data_1Y6R
#
_model_server_result.job_id            l18vHuORAou_ks7b331obw 
_model_server_result.datetime_utc      '2024-11-28 19:04:43' 
_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          1y6r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":234}' 
#
_entry.id    1Y6R 
#
_exptl.entry_id    1Y6R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              297.377 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL 
_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            1Y6R 
_cell.length_a            51.57 
_cell.length_b            69.6 
_cell.length_c            127.57 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Y6R 
_symmetry.cell_setting             ? 
_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 
_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 D N N 
#
_chem_comp.formula           'C12 H19 N5 O2 S' 
_chem_comp.formula_weight    297.377 
_chem_comp.id                MTM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     (1S)-1-(9-DEAZAADENIN-9-YL)-1,4,5-TRIDEOXY-1,4-IMINO-5-METHYLTHIO-D-RIBITOL 
#
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 S5' MTM sing 237 n n 
CS HCS1 MTM sing 238 n n 
CS HCS2 MTM sing 239 n n 
CS HCS3 MTM sing 240 n n 
S5' C5' MTM sing 241 n n 
C5' C4' MTM sing 242 n n 
C5' "H5'1" MTM sing 243 n n 
C5' "H5'2" MTM sing 244 n n 
C4' N4' MTM sing 245 n n 
C4' C3' MTM sing 246 n n 
C4' H4' MTM sing 247 n n 
N4' C1' MTM sing 248 n n 
N4' HN4 MTM sing 249 n n 
C2' O2' MTM sing 250 n n 
C2' C3' MTM sing 251 n n 
C2' C1' MTM sing 252 n n 
C2' H2' MTM sing 253 n n 
O2' "HO'2" MTM sing 254 n n 
C3' O3' MTM sing 255 n n 
C3' H3' MTM sing 256 n n 
O3' H3T MTM sing 257 n n 
C1' C9 MTM sing 258 n n 
C1' H1' MTM sing 259 n n 
C9 C8 MTM doub 260 n y 
C9 C4 MTM sing 261 n y 
C8 N7 MTM sing 262 n y 
C8 H8 MTM sing 263 n n 
N7 C5 MTM sing 264 n y 
N7 H7 MTM sing 265 n n 
C5 C6 MTM sing 266 n n 
C5 C4 MTM doub 267 n y 
C6 N6 MTM sing 268 n n 
C6 N1 MTM sing 269 n n 
C6 H6 MTM sing 270 n n 
N6 H61 MTM sing 271 n n 
N6 H62 MTM sing 272 n n 
N1 C2 MTM sing 273 n n 
N1 HN1 MTM sing 274 n n 
C2 N3 MTM doub 275 n n 
C2 H2 MTM sing 276 n n 
N3 C4 MTM sing 277 n n 
#
_atom_sites.entry_id                     1Y6R 
_atom_sites.fract_transf_matrix[1][1]    0.019391 
_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]    0.014368 
_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]    0.007839 
_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 MTM A 1 233 233 MTM MTM . 
D 2 MTM B 1 234 234 MTM MTM . 
E 3 HOH A 1 234 3 HOH HOH . 
E 3 HOH A 2 235 7 HOH HOH . 
E 3 HOH A 3 236 9 HOH HOH . 
E 3 HOH A 4 237 12 HOH HOH . 
E 3 HOH A 5 238 13 HOH HOH . 
E 3 HOH A 6 239 16 HOH HOH . 
E 3 HOH A 7 240 17 HOH HOH . 
E 3 HOH A 8 241 18 HOH HOH . 
E 3 HOH A 9 242 21 HOH HOH . 
E 3 HOH A 10 243 22 HOH HOH . 
E 3 HOH A 11 244 23 HOH HOH . 
E 3 HOH A 12 245 24 HOH HOH . 
E 3 HOH A 13 246 27 HOH HOH . 
E 3 HOH A 14 247 29 HOH HOH . 
