . J 4 HOH B 29 429 66 HOH HOH . J 4 HOH B 30 430 37 HOH HOH . J 4 HOH B 31 431 75 HOH HOH . J 4 HOH B 32 432 48 HOH HOH . J 4 HOH B 33 433 78 HOH HOH . J 4 HOH B 34 434 65 HOH HOH . J 4 HOH B 35 435 90 HOH HOH . J 4 HOH B 36 436 72 HOH HOH . J 4 HOH B 37 437 88 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 KOJ . . . H 3 23.219 101.605 49.765 1 25.9 ? C1 KOJ 303 B 1 HETATM 2 C C2 KOJ . . . H 3 23.428 101.774 48.393 1 28.27 ? C2 KOJ 303 B 1 HETATM 3 C C3 KOJ . . . H 3 23.173 103.051 47.804 1 30.63 ? C3 KOJ 303 B 1 HETATM 4 C C4 KOJ . . . H 3 22.706 104.117 48.663 1 27.78 ? C4 KOJ 303 B 1 HETATM 5 C C5 KOJ . . . H 3 22.54 103.82 50.002 1 29.92 ? C5 KOJ 303 B 1 HETATM 6 C C6 KOJ . . . H 3 22.056 104.897 50.939 1 33.42 ? C6 KOJ 303 B 1 HETATM 7 O O2 KOJ . . . H 3 23.912 100.637 47.557 1 35.48 ? O2 KOJ 303 B 1 HETATM 8 O O3 KOJ . . . H 3 23.374 103.272 46.398 1 32.07 ? O3 KOJ 303 B 1 HETATM 9 O O5 KOJ . . . H 3 22.793 102.609 50.499 1 34.69 ? O5 KOJ 303 B 1 HETATM 10 O O6 KOJ . . . H 3 22.072 104.366 52.272 1 42.17 ? O6 KOJ 303 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #