data_1PKV
#
_model_server_result.job_id            Xsc0Mm9GTXMhEHdNKS-Znw 
_model_server_result.datetime_utc      '2025-01-26 01:36:00' 
_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          1pkv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":101}' 
#
_entry.id    1PKV 
#
_exptl.entry_id    1PKV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              376.364 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RIBOFLAVIN 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            1PKV 
_cell.length_a            50.161 
_cell.length_b            104.383 
_cell.length_c            85.113 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1PKV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_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,D,E,F 
_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
? 2 C N N 
? 2 D N N 
#
_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 277 n n 
N1 C10 RBF doub 278 n n 
C2 O2 RBF doub 279 n n 
C2 N3 RBF sing 280 n n 
N3 C4 RBF sing 281 n n 
N3 HN3 RBF sing 282 n n 
C4 O4 RBF doub 283 n n 
C4 C4A RBF sing 284 n n 
C4A N5 RBF doub 285 n n 
C4A C10 RBF sing 286 n n 
N5 C5A RBF sing 287 n n 
C5A C6 RBF doub 288 n y 
C5A C9A RBF sing 289 n y 
C6 C7 RBF sing 290 n y 
C6 HC6 RBF sing 291 n n 
C7 C7M RBF sing 292 n n 
C7 C8 RBF doub 293 n y 
C7M HC71 RBF sing 294 n n 
C7M HC72 RBF sing 295 n n 
C7M HC73 RBF sing 296 n n 
C8 C8M RBF sing 297 n n 
C8 C9 RBF sing 298 n y 
C8M HC81 RBF sing 299 n n 
C8M HC82 RBF sing 300 n n 
C8M HC83 RBF sing 301 n n 
C9 C9A RBF doub 302 n y 
C9 HC9 RBF sing 303 n n 
C9A N10 RBF sing 304 n n 
N10 C10 RBF sing 305 n n 
N10 C1' RBF sing 306 n n 
C1' C2' RBF sing 307 n n 
C1' HC11 RBF sing 308 n n 
C1' HC12 RBF sing 309 n n 
C2' O2' RBF sing 310 n n 
C2' C3' RBF sing 311 n n 
C2' HC2' RBF sing 312 n n 
O2' HO2' RBF sing 313 n n 
C3' O3' RBF sing 314 n n 
C3' C4' RBF sing 315 n n 
C3' HC3' RBF sing 316 n n 
O3' HO3' RBF sing 317 n n 
C4' O4' RBF sing 318 n n 
C4' C5' RBF sing 319 n n 
C4' HC4' RBF sing 320 n n 
O4' HO4' RBF sing 321 n n 
C5' O5' RBF sing 322 n n 
C5' HC51 RBF sing 323 n n 
C5' HC52 RBF sing 324 n n 
O5' HO5' RBF sing 325 n n 
#
_atom_sites.entry_id                     1PKV 
_atom_sites.fract_transf_matrix[1][1]    0.019936 
_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]    0.00958 
_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]    0.011749 
_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
C 2 RBF A 1 100 100 RBF RBF . 
D 2 RBF B 1 101 101 RBF RBF . 
E 3 HOH A 1 101 1 HOH HOH . 
E 3 HOH A 2 102 2 HOH HOH . 
E 3 HOH A 3 103 3 HOH HOH . 
E 3 HOH A 4 104 4 HOH HOH . 
E 3 HOH A 5 105 5 HOH HOH . 
E 3 HOH A 6 106 6 HOH HOH . 
E 3 HOH A 7 107 7 HOH HOH . 
E 3 HOH A 8 108 8 HOH HOH . 
E 3 HOH A 9 109 9 HOH HOH . 
E 3 HOH A 10 110 11 HOH HOH . 
E 3 HOH A 11 111 12 HOH HOH . 
E 3 HOH A 12 112 13 HOH HOH . 
E 3 HOH A 13 113 14 HOH HOH . 
E 3 HOH A 14 114 15 HOH HOH . 
E 3 HOH A 15 115 16 HOH HOH . 
E 3 HOH A 16 116 17 HOH HOH . 
E 3 HOH A 17 117 32 HOH HOH . 
E 3 HOH A 18 118 34 HOH HOH . 
E 3 HOH A 19 119 36 HOH HOH . 
E 3 HOH A 20 120 37 HOH HOH . 
F 3 HOH B 1 102 10 HOH HOH . 
F 3 HOH B 2 103 18 HOH HOH . 
F 3 HOH B 3 104 19 HOH HOH . 
