data_2VXA
#
_model_server_result.job_id            yjTKQG5MWb39KaO4B_xxOQ 
_model_server_result.datetime_utc      '2024-11-08 07:02:44' 
_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          2vxa 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"DA","auth_seq_id":200}' 
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_entry.id    2VXA 
#
_exptl.entry_id    2VXA 
_exptl.method      'X-RAY DIFFRACTION' 
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_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    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
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_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            2VXA 
_cell.length_a            85.76 
_cell.length_b            100.51 
_cell.length_c            100.47 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 2VXA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
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_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
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_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
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_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 M N N 
? 2 P N N 
? 2 S N N 
? 2 V N N 
? 2 Z N N 
? 2 DA N N 
? 2 FA N N 
? 2 KA N N 
? 2 MA N N 
? 2 PA N N 
? 2 SA N N 
? 2 VA 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 262 n n 
N1 C10 RBF doub 263 n n 
C2 O2 RBF doub 264 n n 
C2 N3 RBF sing 265 n n 
N3 C4 RBF sing 266 n n 
N3 HN3 RBF sing 267 n n 
C4 O4 RBF doub 268 n n 
C4 C4A RBF sing 269 n n 
C4A N5 RBF doub 270 n n 
C4A C10 RBF sing 271 n n 
N5 C5A RBF sing 272 n n 
C5A C6 RBF doub 273 n y 
C5A C9A RBF sing 274 n y 
C6 C7 RBF sing 275 n y 
C6 HC6 RBF sing 276 n n 
C7 C7M RBF sing 277 n n 
C7 C8 RBF doub 278 n y 
C7M HC71 RBF sing 279 n n 
C7M HC72 RBF sing 280 n n 
C7M HC73 RBF sing 281 n n 
C8 C8M RBF sing 282 n n 
C8 C9 RBF sing 283 n y 
C8M HC81 RBF sing 284 n n 
C8M HC82 RBF sing 285 n n 
C8M HC83 RBF sing 286 n n 
C9 C9A RBF doub 287 n y 
C9 HC9 RBF sing 288 n n 
C9A N10 RBF sing 289 n n 
N10 C10 RBF sing 290 n n 
N10 C1' RBF sing 291 n n 
C1' C2' RBF sing 292 n n 
C1' HC11 RBF sing 293 n n 
C1' HC12 RBF sing 294 n n 
C2' O2' RBF sing 295 n n 
C2' C3' RBF sing 296 n n 
C2' HC2' RBF sing 297 n n 
O2' HO2' RBF sing 298 n n 
C3' O3' RBF sing 299 n n 
C3' C4' RBF sing 300 n n 
C3' HC3' RBF sing 301 n n 
O3' HO3' RBF sing 302 n n 
C4' O4' RBF sing 303 n n 
C4' C5' RBF sing 304 n n 
C4' HC4' RBF sing 305 n n 
O4' HO4' RBF sing 306 n n 
C5' O5' RBF sing 307 n n 
C5' HC51 RBF sing 308 n n 
C5' HC52 RBF sing 309 n n 
O5' HO5' RBF sing 310 n n 
#
_atom_sites.entry_id                     2VXA 
_atom_sites.fract_transf_matrix[1][1]    0.01166 
_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]    0.009949 
_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]    0.009953 
_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
M 2 RBF A 1 200 200 RBF RBF . 
N 3 CL A 1 1069 1069 CL CL . 
O 3 CL A 1 1070 1070 CL CL . 
P 2 RBF B 1 200 200 RBF RBF . 
Q 3 CL B 1 1069 1069 CL CL . 
R 3 CL B 1 1070 1070 CL CL . 
S 2 RBF C 1 200 200 RBF RBF . 
T 3 CL C 1 1069 1069 CL CL . 
U 3 CL C 1 1070 1070 CL CL . 
V 2 RBF D 1 200 200 RBF RBF . 
W 3 CL D 1 1069 1069 CL CL . 
X 3 CL D 1 1070 1070 CL CL . 
Y 3 CL D 1 1071 1071 CL CL . 
Z 2 RBF E 1 200 200 RBF RBF . 
AA 3 CL E 1 1069 1069 CL CL . 
BA 3 CL E 1 1070 1070 CL CL . 
CA 3 CL E 1 1071 1071 CL CL . 
DA 2 RBF F 1 200 200 RBF RBF . 
EA 3 CL F 1 1069 1069 CL CL . 
FA 2 RBF G 1 200 200 RBF RBF . 
GA 3 CL G 1 1069 1069 CL CL . 
HA 3 CL G 1 1070 1070 CL CL . 
IA 3 CL G 1 1071 1071 CL CL . 
JA 3 CL G 1 1072 1072 CL CL . 
