data_1KYV
#
_model_server_result.job_id            it4hZTlqigE546V09QhJlQ 
_model_server_result.datetime_utc      '2024-12-26 22:14:03' 
_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          1kyv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":504}' 
#
_entry.id    1KYV 
#
_exptl.entry_id    1KYV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              376.364 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RIBOFLAVIN 
_entity.pdbx_number_of_molecules    5 
_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            1KYV 
_cell.length_a            111.5 
_cell.length_b            145.523 
_cell.length_c            128.702 
_cell.Z_PDB               40 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1KYV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA pentameric 5 author_and_software_defined_assembly 1 
PISA decameric 10 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 2 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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 111.5 0 64.351 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 G N N 
? 3 I N N 
? 3 K N N 
? 3 M N N 
? 3 O 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 268 n n 
N1 C10 RBF doub 269 n n 
C2 O2 RBF doub 270 n n 
C2 N3 RBF sing 271 n n 
N3 C4 RBF sing 272 n n 
N3 HN3 RBF sing 273 n n 
C4 O4 RBF doub 274 n n 
C4 C4A RBF sing 275 n n 
C4A N5 RBF doub 276 n n 
C4A C10 RBF sing 277 n n 
N5 C5A RBF sing 278 n n 
C5A C6 RBF doub 279 n y 
C5A C9A RBF sing 280 n y 
C6 C7 RBF sing 281 n y 
C6 HC6 RBF sing 282 n n 
C7 C7M RBF sing 283 n n 
C7 C8 RBF doub 284 n y 
C7M HC71 RBF sing 285 n n 
C7M HC72 RBF sing 286 n n 
C7M HC73 RBF sing 287 n n 
C8 C8M RBF sing 288 n n 
C8 C9 RBF sing 289 n y 
C8M HC81 RBF sing 290 n n 
C8M HC82 RBF sing 291 n n 
C8M HC83 RBF sing 292 n n 
C9 C9A RBF doub 293 n y 
C9 HC9 RBF sing 294 n n 
C9A N10 RBF sing 295 n n 
N10 C10 RBF sing 296 n n 
N10 C1' RBF sing 297 n n 
C1' C2' RBF sing 298 n n 
C1' HC11 RBF sing 299 n n 
C1' HC12 RBF sing 300 n n 
C2' O2' RBF sing 301 n n 
C2' C3' RBF sing 302 n n 
C2' HC2' RBF sing 303 n n 
O2' HO2' RBF sing 304 n n 
C3' O3' RBF sing 305 n n 
C3' C4' RBF sing 306 n n 
C3' HC3' RBF sing 307 n n 
O3' HO3' RBF sing 308 n n 
C4' O4' RBF sing 309 n n 
C4' C5' RBF sing 310 n n 
C4' HC4' RBF sing 311 n n 
O4' HO4' RBF sing 312 n n 
C5' O5' RBF sing 313 n n 
C5' HC51 RBF sing 314 n n 
C5' HC52 RBF sing 315 n n 
O5' HO5' RBF sing 316 n n 
#
_atom_sites.entry_id                     1KYV 
_atom_sites.fract_transf_matrix[1][1]    0.008969 
_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]    0.006872 
_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]    0.00777 
_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
F 2 PO4 A 1 1004 4 PO4 PO4 . 
G 3 RBF A 1 501 1 RBF RBF . 
H 2 PO4 B 1 1001 1 PO4 PO4 . 
I 3 RBF B 1 502 2 RBF RBF . 
J 2 PO4 C 1 1003 3 PO4 PO4 . 
K 3 RBF C 1 503 3 RBF RBF . 
L 2 PO4 D 1 1005 5 PO4 PO4 . 
M 3 RBF D 1 504 4 RBF RBF . 
N 2 PO4 E 1 1002 2 PO4 PO4 . 
O 3 RBF E 1 505 5 RBF RBF . 
P 4 HOH A 1 1005 1 HOH HOH . 
P 4 HOH A 2 1006 4 HOH HOH . 
P 4 HOH A 3 1007 8 HOH HOH . 
P 4 HOH A 4 1008 12 HOH HOH . 
P 4 HOH A 5 1009 20 HOH HOH . 
P 4 HOH A 6 1010 30 HOH HOH . 
P 4 HOH A 7 1011 37 HOH HOH . 
P 4 HOH A 8 1012 40 HOH HOH . 
P 4 HOH A 9 1013 44 HOH HOH . 
P 4 HOH A 10 1014 45 HOH HOH . 
