data_1Z5N
#
_model_server_result.job_id            GnRitihnYcoSBrwd9sK6Yg 
_model_server_result.datetime_utc      '2024-10-19 16:36:34' 
_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          1z5n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":233}' 
#
_entry.id    1Z5N 
#
_exptl.entry_id    1Z5N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              180.222 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5-S-methyl-5-thio-alpha-D-ribofuranose 
_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            1Z5N 
_cell.length_a            51.68 
_cell.length_b            69.46 
_cell.length_c            128.36 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Z5N 
_symmetry.cell_setting             orthorhombic 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 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,G,H 
_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 E N N 
#
_chem_comp.formula           'C6 H12 O4 S' 
_chem_comp.formula_weight    180.222 
_chem_comp.id                SR1 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5-S-methyl-5-thio-alpha-D-ribofuranose 
_chem_comp.type              'd-saccharide, alpha linking' 
_chem_comp.pdbx_synonyms     5-S-methyl-5-thio-alpha-D-ribose;5-S-methyl-5-thio-D-ribose;5-S-methyl-5-thio-ribose 
#
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
CS S SR1 sing 306 n n 
CS HS1 SR1 sing 307 n n 
CS HS2 SR1 sing 308 n n 
CS HS3 SR1 sing 309 n n 
S C5 SR1 sing 310 n n 
C5 C4 SR1 sing 311 n n 
C5 H51 SR1 sing 312 n n 
C5 H52 SR1 sing 313 n n 
C4 O4 SR1 sing 314 n n 
C4 C3 SR1 sing 315 n n 
C4 H4 SR1 sing 316 n n 
O4 C1 SR1 sing 317 n n 
C1 O1 SR1 sing 318 n n 
C1 C2 SR1 sing 319 n n 
C1 H1 SR1 sing 320 n n 
O1 HO1 SR1 sing 321 n n 
C2 O2 SR1 sing 322 n n 
C2 C3 SR1 sing 323 n n 
C2 H2 SR1 sing 324 n n 
O2 HO2 SR1 sing 325 n n 
C3 O3 SR1 sing 326 n n 
C3 H3 SR1 sing 327 n n 
O3 HO3 SR1 sing 328 n n 
#
_pdbx_chem_comp_identifier.comp_id            SR1 
_pdbx_chem_comp_identifier.identifier         a-D-Ribf5SMe 
_pdbx_chem_comp_identifier.type               'IUPAC CARBOHYDRATE SYMBOL' 
_pdbx_chem_comp_identifier.program            PDB-CARE 
_pdbx_chem_comp_identifier.program_version    1 
#
_atom_sites.entry_id                     1Z5N 
_atom_sites.fract_transf_matrix[1][1]    0.01935 
_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]    0.014397 
_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]    0.007791 
_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 SR1 A 1 233 233 SR1 SR1 . 
D 3 ADE A 1 234 234 ADE ADE . 
E 2 SR1 B 1 235 235 SR1 SR1 . 
F 3 ADE B 1 236 236 ADE ADE . 
G 4 HOH A 1 235 2 HOH HOH . 
G 4 HOH A 2 236 4 HOH HOH . 
G 4 HOH A 3 237 11 HOH HOH . 
G 4 HOH A 4 238 12 HOH HOH . 
G 4 HOH A 5 239 15 HOH HOH . 
G 4 HOH A 6 240 18 HOH HOH . 
G 4 HOH A 7 241 19 HOH HOH . 
G 4 HOH A 8 242 20 HOH HOH . 
G 4 HOH A 9 243 21 HOH HOH . 
G 4 HOH A 10 244 22 HOH HOH . 
G 4 HOH A 11 245 23 HOH HOH . 
G 4 HOH A 12 246 24 HOH HOH . 
G 4 HOH A 13 247 25 HOH HOH . 
G 4 HOH A 14 248 26 HOH HOH . 
G 4 HOH A 15 249 29 HOH HOH . 
G 4 HOH A 16 250 33 HOH HOH . 
G 4 HOH A 17 251 34 HOH HOH . 
G 4 HOH A 18 252 35 HOH HOH . 
