data_2A58
#
_model_server_result.job_id            DM5sR6dzQuLeHiPP5RyJaw 
_model_server_result.datetime_utc      '2025-03-04 16:34:56' 
_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          2a58 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":304}' 
#
_entry.id    2A58 
#
_exptl.entry_id    2A58 
_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            2A58 
_cell.length_a            111.64 
_cell.length_b            145.13 
_cell.length_c            129.2 
_cell.Z_PDB               40 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2A58 
_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 -1 111.64 0 64.6 
#
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                     2A58 
_atom_sites.fract_transf_matrix[1][1]    0.008957 
_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]    0.00689 
_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]    0.00774 
_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 1 504 504 PO4 PO4 . 
G 3 RBF A 1 300 300 RBF RBF . 
H 2 PO4 B 1 500 500 PO4 PO4 . 
I 3 RBF B 1 301 301 RBF RBF . 
J 2 PO4 C 1 501 501 PO4 PO4 . 
K 3 RBF C 1 302 302 RBF RBF . 
L 2 PO4 D 1 502 502 PO4 PO4 . 
M 3 RBF D 1 303 303 RBF RBF . 
N 2 PO4 E 1 503 503 PO4 PO4 . 
O 3 RBF E 1 304 304 RBF RBF . 
P 4 HOH A 1 505 1 HOH TIP . 
P 4 HOH A 2 506 7 HOH TIP . 
P 4 HOH A 3 507 17 HOH TIP . 
P 4 HOH A 4 508 18 HOH TIP . 
P 4 HOH A 5 509 22 HOH TIP . 
P 4 HOH A 6 510 39 HOH TIP . 
P 4 HOH A 7 511 40 HOH TIP . 
Q 4 HOH B 1 501 12 HOH TIP . 
Q 4 HOH B 2 502 24 HOH TIP . 
Q 4 HOH B 3 503 38 HOH TIP . 
R 4 HOH C 1 502 9 HOH TIP . 
R 4 HOH C 2 503 10 HOH TIP . 
R 4 HOH C 3 504 11 HOH TIP . 
R 4 HOH C 4 505 20 HOH TIP . 
R 4 HOH C 5 506 23 HOH TIP . 
R 4 HOH C 6 507 26 HOH TIP . 
R 4 HOH C 7 508 28 HOH TIP . 
R 4 HOH C 8 509 35 HOH TIP . 
S 4 HOH D 1 503 16 HOH TIP . 
S 4 HOH D 2 504 30 HOH TIP . 
S 4 HOH D 3 505 31 HOH TIP . 
S 4 HOH D 4 506 32 HOH TIP . 
S 4 HOH D 5 507 33 HOH TIP . 
S 4 HOH D 6 508 36 HOH TIP . 
S 4 HOH D 7 509 37 HOH TIP . 
T 4 HOH E 1 504 4 HOH TIP . 
T 4 HOH E 2 505 13 HOH TIP . 
T 4 HOH E 3 506 27 HOH TIP . 
#
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 . . . O 3 67.74 55.813 23.576 0.6 72.75 ? N1 RBF 304 E 1 
HETATM 2 C C2 RBF . . . O 3 67.963 55.977 24.942 0.6 72.34 ? C2 RBF 304 E 1 
HETATM 3 O O2 RBF . . . O 3 69.075 56.283 25.287 0.6 68.48 ? O2 RBF 304 E 1 
HETATM 4 N N3 RBF . . . O 3 66.88 55.767 25.746 0.6 74.83 ? N3 RBF 304 E 1 
HETATM 5 C C4 RBF . . . O 3 65.566 55.407 25.393 0.6 75.69 ? C4 RBF 304 E 1 
HETATM 6 O O4 RBF . . . O 3 64.705 55.255 26.232 0.6 73.5 ? O4 RBF 304 E 1 
HETATM 7 C C4A RBF . . . O 3 65.376 55.235 23.885 0.6 75.22 ? C4A RBF 304 E 1 
HETATM 8 N N5 RBF . . . O 3 64.177 54.89 23.422 0.6 76.41 ? N5 RBF 304 E 1 
HETATM 9 C C5A RBF . . . O 3 64.006 54.726 22.022 0.6 77.04 ? C5A RBF 304 E 1 
HETATM 10 C C6 RBF . . . O 3 62.672 54.339 21.574 0.6 77.19 ? C6 RBF 304 E 1 
HETATM 11 C C7 RBF . . . O 3 62.53 54.172 20.184 0.6 78.94 ? C7 RBF 304 E 1 
HETATM 12 C C7M RBF . . . O 3 61.202 53.759 19.531 0.6 79.12 ? C7M RBF 304 E 1 
HETATM 13 C C8 RBF . . . O 3 63.687 54.389 19.282 0.6 79.43 ? C8 RBF 304 E 1 
HETATM 14 C C8M RBF . . . O 3 63.509 54.185 17.738 0.6 77.88 ? C8M RBF 304 E 1 
HETATM 15 C C9 RBF . . . O 3 64.955 54.762 19.674 0.6 77.78 ? C9 RBF 304 E 1 
HETATM 16 C C9A RBF . . . O 3 65.093 54.928 21.11 0.6 77.54 ? C9A RBF 304 E 1 
HETATM 17 N N10 RBF . . . O 3 66.39 55.316 21.682 0.6 76.61 ? N10 RBF 304 E 1 
HETATM 18 C C10 RBF . . . O 3 66.516 55.459 23.034 0.6 74.95 ? C10 RBF 304 E 1 
HETATM 19 C C1' RBF . . . O 3 67.445 55.511 20.66 0.6 76.2 ? C1' RBF 304 E 1 
HETATM 20 C C2' RBF . . . O 3 68.346 54.263 20.596 0.6 75.14 ? C2' RBF 304 E 1 
HETATM 21 O O2' RBF . . . O 3 69.203 54.237 21.779 0.6 70.67 ? O2' RBF 304 E 1 
HETATM 22 C C3' RBF . . . O 3 69.356 54.332 19.518 0.6 76.23 ? C3' RBF 304 E 1 
HETATM 23 O O3' RBF . . . O 3 70.154 55.516 19.646 0.6 77.27 ? O3' RBF 304 E 1 
HETATM 24 C C4' RBF . . . O 3 68.764 54.324 18.128 0.6 74.8 ? C4' RBF 304 E 1 
HETATM 25 O O4' RBF . . . O 3 67.909 53.239 17.746 0.6 73.43 ? O4' RBF 304 E 1 
HETATM 26 C C5' RBF . . . O 3 70.027 54.438 17.187 0.6 73.06 ? C5' RBF 304 E 1 
HETATM 27 O O5' RBF . . . O 3 70.241 55.839 16.933 0.6 72.49 ? O5' RBF 304 E 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           338 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#