E 3 HOH A 15 248 37 HOH HOH . 
E 3 HOH A 16 249 43 HOH HOH . 
E 3 HOH A 17 250 46 HOH HOH . 
E 3 HOH A 18 251 47 HOH HOH . 
E 3 HOH A 19 252 48 HOH HOH . 
E 3 HOH A 20 253 49 HOH HOH . 
E 3 HOH A 21 254 50 HOH HOH . 
E 3 HOH A 22 255 51 HOH HOH . 
E 3 HOH A 23 256 53 HOH HOH . 
E 3 HOH A 24 257 54 HOH HOH . 
E 3 HOH A 25 258 61 HOH HOH . 
E 3 HOH A 26 259 62 HOH HOH . 
E 3 HOH A 27 260 63 HOH HOH . 
E 3 HOH A 28 261 64 HOH HOH . 
E 3 HOH A 29 262 66 HOH HOH . 
E 3 HOH A 30 263 68 HOH HOH . 
E 3 HOH A 31 264 69 HOH HOH . 
E 3 HOH A 32 265 70 HOH HOH . 
E 3 HOH A 33 266 73 HOH HOH . 
E 3 HOH A 34 267 74 HOH HOH . 
E 3 HOH A 35 268 76 HOH HOH . 
E 3 HOH A 36 269 79 HOH HOH . 
E 3 HOH A 37 270 81 HOH HOH . 
E 3 HOH A 38 271 82 HOH HOH . 
E 3 HOH A 39 272 84 HOH HOH . 
E 3 HOH A 40 273 85 HOH HOH . 
E 3 HOH A 41 274 86 HOH HOH . 
E 3 HOH A 42 275 87 HOH HOH . 
E 3 HOH A 43 276 89 HOH HOH . 
E 3 HOH A 44 277 91 HOH HOH . 
E 3 HOH A 45 278 93 HOH HOH . 
E 3 HOH A 46 279 95 HOH HOH . 
E 3 HOH A 47 280 96 HOH HOH . 
E 3 HOH A 48 281 99 HOH HOH . 
E 3 HOH A 49 282 101 HOH HOH . 
E 3 HOH A 50 283 103 HOH HOH . 
E 3 HOH A 51 284 104 HOH HOH . 
E 3 HOH A 52 285 111 HOH HOH . 
E 3 HOH A 53 286 113 HOH HOH . 
E 3 HOH A 54 287 115 HOH HOH . 
E 3 HOH A 55 288 116 HOH HOH . 
E 3 HOH A 56 289 117 HOH HOH . 
E 3 HOH A 57 290 118 HOH HOH . 
E 3 HOH A 58 291 119 HOH HOH . 
E 3 HOH A 59 292 120 HOH HOH . 
E 3 HOH A 60 293 121 HOH HOH . 
E 3 HOH A 61 294 122 HOH HOH . 
E 3 HOH A 62 295 123 HOH HOH . 
E 3 HOH A 63 296 124 HOH HOH . 
E 3 HOH A 64 297 126 HOH HOH . 
E 3 HOH A 65 298 134 HOH HOH . 
E 3 HOH A 66 299 135 HOH HOH . 
E 3 HOH A 67 300 136 HOH HOH . 
E 3 HOH A 68 301 138 HOH HOH . 
E 3 HOH A 69 302 139 HOH HOH . 
E 3 HOH A 70 303 140 HOH HOH . 
E 3 HOH A 71 304 141 HOH HOH . 
E 3 HOH A 72 305 142 HOH HOH . 
E 3 HOH A 73 306 143 HOH HOH . 
E 3 HOH A 74 307 144 HOH HOH . 
E 3 HOH A 75 308 145 HOH HOH . 
E 3 HOH A 76 309 146 HOH HOH . 
E 3 HOH A 77 310 152 HOH HOH . 
E 3 HOH A 78 311 153 HOH HOH . 
E 3 HOH A 79 312 155 HOH HOH . 
