data_2A59
#
_model_server_result.job_id            9_VBSMFySkD8Tt30kEAUkQ 
_model_server_result.datetime_utc      '2025-03-04 16:00:45' 
_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          2a59 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":304}' 
#
_entry.id    2A59 
#
_exptl.entry_id    2A59 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              290.23 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE 
_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            2A59 
_cell.length_a            111.15 
_cell.length_b            144.81 
_cell.length_c            127.78 
_cell.Z_PDB               40 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2A59 
_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    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 
_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
? 3 G N N 
? 3 I N N 
? 3 K N N 
? 3 M N N 
? 3 O N N 
#
_chem_comp.formula           'C9 H14 N4 O7' 
_chem_comp.formula_weight    290.23 
_chem_comp.id                LMZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 LMZ sing 181 n y 
N1 C6 LMZ sing 182 n y 
N1 HN1 LMZ sing 183 n n 
C2 N3 LMZ sing 184 n y 
C2 O2 LMZ doub 185 n n 
N3 C4 LMZ sing 186 n y 
N3 HN3 LMZ sing 187 n n 
C4 C5 LMZ sing 188 n y 
C4 O4 LMZ doub 189 n n 
C5 C6 LMZ doub 190 n y 
C5 N5 LMZ sing 191 n n 
C6 N7 LMZ sing 192 n n 
N7 C8 LMZ sing 193 n n 
N7 HN7 LMZ sing 194 n n 
C8 C9 LMZ sing 195 n n 
C8 H81 LMZ sing 196 n n 
C8 H82 LMZ sing 197 n n 
C9 O9 LMZ sing 198 n n 
C9 C10 LMZ sing 199 n n 
C9 H9 LMZ sing 200 n n 
O9 HO9 LMZ sing 201 n n 
C10 O10 LMZ sing 202 n n 
C10 C11 LMZ sing 203 n n 
C10 H10 LMZ sing 204 n n 
O10 HO10 LMZ sing 205 n n 
C11 O11 LMZ sing 206 n n 
C11 C12 LMZ sing 207 n n 
C11 H11 LMZ sing 208 n n 
O11 HO11 LMZ sing 209 n n 
C12 O12 LMZ sing 210 n n 
C12 H121 LMZ sing 211 n n 
C12 H122 LMZ sing 212 n n 
O12 HO12 LMZ sing 213 n n 
N5 O52 LMZ doub 214 n n 
#
_atom_sites.entry_id                     2A59 
_atom_sites.fract_transf_matrix[1][1]    0.008997 
_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]    0.006906 
_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]    0.007826 
_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 LMZ A 1 300 300 LMZ LMZ . 
H 2 PO4 B 1 500 500 PO4 PO4 . 
I 3 LMZ B 1 301 301 LMZ LMZ . 
J 2 PO4 C 1 501 501 PO4 PO4 . 
K 3 LMZ C 1 302 302 LMZ LMZ . 
L 2 PO4 D 1 502 502 PO4 PO4 . 
M 3 LMZ D 1 303 303 LMZ LMZ . 
N 2 PO4 E 1 503 503 PO4 PO4 . 
O 3 LMZ E 1 304 304 LMZ LMZ . 
P 4 HOH A 1 505 2 HOH TIP . 
P 4 HOH A 2 506 9 HOH TIP . 
P 4 HOH A 3 507 16 HOH TIP . 
P 4 HOH A 4 508 18 HOH TIP . 
P 4 HOH A 5 509 20 HOH TIP . 
P 4 HOH A 6 510 25 HOH TIP . 
P 4 HOH A 7 511 27 HOH TIP . 
P 4 HOH A 8 512 30 HOH TIP . 
P 4 HOH A 9 513 32 HOH TIP . 
P 4 HOH A 10 514 34 HOH TIP . 
P 4 HOH A 11 515 39 HOH TIP . 
P 4 HOH A 12 516 42 HOH TIP . 
P 4 HOH A 13 517 44 HOH TIP . 
P 4 HOH A 14 518 45 HOH TIP . 
P 4 HOH A 15 519 49 HOH TIP . 
P 4 HOH A 16 520 52 HOH TIP . 
Q 4 HOH B 1 501 3 HOH TIP . 
Q 4 HOH B 2 502 6 HOH TIP . 
Q 4 HOH B 3 503 13 HOH TIP . 
Q 4 HOH B 4 504 15 HOH TIP . 
Q 4 HOH B 5 505 19 HOH TIP . 
Q 4 HOH B 6 506 29 HOH TIP . 
Q 4 HOH B 7 507 36 HOH TIP . 
Q 4 HOH B 8 508 38 HOH TIP . 
Q 4 HOH B 9 509 41 HOH TIP . 
Q 4 HOH B 10 510 54 HOH TIP . 
