data_6V8Y # _model_server_result.job_id Z2N3Z4681sfge4mLhTxMmg _model_server_result.datetime_utc '2024-11-29 03:56:25' _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 6v8y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 6V8Y # _exptl.entry_id 6V8Y _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 (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 8 _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 6V8Y _cell.length_a 81.716 _cell.length_b 88.137 _cell.length_c 49.848 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6V8Y _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,I,J,K,L,M,N,O,P,Q _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_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 24.924 # 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 ? 2 F N N ? 2 G N N ? 2 L N N ? 2 M N N ? 2 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 metalc ? metalc1 A O THR 45 A THR 63 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.889 ? metalc ? metalc2 A OG1 THR 45 A THR 63 1_555 H K K . A K 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc3 A O THR 45 A THR 63 1_555 H K K . A K 406 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc4 A OG1 THR 45 A THR 63 1_555 H K K . A K 406 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc5 A O THR 45 A THR 63 1_555 I K K . A K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? metalc ? metalc6 A O THR 45 A THR 63 1_555 I K K . A K 407 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc7 A O VAL 46 A VAL 64 1_555 I K K . A K 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? metalc ? metalc8 A O VAL 46 A VAL 64 1_555 I K K . A K 407 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc9 A O VAL 46 A VAL 64 1_555 J NA NA . A NA 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.1 ? metalc ? metalc10 A O VAL 46 A VAL 64 1_555 J NA NA . A NA 408 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.097 ? metalc ? metalc11 A O ASP 48 A ASP 66 1_555 K NA NA . A NA 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc12 A O GLY 49 A GLY 67 1_555 O K K . B K 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc13 A O GLY 49 A GLY 67 1_555 O K K . B K 204 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc14 A O PHE 51 A PHE 69 1_555 K NA NA . A NA 409 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc15 A O PHE 51 A PHE 69 1_555 K NA NA . A NA 409 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc16 A OG SER 52 A SER 70 1_555 K NA NA . A NA 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc17 H K K . A K 406 1_555 B O THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc18 H K K . A K 406 1_555 B OG1 THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc19 H K K . A K 406 3_555 B O THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.879 ? metalc ? metalc20 H K K . A K 406 3_555 B OG1 THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? metalc ? metalc21 I K K . A K 407 1_555 B O THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc22 I K K . A K 407 3_555 B O THR 45 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? metalc ? metalc23 I K K . A K 407 1_555 B O VAL 46 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? metalc ? metalc24 I K K . A K 407 3_555 B O VAL 46 