KA 2 RBF H 1 200 200 RBF RBF . 
LA 3 CL H 1 1069 1069 CL CL . 
MA 2 RBF I 1 200 200 RBF RBF . 
NA 3 CL I 1 1069 1069 CL CL . 
OA 3 CL I 1 1070 1070 CL CL . 
PA 2 RBF J 1 200 200 RBF RBF . 
QA 3 CL J 1 1069 1069 CL CL . 
RA 3 CL J 1 1070 1070 CL CL . 
SA 2 RBF K 1 200 200 RBF RBF . 
TA 3 CL K 1 1069 1069 CL CL . 
UA 3 CL K 1 1070 1070 CL CL . 
VA 2 RBF L 1 200 200 RBF RBF . 
#
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 . . . DA 2 -23.276 -42.489 2.991 1 36.73 ? N1 RBF 200 F 1 
HETATM 2 C C2 RBF . . . DA 2 -21.915 -42.413 2.934 1 36.73 ? C2 RBF 200 F 1 
HETATM 3 O O2 RBF . . . DA 2 -21.358 -42.785 1.887 1 36.78 ? O2 RBF 200 F 1 
HETATM 4 N N3 RBF . . . DA 2 -21.159 -41.951 3.954 1 36.74 ? N3 RBF 200 F 1 
HETATM 5 C C4 RBF . . . DA 2 -21.701 -41.557 5.112 1 36.68 ? C4 RBF 200 F 1 
HETATM 6 O O4 RBF . . . DA 2 -20.97 -41.153 6.041 1 36.46 ? O4 RBF 200 F 1 
HETATM 7 C C4A RBF . . . DA 2 -23.182 -41.623 5.263 1 36.34 ? C4A RBF 200 F 1 
HETATM 8 N N5 RBF . . . DA 2 -23.81 -41.246 6.388 1 36.72 ? N5 RBF 200 F 1 
HETATM 9 C C5A RBF . . . DA 2 -25.151 -41.32 6.495 1 36.57 ? C5A RBF 200 F 1 
HETATM 10 C C6 RBF . . . DA 2 -25.757 -40.92 7.666 1 36.83 ? C6 RBF 200 F 1 
HETATM 11 C C7 RBF . . . DA 2 -27.124 -40.986 7.823 1 36.79 ? C7 RBF 200 F 1 
HETATM 12 C C7M RBF . . . DA 2 -27.709 -40.536 9.14 1 36.46 ? C7M RBF 200 F 1 
HETATM 13 C C8 RBF . . . DA 2 -27.956 -41.505 6.697 1 36.93 ? C8 RBF 200 F 1 
HETATM 14 C C8M RBF . . . DA 2 -29.463 -41.614 6.774 1 36.82 ? C8M RBF 200 F 1 
HETATM 15 C C9 RBF . . . DA 2 -27.343 -41.897 5.525 1 36.72 ? C9 RBF 200 F 1 
HETATM 16 C C9A RBF . . . DA 2 -25.975 -41.823 5.375 1 36.68 ? C9A RBF 200 F 1 
HETATM 17 N N10 RBF . . . DA 2 -25.327 -42.227 4.19 1 37.18 ? N10 RBF 200 F 1 
HETATM 18 C C10 RBF . . . DA 2 -23.941 -42.126 4.109 1 36.82 ? C10 RBF 200 F 1 
HETATM 19 C C1' RBF . . . DA 2 -26.032 -42.701 3.031 1 37.72 ? C1' RBF 200 F 1 
HETATM 20 C C2' RBF . . . DA 2 -26.376 -44.147 3.191 1 43.88 ? C2' RBF 200 F 1 
HETATM 21 O O2' RBF . . . DA 2 -25.288 -44.9 2.646 1 43.56 ? O2' RBF 200 F 1 
HETATM 22 C C3' RBF . . . DA 2 -27.725 -44.265 2.472 1 46.96 ? C3' RBF 200 F 1 
HETATM 23 O O3' RBF . . . DA 2 -28.688 -44.931 3.312 1 48.67 ? O3' RBF 200 F 1 
HETATM 24 C C4' RBF . . . DA 2 -27.68 -44.912 1.095 1 49.47 ? C4' RBF 200 F 1 
HETATM 25 O O4' RBF . . . DA 2 -26.54 -44.425 0.416 1 50.38 ? O4' RBF 200 F 1 
HETATM 26 C C5' RBF . . . DA 2 -28.948 -44.552 0.325 1 51.91 ? C5' RBF 200 F 1 
HETATM 27 O O5' RBF . . . DA 2 -30.092 -45.028 1.06 1 53.11 ? O5' RBF 200 F 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           335 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
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