data_2YVJ # _model_server_result.job_id 02dNF8l1lozdltQ7S7VR4g _model_server_result.datetime_utc '2024-11-06 01:37:15' _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":"G","auth_seq_id":502}' # _entry.id 2YVJ # _exptl.entry_id 2YVJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 785.55 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FLAVIN-ADENINE DINUCLEOTIDE' _entity.pdbx_number_of_molecules 2 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G 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 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 'C27 H33 N9 O15 P2' _chem_comp.formula_weight 785.55 _chem_comp.id FAD _chem_comp.mon_nstd_flag . _chem_comp.name 'FLAVIN-ADENINE DINUCLEOTIDE' _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 PA O1A FAD doub 83 n n PA O2A FAD sing 84 n n PA O5B FAD sing 85 n n PA O3P FAD sing 86 n n O2A HOA2 FAD sing 87 n n O5B C5B FAD sing 88 n n C5B C4B FAD sing 89 n n C5B H51A FAD sing 90 n n C5B H52A FAD sing 91 n n C4B O4B FAD sing 92 n n C4B C3B FAD sing 93 n n C4B H4B FAD sing 94 n n O4B C1B FAD sing 95 n n C3B O3B FAD sing 96 n n C3B C2B FAD sing 97 n n C3B H3B FAD sing 98 n n O3B HO3A FAD sing 99 n n C2B O2B FAD sing 100 n n C2B C1B FAD sing 101 n n C2B H2B FAD sing 102 n n O2B HO2A FAD sing 103 n n C1B N9A FAD sing 104 n n C1B H1B FAD sing 105 n n N9A C8A FAD sing 106 n y N9A C4A FAD sing 107 n y C8A N7A FAD doub 108 n y C8A H8A FAD sing 109 n n N7A C5A FAD sing 110 n y C5A C6A FAD sing 111 n y C5A C4A FAD doub 112 n y C6A N6A FAD sing 113 n n C6A N1A FAD doub 114 n y N6A H61A FAD sing 115 n n N6A H62A FAD sing 116 n n N1A C2A FAD sing 117 n y C2A N3A FAD doub 118 n y C2A H2A FAD sing 119 n n N3A C4A FAD sing 120 n y N1 C2 FAD sing 121 n n N1 C10 FAD doub 122 n n C2 O2 FAD doub 123 n n C2 N3 FAD sing 124 n n N3 C4 FAD sing 125 n n N3 HN3 FAD sing 126 n n C4 O4 FAD doub 127 n n C4 C4X FAD sing 128 n n C4X N5 FAD doub 129 n n C4X C10 FAD sing 130 n n N5 C5X FAD sing 131 n n C5X C6 FAD doub 132 n y C5X C9A FAD sing 133 n y C6 C7 FAD sing 134 n y C6 H6 FAD sing 135 n n C7 C7M FAD sing 136 n n C7 C8 FAD doub 137 n y C7M HM71 FAD sing 138 n n C7M HM72 FAD sing 139 n n C7M HM73 FAD sing 140 n n C8 C8M FAD sing 141 n n C8 C9 FAD sing 142 n y C8M HM81 FAD sing 143 n n C8M HM82 FAD sing 144 n n C8M HM83 FAD sing 145 n n C9 C9A FAD doub 146 n y C9 H9 FAD sing 147 n n C9A N10 FAD sing 148 n n N10 C10 FAD sing 149 n n N10 C1' FAD sing 150 n n C1' C2' FAD sing 151 n n C1' "H1'1" FAD sing 152 n n C1' "H1'2" FAD sing 153 n n C2' O2' FAD sing 154 n n C2' C3' FAD sing 155 n n C2' H2' FAD sing 156 n n O2' HO2' FAD sing 157 n n C3' O3' FAD sing 158 n n C3' C4' FAD sing 159 n n C3' H3' FAD sing 160 n n O3' HO3' FAD sing 161 n n C4' O4' FAD sing 162 n n C4' C5' FAD sing 163 n n C4' H4' FAD sing 164 n n O4' HO4' FAD sing 165 n n C5' O5' FAD sing 166 n n C5' "H5'1" FAD sing 167 n n C5' "H5'2" FAD sing 168 n n O5' P FAD sing 169 n n P O1P FAD doub 170 n n P O2P FAD sing 171 n n P O3P FAD sing 172 n n O2P HOP2 FAD sing 173 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 P PA FAD . . . G 3 11.996 20.817 20.651 1 27.35 ? PA FAD 502 P 1 HETATM 2 O O1A FAD . . . G 3 10.685 20.632 20.023 1 30.34 ? O1A FAD 502 P 1 HETATM 3 O O2A FAD . . . G 3 12.209 21.844 21.704 1 34.1 ? O2A FAD 502 P 1 HETATM 4 O O5B FAD . . . G 3 13 21.161 19.436 1 34.91 ? O5B FAD 502 P 1 HETATM 5 C C5B FAD . . . G 3 13.083 20.403 18.227 1 36 ? C5B FAD 502 P 1 HETATM 6 C C4B FAD . . . G 3 13.368 21.404 17.109 1 24.8 ? C4B FAD 502 P 1 HETATM 7 O O4B FAD . . . G 3 13.345 20.623 15.877 