data_2YVJ # _model_server_result.job_id BZcrpoNVUNy1d1iyOOSXjg _model_server_result.datetime_utc '2024-11-24 03:07:25' _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 2yvj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":500}' # _entry.id 2YVJ # _exptl.entry_id 2YVJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 175.82 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FE2/S2 (INORGANIC) 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 115.81 _cell.angle_gamma 90 _cell.entry_id 2YVJ _cell.length_a 60.596 _cell.length_b 173.715 _cell.length_c 60.976 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YVJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_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,K _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 F _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 metalc ? metalc1 B SG CYS 43 B CYS 43 1_555 F FE1 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc2 B ND1 HIS 45 B HIS 45 1_555 F FE2 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc3 B SG CYS 63 B CYS 63 1_555 F FE1 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? metalc ? metalc4 B ND1 HIS 66 B HIS 66 1_555 F FE2 FES . B FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.659 ? # _chem_comp.formula 'Fe2 S2' _chem_comp.formula_weight 175.82 _chem_comp.id FES _chem_comp.mon_nstd_flag . _chem_comp.name 'FE2/S2 (INORGANIC) 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 S1 FES sing 174 n n FE1 S2 FES sing 175 n n FE2 S1 FES sing 176 n n FE2 S2 FES sing 177 n n # _atom_sites.entry_id 2YVJ _atom_sites.fract_transf_matrix[1][1] 0.016503 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007981 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005757 _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] 0.018217 _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 3 FAD A 1 501 501 FAD FAD . E 4 NAI A 1 503 503 NAI NAI . F 5 FES B 1 500 500 FES FES . G 3 FAD P 1 502 502 FAD FAD . H 4 NAI P 1 504 504 NAI NAI . I 6 HOH A 1 504 1 HOH HOH . I 6 HOH A 2 505 2 HOH HOH . I 6 HOH A 3 506 3 HOH HOH . I 6 HOH A 4 507 4 HOH HOH . I 6 HOH A 5 508 7 HOH HOH . I 6 HOH A 6 509 10 HOH HOH . I 6 HOH A 7 510 11 HOH HOH . I 6 HOH A 8 511 13 HOH HOH . I 6 HOH A 9 512 16 HOH HOH . I 6 HOH A 10 513 19 HOH HOH . I 6 HOH A 11 514 21 HOH HOH . I 6 HOH A 12 515 24 HOH HOH . I 6 HOH A 13 516 25 HOH HOH . I 6 HOH A 14 517 28 HOH HOH . I 6 HOH A 15 518 31 HOH HOH . I 6 HOH A 16 519 33 HOH HOH . I 6 HOH A 17 520 43 HOH HOH . I 6 HOH A 18 521 44 HOH HOH . I 6 HOH A 19 522 46 HOH HOH . I 6 HOH A 20 523 50 HOH HOH . I 6 HOH A 21 524 51 HOH HOH . I 6 HOH A 22 525 52 HOH HOH . I 6 HOH A 23 526 54 HOH HOH . I 6 HOH A 24 527 55 HOH HOH . I 6 HOH A 25 528 57 HOH HOH . I 6 HOH A 26 529 60 HOH HOH . I 6 HOH A 27 530 61 HOH HOH . I 6 HOH A 28 531 62 HOH HOH . I 6 HOH A 29 532 66 HOH HOH . I 6 HOH A 30 533 68 HOH HOH . I 6 HOH A 31 534 70 HOH HOH . I 6 HOH A 32 535 77 HOH HOH . J 6 HOH B 1 501 5 HOH HOH . J 6 HOH B 2 502 56 HOH HOH . J 6 HOH B 3 503 64 HOH HOH . J 6 HOH B 4 504 78 HOH HOH . K 6 HOH P 1 505 6 HOH HOH . K 6 HOH P 2 506 8 HOH HOH . K 6 HOH P 3 507 9 HOH HOH . K 6 HOH P 4 508 12 HOH HOH . K 6 HOH P 5 509 14 HOH HOH . K 6 HOH P 6 510 15 HOH HOH . K 6 HOH P 7 511 17 HOH HOH . K 6 HOH P 8 512 18 HOH HOH . K 6 HOH P 9 513 20 HOH HOH . K 6 HOH P 10 514 22 HOH HOH . K 6 HOH P 11 515 23 HOH HOH . K 6 HOH P 12 516 26 HOH HOH . K 6 HOH P 13 517 27 HOH HOH . K 6 HOH P 14 518 29 HOH HOH . K 6 HOH P 15 519 30 HOH HOH . K 6 HOH P 16 520 32 HOH HOH . K 6 HOH P 17 521 34 HOH HOH . K 6 HOH P 18 522 35 HOH HOH . K 6 HOH P 19 523 36 HOH HOH . K 6 HOH P 20 524 37 HOH HOH . K 6 HOH P 21 525 38 HOH HOH . K 6 HOH P 22 526 39 HOH HOH . K 6 HOH P 23 527 40 HOH HOH . K 6 HOH P 24 528 41 HOH HOH . K 6 HOH P 25 529 42 HOH HOH . K 6 HOH P 26 530 45 HOH HOH . K 6 HOH P 27 531 47 HOH HOH . K 6 HOH P 28 532 48 HOH HOH . K 6 HOH P 29 533 49 HOH HOH . K 6 HOH P 30 534 53 HOH HOH . K 6 HOH P 31 535 58 HOH HOH . K 6 HOH P 32 536 59 HOH HOH . K 6 HOH P 33 537 63 HOH HOH . K 6 HOH P 34 538 65 HOH HOH . K 6 HOH P 35 539 67 HOH HOH . K 6 HOH P 36 540 69 HOH HOH . K 6 HOH P 37 541 71 HOH HOH . K 6 HOH P 38 542 72 HOH HOH . K 6 HOH P 39 543 73 HOH HOH . K 6 HOH P 40 544 74 HOH HOH . K 6 HOH P 41 545 75 HOH HOH . K 6 HOH P 42 546 76 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 FES . . . F 5 -4.776 -26.991 2.808 1 37.37 ? FE1 FES 500 B 1 HETATM 2 FE FE2 FES . . . F 5 -4.033 -26.289 5.29 1 35.5 ? FE2 FES 500 B 1 HETATM 3 S S1 FES . . . F 5 -5.53 -27.814 4.707 1 37.54 ? S1 FES 500 B 1 HETATM 4 S S2 FES . . . F 5 -3.066 -25.714 3.39 1 34.13 ? S2 FES 500 B 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 362 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 4 #