data_6NDZ # _model_server_result.job_id RMUrdhCKw2UWRY3GWb0K3Q _model_server_result.datetime_utc '2024-11-05 00:07:21' _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 6ndz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":201}' # _entry.id 6NDZ # _exptl.entry_id 6NDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 4 _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 6NDZ _cell.length_a 79.93 _cell.length_b 109.015 _cell.length_c 114.373 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,K,L,M,N,Q,R 1 1 C,D,O,S,T 2 1 E,F,P,U,V 3 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 L N N ? 3 M N N ? 3 N 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 4 A CYS 8 1_555 A SG CYS 65 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 12 A CYS 16 1_555 A SG CYS 58 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 49 A CYS 53 1_555 A SG CYS 87 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 76 A CYS 80 1_555 A SG CYS 117 A CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 80 A CYS 84 1_555 A SG CYS 104 A CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 C SG CYS 4 C CYS 8 1_555 C SG CYS 65 C CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 C SG CYS 12 C CYS 16 1_555 C SG CYS 58 C CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 C SG CYS 49 C CYS 53 1_555 C SG CYS 87 C CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 C SG CYS 76 C CYS 80 1_555 C SG CYS 117 C CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 C SG CYS 80 C CYS 84 1_555 C SG CYS 104 C CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 E SG CYS 4 E CYS 8 1_555 E SG CYS 65 E CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 E SG CYS 12 E CYS 16 1_555 E SG CYS 58 E CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 E SG CYS 49 E CYS 53 1_555 E SG CYS 87 E CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 E SG CYS 76 E CYS 80 1_555 E SG CYS 117 E CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 E SG CYS 80 E CYS 84 1_555 E SG CYS 104 E CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _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 MPD sing 250 n n C1 H11 MPD sing 251 n n C1 H12 MPD sing 252 n n C1 H13 MPD sing 253 n n C2 O2 MPD sing 254 n n C2 CM MPD sing 255 n n C2 C3 MPD sing 256 n n O2 HO2 MPD sing 257 n n CM HM1 MPD sing 258 n n CM HM2 MPD sing 259 n n CM HM3 MPD sing 260 n n C3 C4 MPD sing 261 n n C3 H31 MPD sing 262 n n C3 H32 MPD sing 263 n n C4 O4 MPD sing 264 n n C4 C5 MPD sing 265 n n C4 H4 MPD sing 266 n n O4 HO4 MPD sing 267 n n C5 H51 MPD sing 268 n n C5 H52 MPD sing 269 n