data_4YT4 # _model_server_result.job_id Ob-sfXOjqxAYZOKhcmwRPA _model_server_result.datetime_utc '2024-11-07 08:55:07' _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 4yt4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4YT4 # _exptl.entry_id 4YT4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 686.323 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'iron-guanylyl pyridinol cofactor' _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 4YT4 _cell.length_a 59.81 _cell.length_b 59.81 _cell.length_c 183.43 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YT4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_465 y-1,x+1,-z 0 1 0 1 0 0 0 0 -1 -59.81 59.81 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 127 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 127 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id FE9 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id FE9 _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 2.384 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C21 H23 Fe N6 O13 P S 4' _chem_comp.formula_weight 686.323 _chem_comp.id FE9 _chem_comp.mon_nstd_flag . _chem_comp.name 'iron-guanylyl pyridinol cofactor' _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 O2' C2' FE9 sing 83 n n O6A C6A FE9 doub 84 n n C6A N1A FE9 sing 85 n n C6A C5A FE9 sing 86 n n N1A C2A FE9 sing 87 n n N7A C5A FE9 sing 88 n y N7A C8A FE9 doub 89 n y C5A C4A FE9 doub 90 n y C8A N9A FE9 sing 91 n y C2A N2A FE9 sing 92 n n C2A N3A FE9 doub 93 n n C2' C1' FE9 sing 94 n n C2' C3' FE9 sing 95 n n C4A N3A FE9 sing 96 n n C4A N9A FE9 sing 97 n y N9A C1' FE9 sing 98 n n O3' C3' FE9 sing 99 n n C1' O4' FE9 sing 100 n n C3' C4' FE9 sing 101 n n O4' C4' FE9 sing 102 n n C4' C5' FE9 sing 103 n n O1P P1 FE9 doub 104 n n C5' O5' FE9 sing 105 n n O5' P1 FE9 sing 106 n n P1 O2P FE9 sing 107 n n P1 O3P FE9 sing 108 n n O3P C4 FE9 sing 109 n n C3M C3 FE9 sing 110 n n C4 C3 FE9 doub 111 n n C4 C5 FE9 sing 112 n n C5M C5 FE9 sing 113 n n C3 C2 FE9 sing 114 n n C5 C6 FE9 doub 115 n n C2 O2 FE9 doub 116 n n C2 N1 FE9 sing 117 n n C6 N1 FE9 sing 118 n n C6 C7 FE9 sing 119 n n N1 FE FE9 sing 120 n n O1F C1F FE9 trip 121 n n C7 C8 FE9 sing 122 n n C1F FE FE9 sing 123 n n C8 FE FE9 sing 124 n n C8 O18 FE9 doub 125 n n FE C2F FE9 sing 126 n n C2F O2F FE9 trip 127 n n C7 H8 FE9 sing 128 n n C5M H9 FE9 sing 129 n n C5M H10 FE9 sing 130 n n C5M H11 FE9 sing 131 n n C3M H12 