data_1P59 # _model_server_result.job_id 8tNhzeJhoisObFiwzghmDg _model_server_result.datetime_utc '2024-11-25 15:59:35' _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 1p59 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":300}' # _entry.id 1P59 # _exptl.entry_id 1P59 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.64 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'IRON/SULFUR CLUSTER' _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 90 _cell.angle_gamma 90 _cell.entry_id 1P59 _cell.length_a 66.321 _cell.length_b 105.896 _cell.length_c 41.518 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1P59 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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,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 5 _struct_asym.id E _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 O3' DG 6 B DG 6 1_555 A P 5IU 7 B 5IU 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? covale ? covale2 A O3' 5IU 7 B 5IU 7 1_555 A P DG 8 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? covale ? covale3 B O3' DG 2 C DG 13 1_555 B P 5IU 3 C 5IU 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale4 B O3' 5IU 3 C 5IU 14 1_555 B P DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? covale ? covale5 B O3' DA 6 C DA 17 1_555 B P 3DR 7 C 3DR 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.619 ? covale ? covale6 B O3' 3DR 7 C 3DR 18 1_555 B P DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? covale ? covale7 B O3' DG 8 C DG 19 1_555 B P 5IU 9 C 5IU 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? covale ? covale8 B O3' 5IU 9 C 5IU 20 1_555 B P DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 B OP1 DC 10 C DC 21 1_555 D NA NA . A NA 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc2 C O MET 116 A MET 113 1_555 D NA NA . A NA 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc3 C O LEU 118 A LEU 115 1_555 D NA NA . A NA 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc4 C O VAL 121 A VAL 118 1_555 D NA NA . A NA 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc5 C SG CYS 192 A CYS 189 1_555 E FE2 SF4 . A SF4 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc6 C SG CYS 199 A CYS 196 1_555 E FE3 SF4 . A SF4 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc7 C SG CYS 202 A CYS 199 1_555 E FE1 SF4 . A SF4 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc8 C SG CYS 208 A CYS 205 1_555 E FE4 SF4 . A SF4 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? hydrog WATSON-CRICK hydrog1 A N1 DA 2 B DA 2 1_555 B N3 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N6 DA 2 B DA 2 1_555 B O4 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 DG 3 B DG 3 1_555 B N3 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 DG 3 B DG 3 1_555 B O2 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 DG 3 B DG 3 1_555 B N4 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 4 B DA 4 1_555 B N3 5IU 9 C 5IU 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 4 B DA 4 1_555 B O4 5IU 9 C 5IU 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 DC 5 B DC 5 1_555 B N1 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N4 DC 5 B DC 5 1_555 B O6 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O2 DC 5 B DC 5 1_555 B N2 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 5IU 7 B 5IU 7 1_555 B N1 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 5IU 7 B 5IU 7 1_555 B N6 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DG 8 B DG 8 1_555 B N3 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N2 DG 8 B DG 8 1_555 B O2 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O6 DG 8 B DG 8 1_555 B N4 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DG 9 B DG 9 1_555 B N3 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 DG 9 B DG 9 1_555 B O2 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 DG 9 B DG 9 1_555 B N4 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 DA 10 B DA 10 1_555 B N3 5IU 3 C 5IU 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N6 DA 10 B DA 10 1_555 B O4 5IU 3 C 5IU 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 DC 11 B DC 11 1_555 B N1 DG 2 C DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 DC 11 B DC 11 1_555 B O6 DG 2 C DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 DC 11 B DC 11 1_555 B N2 DG 2 C DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Fe4 S4' _chem_comp.formula_weight 351.64 _chem_comp.id SF4 _chem_comp.mon_nstd_flag . _chem_comp.name 'IRON/SULFUR CLUSTER' _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 FE1 S2 SF4 sing 496 n n FE1 S3 SF4 sing 497 n n FE1 S4 SF4 sing 498 n n FE2 S1 SF4 sing 499 n n FE2 S3 SF4 sing 500 n n FE2 S4 SF4 sing 501 n n FE3 S1 SF4 sing 502 n n FE3 S2 SF4 sing 503 n n FE3 S4 SF4 sing 504 n n FE4 S1 SF4 sing 505 n n FE4 S2 SF4 sing 506 n n FE4 S3 SF4 sing 507 n n # _atom_sites.entry_id 1P59 _atom_sites.fract_transf_matrix[1][1] 0.015078 _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] 0.009443 _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] 0.024086 _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 A 1 224 1 NA NA1 . E 5 SF4 A 1 300 300 SF4 FS4 . F 6 HOH B 1 12 9 HOH HOH . F 6 HOH B 2 13 20 HOH HOH . F 6 HOH B 3 14 21 HOH HOH . G 6 HOH C 1 23 2 HOH HOH . G 6 HOH C 2 24 18 HOH HOH . G 6 HOH C 3 25 19 HOH HOH . G 6 HOH C 4 26 22 HOH HOH . G 6 HOH C 5 27 29 HOH HOH . H 6 HOH A 1 301 1 HOH HOH . H 6 HOH A 2 302 3 HOH HOH . H 6 HOH A 3 303 4 HOH HOH . H 6 HOH A 4 304 5 HOH HOH . H 6 HOH A 5 305 6 HOH HOH . H 6 HOH A 6 306 7 HOH HOH . H 6 HOH A 7 307 8 HOH HOH . H 6 HOH A 8 308 10 HOH HOH . H 6 HOH A 9 309 11 HOH HOH . H 6 HOH A 10 310 12 HOH HOH . H 6 HOH A 11 311 13 HOH HOH . H 6 HOH A 12 312 14 HOH HOH . H 6 HOH A 13 313 15 HOH HOH . H 6 HOH A 14 314 16 HOH HOH . H 6 HOH A 15 315 17 HOH HOH . H 6 HOH A 16 316 23 HOH HOH . H 6 HOH A 17 317 24 HOH HOH . H 6 HOH A 18 318 25 HOH HOH . H 6 HOH A 19 319 26 HOH HOH . H 6 HOH A 20 320 27 HOH HOH . H 6 HOH A 21 321 28 HOH HOH . H 6 HOH A 22 322 30 HOH HOH . H 6 HOH A 23 323 31 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 FE FE1 SF4 . . . E 5 51.221 52.487 10.623 1 38.87 ? FE1 SF4 300 A 1 HETATM 2 FE FE2 SF4 . . . E 5 48.971 50.822 10.805 1 39.23 ? FE2 SF4 300 A 1 HETATM 3 FE FE3 SF4 . . . E 5 49.354 52.872 12.423 1 38.62 ? FE3 SF4 300 A 1 HETATM 4 FE FE4 SF4 . . . E 5 48.681 53.159 9.83 1 37.29 ? FE4 SF4 300 A 1 HETATM 5 S S1 SF4 . . . E 5 47.4 52.203 11.506 1 37.45 ? S1 SF4 300 A 1 HETATM 6 S S2 SF4 . . . E 5 50.049 54.255 10.988 1 38.74 ? S2 SF4 300 A 1 HETATM 7 S S3 SF4 . . . E 5 49.892 51.431 8.927 1 37.25 ? S3 SF4 300 A 1 HETATM 8 S S4 SF4 . . . E 5 50.655 51.228 12.37 1 37.54 ? S4 SF4 300 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 8 #