n C5 H53 MPD sing 270 n n # _atom_sites.entry_id 6NDZ _atom_sites.fract_transf_matrix[1][1] 0.012511 _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] 0.009173 _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] 0.008743 _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 G 3 MPD A 1 201 5 MPD MPD . H 4 ACT A 1 202 1 ACT ACT . I 4 ACT A 1 203 2 ACT ACT . J 4 ACT A 1 204 3 ACT ACT . K 5 ACY A 1 205 1 ACY ACY . L 3 MPD B 1 201 1 MPD MPD . M 3 MPD B 1 202 3 MPD MPD . N 3 MPD B 1 203 6 MPD MPD . O 4 ACT C 1 201 4 ACT ACT . P 5 ACY F 1 201 2 ACY ACY . Q 6 HOH A 1 301 168 HOH HOH . Q 6 HOH A 2 302 57 HOH HOH . Q 6 HOH A 3 303 5 HOH HOH . Q 6 HOH A 4 304 198 HOH HOH . Q 6 HOH A 5 305 4 HOH HOH . Q 6 HOH A 6 306 267 HOH HOH . Q 6 HOH A 7 307 82 HOH HOH . Q 6 HOH A 8 308 194 HOH HOH . Q 6 HOH A 9 309 268 HOH HOH . Q 6 HOH A 10 310 21 HOH HOH . Q 6 HOH A 11 311 60 HOH HOH . Q 6 HOH A 12 312 14 HOH HOH . Q 6 HOH A 13 313 3 HOH HOH . Q 6 HOH A 14 314 109 HOH HOH . Q 6 HOH A 15 315 206 HOH HOH . Q 6 HOH A 16 316 99 HOH HOH . Q 6 HOH A 17 317 38 HOH HOH . Q 6 HOH A 18 318 203 HOH HOH . Q 6 HOH A 19 319 59 HOH HOH . Q 6 HOH A 20 320 63 HOH HOH . Q 6 HOH A 21 321 137 HOH HOH . Q 6 HOH A 22 322 225 HOH HOH . Q 6 HOH A 23 323 201 HOH HOH . Q 6 HOH A 24 324 17 HOH HOH . Q 6 HOH A 25 325 191 HOH HOH . Q 6 HOH A 26 326 65 HOH HOH . Q 6 HOH A 27 327 205 HOH HOH . Q 6 HOH A 28 328 12 HOH HOH . Q 6 HOH A 29 329 11 HOH HOH . Q 6 HOH A 30 330 83 HOH HOH . Q 6 HOH A 31 331 8 HOH HOH . Q 6 HOH A 32 332 241 HOH HOH . Q 6 HOH A 33 333 76 HOH HOH . Q 6 HOH A 34 334 41 HOH HOH . Q 6 HOH A 35 335 202 HOH HOH . Q 6 HOH A 36 336 181 HOH HOH . Q 6 HOH A 37 337 15 HOH HOH . Q 6 HOH A 38 338 111 HOH HOH . Q 6 HOH A 39 339 199 HOH HOH . Q 6 HOH A 40 340 34 HOH HOH . Q 6 HOH A 41 341 188 HOH HOH . Q 6 HOH A 42 342 90 HOH HOH . Q 6 HOH A 43 343 55 HOH HOH . Q 6 HOH A 44 344 35 HOH HOH . Q 6 HOH A 45 345 46 HOH HOH . Q 6 HOH A 46 346 132 HOH HOH . Q 6 HOH A 47 347 70 HOH HOH . Q 6 HOH A 48 348 120 HOH HOH . Q 6 HOH A 49 349 200 HOH HOH . Q 6 HOH A 50 350 240 HOH HOH . Q 6 HOH A 51 351 187 HOH HOH . Q 6 HOH A 52 352 242 HOH HOH . Q 6 HOH A 53 353 110 HOH HOH . Q 6 HOH A 54 354 243 HOH HOH . Q 6 HOH A 55 355 182 HOH HOH . Q 6 HOH A 56 356 221 HOH HOH . Q 6 HOH A 57 357 212 HOH HOH . Q 6 HOH A 58 358 222 HOH HOH . Q 6 HOH A 59 359 40 HOH HOH . R 6 HOH B 1 301 1 HOH HOH . R 6 HOH B 2 302 143 HOH HOH . R 6 HOH B 3 303 101 HOH HOH . R 6 HOH B 4 304 138 HOH HOH . R 6 HOH B 5 305 51 HOH HOH . R 6 HOH B 6 306 246 HOH HOH . R 6 HOH B 7 307 71 HOH HOH . R 6 HOH B 8 308 114 HOH HOH . R 6 HOH B 9 309 39 HOH HOH . R 6 HOH B 10 310 247 HOH HOH . R 6 HOH B 11 311 249 HOH HOH . R 6 HOH B 12 312 248 HOH HOH . R 6 HOH B 13 313 125 HOH HOH . R 6 HOH B 14 314 56 HOH HOH . R 6 HOH B 15 315 64 HOH HOH . R 6 HOH B 16 316 269 HOH HOH . R 6 HOH B 17 317 18 HOH HOH . R 6 HOH B 18 318 209 HOH HOH . R 6 HOH B 19 319 238 HOH HOH . R 6 HOH B 20 320 167 HOH HOH . R 6 HOH B 21 321 159 HOH HOH . R 6 HOH B 22 322 163 HOH HOH . R 6 HOH B 23 323 239 HOH HOH . R 6 HOH B 24 324 135 HOH HOH . R 6 HOH B 25 325 166 HOH HOH . R 6 HOH B 26 326 131 HOH HOH . R 6 HOH B 27 327 169 HOH HOH . R 6 HOH B 28 328 119 HOH HOH . R 6 HOH B 29 329 136 HOH HOH . R 6 HOH B 30 330 266 HOH HOH . R 6 HOH B 31 331 44 HOH HOH . R 6 HOH B 32 332 192 HOH HOH . R 6 HOH B 33 333 117 HOH HOH . R 6 HOH B 34 334 245 HOH HOH . R 6 HOH B 35 335 237 HOH HOH . R 6 HOH B 36 336 126 HOH HOH . R 6 HOH B 37 337 193 HOH HOH . R 6 HOH B 38 338 130 HOH HOH . R 6 HOH B 39 339 195 HOH HOH . R 6 HOH B 40 340 244 HOH HOH . R 6 HOH B 41 341 19 HOH HOH . R 6 HOH B 42 342 175 HOH HOH . R 6 HOH B 43 343 207 HOH HOH . R 6 HOH B 44 344 229 HOH HOH . R 6 HOH B 45 345 211 HOH HOH . R 6 HOH B 46 346 24 HOH HOH . R 6 HOH B 47 347 148 HOH HOH . S 6 HOH C 1 301 28 HOH HOH . S 6 HOH C 2 302 251 HOH HOH . S 6 HOH C 3 303 250 HOH HOH . S 6 HOH C 4 304 93 HOH HOH . S 6 HOH C 5 305 164 HOH HOH . S 6 HOH C 6 306 139 HOH HOH . S 6 HOH C 7 307 6 HOH HOH . S 6 HOH C 8 308 67 HOH HOH . S 6 HOH C 9 309 32 HOH HOH . S 6 HOH C 10 310 133 HOH HOH . S 6 HOH C 11 311 54 HOH HOH . S 6 HOH C 12 312 141 HOH HOH . S 6 HOH C 13 313 89 HOH HOH . S 6 HOH C 14 314 77 HOH HOH . S 6 HOH C 15 315 91 HOH HOH . S 6 HOH C 16 316 23 HOH HOH . S 6 HOH C 17 317 50 HOH HOH . S 6 HOH C 18 318 213 HOH HOH . S 6 HOH C 19 319 151 HOH HOH . S 6 HOH C 20 320 92 HOH HOH . S 6 HOH C 21 321 86 HOH HOH . S 6 HOH C 22 322 16 HOH HOH . S 6 HOH C 23 323 7 HOH HOH . S 6 HOH C 24 324 10 HOH HOH . S 6 HOH C 25 325 27 HOH HOH . S 6 HOH C 26 326 254 HOH HOH . S 6 HOH C 27 327 232 HOH HOH . S 6 HOH C 28 328 217 HOH HOH . S 6 HOH C 29 329 154 HOH HOH . S 6 HOH C 30 330 81 HOH HOH . S 6 HOH C 31 331 13 HOH HOH . S 6 HOH C 32 332 178 HOH HOH . S 6 HOH C 33 333 62 HOH HOH . S 6 HOH C 34 334 214 HOH HOH . S 6 HOH C 35 335 48 HOH HOH . S 6 HOH C 36 336 100 HOH HOH . S 6 HOH C 37 337 58 HOH HOH . S 6 HOH C 38 338 94 HOH HOH . S 6 HOH C 39 339 155 HOH HOH . T 6 HOH D 1 201 103 HOH HOH . T 6 HOH D 2 202 256 HOH HOH . T 6 HOH D 3 203 113 HOH HOH . T 6 HOH D 4 204 129 HOH HOH . T 6 HOH D 5 205 157 HOH HOH . T 6 HOH D 6 206 80 HOH HOH . T 6 HOH D 7 207 179 HOH HOH . T 6 