data_5X4V # _model_server_result.job_id xDxG9SA5cC1bMgf1c9i_7g _model_server_result.datetime_utc '2025-07-17 14:25:03' _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 5x4v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5X4V # _exptl.entry_id 5X4V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 405.405 _entity.id 2 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol _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 120 _cell.entry_id 5X4V _cell.length_a 76.872 _cell.length_b 76.872 _cell.length_c 204.785 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X4V _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 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' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 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 # _chem_comp.formula 'C18 H23 N5 O6' _chem_comp.formula_weight 405.405 _chem_comp.id RS3 _chem_comp.mon_nstd_flag . _chem_comp.name 1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Roseoflavin # 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 C4 C4A RS3 sing 277 n n C4 O4 RS3 doub 278 n n N3 C4 RS3 sing 279 n n N3 HN3 RS3 sing 280 n n C2 N1 RS3 sing 281 n n C2 N3 RS3 sing 282 n n O2 C2 RS3 doub 283 n n C4A N5 RS3 doub 284 n n C10 N10 RS3 sing 285 n n C10 C4A RS3 sing 286 n n N1 C10 RS3 doub 287 n n N5 C5A RS3 sing 288 n n C5A C6 RS3 doub 289 n y C6 C7 RS3 sing 290 n y C6 H6 RS3 sing 291 n n C7 C7M RS3 sing 292 n n C7M H17M RS3 sing 293 n n C7M H27M RS3 sing 294 n n C7M H37M RS3 sing 295 n n C8 N8 RS3 sing 296 n n C8 C7 RS3 doub 297 n y N8 C20 RS3 sing 298 n n C19 N8 RS3 sing 299 n n C19 H119 RS3 sing 300 n n C19 H219 RS3 sing 301 n n C19 H319 RS3 sing 302 n n C20 H120 RS3 sing 303 n n C20 H220 RS3 sing 304 n n C20 H320 RS3 sing 305 n n C9 C8 RS3 sing 306 n y C9 H9 RS3 sing 307 n n C9A C9 RS3 doub 308 n y C9A C5A RS3 sing 309 n y N10 C9A RS3 sing 310 n n C1' N10 RS3 sing 311 n n C1' H11' RS3 sing 312 n n C1' H21' RS3 sing 313 n n C2' C1' RS3 sing 314 n n C2' H2' RS3 sing 315 n n O2' C2' RS3 sing 316 n n O2' HO2' RS3 sing 317 n n C3' C4' RS3 sing 318 n n C3' C2' RS3 sing 319 n n C3' H3' RS3 sing 320 n n O3' C3' RS3 sing 321 n n O3' HO3' RS3 sing 322 n n C4' O4' RS3 sing 323 n n C4' H4' RS3 sing 324 n n O4' HO4' RS3 sing 325 n n C5' C4' RS3 sing 326 n n C5' H15' RS3 sing 327 n n C5' H25' RS3 sing 328 n n O5' C5' RS3 sing 329 n n O5' HO5' RS3 sing 330 n n # _atom_sites.entry_id 5X4V _atom_sites.fract_transf_matrix[1][1] 0.013009 _atom_sites.fract_transf_matrix[1][2] 0.007511 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015021 _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] 0.004883 _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 RS3 A 1 401 1 RS3 RS3 . C 3 HOH A 1 501 60 HOH HOH . C 3 HOH A 2 502 74 HOH HOH . C 3 HOH A 3 503 22 HOH HOH . C 3 HOH A 4 504 77 HOH HOH . C 3 HOH A 5 505 40 HOH HOH . C 3 HOH A 6 506 61 HOH HOH . C 3 HOH A 7 507 66 HOH HOH . C 3 HOH A 8 508 27 HOH HOH . C 3 HOH A 9 510 54 HOH HOH . C 3 HOH A 10 511 9 HOH HOH . C 3 HOH A 11 512 57 HOH HOH . C 3 HOH A 12 513 80 HOH HOH . C 3 HOH A 13 514 19 HOH HOH . C 3 HOH A 14 515 46 HOH HOH . C 3 HOH A 15 516 11 HOH HOH . C 3 HOH A 16 517 62 HOH HOH . C 3 HOH A 17 518 35 HOH HOH . C 3 HOH A 18 519 16 HOH HOH . C 3 HOH A 19 520 58 HOH HOH . C 3 HOH A 20 521 68 HOH HOH . C 3 HOH A 21 522 44 HOH HOH . C 3 HOH A 22 523 78 HOH HOH . C 3 HOH A 23 524 7 HOH HOH . C 3 HOH A 24 525 8 HOH HOH . C 3 HOH A 25 526 15 HOH HOH . C 3 HOH A 26 527 41 HOH HOH . C 3 HOH A 27 528 25 HOH HOH . C 3 HOH A 28 529 37 HOH HOH . C 3 HOH A 29 530 71 HOH HOH . C 3 HOH A 30 531 39 HOH HOH . C 3 HOH A 31 532 33 HOH HOH . C 3 HOH A 32 533 59 HOH HOH . C 3 HOH A 33 534 23 HOH HOH . C 3 HOH A 34 535 21 HOH HOH . C 3 HOH A 35 536 64 HOH HOH . C 3 HOH A 36 537 2 HOH HOH . C 3 HOH A 37 538 30 HOH HOH . C 3 HOH A 38 539 51 HOH HOH . C 3 HOH A 39 540 79 HOH HOH . C 3 HOH A 40 541 85 HOH HOH . C 3 HOH A 41 542 17 HOH HOH . C 3 HOH A 42 543 13 HOH HOH . C 3 HOH A 43 544 45 HOH HOH . C 3 HOH A 44 545 28 HOH HOH . C 3 HOH A 45 546 55 HOH HOH . C 3 HOH A 46 547 1 HOH HOH . C 3 HOH A 47 548 42 HOH HOH . C 3 HOH A 48 549 18 HOH HOH . C 3 HOH A 49 550 47 HOH HOH . C 3 HOH A 50 551 29 HOH HOH . C 3 HOH A 51 552 12 HOH HOH . C 3 HOH A 52 553 52 HOH HOH . C 3 HOH A 53 554 48 HOH HOH . C 3 HOH A 54 555 6 HOH HOH . C 3 HOH A 55 556 43 HOH HOH . C 3 HOH A 56 557 36 HOH HOH . C 3 HOH A 57 558 63 HOH HOH . C 3 HOH A 58 559 4 HOH HOH . C 3 HOH A 59 560 34 HOH HOH . C 3 HOH A 60 561 31 HOH HOH . C 3 HOH A 61 562 69 HOH HOH . C 3 HOH A 62 563 49 HOH HOH . C 3 HOH A 63 564 73 HOH HOH . C 3 HOH A 64 565 84 HOH HOH . C 3 HOH A 65 566 70 HOH HOH . C 3 HOH A 66 567 20 HOH HOH . C 3 HOH A 67 568 24 HOH HOH . C 3 HOH A 68 569 5 HOH HOH . C 3 HOH A 69 570 3 HOH HOH . C 3 HOH A 70 571 72 HOH HOH . C 3 HOH A 71 572 67 HOH HOH . C 3 HOH A 72 573 10 HOH HOH . C 3 HOH A 73 574 