data_1NB9
#
_model_server_result.job_id            kCYEvgCrHxBW9x2nbo_ZVw 
_model_server_result.datetime_utc      '2024-10-24 04:21:50' 
_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          1nb9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    1NB9 
#
_exptl.entry_id    1NB9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              376.364 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RIBOFLAVIN 
_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            1NB9 
_cell.length_a            56.957 
_cell.length_b            56.957 
_cell.length_c            82.501 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1NB9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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
metalc ? metalc1 A O THR 26 A THR 34 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc2 A OG1 THR 26 A THR 34 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc3 B MG MG . A MG 201 1_555 C O1B ADP . A ADP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc4 B MG MG . A MG 201 1_555 C O2A ADP . A ADP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc5 B MG MG . A MG 201 1_555 E O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
metalc ? metalc6 B MG MG . A MG 201 1_555 E O HOH . A HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
#
_chem_comp.formula           'C17 H20 N4 O6' 
_chem_comp.formula_weight    376.364 
_chem_comp.id                RBF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              RIBOFLAVIN 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'RIBOFLAVINE;VITAMIN B2' 
#
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
N1 C2 RBF sing 321 n n 
N1 C10 RBF doub 322 n n 
C2 O2 RBF doub 323 n n 
C2 N3 RBF sing 324 n n 
N3 C4 RBF sing 325 n n 
N3 HN3 RBF sing 326 n n 
C4 O4 RBF doub 327 n n 
C4 C4A RBF sing 328 n n 
C4A N5 RBF doub 329 n n 
C4A C10 RBF sing 330 n n 
N5 C5A RBF sing 331 n n 
C5A C6 RBF doub 332 n y 
C5A C9A RBF sing 333 n y 
C6 C7 RBF sing 334 n y 
C6 HC6 RBF sing 335 n n 
C7 C7M RBF sing 336 n n 
C7 C8 RBF doub 337 n y 
C7M HC71 RBF sing 338 n n 
C7M HC72 RBF sing 339 n n 
C7M HC73 RBF sing 340 n n 
C8 C8M RBF sing 341 n n 
C8 C9 RBF sing 342 n y 
C8M HC81 RBF sing 343 n n 
C8M HC82 RBF sing 344 n n 
C8M HC83 RBF sing 345 n n 
C9 C9A RBF doub 346 n y 
C9 HC9 RBF sing 347 n n 
C9A N10 RBF sing 348 n n 
N10 C10 RBF sing 349 n n 
N10 C1' RBF sing 350 n n 
C1' C2' RBF sing 351 n n 
C1' HC11 RBF sing 352 n n 
C1' HC12 RBF sing 353 n n 
C2' O2' RBF sing 354 n n 
C2' C3' RBF sing 355 n n 
C2' HC2' RBF sing 356 n n 
O2' HO2' RBF sing 357 n n 
C3' O3' RBF sing 358 n n 
C3' C4' RBF sing 359 n n 
C3' HC3' RBF sing 360 n n 
O3' HO3' RBF sing 361 n n 
C4' O4' RBF sing 362 n n 
C4' C5' RBF sing 363 n n 
C4' HC4' RBF sing 364 n n 
O4' HO4' RBF sing 365 n n 
C5' O5' RBF sing 366 n n 
C5' HC51 RBF sing 367 n n 
C5' HC52 RBF sing 368 n n 
O5' HO5' RBF sing 369 n n 
#
_atom_sites.entry_id                     1NB9 
_atom_sites.fract_transf_matrix[1][1]    0.017557 
_atom_sites.fract_transf_matrix[1][2]    0.010137 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020273 
_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]    0.012121 
_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 MG A 1 201 301 MG MG . 
C 3 ADP A 1 301 201 ADP ADP . 
D 4 RBF A 1 401 401 RBF RBF . 
E 5 HOH A 1 501 501 HOH HOH . 
E 5 HOH A 2 502 502 HOH HOH . 
E 5 HOH A 3 503 503 HOH HOH . 
E 5 HOH A 4 504 504 HOH HOH . 
E 5 HOH A 5 505 505 HOH HOH . 
E 5 HOH A 6 506 506 HOH HOH . 
E 5 HOH A 7 507 507 HOH HOH . 
E 5 HOH A 8 508 508 HOH HOH . 
E 5 HOH A 9 509 509 HOH HOH . 
E 5 HOH A 10 510 510 HOH HOH . 
E 5 HOH A 11 511 511 HOH HOH . 
E 5 HOH A 12 512 512 HOH HOH . 
E 5 HOH A 13 513 513 HOH HOH . 
E 5 HOH A 14 514 514 HOH HOH . 
E 5 HOH A 15 515 515 HOH HOH . 
E 5 HOH A 16 516 516 HOH HOH . 
E 5 HOH A 17 517 517 HOH HOH . 
E 5 HOH A 18 518 518 HOH HOH . 