G 4 HOH A 19 253 37 HOH HOH . 
G 4 HOH A 20 254 38 HOH HOH . 
G 4 HOH A 21 255 39 HOH HOH . 
G 4 HOH A 22 256 40 HOH HOH . 
G 4 HOH A 23 257 41 HOH HOH . 
G 4 HOH A 24 258 42 HOH HOH . 
G 4 HOH A 25 259 44 HOH HOH . 
G 4 HOH A 26 260 50 HOH HOH . 
G 4 HOH A 27 261 53 HOH HOH . 
G 4 HOH A 28 262 54 HOH HOH . 
G 4 HOH A 29 263 55 HOH HOH . 
G 4 HOH A 30 264 56 HOH HOH . 
G 4 HOH A 31 265 57 HOH HOH . 
G 4 HOH A 32 266 60 HOH HOH . 
G 4 HOH A 33 267 62 HOH HOH . 
G 4 HOH A 34 268 66 HOH HOH . 
G 4 HOH A 35 269 68 HOH HOH . 
G 4 HOH A 36 270 71 HOH HOH . 
G 4 HOH A 37 271 72 HOH HOH . 
G 4 HOH A 38 272 73 HOH HOH . 
G 4 HOH A 39 273 74 HOH HOH . 
G 4 HOH A 40 274 75 HOH HOH . 
G 4 HOH A 41 275 77 HOH HOH . 
G 4 HOH A 42 276 79 HOH HOH . 
G 4 HOH A 43 277 80 HOH HOH . 
G 4 HOH A 44 278 85 HOH HOH . 
G 4 HOH A 45 279 88 HOH HOH . 
G 4 HOH A 46 280 92 HOH HOH . 
G 4 HOH A 47 281 94 HOH HOH . 
G 4 HOH A 48 282 95 HOH HOH . 
G 4 HOH A 49 283 96 HOH HOH . 
G 4 HOH A 50 284 100 HOH HOH . 
G 4 HOH A 51 285 102 HOH HOH . 
G 4 HOH A 52 286 103 HOH HOH . 
G 4 HOH A 53 287 107 HOH HOH . 
G 4 HOH A 54 288 108 HOH HOH . 
G 4 HOH A 55 289 109 HOH HOH . 
G 4 HOH A 56 290 110 HOH HOH . 
G 4 HOH A 57 291 111 HOH HOH . 
G 4 HOH A 58 292 113 HOH HOH . 
G 4 HOH A 59 293 118 HOH HOH . 
G 4 HOH A 60 294 119 HOH HOH . 
G 4 HOH A 61 295 120 HOH HOH . 
G 4 HOH A 62 296 121 HOH HOH . 
G 4 HOH A 63 297 125 HOH HOH . 
H 4 HOH B 1 237 1 HOH HOH . 
H 4 HOH B 2 238 3 HOH HOH . 
H 4 HOH B 3 239 5 HOH HOH . 
H 4 HOH B 4 240 6 HOH HOH . 
H 4 HOH B 5 241 7 HOH HOH . 
H 4 HOH B 6 242 8 HOH HOH . 
H 4 HOH B 7 243 9 HOH HOH . 
H 4 HOH B 8 244 10 HOH HOH . 
H 4 HOH B 9 245 13 HOH HOH . 
H 4 HOH B 10 246 14 HOH HOH . 
H 4 HOH B 11 247 16 HOH HOH . 
H 4 HOH B 12 248 17 HOH HOH . 
H 4 HOH B 13 249 27 HOH HOH . 
H 4 HOH B 14 250 28 HOH HOH . 
H 4 HOH B 15 251 30 HOH HOH . 
H 4 HOH B 16 252 31 HOH HOH . 
H 4 HOH B 17 253 32 HOH HOH . 
H 4 HOH B 18 254 36 HOH HOH . 
H 4 HOH B 19 255 43 HOH HOH . 
H 4 HOH B 20 256 45 HOH HOH . 
H 4 HOH B 21 257 46 HOH HOH . 
H 4 HOH B 22 258 47 HOH HOH . 