HOH D 8 208 184 HOH HOH . T 6 HOH D 9 209 145 HOH HOH . U 6 HOH E 1 201 176 HOH HOH . U 6 HOH E 2 202 78 HOH HOH . U 6 HOH E 3 203 29 HOH HOH . U 6 HOH E 4 204 128 HOH HOH . U 6 HOH E 5 205 262 HOH HOH . U 6 HOH E 6 206 33 HOH HOH . U 6 HOH E 7 207 105 HOH HOH . U 6 HOH E 8 208 228 HOH HOH . U 6 HOH E 9 209 265 HOH HOH . U 6 HOH E 10 210 68 HOH HOH . U 6 HOH E 11 211 270 HOH HOH . U 6 HOH E 12 212 152 HOH HOH . U 6 HOH E 13 213 85 HOH HOH . U 6 HOH E 14 214 260 HOH HOH . U 6 HOH E 15 215 104 HOH HOH . U 6 HOH E 16 216 160 HOH HOH . U 6 HOH E 17 217 146 HOH HOH . U 6 HOH E 18 218 87 HOH HOH . U 6 HOH E 19 219 53 HOH HOH . U 6 HOH E 20 220 116 HOH HOH . U 6 HOH E 21 221 61 HOH HOH . U 6 HOH E 22 222 97 HOH HOH . U 6 HOH E 23 223 9 HOH HOH . U 6 HOH E 24 224 72 HOH HOH . U 6 HOH E 25 225 73 HOH HOH . U 6 HOH E 26 226 75 HOH HOH . U 6 HOH E 27 227 147 HOH HOH . U 6 HOH E 28 228 258 HOH HOH . U 6 HOH E 29 229 2 HOH HOH . U 6 HOH E 30 230 30 HOH HOH . U 6 HOH E 31 231 47 HOH HOH . U 6 HOH E 32 232 149 HOH HOH . U 6 HOH E 33 233 259 HOH HOH . U 6 HOH E 34 234 223 HOH HOH . U 6 HOH E 35 235 66 HOH HOH . U 6 HOH E 36 236 106 HOH HOH . U 6 HOH E 37 237 26 HOH HOH . U 6 HOH E 38 238 121 HOH HOH . U 6 HOH E 39 239 107 HOH HOH . U 6 HOH E 40 240 230 HOH HOH . U 6 HOH E 41 241 95 HOH HOH . U 6 HOH E 42 242 173 HOH HOH . V 6 HOH F 1 301 96 HOH HOH . V 6 HOH F 2 302 98 HOH HOH . V 6 HOH F 3 303 79 HOH HOH . V 6 HOH F 4 304 31 HOH HOH . V 6 HOH F 5 305 25 HOH HOH . V 6 HOH F 6 306 22 HOH HOH . V 6 HOH F 7 307 261 HOH HOH . V 6 HOH F 8 308 123 HOH HOH . V 6 HOH F 9 309 74 HOH HOH . V 6 HOH F 10 310 224 HOH HOH . V 6 HOH F 11 311 124 HOH HOH . V 6 HOH F 12 312 108 HOH HOH . V 6 HOH F 13 313 231 HOH HOH . V 6 HOH F 14 314 112 HOH HOH . V 6 HOH F 15 315 122 HOH HOH . V 6 HOH F 16 316 43 HOH HOH . V 6 HOH F 17 317 235 HOH HOH . V 6 HOH F 18 318 183 HOH HOH . V 6 HOH F 19 319 150 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 MPD . . . L 3 161.247 345.518 26.858 1 81.49 ? C1 MPD 201 B 1 HETATM 2 C C2 MPD . . . L 3 161.991 346.735 27.395 1 84.27 ? C2 MPD 201 B 1 HETATM 3 O O2 MPD . . . L 3 162.789 347.296 26.323 1 88.43 ? O2 MPD 201 B 1 HETATM 4 C CM MPD . . . L 3 161.006 347.804 27.844 1 82.64 ? CM MPD 201 B 1 HETATM 5 C C3 MPD . . . L 3 162.9 346.337 28.556 1 81.35 ? C3 MPD 201 B 1 HETATM 6 C C4 MPD . . . L 3 164.231 345.769 28.071 1 77.91 ? C4 MPD 201 B 1 HETATM 7 O O4 MPD . . . L 3 164.713 346.548 27.001 1 86.24 ? O4 MPD 201 B 1 HETATM 8 C C5 MPD . . . L 3 165.274 345.752 29.184 1 69.18 ? C5 MPD 201 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 8 #