E 5 HOH A 19 519 519 HOH HOH . 
E 5 HOH A 20 520 520 HOH HOH . 
E 5 HOH A 21 521 521 HOH HOH . 
E 5 HOH A 22 522 522 HOH HOH . 
E 5 HOH A 23 523 523 HOH HOH . 
E 5 HOH A 24 524 524 HOH HOH . 
E 5 HOH A 25 525 525 HOH HOH . 
E 5 HOH A 26 526 526 HOH HOH . 
E 5 HOH A 27 527 527 HOH HOH . 
E 5 HOH A 28 528 528 HOH HOH . 
E 5 HOH A 29 529 529 HOH HOH . 
E 5 HOH A 30 530 530 HOH HOH . 
E 5 HOH A 31 531 531 HOH HOH . 
E 5 HOH A 32 532 532 HOH HOH . 
E 5 HOH A 33 533 533 HOH HOH . 
E 5 HOH A 34 534 534 HOH HOH . 
E 5 HOH A 35 535 535 HOH HOH . 
E 5 HOH A 36 536 536 HOH HOH . 
E 5 HOH A 37 537 537 HOH HOH . 
E 5 HOH A 38 538 538 HOH HOH . 
E 5 HOH A 39 539 539 HOH HOH . 
E 5 HOH A 40 540 540 HOH HOH . 
E 5 HOH A 41 541 541 HOH HOH . 
E 5 HOH A 42 542 542 HOH HOH . 
E 5 HOH A 43 543 543 HOH HOH . 
E 5 HOH A 44 544 544 HOH HOH . 
E 5 HOH A 45 545 545 HOH HOH . 
E 5 HOH A 46 546 546 HOH HOH . 
E 5 HOH A 47 547 547 HOH HOH . 
E 5 HOH A 48 548 548 HOH HOH . 
E 5 HOH A 49 549 549 HOH HOH . 
E 5 HOH A 50 550 550 HOH HOH . 
E 5 HOH A 51 551 551 HOH HOH . 
E 5 HOH A 52 552 552 HOH HOH . 
E 5 HOH A 53 553 553 HOH HOH . 
E 5 HOH A 54 554 554 HOH HOH . 
E 5 HOH A 55 555 555 HOH HOH . 
E 5 HOH A 56 556 556 HOH HOH . 
E 5 HOH A 57 557 557 HOH HOH . 
E 5 HOH A 58 558 558 HOH HOH . 
E 5 HOH A 59 559 559 HOH HOH . 
E 5 HOH A 60 560 560 HOH HOH . 
E 5 HOH A 61 561 561 HOH HOH . 
E 5 HOH A 62 562 562 HOH HOH . 
E 5 HOH A 63 563 563 HOH HOH . 
E 5 HOH A 64 564 564 HOH HOH . 
E 5 HOH A 65 565 565 HOH HOH . 
E 5 HOH A 66 566 566 HOH HOH . 
E 5 HOH A 67 567 567 HOH HOH . 
E 5 HOH A 68 568 568 HOH HOH . 
E 5 HOH A 69 569 569 HOH HOH . 
E 5 HOH A 70 570 570 HOH HOH . 
E 5 HOH A 71 571 571 HOH HOH . 
E 5 HOH A 72 572 572 HOH HOH . 
E 5 HOH A 73 573 573 HOH HOH . 
E 5 HOH A 74 574 574 HOH HOH . 
E 5 HOH A 75 575 575 HOH HOH . 
E 5 HOH A 76 576 576 HOH HOH . 
E 5 HOH A 77 577 577 HOH HOH . 
E 5 HOH A 78 578 578 HOH HOH . 
E 5 HOH A 79 579 579 HOH HOH . 
E 5 HOH A 80 580 580 HOH HOH . 
E 5 HOH A 81 581 581 HOH HOH . 
E 5 HOH A 82 582 582 HOH HOH . 
E 5 HOH A 83 583 583 HOH HOH . 
E 5 HOH A 84 584 584 HOH HOH . 
E 5 HOH A 85 585 585 HOH HOH . 
E 5 HOH A 86 586 586 HOH HOH . 
E 5 HOH A 87 587 587 HOH HOH . 
E 5 HOH A 88 588 588 HOH HOH . 
E 5 HOH A 89 589 589 HOH HOH . 
E 5 HOH A 90 590 590 HOH HOH . 
E 5 HOH A 91 591 591 HOH HOH . 
E 5 HOH A 92 592 592 HOH HOH . 
E 5 HOH A 93 593 593 HOH HOH . 
E 5 HOH A 94 594 594 HOH HOH . 
E 5 HOH A 95 595 595 HOH HOH . 
E 5 HOH A 96 596 596 HOH HOH . 
E 5 HOH A 97 597 597 HOH HOH . 
E 5 HOH A 98 598 598 HOH HOH . 
E 5 HOH A 99 599 599 HOH HOH . 
