data_3NRF
#
_model_server_result.job_id            43k23D6SiCFcspz0IGXe5w 
_model_server_result.datetime_utc      '2025-08-31 10:53:37' 
_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          3nrf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":129}' 
#
_entry.id    3NRF 
#
_exptl.entry_id    3NRF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4R)-2-METHYLPENTANE-2,4-DIOL 
_entity.pdbx_number_of_molecules    3 
_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            3NRF 
_cell.length_a            69.343 
_cell.length_b            96.491 
_cell.length_c            61.788 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NRF 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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    1,2 
#
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_656 -x+1,y,-z+3/2 -1 0 0 0 1 0 0 0 -1 69.343 0 92.682 
#
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 
? 2 E N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
disulf ? disulf1 A SG CYS 49 A CYS 69 1_555 A SG CYS 105 A CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
disulf ? disulf2 B SG CYS 49 B CYS 69 1_555 B SG CYS 105 B CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
covale ? covale1 A C VAL 7 A VAL 27 1_555 A N MSE 8 A MSE 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale2 A C MSE 8 A MSE 28 1_555 A N VAL 9 A VAL 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale3 B C VAL 7 B VAL 27 1_555 B N MSE 8 B MSE 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? 
covale ? covale4 B C MSE 8 B MSE 28 1_555 B N VAL 9 B VAL 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MRD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4R)-2-METHYLPENTANE-2,4-DIOL 
_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
C1 C2 MRD sing 228 n n 
C1 H1C1 MRD sing 229 n n 
C1 H1C2 MRD sing 230 n n 
C1 H1C3 MRD sing 231 n n 
C2 O2 MRD sing 232 n n 
C2 CM MRD sing 233 n n 
C2 C3 MRD sing 234 n n 
O2 H2 MRD sing 235 n n 
CM HMC1 MRD sing 236 n n 
CM HMC2 MRD sing 237 n n 
CM HMC3 MRD sing 238 n n 
C3 C4 MRD sing 239 n n 
C3 H3C1 MRD sing 240 n n 
C3 H3C2 MRD sing 241 n n 
C4 O4 MRD sing 242 n n 
C4 C5 MRD sing 243 n n 
C4 H4 MRD sing 244 n n 
O4 HA MRD sing 245 n n 
C5 H5C1 MRD sing 246 n n 
C5 H5C2 MRD sing 247 n n 
C5 H5C3 MRD sing 248 n n 
#
_atom_sites.entry_id                     3NRF 
_atom_sites.fract_transf_matrix[1][1]    0.014421 
_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]    0.010364 
_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]    0.016184 
_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 MRD A 1 128 128 MRD MRD . 
D 2 MRD B 1 127 127 MRD MRD . 
E 2 MRD B 1 129 129 MRD MRD . 
F 3 CAC B 1 130 130 CAC CAC . 
G 4 HOH A 1 132 132 HOH HOH . 
G 4 HOH A 2 133 133 HOH HOH . 
G 4 HOH A 3 135 135 HOH HOH . 
G 4 HOH A 4 137 137 HOH HOH . 
G 4 HOH A 5 139 139 HOH HOH . 
G 4 HOH A 6 140 140 HOH HOH . 
G 4 HOH A 7 141 141 HOH HOH . 
G 4 HOH A 8 142 142 HOH HOH . 
G 4 HOH A 9 143 143 HOH HOH . 
G 4 HOH A 10 146 146 HOH HOH . 
G 4 HOH A 11 147 147 HOH HOH . 
G 4 HOH A 12 148 148 HOH HOH . 
G 4 HOH A 13 150 150 HOH HOH . 
G 4 HOH A 14 152 152 HOH HOH . 
G 4 HOH A 15 153 153 HOH HOH . 
G 4 HOH A 16 157 157 HOH HOH . 
G 4 HOH A 17 158 158 HOH HOH . 
G 4 HOH A 18 161 161 HOH HOH . 
G 4 HOH A 19 162 162 HOH HOH . 
G 4 HOH A 20 165 165 HOH HOH . 
G 4 HOH A 21 167 167 HOH HOH . 
G 4 HOH A 22 169 169 HOH HOH . 
G 4 HOH A 23 171 171 HOH HOH . 