38 HOH HOH . C 3 HOH A 74 575 65 HOH HOH . C 3 HOH A 75 576 86 HOH HOH . C 3 HOH A 76 577 14 HOH HOH . C 3 HOH A 77 578 26 HOH HOH . C 3 HOH A 78 579 56 HOH HOH . C 3 HOH A 79 580 83 HOH HOH . C 3 HOH A 80 581 75 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 O4 RS3 . . . B 2 2.299 19.817 2.315 1 54.69 ? O4 RS3 401 A 1 HETATM 2 C C4 RS3 . . . B 2 2.735 20.613 3.176 1 52.48 ? C4 RS3 401 A 1 HETATM 3 N N3 RS3 . . . B 2 2.781 21.931 2.933 1 54.75 ? N3 RS3 401 A 1 HETATM 4 C C2 RS3 . . . B 2 3.248 22.791 3.845 1 52.91 ? C2 RS3 401 A 1 HETATM 5 O O2 RS3 . . . B 2 3.264 24.018 3.575 1 47.73 ? O2 RS3 401 A 1 HETATM 6 C C4A RS3 . . . B 2 3.211 20.088 4.481 1 52.05 ? C4A RS3 401 A 1 HETATM 7 C C10 RS3 . . . B 2 3.716 21.068 5.465 1 51.89 ? C10 RS3 401 A 1 HETATM 8 N N1 RS3 . . . B 2 3.689 22.359 5.052 1 57.14 ? N1 RS3 401 A 1 HETATM 9 N N5 RS3 . . . B 2 3.172 18.768 4.737 1 52.1 ? N5 RS3 401 A 1 HETATM 10 C C5A RS3 . . . B 2 3.597 18.293 5.918 1 49.9 ? C5A RS3 401 A 1 HETATM 11 C C6 RS3 . . . B 2 3.54 16.921 6.135 1 45.16 ? C6 RS3 401 A 1 HETATM 12 C C7 RS3 . . . B 2 3.967 16.365 7.333 1 46.79 ? C7 RS3 401 A 1 HETATM 13 C C7M RS3 . . . B 2 3.864 14.856 7.433 1 40.03 ? C7M RS3 401 A 1 HETATM 14 C C8 RS3 . . . B 2 4.499 17.303 8.39 1 49.26 ? C8 RS3 401 A 1 HETATM 15 N N8 RS3 . . . B 2 4.969 16.987 9.688 1 44.91 ? N8 RS3 401 A 1 HETATM 16 C C19 RS3 . . . B 2 4.001 16.249 10.512 1 39.02 ? C19 RS3 401 A 1 HETATM 17 C C20 RS3 . . . B 2 6.266 16.341 9.679 1 43.18 ? C20 RS3 401 A 1 HETATM 18 C C9 RS3 . . . B 2 4.551 18.666 8.149 1 48.02 ? C9 RS3 401 A 1 HETATM 19 C C9A RS3 . . . B 2 4.121 19.217 6.957 1 47.33 ? C9A RS3 401 A 1 HETATM 20 N N10 RS3 . . . B 2 4.174 20.613 6.74 1 50.4 ? N10 RS3 401 A 1 HETATM 21 C C1' RS3 . . . B 2 4.718 21.453 7.832 1 48.97 ? C1' RS3 401 A 1 HETATM 22 C C2' RS3 . . . B 2 4.686 22.944 7.53 1 57.83 ? C2' RS3 401 A 1 HETATM 23 O O2' RS3 . . . B 2 5.835 23.234 6.728 1 59.26 ? O2' RS3 401 A 1 HETATM 24 C C3' RS3 . . . B 2 4.72 23.918 8.701 1 59.79 ? C3' RS3 401 A 1 HETATM 25 O O3' RS3 . . . B 2 3.795 23.467 9.699 1 54.2 ? O3' RS3 401 A 1 HETATM 26 C C4' RS3 . . . B 2 4.329 25.33 8.203 1 56.95 ? C4' RS3 401 A 1 HETATM 27 O O4' RS3 . . . B 2 4.122 25.368 6.779 1 54.52 ? O4' RS3 401 A 1 HETATM 28 C C5' RS3 . . . B 2 5.348 26.421 8.532 1 48.78 ? C5' RS3 401 A 1 HETATM 29 O O5' RS3 . . . B 2 4.717 27.698 8.384 1 51.56 ? O5' RS3 401 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 29 #