E 3 HOH A 80 313 157 HOH HOH . 
E 3 HOH A 81 314 159 HOH HOH . 
E 3 HOH A 82 315 160 HOH HOH . 
E 3 HOH A 83 316 161 HOH HOH . 
E 3 HOH A 84 317 163 HOH HOH . 
F 3 HOH B 1 235 1 HOH HOH . 
F 3 HOH B 2 236 2 HOH HOH . 
F 3 HOH B 3 237 4 HOH HOH . 
F 3 HOH B 4 238 5 HOH HOH . 
F 3 HOH B 5 239 6 HOH HOH . 
F 3 HOH B 6 240 8 HOH HOH . 
F 3 HOH B 7 241 10 HOH HOH . 
F 3 HOH B 8 242 11 HOH HOH . 
F 3 HOH B 9 243 14 HOH HOH . 
F 3 HOH B 10 244 15 HOH HOH . 
F 3 HOH B 11 245 19 HOH HOH . 
F 3 HOH B 12 246 20 HOH HOH . 
F 3 HOH B 13 247 25 HOH HOH . 
F 3 HOH B 14 248 26 HOH HOH . 
F 3 HOH B 15 249 28 HOH HOH . 
F 3 HOH B 16 250 30 HOH HOH . 
F 3 HOH B 17 251 31 HOH HOH . 
F 3 HOH B 18 252 32 HOH HOH . 
F 3 HOH B 19 253 33 HOH HOH . 
F 3 HOH B 20 254 34 HOH HOH . 
F 3 HOH B 21 255 35 HOH HOH . 
F 3 HOH B 22 256 36 HOH HOH . 
F 3 HOH B 23 257 38 HOH HOH . 
F 3 HOH B 24 258 39 HOH HOH . 
F 3 HOH B 25 259 40 HOH HOH . 
F 3 HOH B 26 260 41 HOH HOH . 
F 3 HOH B 27 261 42 HOH HOH . 
F 3 HOH B 28 262 44 HOH HOH . 
F 3 HOH B 29 263 45 HOH HOH . 
F 3 HOH B 30 264 52 HOH HOH . 
F 3 HOH B 31 265 55 HOH HOH . 
F 3 HOH B 32 266 56 HOH HOH . 
F 3 HOH B 33 267 57 HOH HOH . 
F 3 HOH B 34 268 58 HOH HOH . 
F 3 HOH B 35 269 59 HOH HOH . 
F 3 HOH B 36 270 60 HOH HOH . 
F 3 HOH B 37 271 65 HOH HOH . 
F 3 HOH B 38 272 67 HOH HOH . 
F 3 HOH B 39 273 71 HOH HOH . 
F 3 HOH B 40 274 72 HOH HOH . 
F 3 HOH B 41 275 75 HOH HOH . 
F 3 HOH B 42 276 77 HOH HOH . 
F 3 HOH B 43 277 78 HOH HOH . 
F 3 HOH B 44 278 80 HOH HOH . 
F 3 HOH B 45 279 83 HOH HOH . 
F 3 HOH B 46 280 88 HOH HOH . 
F 3 HOH B 47 281 90 HOH HOH . 
F 3 HOH B 48 282 92 HOH HOH . 
F 3 HOH B 49 283 94 HOH HOH . 
F 3 HOH B 50 284 97 HOH HOH . 
F 3 HOH B 51 285 98 HOH HOH . 
F 3 HOH B 52 286 100 HOH HOH . 
F 3 HOH B 53 287 102 HOH HOH . 
F 3 HOH B 54 288 105 HOH HOH . 
F 3 HOH B 55 289 106 HOH HOH . 
F 3 HOH B 56 290 107 HOH HOH . 
F 3 HOH B 57 291 108 HOH HOH . 
F 3 HOH B 58 292 109 HOH HOH . 
F 3 HOH B 59 293 110 HOH HOH . 
F 3 HOH B 60 294 112 HOH HOH . 