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc25 J NA NA . A NA 408 1_555 P O HOH . A HOH 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc26 J NA NA . A NA 408 1_555 P O HOH . A HOH 524 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc27 J NA NA . A NA 408 1_555 B O VAL 46 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.113 ? metalc ? metalc28 J NA NA . A NA 408 3_555 B O VAL 46 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.107 ? metalc ? metalc29 J NA NA . A NA 408 1_555 Q O HOH . B HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc30 J NA NA . A NA 408 1_555 Q O HOH . B HOH 327 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc31 K NA NA . A NA 409 3_555 B O ASP 48 B ASP 66 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.284 ? metalc ? metalc32 K NA NA . A NA 409 1_555 Q O HOH . B HOH 301 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc33 K NA NA . A NA 409 1_555 Q O HOH . B HOH 303 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? metalc ? metalc34 K NA NA . A NA 409 1_555 Q O HOH . B HOH 324 3_555 ? ? ? ? A ? ? ? ? ? ? ? 2.629 ? metalc ? metalc35 P O HOH . A HOH 504 1_555 O K K . B K 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc36 P O HOH . A HOH 504 3_555 O K K . B K 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc37 B O GLY 49 B GLY 67 1_555 O K K . B K 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc38 B O GLY 49 B GLY 67 1_555 O K K . B K 204 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc39 B O GLY 49 B GLY 67 1_555 O K K . B K 204 3_555 ? A ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc40 B O GLY 49 B GLY 67 1_555 O K K . B K 204 3_555 ? B ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc41 O K K . B K 204 1_555 Q O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc42 O K K . B K 204 1_555 Q O HOH . B HOH 304 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? # _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 205 n n C1 H11 MPD sing 206 n n C1 H12 MPD sing 207 n n C1 H13 MPD sing 208 n n C2 O2 MPD sing 209 n n C2 CM MPD sing 210 n n C2 C3 MPD sing 211 n n O2 HO2 MPD sing 212 n n CM HM1 MPD sing 213 n n CM HM2 MPD sing 214 n n CM HM3 MPD sing 215 n n C3 C4 MPD sing 216 n n C3 H31 MPD sing 217 n n C3 H32 MPD sing 218 n n C4 O4 MPD sing 219 n n C4 C5 MPD sing 220 n n C4 H4 MPD sing 221 n n O4 HO4 MPD sing 222 n n C5 H51 MPD sing 223 n n C5 H52 MPD sing 224 n n C5 H53 MPD sing 225 n n # _atom_sites.entry_id 6V8Y _atom_sites.fract_transf_matrix[1][1] 0.012238 _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] 0.011346 _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] 0.020061 _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 MPD A 1 401 401 MPD MPD . D 2 MPD A 1 402 201 MPD MPD . E 2 MPD A 1 403 301 MPD MPD . F 2 MPD A 1 404 401 MPD MPD . G 2 MPD A 1 405 501 MPD MPD . H 3 K A 1 406 1 K K . I 3 K A 1 407 2 K K . J 4 NA A 1 408 1 NA NA . K 4 NA A 1 409 2 NA NA . L 2 MPD B 1 201 201 MPD MPD . M 2 MPD B 1 202 301 MPD MPD . N 2 MPD B 1 203 501 MPD MPD . O 3 K B 1 204 4 K K . P 5 HOH A 1 501 30 HOH HOH . P 5 HOH A 2 502 54 HOH HOH . P 5 HOH A 3 503 21 HOH HOH . P 5 HOH A 4 504 60 HOH HOH . P 5 HOH A 5 505 27 HOH HOH . P 5 HOH A 6 506 17 HOH HOH . P 5 HOH A 7 507 37 HOH HOH . P 5 HOH