P 4 HOH A 11 1015 46 HOH HOH . 
P 4 HOH A 12 1016 48 HOH HOH . 
P 4 HOH A 13 1017 49 HOH HOH . 
P 4 HOH A 14 1018 50 HOH HOH . 
P 4 HOH A 15 1019 51 HOH HOH . 
P 4 HOH A 16 1020 52 HOH HOH . 
P 4 HOH A 17 1021 53 HOH HOH . 
P 4 HOH A 18 1022 54 HOH HOH . 
P 4 HOH A 19 1023 57 HOH HOH . 
P 4 HOH A 20 1024 58 HOH HOH . 
P 4 HOH A 21 1025 59 HOH HOH . 
P 4 HOH A 22 1026 62 HOH HOH . 
P 4 HOH A 23 1027 94 HOH HOH . 
Q 4 HOH B 1 1002 2 HOH HOH . 
Q 4 HOH B 2 1003 10 HOH HOH . 
Q 4 HOH B 3 1004 16 HOH HOH . 
Q 4 HOH B 4 1005 22 HOH HOH . 
Q 4 HOH B 5 1006 33 HOH HOH . 
Q 4 HOH B 6 1007 38 HOH HOH . 
Q 4 HOH B 7 1008 42 HOH HOH . 
Q 4 HOH B 8 1009 55 HOH HOH . 
Q 4 HOH B 9 1010 56 HOH HOH . 
Q 4 HOH B 10 1011 60 HOH HOH . 
Q 4 HOH B 11 1012 61 HOH HOH . 
Q 4 HOH B 12 1013 63 HOH HOH . 
Q 4 HOH B 13 1014 64 HOH HOH . 
Q 4 HOH B 14 1015 65 HOH HOH . 
Q 4 HOH B 15 1016 69 HOH HOH . 
Q 4 HOH B 16 1017 70 HOH HOH . 
R 4 HOH C 1 1004 3 HOH HOH . 
R 4 HOH C 2 1005 7 HOH HOH . 
R 4 HOH C 3 1006 13 HOH HOH . 
R 4 HOH C 4 1007 14 HOH HOH . 
R 4 HOH C 5 1008 25 HOH HOH . 
R 4 HOH C 6 1009 28 HOH HOH . 
R 4 HOH C 7 1010 29 HOH HOH . 
R 4 HOH C 8 1011 31 HOH HOH . 
R 4 HOH C 9 1012 32 HOH HOH . 
R 4 HOH C 10 1013 34 HOH HOH . 
R 4 HOH C 11 1014 36 HOH HOH . 
R 4 HOH C 12 1015 41 HOH HOH . 
R 4 HOH C 13 1016 68 HOH HOH . 
R 4 HOH C 14 1017 71 HOH HOH . 
R 4 HOH C 15 1018 72 HOH HOH . 
R 4 HOH C 16 1019 73 HOH HOH . 
R 4 HOH C 17 1020 74 HOH HOH . 
R 4 HOH C 18 1021 77 HOH HOH . 
R 4 HOH C 19 1022 80 HOH HOH . 
R 4 HOH C 20 1023 92 HOH HOH . 
R 4 HOH C 21 1024 93 HOH HOH . 
S 4 HOH D 1 1006 5 HOH HOH . 
S 4 HOH D 2 1007 6 HOH HOH . 
S 4 HOH D 3 1008 18 HOH HOH . 
S 4 HOH D 4 1009 23 HOH HOH . 
S 4 HOH D 5 1010 26 HOH HOH . 
S 4 HOH D 6 1011 27 HOH HOH . 
S 4 HOH D 7 1012 35 HOH HOH . 
S 4 HOH D 8 1013 39 HOH HOH . 
S 4 HOH D 9 1014 75 HOH HOH . 
S 4 HOH D 10 1015 76 HOH HOH . 
S 4 HOH D 11 1016 78 HOH HOH . 
S 4 HOH D 12 1017 79 HOH HOH . 
S 4 HOH D 13 1018 81 HOH HOH . 
S 4 HOH D 14 1019 82 HOH HOH . 
S 4 HOH D 15 1020 83 HOH HOH . 
S 4 HOH D 16 1021 91 HOH HOH . 
T 4 HOH E 1 1003 9 HOH HOH . 
T 4 HOH E 2 1004 11 HOH HOH . 
T 4 HOH E 3 1005 15 HOH HOH . 
T 4 HOH E 4 1006 17 HOH HOH . 
T 4 HOH E 5 1007 19 HOH HOH . 