F 3 HOH B 4 105 20 HOH HOH . 
F 3 HOH B 5 106 21 HOH HOH . 
F 3 HOH B 6 107 22 HOH HOH . 
F 3 HOH B 7 108 23 HOH HOH . 
F 3 HOH B 8 109 24 HOH HOH . 
F 3 HOH B 9 110 25 HOH HOH . 
F 3 HOH B 10 111 26 HOH HOH . 
F 3 HOH B 11 112 27 HOH HOH . 
F 3 HOH B 12 113 28 HOH HOH . 
F 3 HOH B 13 114 29 HOH HOH . 
F 3 HOH B 14 115 30 HOH HOH . 
F 3 HOH B 15 116 31 HOH HOH . 
F 3 HOH B 16 117 33 HOH HOH . 
F 3 HOH B 17 118 35 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 2 -1.354 19.869 41.755 1 27.46 ? N1 RBF 101 B 1 
HETATM 2 C C2 RBF . . . D 2 -1.743 18.594 41.443 1 28.78 ? C2 RBF 101 B 1 
HETATM 3 O O2 RBF . . . D 2 -2.183 18.286 40.293 1 26.24 ? O2 RBF 101 B 1 
HETATM 4 N N3 RBF . . . D 2 -1.696 17.596 42.327 1 27.98 ? N3 RBF 101 B 1 
HETATM 5 C C4 RBF . . . D 2 -1.258 17.747 43.593 1 28.36 ? C4 RBF 101 B 1 
HETATM 6 O O4 RBF . . . D 2 -1.195 16.747 44.387 1 29.56 ? O4 RBF 101 B 1 
HETATM 7 C C4A RBF . . . D 2 -0.815 19.094 44.008 1 26.13 ? C4A RBF 101 B 1 
HETATM 8 N N5 RBF . . . D 2 -0.392 19.354 45.28 1 24.91 ? N5 RBF 101 B 1 
HETATM 9 C C5A RBF . . . D 2 0.014 20.63 45.616 1 25.44 ? C5A RBF 101 B 1 
HETATM 10 C C6 RBF . . . D 2 0.52 20.884 46.886 1 26.92 ? C6 RBF 101 B 1 
HETATM 11 C C7 RBF . . . D 2 0.945 22.149 47.282 1 25.79 ? C7 RBF 101 B 1 
HETATM 12 C C7M RBF . . . D 2 1.464 22.373 48.698 1 22.91 ? C7M RBF 101 B 1 
HETATM 13 C C8 RBF . . . D 2 0.894 23.228 46.262 1 29.27 ? C8 RBF 101 B 1 
HETATM 14 C C8M RBF . . . D 2 1.352 24.631 46.564 1 30.47 ? C8M RBF 101 B 1 
HETATM 15 C C9 RBF . . . D 2 0.422 23.007 44.967 1 28.77 ? C9 RBF 101 B 1 
HETATM 16 C C9A RBF . . . D 2 -0.02 21.743 44.619 1 25.49 ? C9A RBF 101 B 1 
HETATM 17 N N10 RBF . . . D 2 -0.46 21.497 43.325 1 26.06 ? N10 RBF 101 B 1 
HETATM 18 C C10 RBF . . . D 2 -0.875 20.17 42.991 1 27.1 ? C10 RBF 101 B 1 
HETATM 19 C C1' RBF . . . D 2 -0.563 22.567 42.342 1 23.62 ? C1' RBF 101 B 1 
HETATM 20 C C2' RBF . . . D 2 0.459 22.398 41.27 1 23.23 ? C2' RBF 101 B 1 
HETATM 21 O O2' RBF . . . D 2 1.737 22.533 41.876 1 23.01 ? O2' RBF 101 B 1 
HETATM 22 C C3' RBF . . . D 2 0.219 23.485 40.252 1 23.31 ? C3' RBF 101 B 1 
HETATM 23 O O3' RBF . . . D 2 -1.069 23.356 39.666 1 25.31 ? O3' RBF 101 B 1 
HETATM 24 C C4' RBF . . . D 2 1.226 23.416 39.126 1 23.59 ? C4' RBF 101 B 1 
HETATM 25 O O4' RBF . . . D 2 2.5 23.69 39.704 1 23.23 ? O4' RBF 101 B 1 
HETATM 26 C C5' RBF . . . D 2 0.875 24.427 38.011 1 23.62 ? C5' RBF 101 B 1 
HETATM 27 O O5' RBF . . . D 2 0.909 25.774 38.574 1 29.05 ? O5' RBF 101 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#