G 4 HOH A 24 172 172 HOH HOH . 
G 4 HOH A 25 178 178 HOH HOH . 
G 4 HOH A 26 180 180 HOH HOH . 
G 4 HOH A 27 181 181 HOH HOH . 
G 4 HOH A 28 182 182 HOH HOH . 
G 4 HOH A 29 183 183 HOH HOH . 
G 4 HOH A 30 185 185 HOH HOH . 
G 4 HOH A 31 190 190 HOH HOH . 
G 4 HOH A 32 191 191 HOH HOH . 
G 4 HOH A 33 195 195 HOH HOH . 
G 4 HOH A 34 196 196 HOH HOH . 
G 4 HOH A 35 199 199 HOH HOH . 
G 4 HOH A 36 200 200 HOH HOH . 
G 4 HOH A 37 202 202 HOH HOH . 
G 4 HOH A 38 203 203 HOH HOH . 
G 4 HOH A 39 210 210 HOH HOH . 
G 4 HOH A 40 216 216 HOH HOH . 
G 4 HOH A 41 218 218 HOH HOH . 
G 4 HOH A 42 221 221 HOH HOH . 
G 4 HOH A 43 222 222 HOH HOH . 
G 4 HOH A 44 223 223 HOH HOH . 
G 4 HOH A 45 228 228 HOH HOH . 
G 4 HOH A 46 229 229 HOH HOH . 
G 4 HOH A 47 230 230 HOH HOH . 
G 4 HOH A 48 231 231 HOH HOH . 
G 4 HOH A 49 232 232 HOH HOH . 
G 4 HOH A 50 233 233 HOH HOH . 
G 4 HOH A 51 234 234 HOH HOH . 
G 4 HOH A 52 238 238 HOH HOH . 
G 4 HOH A 53 240 240 HOH HOH . 
G 4 HOH A 54 243 243 HOH HOH . 
G 4 HOH A 55 244 244 HOH HOH . 
G 4 HOH A 56 245 245 HOH HOH . 
G 4 HOH A 57 247 247 HOH HOH . 
G 4 HOH A 58 248 248 HOH HOH . 
G 4 HOH A 59 251 251 HOH HOH . 
G 4 HOH A 60 252 252 HOH HOH . 
G 4 HOH A 61 256 256 HOH HOH . 
G 4 HOH A 62 257 257 HOH HOH . 
G 4 HOH A 63 259 259 HOH HOH . 
G 4 HOH A 64 261 261 HOH HOH . 
G 4 HOH A 65 263 263 HOH HOH . 
G 4 HOH A 66 265 265 HOH HOH . 
G 4 HOH A 67 267 267 HOH HOH . 
G 4 HOH A 68 268 268 HOH HOH . 
G 4 HOH A 69 269 269 HOH HOH . 
G 4 HOH A 70 270 270 HOH HOH . 
G 4 HOH A 71 271 271 HOH HOH . 
G 4 HOH A 72 275 275 HOH HOH . 
G 4 HOH A 73 276 276 HOH HOH . 
G 4 HOH A 74 277 277 HOH HOH . 
G 4 HOH A 75 278 278 HOH HOH . 
G 4 HOH A 76 279 279 HOH HOH . 
G 4 HOH A 77 280 280 HOH HOH . 
G 4 HOH A 78 281 281 HOH HOH . 
G 4 HOH A 79 282 282 HOH HOH . 
G 4 HOH A 80 283 283 HOH HOH . 
G 4 HOH A 81 284 284 HOH HOH . 
G 4 HOH A 82 285 285 HOH HOH . 
G 4 HOH A 83 286 286 HOH HOH . 
G 4 HOH A 84 287 287 HOH HOH . 
G 4 HOH A 85 288 288 HOH HOH . 
G 4 HOH A 86 289 289 HOH HOH . 
G 4 HOH A 87 290 290 HOH HOH . 
G 4 HOH A 88 291 291 HOH HOH . 
G 4 HOH A 89 300 300 HOH HOH . 
G 4 HOH A 90 301 301 HOH HOH . 
G 4 HOH A 91 305 305 HOH HOH . 
G 4 HOH A 92 306 306 HOH HOH . 