FE9 sing 132 n n C3M H13 FE9 sing 133 n n C3M H14 FE9 sing 134 n n O2P H15 FE9 sing 135 n n C5' H16 FE9 sing 136 n n C5' H17 FE9 sing 137 n n C4' H18 FE9 sing 138 n n C1' H19 FE9 sing 139 n n C2' H20 FE9 sing 140 n n O2' H21 FE9 sing 141 n n C3' H22 FE9 sing 142 n n O3' H23 FE9 sing 143 n n N2A H24 FE9 sing 144 n n N2A H25 FE9 sing 145 n n N1A H26 FE9 sing 146 n n C8A H27 FE9 sing 147 n n C7 H1 FE9 sing 148 n n FE O1 FE9 sing 149 n n FE S1 FE9 sing 150 n n S1 HS1 FE9 sing 151 n n O1 H2 FE9 sing 152 n n # _atom_sites.entry_id 4YT4 _atom_sites.fract_transf_matrix[1][1] 0.01672 _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] 0.01672 _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] 0.005452 _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 B 2 FE9 A 1 401 1 FE9 FE9 . C 3 HOH A 1 501 105 HOH HOH . C 3 HOH A 2 502 41 HOH HOH . C 3 HOH A 3 503 109 HOH HOH . C 3 HOH A 4 504 66 HOH HOH . C 3 HOH A 5 505 34 HOH HOH . C 3 HOH A 6 506 104 HOH HOH . C 3 HOH A 7 507 47 HOH HOH . C 3 HOH A 8 508 62 HOH HOH . C 3 HOH A 9 509 48 HOH HOH . C 3 HOH A 10 510 52 HOH HOH . C 3 HOH A 11 511 9 HOH HOH . C 3 HOH A 12 512 3 HOH HOH . C 3 HOH A 13 513 58 HOH HOH . C 3 HOH A 14 514 10 HOH HOH . C 3 HOH A 15 515 8 HOH HOH . C 3 HOH A 16 516 92 HOH HOH . C 3 HOH A 17 517 55 HOH HOH . C 3 HOH A 18 518 70 HOH HOH . C 3 HOH A 19 519 107 HOH HOH . C 3 HOH A 20 520 78 HOH HOH . C 3 HOH A 21 521 15 HOH HOH . C 3 HOH A 22 522 79 HOH HOH . C 3 HOH A 23 523 68 HOH HOH . C 3 HOH A 24 524 51 HOH HOH . C 3 HOH A 25 525 24 HOH HOH . C 3 HOH A 26 526 40 HOH HOH . C 3 HOH A 27 527 29 HOH HOH . C 3 HOH A 28 528 82 HOH HOH . C 3 HOH A 29 529 45 HOH HOH . C 3 HOH A 30 530 50 HOH HOH . C 3 HOH A 31 531 46 HOH HOH . C 3 HOH A 32 532 11 HOH HOH . C 3 HOH A 33 533 20 HOH HOH . C 3 HOH A 34 534 57 HOH HOH . C 3 HOH A 35 535 110 HOH HOH . C 3 HOH A 36 536 53 HOH HOH . C 3 HOH A 37 537 60 HOH HOH . C 3 HOH A 38 538 74 HOH HOH . C 3 HOH A 39 539 76 HOH HOH . C 3 HOH A 40 540 102 HOH HOH . C 3 HOH A 41 541 101 HOH HOH . C 3 HOH A 42 542 19 HOH HOH . C 3 HOH A 43 543 69 HOH HOH . C 3 HOH A 44 544 108 HOH HOH . C 3 HOH A 45 545 95 HOH HOH . C 3 HOH A 46 546 28 HOH HOH . C 3 HOH A 47 547 96 HOH HOH . C 3 HOH A 48 548 61 HOH HOH . C 3 HOH A 49 549 100 HOH HOH . C 3 HOH A 50 550 89 HOH HOH . C 3 HOH A 51 551 85 HOH HOH . C 3 HOH A 52 552 1 HOH HOH . C 3 HOH A 53 553 2 HOH HOH . C 3 HOH A 54 554 4 HOH HOH . C 3 HOH A 55 555 5 HOH HOH . C 3 HOH A 56 556 6 HOH HOH . C 3 HOH A 57 557 12 HOH HOH . C 3 HOH A 58 558 13 HOH HOH . C 3 HOH A 59 559 14 HOH HOH . C 3 HOH A 60 560 16 HOH HOH . C 3 HOH A 61 561 17 HOH HOH . C 3 HOH A 62 562 18 HOH HOH . C 3 HOH A 63 563 21 HOH HOH . C 3 HOH A 64 564 22 HOH HOH . C 3 HOH A 65 565 23 HOH HOH . C 3 HOH A 66 566 25 HOH HOH . C 3 HOH A 67 567 26 HOH HOH . C 3 HOH A 68 568 27 HOH HOH . C 3 HOH A 69 569 30 HOH HOH . C 3 HOH A 70 570 31 HOH HOH . C 3 HOH A 71 571 32 HOH HOH . C 3 HOH A 72 572 33 HOH HOH . C 3 HOH A 73 573 35 HOH HOH . C 3 HOH A 74 574 36 HOH HOH . C 3 HOH A 75 575 37 HOH HOH . C 3 HOH A 76 576 38 HOH HOH . C 3 HOH A 77 577 39 HOH HOH . C 3 HOH A 78 578 42 HOH HOH . C 3 HOH A 79 579 43 HOH HOH . C 3 HOH A 80 580 44 HOH HOH . C 3 HOH A 81 581 49 HOH HOH . C 3 HOH A 82 582 54 HOH HOH . C 3 HOH A 83 583 56 HOH HOH . C 3 HOH A 84 584 59 HOH HOH . C 3 HOH A 85 585 63 HOH HOH . C 3 HOH A 86 586 64 HOH HOH . C 3 HOH A 87 587 65 HOH HOH . C 3 HOH A 88 588 67 HOH HOH . C 3 HOH A 89 589 71 HOH HOH . C 3 HOH A 90 590 72 HOH HOH . C 3 HOH A 91 591 73 HOH HOH . C 3 HOH A 92 592 75 HOH HOH . C 3 HOH A 93 593 77 HOH HOH . C 3 HOH A 94 594 80 HOH HOH . C 3 HOH A 95 595 81 HOH HOH . C 3 HOH A 96 596 83 HOH HOH . C 3 HOH A 97 597 84 HOH HOH . C 3 HOH A 98 598 86 HOH HOH . C 3 HOH A 99 599 87 HOH HOH . C 3 HOH A 100 600 88 HOH HOH . C 3 HOH A 101 601 90 HOH HOH . C 3 HOH A 102 602 91 HOH HOH . C 3 HOH A 103 603 93 HOH HOH . C 3 HOH A 104 604 94 HOH HOH . C 3 HOH A 105 605 97 HOH HOH . C 3 HOH A 106 606 98 HOH HOH . C 3 HOH A 107 607 99 HOH HOH . C 3 HOH A 108 608 103 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 O O2 FE9 . . . B 2 -7.398 20.073 -3.508 1 74.95 ? O2 FE9 401 A 1 HETATM 2 FE FE FE9 . . . B 2 -7.956 21.286 -6.481 1 83.47 2 FE FE9 401 A 1 HETATM 3 C C1F FE9 . . . B 2 -8.471 19.339 -7.288 1 77.29 ? C1F FE9 401 A 1 HETATM 4 O O1F FE9 . . . B 2 -8.73 18.308 -7.705 1 78.72 ? O1F FE9 401 A 1 HETATM 5 C C2F FE9 . . . B 2 -9.703 21.988 -7.547 1 75.71 ? C2F FE9 401 A 1 HETATM 6 O O2F FE9 . . . B 2 -10.642 22.351 -8.075 1 73.75 ? O2F FE9 401 A 1 HETATM 7 C C8 FE9 . . . B 2 -7.163 21.913 -8.096 1 74.03 ? C8 FE9 401 A 1 HETATM 8 O O18 FE9 . . . B 2 -7.582 22.517 -9.125 1 65.55 ? O18 FE9 401 A 1 HETATM 9 C C7 FE9 . . . B 2 -5.538 21.456 -8.007 1 70.15 ? C7 FE9 401 A 1 HETATM 10 C C6 FE9 . . . B 2 -5.164 20.74 -6.316 1 72.44 ? C6 FE9 401 A 1 HETATM 11 N N1 FE9 . . . B 2 -6.501 20.679 -5.554 1 75.24 ? N1 FE9 401 A 1 HETATM 12 C C5 FE9 . . . B 2 -3.875 20.295 -5.763 1 68.96 ? C5 FE9 401 A 1 HETATM 13 C C5M FE9 . . . B 2 -2.7 20.484 -6.705 1 66.75 ? C5M FE9 401 A 1 HETATM 14 C C4 FE9 . . . B 2 -3.786 19.767 -4.371 1 69.37 ? C4 FE9 401 A 1 HETATM 15 C C3 FE9 . . . B 2 -5.084 19.702 -3.594 1 69.38 ? C3 FE9 401 A 1 HETATM 16 C C3M FE9 . . . B 2 -5.023 19.163 -2.19 1 63.95 ? C3M FE9 401 A 1 HETATM 17 C C2 FE9 . . . B 2 -6.425 20.163 -4.197 1 72.14 ? C2 FE9 401 A 1 HETATM 18 O O3P FE9 . . . B 2 -2.584 19.331 -3.779 1 72.49 ? O3P FE9 401 A 1 HETATM 19 P P1 FE9 . . . B 2 -1.974 17.875 -4.131 1 81.46 ? P1 FE9 401 A 1 HETATM 20 O O1P FE9 . . . B 2 -3.008 16.792 -4.335 1 77.74 ? O1P FE9 401 A 1 HETATM 21 O O2P FE9 . . . B 2 -0.96 17.535 -3.05 1 74.32 -1 O2P FE9 401 A 1 HETATM 22 O O5' FE9 . . . B 2 -1.174 17.772 -5.508 1 77.22 ? O5' FE9 401 A 1 HETATM 23 C C5' FE9 . . . B 2 0.18 18.162 -5.491 1 70.45 ? C5' FE9 401 A 1 HETATM 24 C C4' FE9 . . . B 2 0.976 17.291 -6.464 1 66.57 ? C4' FE9 401 A 1 HETATM 25 O O4' FE9 . . . B 2 2.259 18.131 -6.861 1 61.71 ? O4' FE9 401 A 1 HETATM 26 C C1' FE9 . . . B 2 3.438 17.222 -6.353 1 61.06 ? C1' FE9 401 A 1 HETATM 27 C C2' FE9 . . . B 2 2.946 16.452 -5.377 1 61.6 ? C2' FE9 401 A 1 HETATM 28 O O2' FE9 . . . B 2 3.687 15.232 -5.087 1 59.42 ? O2' FE9 401 A 1 HETATM 29 C C3' FE9 . . . B 2 1.371 16.172 -5.884 1 64.1 ? C3' FE9 401 A 1 HETATM 30 O O3' FE9 . . . B 2 1.229 15.015 -6.757 1 59.96 ? O3' FE9 401 A 1 HETATM 31 N N9A FE9 . . . B 2 4.696 17.919 -6.062 1 58.8 ? N9A FE9 401 A 1 HETATM 32 C C4A FE9 . . . B 2 5.48 18.299 -7.126 1 53.46 ? C4A FE9 401 A 1 HETATM 33 N N3A FE9 . . . B 2 5.266 18.168 -8.565 1 52.24 ? N3A FE9 401 A 1 HETATM 34 C C2A FE9 . . . B 2 6.268 18.661 -9.484 1 48.42 ? C2A FE9 401 A 1 HETATM 35 N N2A FE9 . . . B 2 6.058 18.533 -10.88 1 45.26 ? N2A FE9 401 A 1 HETATM 36 N N1A FE9 . . . B 2 7.473 19.264 -9.003 1 48.92 ? N1A FE9 401 A 1 HETATM 37 C C6A FE9 . . . B 2 7.687 19.387 -7.615 1 51.36 ? C6A FE9 401 A 1 HETATM 38 O O6A FE9 . . . B 2 8.716 19.923 -7.219 1 51.41 ? O6A FE9 401 A 1 HETATM 39 C C5A FE9 . . . B 2 6.623 18.88 -6.638 1 54.21 ? C5A FE9 401 A 1 HETATM 40 N N7A FE9 . . . B 2 6.529 18.846 -5.267 1 54.58 ? N7A FE9 401 A 1 HETATM 41 C C8A FE9 . . . B 2 5.354 18.254 -4.912 1 55.22 ? C8A FE9 401 A 1 HETATM 42 O O1 FE9 . . . B 2 -9.389 21.165 -4.893 1 72.96 ? O1 FE9 401 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 42 #