T 4 HOH E 6 1008 21 HOH HOH . 
T 4 HOH E 7 1009 24 HOH HOH . 
T 4 HOH E 8 1010 43 HOH HOH . 
T 4 HOH E 9 1011 47 HOH HOH . 
T 4 HOH E 10 1012 66 HOH HOH . 
T 4 HOH E 11 1013 67 HOH HOH . 
T 4 HOH E 12 1014 84 HOH HOH . 
T 4 HOH E 13 1015 85 HOH HOH . 
T 4 HOH E 14 1016 86 HOH HOH . 
T 4 HOH E 15 1017 87 HOH HOH . 
T 4 HOH E 16 1018 88 HOH HOH . 
T 4 HOH E 17 1019 89 HOH HOH . 
T 4 HOH E 18 1020 90 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 . . . M 3 61.028 39.503 8.683 1 64.3 ? N1 RBF 504 D 1 
HETATM 2 C C2 RBF . . . M 3 60.754 40.817 9.047 1 63.28 ? C2 RBF 504 D 1 
HETATM 3 O O2 RBF . . . M 3 61.492 41.676 8.619 1 58.64 ? O2 RBF 504 D 1 
HETATM 4 N N3 RBF . . . M 3 59.667 40.984 9.859 1 65.09 ? N3 RBF 504 D 1 
HETATM 5 C C4 RBF . . . M 3 58.779 40.012 10.38 1 66.81 ? C4 RBF 504 D 1 
HETATM 6 O O4 RBF . . . M 3 57.853 40.32 11.091 1 64.05 ? O4 RBF 504 D 1 
HETATM 7 C C4A RBF . . . M 3 59.128 38.585 9.956 1 69.11 ? C4A RBF 504 D 1 
HETATM 8 N N5 RBF . . . M 3 58.371 37.58 10.377 1 72.08 ? N5 RBF 504 D 1 
HETATM 9 C C5A RBF . . . M 3 58.7 36.259 9.979 1 73.93 ? C5A RBF 504 D 1 
HETATM 10 C C6 RBF . . . M 3 57.822 35.201 10.488 1 74.4 ? C6 RBF 504 D 1 
HETATM 11 C C7 RBF . . . M 3 58.16 33.893 10.089 1 74.9 ? C7 RBF 504 D 1 
HETATM 12 C C7M RBF . . . M 3 57.355 32.652 10.534 1 74.97 ? C7M RBF 504 D 1 
HETATM 13 C C8 RBF . . . M 3 59.329 33.659 9.209 1 73.17 ? C8 RBF 504 D 1 
HETATM 14 C C8M RBF . . . M 3 59.675 32.183 8.793 1 70.45 ? C8M RBF 504 D 1 
HETATM 15 C C9 RBF . . . M 3 60.18 34.645 8.703 1 71.81 ? C9 RBF 504 D 1 
HETATM 16 C C9A RBF . . . M 3 59.826 35.991 9.121 1 72.24 ? C9A RBF 504 D 1 
HETATM 17 N N10 RBF . . . M 3 60.62 37.164 8.688 1 70.54 ? N10 RBF 504 D 1 
HETATM 18 C C10 RBF . . . M 3 60.263 38.405 9.099 1 70.3 ? C10 RBF 504 D 1 
HETATM 19 C C1' RBF . . . M 3 61.778 36.923 7.803 1 68.21 ? C1' RBF 504 D 1 
HETATM 20 C C2' RBF . . . M 3 63.161 36.55 8.356 1 65.79 ? C2' RBF 504 D 1 
HETATM 21 O O2' RBF . . . M 3 63.759 37.79 8.844 1 54.86 ? O2' RBF 504 D 1 
HETATM 22 C C3' RBF . . . M 3 63.901 35.85 7.235 1 67.64 ? C3' RBF 504 D 1 
HETATM 23 O O3' RBF . . . M 3 63.945 36.41 5.918 1 63.55 ? O3' RBF 504 D 1 
HETATM 24 C C4' RBF . . . M 3 63.489 34.463 6.857 1 66.17 ? C4' RBF 504 D 1 
HETATM 25 O O4' RBF . . . M 3 63.311 33.699 8.067 1 58.64 ? O4' RBF 504 D 1 
HETATM 26 C C5' RBF . . . M 3 64.472 33.565 5.99 1 59.19 ? C5' RBF 504 D 1 
HETATM 27 O O5' RBF . . . M 3 65.814 33.717 6.488 1 58.88 ? O5' RBF 504 D 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           300 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#