G 4 HOH A 93 309 309 HOH HOH . 
G 4 HOH A 94 311 311 HOH HOH . 
G 4 HOH A 95 312 312 HOH HOH . 
G 4 HOH A 96 314 314 HOH HOH . 
G 4 HOH A 97 315 315 HOH HOH . 
G 4 HOH A 98 319 319 HOH HOH . 
G 4 HOH A 99 320 320 HOH HOH . 
G 4 HOH A 100 321 321 HOH HOH . 
G 4 HOH A 101 322 322 HOH HOH . 
G 4 HOH A 102 323 323 HOH HOH . 
G 4 HOH A 103 325 325 HOH HOH . 
G 4 HOH A 104 326 326 HOH HOH . 
G 4 HOH A 105 327 327 HOH HOH . 
G 4 HOH A 106 328 328 HOH HOH . 
G 4 HOH A 107 329 329 HOH HOH . 
G 4 HOH A 108 332 332 HOH HOH . 
G 4 HOH A 109 334 334 HOH HOH . 
G 4 HOH A 110 335 335 HOH HOH . 
G 4 HOH A 111 336 336 HOH HOH . 
G 4 HOH A 112 337 337 HOH HOH . 
G 4 HOH A 113 339 339 HOH HOH . 
G 4 HOH A 114 340 340 HOH HOH . 
G 4 HOH A 115 342 342 HOH HOH . 
H 4 HOH B 1 131 131 HOH HOH . 
H 4 HOH B 2 134 134 HOH HOH . 
H 4 HOH B 3 136 136 HOH HOH . 
H 4 HOH B 4 138 138 HOH HOH . 
H 4 HOH B 5 144 144 HOH HOH . 
H 4 HOH B 6 145 145 HOH HOH . 
H 4 HOH B 7 149 149 HOH HOH . 
H 4 HOH B 8 151 151 HOH HOH . 
H 4 HOH B 9 154 154 HOH HOH . 
H 4 HOH B 10 155 155 HOH HOH . 
H 4 HOH B 11 156 156 HOH HOH . 
H 4 HOH B 12 159 159 HOH HOH . 
H 4 HOH B 13 160 160 HOH HOH . 
H 4 HOH B 14 163 163 HOH HOH . 
H 4 HOH B 15 164 164 HOH HOH . 
H 4 HOH B 16 166 166 HOH HOH . 
H 4 HOH B 17 168 168 HOH HOH . 
H 4 HOH B 18 170 170 HOH HOH . 
H 4 HOH B 19 173 173 HOH HOH . 
H 4 HOH B 20 174 174 HOH HOH . 
H 4 HOH B 21 175 175 HOH HOH . 
H 4 HOH B 22 176 176 HOH HOH . 
H 4 HOH B 23 177 177 HOH HOH . 
H 4 HOH B 24 179 179 HOH HOH . 
H 4 HOH B 25 184 184 HOH HOH . 
H 4 HOH B 26 186 186 HOH HOH . 
H 4 HOH B 27 187 187 HOH HOH . 
H 4 HOH B 28 188 188 HOH HOH . 
H 4 HOH B 29 189 189 HOH HOH . 
H 4 HOH B 30 192 192 HOH HOH . 
H 4 HOH B 31 193 193 HOH HOH . 
H 4 HOH B 32 194 194 HOH HOH . 
H 4 HOH B 33 197 197 HOH HOH . 
H 4 HOH B 34 198 198 HOH HOH . 
H 4 HOH B 35 201 201 HOH HOH . 
H 4 HOH B 36 204 204 HOH HOH . 
H 4 HOH B 37 205 205 HOH HOH . 
H 4 HOH B 38 206 206 HOH HOH . 
H 4 HOH B 39 207 207 HOH HOH . 
H 4 HOH B 40 208 208 HOH HOH . 
H 4 HOH B 41 209 209 HOH HOH . 
H 4 HOH B 42 211 211 HOH HOH . 
H 4 HOH B 43 212 212 HOH HOH . 
H 4 HOH B 44 213 213 HOH HOH . 
H 4 HOH B 45 214 214 HOH HOH . 
H 4 HOH B 46 215 215 HOH HOH . 
H 4 HOH B 47 217 217 HOH HOH . 