H 4 HOH B 23 259 48 HOH HOH . 
H 4 HOH B 24 260 49 HOH HOH . 
H 4 HOH B 25 261 51 HOH HOH . 
H 4 HOH B 26 262 52 HOH HOH . 
H 4 HOH B 27 263 58 HOH HOH . 
H 4 HOH B 28 264 59 HOH HOH . 
H 4 HOH B 29 265 61 HOH HOH . 
H 4 HOH B 30 266 63 HOH HOH . 
H 4 HOH B 31 267 64 HOH HOH . 
H 4 HOH B 32 268 65 HOH HOH . 
H 4 HOH B 33 269 67 HOH HOH . 
H 4 HOH B 34 270 69 HOH HOH . 
H 4 HOH B 35 271 70 HOH HOH . 
H 4 HOH B 36 272 76 HOH HOH . 
H 4 HOH B 37 273 78 HOH HOH . 
H 4 HOH B 38 274 81 HOH HOH . 
H 4 HOH B 39 275 82 HOH HOH . 
H 4 HOH B 40 276 83 HOH HOH . 
H 4 HOH B 41 277 84 HOH HOH . 
H 4 HOH B 42 278 86 HOH HOH . 
H 4 HOH B 43 279 87 HOH HOH . 
H 4 HOH B 44 280 89 HOH HOH . 
H 4 HOH B 45 281 90 HOH HOH . 
H 4 HOH B 46 282 91 HOH HOH . 
H 4 HOH B 47 283 93 HOH HOH . 
H 4 HOH B 48 284 97 HOH HOH . 
H 4 HOH B 49 285 98 HOH HOH . 
H 4 HOH B 50 286 99 HOH HOH . 
H 4 HOH B 51 287 101 HOH HOH . 
H 4 HOH B 52 288 104 HOH HOH . 
H 4 HOH B 53 289 105 HOH HOH . 
H 4 HOH B 54 290 106 HOH HOH . 
H 4 HOH B 55 291 112 HOH HOH . 
H 4 HOH B 56 292 114 HOH HOH . 
H 4 HOH B 57 293 115 HOH HOH . 
H 4 HOH B 58 294 116 HOH HOH . 
H 4 HOH B 59 295 117 HOH HOH . 
H 4 HOH B 60 296 122 HOH HOH . 
H 4 HOH B 61 297 123 HOH HOH . 
H 4 HOH B 62 298 124 HOH HOH . 
H 4 HOH B 63 299 126 HOH HOH . 
H 4 HOH B 64 300 127 HOH HOH . 
H 4 HOH B 65 301 128 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 C CS SR1 . . . C 2 56.725 68.946 22.794 1 27.63 ? CS SR1 233 A 1 
HETATM 2 S S SR1 . . . C 2 56.082 70.572 23.239 1 25.97 ? S SR1 233 A 1 
HETATM 3 C C5 SR1 . . . C 2 56.965 71.593 22.048 1 27.34 ? C5 SR1 233 A 1 
HETATM 4 C C4 SR1 . . . C 2 58.391 71.873 22.477 1 27.26 ? C4 SR1 233 A 1 
HETATM 5 O O4 SR1 . . . C 2 59.143 72.332 21.317 1 28.04 ? O4 SR1 233 A 1 
HETATM 6 C C1 SR1 . . . C 2 59.405 73.72 21.437 1 26.92 ? C1 SR1 233 A 1 
HETATM 7 O O1 SR1 . . . C 2 60.794 73.919 21.775 1 32.57 ? O1 SR1 233 A 1 
HETATM 8 C C2 SR1 . . . C 2 58.513 74.207 22.573 1 25.69 ? C2 SR1 233 A 1 
HETATM 9 O O2 SR1 . . . C 2 59.023 75.39 23.137 1 24.86 ? O2 SR1 233 A 1 
HETATM 10 C C3 SR1 . . . C 2 58.55 72.995 23.498 1 28.06 ? C3 SR1 233 A 1 
HETATM 11 O O3 SR1 . . . C 2 59.812 72.87 24.16 1 27.88 ? O3 SR1 233 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           11 
#