data_2YVJ # _model_server_result.job_id tn2sFb8wYX7umziLzBjC5Q _model_server_result.datetime_utc '2024-11-06 01:36:01' _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":"D","auth_seq_id":501}' # _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 . . . D 3 10.036 -20.974 16.632 1 28.77 ? PA FAD 501 A 1 HETATM 2 O O1A FAD . . . D 3 9.979 -21.259 18.088 1 33.6 ? O1A FAD 501 A 1 HETATM 3 O O2A FAD . . . D 3 9.152 -21.713 15.701 1 33.43 ? O2A FAD 501 A 1 HETATM 4 O O5B FAD . . . D 3 11.581 -21.218 16.243 1 30.74 ? O5B FAD 501 A 1 HETATM 5 C C5B FAD . . . D 3 12.567 -20.828 17.22 1 28.26 ? C5B FAD 501 A 1 HETATM 6 C C4B FAD . . . D 3 13.715 -21.828 17.148 1 31.37 ? C4B FAD 501 A 1 HETATM 7 O O4B FAD . . . D 3 14.842 -21.138 17.761 1 21.46 ? O4B FAD 501 A 1 HETATM 8 C C3B FAD . . . D 3 13.523 -23.112 17.999 1 32.39 ? C3B FAD 501 A 1 HETATM 9 O O3B FAD . . . D 3 14.261 -24.216 17.497 1 39.13 ? O3B FAD 501 A 1 HETATM 10 C C2B FAD . . . D 3 14.138 -22.577 19.303 1 35.98 ? C2B FAD 501 A 1 HETATM 11 O O2B FAD . . . D 3 14.36 -23.471 20.364 1 50.28 ? O2B FAD 501 A 1 HETATM 12 C C1B FAD . . . D 3 15.422 -21.956 18.755 1 19.9 ? C1B FAD 501 A 1 HETATM 13 N N9A FAD . . . D 3 16.143 -21.123 19.682 1 34.89 ? N9A FAD 501 A 1 HETATM 14 C C8A FAD . . . D 3 15.69 -20.241 20.611 1 33.92 ? C8A FAD 501 A 1 HETATM 15 N N7A FAD . . . D 3 16.649 -19.663 21.321 1 37.12 ? N7A FAD 501 A 1 HETATM 16 C C5A FAD . . . D 3 17.823 -20.159 20.751 1 46.49 ? C5A FAD 501 A 1 HETATM 17 C C6A FAD . . . D 3 19.205 -19.958 21.044 1 43.93 ? C6A FAD 501 A 1 HETATM 18 N N6A FAD . . . D 3 19.615 -19.121 22.005 1 64.02 ? N6A FAD 501 A 1 HETATM 19 N N1A FAD . . . D 3 20.105 -20.703 20.374 1 28.28 ? N1A FAD 501 A 1 HETATM 20 C C2A FAD . . . D 3 19.667 -21.522 19.402 1 31.92 ? C2A FAD 501 A 1 HETATM 21 N N3A FAD . . . D 3 18.414 -21.779 19.019 1 46.77 ? N3A FAD 501 A 1 HETATM 22 C C4A FAD . . . D 3 17.529 -21.031 19.768 1 47.44 ? C4A FAD 501 A 1 HETATM 23 N N1 FAD . . . D 3 0.05 -20.606 14.31 1 33.48 ? N1 FAD 501 A 1 HETATM 24 C C2 FAD . . . D 3 -0.963 -20.483 13.432 1 31.9 ? C2 FAD 501 A 1 HETATM 25 O O2 FAD . . . D 3 -1.077 -19.524 12.618 1 26.12 ? O2 FAD 501 A 1 HETATM 26 N N3 FAD . . . D 3 -1.959 -21.45 13.407 1 34.79 ? N3 FAD 501 A 1 HETATM 27 C C4 FAD . . . D 3 -2.01 -22.557 14.227 1 39.26 ? C4 FAD 501 A 1 HETATM 28 O O4 FAD . . . D 3 -2.938 -23.391 14.102 1 32.44 ? O4 FAD 501 A 1 HETATM 29 C C4X FAD . . . D 3 -0.93 -22.67 15.12 1 44.64 ? C4X FAD 501 A 1 HETATM 30 N N5 FAD . . . D 3 -0.892 -23.772 15.987 1 31.16 ? N5 FAD 501 A 1 HETATM 31 C C5X FAD . . . D 3 0.163 -23.848 16.872 1 29.94 ? C5X FAD 501 A 1 HETATM 32 C C6 FAD . . . D 3 0.203 -24.944 17.762 1 26.79 ? C6 FAD 501 A 1 HETATM 33 C C7 FAD . . . D 3 1.249 -25.14 18.596 1 32.05 ? C7 FAD 501 A 1 HETATM 34 C C7M FAD . . . D 3 1.252 -26.331 19.55 1 29.19 ? C7M FAD 501 A 1 HETATM 35 C C8 FAD . . . D 3 2.319 -24.262 18.559 1 28.74 ? C8 FAD 501 A 1 HETATM 36 C C8M FAD . . . D 3 3.471 -24.448 19.517 1 43.32 ? C8M FAD 501 A 1 HETATM 37 C C9 FAD . . . D 3 2.269 -23.117 17.714 1 28.29 ? C9 FAD 501 A 1 HETATM 38 C C9A FAD . . . D 3 1.222 -22.907 16.855 1 25.06 ? C9A FAD 501 A 1 HETATM 39 N N10 FAD . . . D 3 1.114 -21.788 15.994 1 26.56 ? N10 FAD 501 A 1 HETATM 40 C C10 FAD . . . D 3 0.077 -21.683 15.128 1 35.01 ? C10 FAD 501 A 1 HETATM 41 C C1' FAD . . . D 3 2.088 -20.679 16.018 1 32.58 ? C1' FAD 501 A 1 HETATM 42 C C2' FAD . . . D 3 3.292 -20.968 15.114 1 30.26 ? C2' FAD 501 A 1 HETATM 43 O O2' FAD . . . D 3 3.723 -22.321 15.295 1 37.23 ? O2' FAD 501 A 1 HETATM 44 C C3' FAD . . . D 3 4.377 -19.953 15.416 1 34.42 ? C3' FAD 501 A 1 HETATM 45 O O3' FAD . . . D 3 3.858 -18.684 15.063 1 66.55 ? O3' FAD 501 A 1 HETATM 46 C C4' FAD . . . D 3 5.649 -20.24 14.607 1 24.15 ? C4' FAD 501 A 1 HETATM 47 O O4' FAD . . . D 3 6.137 -21.534 15.002 1 33.58 ? O4' FAD 501 A 1 HETATM 48 C C5' FAD . . . D 3 6.729 -19.195 14.848 1 22.53 ? C5' FAD 501 A 1 HETATM 49 O O5' FAD . . . D 3 7.989 -19.838 14.652 1 35.91 ? O5' FAD 501 A 1 HETATM 50 P P FAD . . . D 3 9.375 -19.075 14.831 1 26.43 ? P FAD 501 A 1 HETATM 51 O O1P FAD . . . D 3 10.289 -19.7 13.852 1 54.5 ? O1P FAD 501 A 1 HETATM 52 O O2P FAD . . . D 3 9.15 -17.617 14.821 1 20.29 ? O2P FAD 501 A 1 HETATM 53 O O3P FAD . . . D 3 9.822 -19.423 16.341 1 15.29 ? O3P FAD 501 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 53 #