H 4 HOH B 48 219 219 HOH HOH . 
H 4 HOH B 49 220 220 HOH HOH . 
H 4 HOH B 50 224 224 HOH HOH . 
H 4 HOH B 51 225 225 HOH HOH . 
H 4 HOH B 52 226 226 HOH HOH . 
H 4 HOH B 53 227 227 HOH HOH . 
H 4 HOH B 54 235 235 HOH HOH . 
H 4 HOH B 55 236 236 HOH HOH . 
H 4 HOH B 56 237 237 HOH HOH . 
H 4 HOH B 57 239 239 HOH HOH . 
H 4 HOH B 58 241 241 HOH HOH . 
H 4 HOH B 59 242 242 HOH HOH . 
H 4 HOH B 60 246 246 HOH HOH . 
H 4 HOH B 61 249 249 HOH HOH . 
H 4 HOH B 62 250 250 HOH HOH . 
H 4 HOH B 63 253 253 HOH HOH . 
H 4 HOH B 64 254 254 HOH HOH . 
H 4 HOH B 65 255 255 HOH HOH . 
H 4 HOH B 66 258 258 HOH HOH . 
H 4 HOH B 67 260 260 HOH HOH . 
H 4 HOH B 68 262 262 HOH HOH . 
H 4 HOH B 69 264 264 HOH HOH . 
H 4 HOH B 70 266 266 HOH HOH . 
H 4 HOH B 71 272 272 HOH HOH . 
H 4 HOH B 72 273 273 HOH HOH . 
H 4 HOH B 73 274 274 HOH HOH . 
H 4 HOH B 74 292 292 HOH HOH . 
H 4 HOH B 75 293 293 HOH HOH . 
H 4 HOH B 76 294 294 HOH HOH . 
H 4 HOH B 77 295 295 HOH HOH . 
H 4 HOH B 78 296 296 HOH HOH . 
H 4 HOH B 79 297 297 HOH HOH . 
H 4 HOH B 80 298 298 HOH HOH . 
H 4 HOH B 81 299 299 HOH HOH . 
H 4 HOH B 82 302 302 HOH HOH . 
H 4 HOH B 83 303 303 HOH HOH . 
H 4 HOH B 84 304 304 HOH HOH . 
H 4 HOH B 85 307 307 HOH HOH . 
H 4 HOH B 86 308 308 HOH HOH . 
H 4 HOH B 87 310 310 HOH HOH . 
H 4 HOH B 88 313 313 HOH HOH . 
H 4 HOH B 89 316 316 HOH HOH . 
H 4 HOH B 90 317 317 HOH HOH . 
H 4 HOH B 91 318 318 HOH HOH . 
H 4 HOH B 92 324 324 HOH HOH . 
H 4 HOH B 93 330 330 HOH HOH . 
H 4 HOH B 94 331 331 HOH HOH . 
H 4 HOH B 95 333 333 HOH HOH . 
H 4 HOH B 96 338 338 HOH HOH . 
H 4 HOH B 97 341 341 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 C1 MRD . . . E 2 14.496 2.814 42.551 1 36.92 ? C1 MRD 129 B 1 
HETATM 2 C C2 MRD . . . E 2 13.844 4.203 42.627 1 36.95 ? C2 MRD 129 B 1 
HETATM 3 O O2 MRD . . . E 2 13.92 4.899 41.365 1 35.11 ? O2 MRD 129 B 1 
HETATM 4 C CM MRD . . . E 2 12.36 4.002 42.927 1 32.05 ? CM MRD 129 B 1 
HETATM 5 C C3 MRD . . . E 2 14.487 5.103 43.714 1 30.65 ? C3 MRD 129 B 1 
HETATM 6 C C4 MRD . . . E 2 15.961 5.545 43.553 1 35.7 ? C4 MRD 129 B 1 
HETATM 7 O O4 MRD . . . E 2 16.36 6.457 44.633 1 33.72 ? O4 MRD 129 B 1 
HETATM 8 C C5 MRD . . . E 2 16.231 6.243 42.215 1 27.95 ? C5 MRD 129 B 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           383 
_model_server_stats.encode_time_ms          53 
_model_server_stats.element_count           8 
#