1 30.32 ? O4B FAD 502 P 1 HETATM 8 C C3B FAD . . . G 3 12.261 22.472 16.947 1 27.09 ? C3B FAD 502 P 1 HETATM 9 O O3B FAD . . . G 3 12.756 23.794 16.925 1 28.68 ? O3B FAD 502 P 1 HETATM 10 C C2B FAD . . . G 3 11.621 22.09 15.613 1 30.95 ? C2B FAD 502 P 1 HETATM 11 O O2B FAD . . . G 3 11.036 23.124 14.85 1 34.49 ? O2B FAD 502 P 1 HETATM 12 C C1B FAD . . . G 3 12.804 21.46 14.87 1 36.6 ? C1B FAD 502 P 1 HETATM 13 N N9A FAD . . . G 3 12.348 20.736 13.707 1 25.64 ? N9A FAD 502 P 1 HETATM 14 C C8A FAD . . . G 3 11.312 19.882 13.583 1 22.96 ? C8A FAD 502 P 1 HETATM 15 N N7A FAD . . . G 3 11.183 19.386 12.367 1 32.84 ? N7A FAD 502 P 1 HETATM 16 C C5A FAD . . . G 3 12.257 19.946 11.679 1 32.96 ? C5A FAD 502 P 1 HETATM 17 C C6A FAD . . . G 3 12.611 19.892 10.298 1 26.47 ? C6A FAD 502 P 1 HETATM 18 N N6A FAD . . . G 3 11.935 19.124 9.439 1 21.84 ? N6A FAD 502 P 1 HETATM 19 N N1A FAD . . . G 3 13.701 20.581 9.914 1 19.78 ? N1A FAD 502 P 1 HETATM 20 C C2A FAD . . . G 3 14.32 21.346 10.831 1 16.8 ? C2A FAD 502 P 1 HETATM 21 N N3A FAD . . . G 3 14.022 21.597 12.102 1 21.2 ? N3A FAD 502 P 1 HETATM 22 C C4A FAD . . . G 3 12.936 20.803 12.455 1 32.27 ? C4A FAD 502 P 1 HETATM 23 N N1 FAD . . . G 3 9.671 20.579 30.434 1 35.81 ? N1 FAD 502 P 1 HETATM 24 C C2 FAD . . . G 3 9.944 20.469 31.752 1 36.74 ? C2 FAD 502 P 1 HETATM 25 O O2 FAD . . . G 3 10.478 19.433 32.229 1 39.67 ? O2 FAD 502 P 1 HETATM 26 N N3 FAD . . . G 3 9.615 21.501 32.632 1 27.43 ? N3 FAD 502 P 1 HETATM 27 C C4 FAD . . . G 3 9.01 22.677 32.214 1 30.71 ? C4 FAD 502 P 1 HETATM 28 O O4 FAD . . . G 3 8.775 23.591 33.04 1 29.77 ? O4 FAD 502 P 1 HETATM 29 C C4X FAD . . . G 3 8.731 22.766 30.835 1 31.03 ? C4X FAD 502 P 1 HETATM 30 N N5 FAD . . . G 3 8.137 23.943 30.352 1 27.69 ? N5 FAD 502 P 1 HETATM 31 C C5X FAD . . . G 3 7.848 23.989 28.994 1 29.44 ? C5X FAD 502 P 1 HETATM 32 C C6 FAD . . . G 3 7.261 25.151 28.442 1 34.1 ? C6 FAD 502 P 1 HETATM 33 C C7 FAD . . . G 3 6.918 25.223 27.129 1 27.15 ? C7 FAD 502 P 1 HETATM 34 C C7M FAD . . . G 3 6.284 26.495 26.57 1 32.97 ? C7M FAD 502 P 1 HETATM 35 C C8 FAD . . . G 3 7.256 24.189 26.267 1 19.38 ? C8 FAD 502 P 1 HETATM 36 C C8M FAD . . . G 3 6.935 24.27 24.793 1 35.07 ? C8M FAD 502 P 1 HETATM 37 C C9 FAD . . . G 3 7.872 23.037 26.799 1 25.41 ? C9 FAD 502 P 1 HETATM 38 C C9A FAD . . . G 3 8.173 22.917 28.124 1 27.88 ? C9A FAD 502 P 1 HETATM 39 N N10 FAD . . . G 3 8.832 21.77 28.639 1 31.97 ? N10 FAD 502 P 1 HETATM 40 C C10 FAD . . . G 3 9.084 21.706 29.973 1 30.6 ? C10 FAD 502 P 1 HETATM 41 C C1' FAD . . . G 3 9.231 20.658 27.778 1 44.59 ? C1' FAD 502 P 1 HETATM 42 C C2' FAD . . . G 3 10.658 20.733 27.234 1 44.13 ? C2' FAD 502 P 1 HETATM 43 O O2' FAD . . . G 3 11.084 22.082 27.063 1 62.13 ? O2' FAD 502 P 1 HETATM 44 C C3' FAD . . . G 3 10.691 19.921 25.944 1 26.41 ? C3' FAD 502 P 1 HETATM 45 O O3' FAD . . . G 3 10.675 18.57 26.416 1 37.9 ? O3' FAD 502 P 1 HETATM 46 C C4' FAD . . . G 3 11.998 20.138 25.162 1 35.23 ? C4' FAD 502 P 1 HETATM 47 O O4' FAD . . . G 3 12.097 21.47 24.677 1 29.6 ? O4' FAD 502 P 1 HETATM 48 C C5' FAD . . . G 3 12.122 19.125 24.05 1 38.14 ? C5' FAD 502 P 1 HETATM 49 O O5' FAD . . . G 3 13.466 19.063 23.582 1 33.4 ? O5' FAD 502 P 1 HETATM 50 P P FAD . . . G 3 13.772 18.754 22.034 1 29.86 ? P FAD 502 P 1 HETATM 51 O O1P FAD . . . G 3 15.054 19.486 21.821 1 27.94 ? O1P FAD 502 P 1 HETATM 52 O O2P FAD . . . G 3 13.661 17.321 21.772 1 17.26 ? O2P FAD 502 P 1 HETATM 53 O O3P FAD . . . G 3 12.574 19.434 21.219 1 22.52 ? O3P FAD 502 P 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 53 #