F 3 HOH B 61 295 114 HOH HOH . 
F 3 HOH B 62 296 125 HOH HOH . 
F 3 HOH B 63 297 127 HOH HOH . 
F 3 HOH B 64 298 128 HOH HOH . 
F 3 HOH B 65 299 129 HOH HOH . 
F 3 HOH B 66 300 130 HOH HOH . 
F 3 HOH B 67 301 131 HOH HOH . 
F 3 HOH B 68 302 132 HOH HOH . 
F 3 HOH B 69 303 133 HOH HOH . 
F 3 HOH B 70 304 137 HOH HOH . 
F 3 HOH B 71 305 147 HOH HOH . 
F 3 HOH B 72 306 148 HOH HOH . 
F 3 HOH B 73 307 149 HOH HOH . 
F 3 HOH B 74 308 150 HOH HOH . 
F 3 HOH B 75 309 151 HOH HOH . 
F 3 HOH B 76 310 154 HOH HOH . 
F 3 HOH B 77 311 156 HOH HOH . 
F 3 HOH B 78 312 158 HOH HOH . 
F 3 HOH B 79 313 162 HOH HOH . 
F 3 HOH B 80 314 164 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 MTM . . . D 2 47.219 90.991 40.792 1 27.31 ? CS MTM 234 B 1 
HETATM 2 S S5' MTM . . . D 2 47.138 89.326 40.029 1 22.56 ? S5' MTM 234 B 1 
HETATM 3 C C5' MTM . . . D 2 46.535 88.353 41.457 1 17.74 ? C5' MTM 234 B 1 
HETATM 4 C C4' MTM . . . D 2 47.621 87.907 42.459 1 22.06 ? C4' MTM 234 B 1 
HETATM 5 N N4' MTM . . . D 2 46.957 87.309 43.655 1 20.81 ? N4' MTM 234 B 1 
HETATM 6 C C2' MTM . . . D 2 47.719 85.52 42.305 1 16.12 ? C2' MTM 234 B 1 
HETATM 7 O O2' MTM . . . D 2 48.622 84.446 42.689 1 15.15 ? O2' MTM 234 B 1 
HETATM 8 C C3' MTM . . . D 2 48.553 86.838 41.928 1 17.25 ? C3' MTM 234 B 1 
HETATM 9 O O3' MTM . . . D 2 49.836 86.875 42.635 1 17.26 ? O3' MTM 234 B 1 
HETATM 10 C C1' MTM . . . D 2 46.695 85.867 43.466 1 17.08 ? C1' MTM 234 B 1 
HETATM 11 C C9 MTM . . . D 2 45.216 85.771 43.123 1 19.44 ? C9 MTM 234 B 1 
HETATM 12 C C8 MTM . . . D 2 44.168 86.098 43.991 1 18.58 ? C8 MTM 234 B 1 
HETATM 13 N N7 MTM . . . D 2 42.952 85.962 43.478 1 16.73 ? N7 MTM 234 B 1 
HETATM 14 C C5 MTM . . . D 2 43.193 85.519 42.191 1 17.2 ? C5 MTM 234 B 1 
HETATM 15 C C6 MTM . . . D 2 42.332 85.189 41.091 1 16.87 ? C6 MTM 234 B 1 
HETATM 16 N N6 MTM . . . D 2 40.994 85.277 41.172 1 18.03 ? N6 MTM 234 B 1 
HETATM 17 N N1 MTM . . . D 2 42.936 84.775 39.922 1 15.75 ? N1 MTM 234 B 1 
HETATM 18 C C2 MTM . . . D 2 44.293 84.686 39.833 1 17.5 ? C2 MTM 234 B 1 
HETATM 19 N N3 MTM . . . D 2 45.2 84.975 40.805 1 18.14 ? N3 MTM 234 B 1 
HETATM 20 C C4 MTM . . . D 2 44.575 85.387 41.956 1 14.68 ? C4 MTM 234 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           20 
#