data_3PDI # _model_server_result.job_id XC0OaHnTrzwE1ga1QAE0aQ _model_server_result.datetime_utc '2024-12-26 20:50:21' _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 3pdi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":502}' # _entry.id 3PDI # _exptl.entry_id 3PDI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 741.393 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'L-Cluster (Fe8S9)' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.5 _cell.angle_gamma 90 _cell.entry_id 3PDI _cell.length_a 146.07 _cell.length_b 95.22 _cell.length_c 149.98 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,K,L 1 1 E,F,G,H,M,N,O,P 2 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 J N N ? 4 L N N ? 4 N N N ? 4 P 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 SG CYS 45 A CYS 37 1_555 I FE1 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc2 A SG CYS 132 A CYS 124 1_555 I FE3 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc3 I FE4 SF4 . A SF4 501 1_555 B SG CYS 44 B CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc4 C SG CYS 45 C CYS 37 1_555 K FE1 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc5 C SG CYS 132 C CYS 124 1_555 K FE3 SF4 . C SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc6 K FE4 SF4 . C SF4 501 1_555 D SG CYS 44 D CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc7 E SG CYS 45 E CYS 37 1_555 M FE1 SF4 . E SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc8 E SG CYS 132 E CYS 124 1_555 M FE3 SF4 . E SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc9 M FE4 SF4 . E SF4 501 1_555 F SG CYS 44 F CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc10 G SG CYS 45 G CYS 37 1_555 O FE1 SF4 . G SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc11 G SG CYS 132 G CYS 124 1_555 O FE3 SF4 . G SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc12 O FE4 SF4 . G SF4 501 1_555 H SG CYS 44 H CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? # _chem_comp.formula 'Fe8 H6 S9' _chem_comp.formula_weight 741.393 _chem_comp.id CZL _chem_comp.mon_nstd_flag . _chem_comp.name 'L-Cluster (Fe8S9)' _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 S1A FE1 CZL sing 83 n n FE4 FE1 CZL sing 84 n n FE3 FE1 CZL sing 85 n n S2A FE1 CZL sing 86 n n FE1 S4A CZL sing 87 n n S2B FE2 CZL sing 88 n n FE2 S1A CZL sing 89 n n FE2 FE4 CZL sing 90 n n FE2 FE3 CZL sing 91 n n FE2 S2A CZL sing 92 n n FE7 FE3 CZL sing 93 n n FE3 S2A CZL sing 94 n n FE3 S5A CZL sing 95 n n FE3 S4A CZL sing 96 n n FE5 FE4 CZL sing 97 n n S3A FE4 CZL sing 98 n n S1A FE4 CZL sing 99 n n FE4 S4A CZL sing 100 n n S1B FE5 CZL sing 101 n n FE6 FE5 CZL sing 102 n n FE5 S4B CZL sing 103 n n FE5 FE7 CZL sing 104 n n FE5 S3A CZL sing 105 n n S1B FE6 CZL sing 106 n n FE8 FE6 CZL sing 107 n n S3B FE6 CZL sing 108 n n FE6 S2B CZL sing 109 n n FE6 FE7 CZL sing 110 n n S3B FE7 CZL sing 111 n n S4B FE7 CZL sing 112 n n FE7 S5A CZL sing 113 n n S1B FE8 CZL sing 114 n n FE8 S3B CZL sing 115 n n FE8 S4B CZL sing 116 n n S1A HS1A CZL sing 117 n n S1B HS1B CZL sing 118 n n S2A HS2A CZL sing 119 n n S3B HS3B CZL sing 120 n n S4A HS4A CZL sing 121 n n S4B HS4B CZL sing 122 n n # _atom_sites.entry_id 3PDI _atom_sites.fract_transf_matrix[1][1] 0.006846 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000659 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010502 _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] 0.006698 _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 I 3 SF4 A 1 501 501 SF4 FS4 . J 4 CZL A 1 502 502 CZL CZL . K 3 SF4 C 1 501 501 SF4 FS4 . L 4 CZL C 1 502 502 CZL CZL . M 3 SF4 E 1 501 501 SF4 FS4 . N 4 CZL E 1 502 502 CZL CZL . O 3 SF4 G 1 501 501 SF4 FS4 . P 4 CZL G 1 502 502 CZL CZL . # 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 CZL . . . P 4 60.965 31.542 68.247 1 129.14 ? FE1 CZL 502 G 1 HETATM 2 FE FE2 CZL . . . P 4 60.387 31.042 70.8 1 91.55 ? FE2 CZL 502 G 1 HETATM 3 FE FE3 CZL . . . P 4 58.567 30.621 68.929 1 123.91 ? FE3 CZL 502 G 1 HETATM 4 FE FE4 CZL . . . P 4 59.287 33.102 69.559 1 82.4 ? FE4 CZL 502 G 1 HETATM 5 FE FE5 CZL . . . P 4 57.375 32.722 71.357 1 88.58 ? FE5 CZL 502 G 1 HETATM 6 FE FE6 CZL . . . P 4 58.548 30.761 72.702 1 62.63 ? FE6 CZL 502 G 1 HETATM 7 FE FE7 CZL . . . P 4 56.771 30.219 70.825 1 87.74 ? FE7 CZL 502 G 1 HETATM 8 FE FE8 CZL . . . P 4 55.992 31.277 73.144 1 82.43 ? FE8 CZL 502 G 1 HETATM 9 S S1A CZL . . . P 4 61.492 32.895 70.041 1 107.04 ? S1A CZL 502 G 1 HETATM 10 S S1B CZL . . . P 4 57.769 32.685 73.604 1 83.18 ? S1B CZL 502 G 1 HETATM 11 S S2A CZL . . . P 4 60.532 29.486 69.15 1 95.58 ? S2A CZL 502 G 1 HETATM 12 S S2B CZL . . . P 4 60.745 30.234 72.904 1 64.83 ? S2B CZL 502 G 1 HETATM 13 S S3A CZL . . . P 4 57.844 34.679 70.291 1 81.22 ? S3A CZL 502 G 1 HETATM 14 S S3B CZL . . . P 4 56.898 29.198 72.845 1 55 ? S3B CZL 502 G 1 HETATM 15 S S4A CZL . . . P 4 58.949 32.314 67.448 1 107.2 ? S4A CZL 502 G 1 HETATM 16 S S4B CZL . . . P 4 55.269 31.911 71.066 1 110.76 ? S4B CZL 502 G 1 HETATM 17 S S5A CZL . . . P 4 56.87 29.153 68.748 1 98.47 ? S5A CZL 502 G 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 408 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 17 #