data_4YPH # _model_server_result.job_id CVyRI0Cxpo8NrCD82k7tbg _model_server_result.datetime_utc '2024-11-02 22:33:03' _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 4yph # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 4YPH # _exptl.entry_id 4YPH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.64 _entity.id 4 _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 4YPH _cell.length_a 37.636 _cell.length_b 83.757 _cell.length_c 142.735 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YPH _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 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 _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 4 _struct_asym.id D _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 B O3' DC 5 B DC 5 1_555 B P 8OG 6 B 8OG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? covale ? covale2 B O3' 8OG 6 B 8OG 6 1_555 B P DT 7 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 A O SER 121 A SER 118 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc2 A O LEU 123 A LEU 120 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? metalc ? metalc3 A O VAL 126 A VAL 123 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc4 A SG CYS 201 A CYS 198 1_555 D FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc5 A SG CYS 208 A CYS 205 1_555 D FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc6 A SG CYS 211 A CYS 208 1_555 D FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc7 A SG CYS 217 A CYS 214 1_555 D FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc8 E NA NA . A NA 402 1_555 F O HOH . A HOH 540 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc9 E NA NA . A NA 402 1_555 C OP1 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? hydrog WATSON-CRICK hydrog1 B N1 DA 2 B DA 2 1_555 C N3 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 2 B DA 2 1_555 C O4 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 3 B DG 3 1_555 C N3 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 3 B DG 3 1_555 C O2 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 3 B DG 3 1_555 C N4 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 4 B DA 4 1_555 C N3 DT 9 C DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 4 B DA 4 1_555 C O4 DT 9 C DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 5 B DC 5 1_555 C N1 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 5 B DC 5 1_555 C O6 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 5 B DC 5 1_555 C N2 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog11 B N3 DT 7 B DT 7 1_555 C N1 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog12 B O2 DT 7 B DT 7 1_555 C N6 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 8 B DG 8 1_555 C N3 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 8 B DG 8 1_555 C O2 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 8 B DG 8 1_555 C N4 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 9 B DG 9 1_555 C N3 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 9 B DG 9 1_555 C O2 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 9 B DG 9 1_555 C N4 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DA 10 B DA 10 1_555 C N3 DT 3 C DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N6 DA 10 B DA 10 1_555 C O4 DT 3 C DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog21 B O2 DC 11 B DC 11 1_555 C 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 479 n n FE1 S3 SF4 sing 480 n n FE1 S4 SF4 sing 481 n n FE2 S1 SF4 sing 482 n n FE2 S3 SF4 sing 483 n n FE2 S4 SF4 sing 484 n n FE3 S1 SF4 sing 485 n n FE3 S2 SF4 sing 486 n n FE3 S4 SF4 sing 487 n n FE4 S1 SF4 sing 488 n n FE4 S2 SF4 sing 489 n n FE4 S3 SF4 sing 490 n n # _atom_sites.entry_id 4YPH _atom_sites.fract_transf_matrix[1][1] 0.02657 _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] 0.011939 _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] 0.007006 _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 SF4 A 1 401 400 SF4 SF4 . E 5 NA A 1 402 1 NA NA . F 6 HOH A 1 501 22 HOH HOH . F 6 HOH A 2 502 45 HOH HOH . F 6 HOH A 3 503 47 HOH HOH . F 6 HOH A 4 504 10 HOH HOH . F 6 HOH A 5 505 55 HOH HOH . F 6 HOH A 6 506 8 HOH HOH . F 6 HOH A 7 507 48 HOH HOH . F 6 HOH A 8 508 39 HOH HOH . F 6 HOH A 9 509 25 HOH HOH . F 6 HOH A 10 510 34 HOH HOH . F 6 HOH A 11 511 16 HOH HOH . F 6 HOH A 12 512 7 HOH HOH . F 6 HOH A 13 513 24 HOH HOH . F 6 HOH A 14 514 4 HOH HOH . F 6 HOH A 15 515 15 HOH HOH . F 6 HOH A 16 516 12 HOH HOH . F 6 HOH A 17 517 9 HOH HOH . F 6 HOH A 18 518 28 HOH HOH . F 6 HOH A 19 519 13 HOH HOH . F 6 HOH A 20 520 21 HOH HOH . F 6 HOH A 21 521 11 HOH HOH . F 6 HOH A 22 522 33 HOH HOH . F 6 HOH A 23 523 23 HOH HOH . F 6 HOH A 24 524 51 HOH HOH . F 6 HOH A 25 525 20 HOH HOH . F 6 HOH A 26 526 17 HOH HOH . F 6 HOH A 27 527 6 HOH HOH . F 6 HOH A 28 528 57 HOH HOH . F 6 HOH A 29 529 44 HOH HOH . F 6 HOH A 30 530 46 HOH HOH . F 6 HOH A 31 531 49 HOH HOH . F 6 HOH A 32 532 65 HOH HOH . F 6 HOH A 33 533 3 HOH HOH . F 6 HOH A 34 534 30 HOH HOH . F 6 HOH A 35 535 36 HOH HOH . F 6 HOH A 36 536 60 HOH HOH . F 6 HOH A 37 537 29 HOH HOH . F 6 HOH A 38 538 52 HOH HOH . F 6 HOH A 39 539 61 HOH HOH . F 6 HOH A 40 540 26 HOH HOH . F 6 HOH A 41 541 62 HOH HOH . F 6 HOH A 42 542 31 HOH HOH . F 6 HOH A 43 543 18 HOH HOH . G 6 HOH B 1 101 32 HOH HOH . G 6 HOH B 2 102 38 HOH HOH . G 6 HOH B 3 103 27 HOH HOH . G 6 HOH B 4 104 35 HOH HOH . G 6 HOH B 5 105 37 HOH HOH . G 6 HOH B 6 106 5 HOH HOH . H 6 HOH C 1 101 14 HOH HOH . H 6 HOH C 2 102 67 HOH HOH . H 6 HOH C 3 103 19 HOH HOH . H 6 HOH C 4 104 66 HOH HOH . H 6 HOH C 5 105 41 HOH HOH . H 6 HOH C 6 106 64 HOH HOH . H 6 HOH C 7 107 40 HOH HOH . H 6 HOH C 8 108 63 HOH HOH . H 6 HOH C 9 109 56 HOH HOH . H 6 HOH C 10 110 54 HOH HOH . H 6 HOH C 11 111 43 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 . . . D 4 -9.328 -15.863 1.423 1 44.04 ? FE1 SF4 401 A 1 HETATM 2 FE FE2 SF4 . . . D 4 -10.737 -13.365 1.092 1 48.33 ? FE2 SF4 401 A 1 HETATM 3 FE FE3 SF4 . . . D 4 -8.617 -13.603 3.016 1 43.15 ? FE3 SF4 401 A 1 HETATM 4 FE FE4 SF4 . . . D 4 -11.145 -14.884 3.506 1 48.31 ? FE4 SF4 401 A 1 HETATM 5 S S1 SF4 . . . D 4 -10.665 -12.789 3.176 1 40.81 ? S1 SF4 401 A 1 HETATM 6 S S2 SF4 . . . D 4 -9.09 -15.641 3.59 1 47.54 ? S2 SF4 401 A 1 HETATM 7 S S3 SF4 . . . D 4 -11.453 -15.365 1.411 1 43.13 ? S3 SF4 401 A 1 HETATM 8 S S4 SF4 . . . D 4 -8.643 -13.899 0.837 1 40.57 ? S4 SF4 401 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 8 #