Q 4 HOH B 11 511 55 HOH TIP . 
Q 4 HOH B 12 512 56 HOH TIP . 
R 4 HOH C 1 502 1 HOH TIP . 
R 4 HOH C 2 503 7 HOH TIP . 
R 4 HOH C 3 504 8 HOH TIP . 
R 4 HOH C 4 505 14 HOH TIP . 
R 4 HOH C 5 506 21 HOH TIP . 
R 4 HOH C 6 507 22 HOH TIP . 
R 4 HOH C 7 508 31 HOH TIP . 
R 4 HOH C 8 509 33 HOH TIP . 
R 4 HOH C 9 510 37 HOH TIP . 
R 4 HOH C 10 511 46 HOH TIP . 
R 4 HOH C 11 512 48 HOH TIP . 
R 4 HOH C 12 513 57 HOH TIP . 
R 4 HOH C 13 514 58 HOH TIP . 
S 4 HOH D 1 503 4 HOH TIP . 
S 4 HOH D 2 504 5 HOH TIP . 
S 4 HOH D 3 505 12 HOH TIP . 
S 4 HOH D 4 506 17 HOH TIP . 
S 4 HOH D 5 507 28 HOH TIP . 
S 4 HOH D 6 508 35 HOH TIP . 
S 4 HOH D 7 509 43 HOH TIP . 
S 4 HOH D 8 510 53 HOH TIP . 
T 4 HOH E 1 504 10 HOH TIP . 
T 4 HOH E 2 505 11 HOH TIP . 
T 4 HOH E 3 506 23 HOH TIP . 
T 4 HOH E 4 507 24 HOH TIP . 
T 4 HOH E 5 508 26 HOH TIP . 
T 4 HOH E 6 509 40 HOH TIP . 
T 4 HOH E 7 510 47 HOH TIP . 
T 4 HOH E 8 511 50 HOH TIP . 
T 4 HOH E 9 512 51 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 LMZ . . . O 3 67.771 55.208 23.615 1 38.3 ? N1 LMZ 304 E 1 
HETATM 2 C C2 LMZ . . . O 3 68.012 55.346 24.983 1 37.27 ? C2 LMZ 304 E 1 
HETATM 3 N N3 LMZ . . . O 3 66.945 55.185 25.803 1 38.81 ? N3 LMZ 304 E 1 
HETATM 4 C C4 LMZ . . . O 3 65.641 54.895 25.383 1 39.75 ? C4 LMZ 304 E 1 
HETATM 5 C C5 LMZ . . . O 3 65.407 54.747 23.893 1 39.79 ? C5 LMZ 304 E 1 
HETATM 6 C C6 LMZ . . . O 3 66.512 54.916 23.027 1 40.4 ? C6 LMZ 304 E 1 
HETATM 7 N N7 LMZ . . . O 3 66.406 54.802 21.651 1 40.49 ? N7 LMZ 304 E 1 
HETATM 8 C C8 LMZ . . . O 3 67.529 55.395 20.928 1 37.83 ? C8 LMZ 304 E 1 
HETATM 9 C C9 LMZ . . . O 3 68.46 54.34 20.252 1 41.51 ? C9 LMZ 304 E 1 
HETATM 10 O O9 LMZ . . . O 3 69.347 53.978 21.28 1 42.88 ? O9 LMZ 304 E 1 
HETATM 11 C C10 LMZ . . . O 3 69.36 54.749 18.999 1 44.36 ? C10 LMZ 304 E 1 
HETATM 12 O O10 LMZ . . . O 3 69.74 56.11 19.074 1 47.44 ? O10 LMZ 304 E 1 
HETATM 13 C C11 LMZ . . . O 3 68.812 54.479 17.464 1 43.18 ? C11 LMZ 304 E 1 
HETATM 14 O O11 LMZ . . . O 3 67.586 53.812 17.788 1 42.4 ? O11 LMZ 304 E 1 
HETATM 15 C C12 LMZ . . . O 3 69.384 53.453 16.455 1 45.2 ? C12 LMZ 304 E 1 
HETATM 16 O O12 LMZ . . . O 3 70.689 53.887 16.305 1 48.74 ? O12 LMZ 304 E 1 
HETATM 17 N N5 LMZ . . . O 3 64.096 54.447 23.455 1 44.9 ? N5 LMZ 304 E 1 
HETATM 18 O O52 LMZ . . . O 3 63.882 54.312 22.228 1 49.08 ? O52 LMZ 304 E 1 
HETATM 19 O O4 LMZ . . . O 3 64.711 54.773 26.403 1 42.63 ? O4 LMZ 304 E 1 
HETATM 20 O O2 LMZ . . . O 3 69.28 55.629 25.358 1 36.84 ? O2 LMZ 304 E 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           20 
#