E 5 HOH A 100 600 600 HOH HOH . 
E 5 HOH A 101 601 601 HOH HOH . 
E 5 HOH A 102 602 602 HOH HOH . 
E 5 HOH A 103 603 603 HOH HOH . 
E 5 HOH A 104 604 604 HOH HOH . 
E 5 HOH A 105 605 605 HOH HOH . 
E 5 HOH A 106 606 606 HOH HOH . 
E 5 HOH A 107 607 607 HOH HOH . 
E 5 HOH A 108 608 608 HOH HOH . 
E 5 HOH A 109 609 609 HOH HOH . 
E 5 HOH A 110 610 610 HOH HOH . 
E 5 HOH A 111 611 611 HOH HOH . 
E 5 HOH A 112 612 612 HOH HOH . 
E 5 HOH A 113 613 613 HOH HOH . 
E 5 HOH A 114 614 614 HOH HOH . 
E 5 HOH A 115 615 615 HOH HOH . 
E 5 HOH A 116 616 616 HOH HOH . 
E 5 HOH A 117 617 617 HOH HOH . 
E 5 HOH A 118 618 618 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 N N1 RBF . . . D 4 0.414 34.782 34.454 1 25.93 ? N1 RBF 401 A 1 
HETATM 2 C C2 RBF . . . D 4 0.49 35.826 35.328 1 29.05 ? C2 RBF 401 A 1 
HETATM 3 O O2 RBF . . . D 4 0.609 36.993 34.866 1 31.18 ? O2 RBF 401 A 1 
HETATM 4 N N3 RBF . . . D 4 0.464 35.665 36.668 1 25.31 ? N3 RBF 401 A 1 
HETATM 5 C C4 RBF . . . D 4 0.327 34.457 37.255 1 21.16 ? C4 RBF 401 A 1 
HETATM 6 O O4 RBF . . . D 4 0.226 34.327 38.5 1 21.35 ? O4 RBF 401 A 1 
HETATM 7 C C4A RBF . . . D 4 0.233 33.277 36.385 1 19.07 ? C4A RBF 401 A 1 
HETATM 8 N N5 RBF . . . D 4 0.139 32.046 36.917 1 19.9 ? N5 RBF 401 A 1 
HETATM 9 C C5A RBF . . . D 4 0.073 30.969 36.094 1 18.5 ? C5A RBF 401 A 1 
HETATM 10 C C6 RBF . . . D 4 -0.014 29.693 36.66 1 19.21 ? C6 RBF 401 A 1 
HETATM 11 C C7 RBF . . . D 4 -0.11 28.571 35.812 1 17.84 ? C7 RBF 401 A 1 
HETATM 12 C C7M RBF . . . D 4 -0.239 27.187 36.371 1 20.48 ? C7M RBF 401 A 1 
HETATM 13 C C8 RBF . . . D 4 -0.087 28.755 34.346 1 21.63 ? C8 RBF 401 A 1 
HETATM 14 C C8M RBF . . . D 4 -0.189 27.553 33.435 1 21.06 ? C8M RBF 401 A 1 
HETATM 15 C C9 RBF . . . D 4 0.001 30.025 33.789 1 19.87 ? C9 RBF 401 A 1 
HETATM 16 C C9A RBF . . . D 4 0.096 31.15 34.611 1 19.17 ? C9A RBF 401 A 1 
HETATM 17 N N10 RBF . . . D 4 0.217 32.436 34.056 1 20.72 ? N10 RBF 401 A 1 
HETATM 18 C C10 RBF . . . D 4 0.301 33.507 34.928 1 21.3 ? C10 RBF 401 A 1 
HETATM 19 C C1' RBF . . . D 4 0.187 32.751 32.603 1 22.26 ? C1' RBF 401 A 1 
HETATM 20 C C2' RBF . . . D 4 1.316 32.274 31.761 0.5 25.48 ? C2' RBF 401 A 1 
HETATM 21 O O2' RBF . . . D 4 2.151 33.396 31.932 0.5 29.37 ? O2' RBF 401 A 1 
HETATM 22 C C3' RBF . . . D 4 0.674 31.957 30.386 0.5 29.68 ? C3' RBF 401 A 1 
HETATM 23 O O3' RBF . . . D 4 0.543 30.552 30.307 0.5 28.35 ? O3' RBF 401 A 1 
HETATM 24 C C4' RBF . . . D 4 1.358 32.331 29.078 0.3 32.55 ? C4' RBF 401 A 1 
HETATM 25 O O4' RBF . . . D 4 2.043 33.541 29.328 1 41.54 ? O4' RBF 401 A 1 
HETATM 26 C C5' RBF . . . D 4 0.355 32.476 27.907 0.1 31.89 ? C5' RBF 401 A 1 
HETATM 27 O O5' RBF . . . D 4 -0.409 31.303 27.536 1 28.56 ? O5' RBF 401 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           236 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#