A 8 508 28 HOH HOH . P 5 HOH A 9 509 10 HOH HOH . P 5 HOH A 10 510 7 HOH HOH . P 5 HOH A 11 511 15 HOH HOH . P 5 HOH A 12 512 41 HOH HOH . P 5 HOH A 13 513 72 HOH HOH . P 5 HOH A 14 514 31 HOH HOH . P 5 HOH A 15 515 4 HOH HOH . P 5 HOH A 16 516 52 HOH HOH . P 5 HOH A 17 517 40 HOH HOH . P 5 HOH A 18 518 24 HOH HOH . P 5 HOH A 19 519 35 HOH HOH . P 5 HOH A 20 520 25 HOH HOH . P 5 HOH A 21 521 45 HOH HOH . P 5 HOH A 22 522 1 HOH HOH . P 5 HOH A 23 523 14 HOH HOH . P 5 HOH A 24 524 11 HOH HOH . P 5 HOH A 25 525 57 HOH HOH . P 5 HOH A 26 526 36 HOH HOH . P 5 HOH A 27 527 53 HOH HOH . P 5 HOH A 28 528 73 HOH HOH . P 5 HOH A 29 529 61 HOH HOH . P 5 HOH A 30 530 66 HOH HOH . P 5 HOH A 31 531 42 HOH HOH . P 5 HOH A 32 532 65 HOH HOH . P 5 HOH A 33 533 48 HOH HOH . P 5 HOH A 34 534 68 HOH HOH . P 5 HOH A 35 535 58 HOH HOH . P 5 HOH A 36 536 67 HOH HOH . P 5 HOH A 37 537 62 HOH HOH . Q 5 HOH B 1 301 70 HOH HOH . Q 5 HOH B 2 302 34 HOH HOH . Q 5 HOH B 3 303 74 HOH HOH . Q 5 HOH B 4 304 69 HOH HOH . Q 5 HOH B 5 305 18 HOH HOH . Q 5 HOH B 6 306 8 HOH HOH . Q 5 HOH B 7 307 23 HOH HOH . Q 5 HOH B 8 308 9 HOH HOH . Q 5 HOH B 9 309 55 HOH HOH . Q 5 HOH B 10 310 44 HOH HOH . Q 5 HOH B 11 311 26 HOH HOH . Q 5 HOH B 12 312 13 HOH HOH . Q 5 HOH B 13 313 38 HOH HOH . Q 5 HOH B 14 314 6 HOH HOH . Q 5 HOH B 15 315 5 HOH HOH . Q 5 HOH B 16 316 39 HOH HOH . Q 5 HOH B 17 317 46 HOH HOH . Q 5 HOH B 18 318 16 HOH HOH . Q 5 HOH B 19 319 19 HOH HOH . Q 5 HOH B 20 320 12 HOH HOH . Q 5 HOH B 21 321 29 HOH HOH . Q 5 HOH B 22 322 33 HOH HOH . Q 5 HOH B 23 323 51 HOH HOH . Q 5 HOH B 24 324 22 HOH HOH . Q 5 HOH B 25 325 3 HOH HOH . Q 5 HOH B 26 326 20 HOH HOH . Q 5 HOH B 27 327 32 HOH HOH . Q 5 HOH B 28 328 59 HOH HOH . Q 5 HOH B 29 329 56 HOH HOH . Q 5 HOH B 30 330 43 HOH HOH . Q 5 HOH B 31 331 49 HOH HOH . Q 5 HOH B 32 332 63 HOH HOH . Q 5 HOH B 33 333 64 HOH HOH . Q 5 HOH B 34 334 50 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 . . . D 2 20.316 21.462 26.956 1 42.69 ? C1 MPD 402 A 1 HETATM 2 C C2 MPD . . . D 2 20.884 22.788 26.471 1 25.78 ? C2 MPD 402 A 1 HETATM 3 O O2 MPD . . . D 2 20.847 22.814 25.028 1 23.34 ? O2 MPD 402 A 1 HETATM 4 C CM MPD . . . D 2 19.973 23.906 26.951 1 28.93 ? CM MPD 402 A 1 HETATM 5 C C3 MPD . . . D 2 22.309 23.073 26.953 1 22.67 ? C3 MPD 402 A 1 HETATM 6 C C4 MPD . . . D 2 23.433 22.323 26.258 1 29.35 ? C4 MPD 402 A 1 HETATM 7 O O4 MPD . . . D 2 24.67 22.614 26.933 1 37.44 ? O4 MPD 402 A 1 HETATM 8 C C5 MPD . . . D 2 23.215 20.825 26.333 1 28.01 ? C5 MPD 402 A 1 HETATM 9 H H11 MPD . . . D 2 19.431 21.647 27.564 1 51.24 ? H11 MPD 402 A 1 HETATM 10 H H12 MPD . . . D 2 20.045 20.847 26.098 1 51.24 ? H12 MPD 402 A 1 HETATM 11 H H13 MPD . . . D 2 21.065 20.943 27.554 1 51.24 ? H13 MPD 402 A 1 HETATM 12 H HO2 MPD . . . D 2 21.671 23.223 24.688 1 28.02 ? HO2 MPD 402 A 1 HETATM 13 H HM1 MPD . . . D 2 20.555 24.819 27.077 1 34.73 ? HM1 MPD 402 A 1 HETATM 14 H HM2 MPD . . . D 2 19.525 23.626 27.904 1 34.73 ? HM2 MPD 402 A 1 HETATM 15 H HM3 MPD . . . D 2 19.187 24.075 26.215 1 34.73 ? HM3 MPD 402 A 1 HETATM 16 H H31 MPD . . . D 2 22.496 24.14 26.836 1 27.22 ? H31 MPD 402 A 1 HETATM 17 H H32 MPD . . . D 2 22.357 22.839 28.016 1 27.22 ? H32 MPD 402 A 1 HETATM 18 H H4 MPD . . . D 2 23.463 22.637 25.215 1 35.23 ? H4 MPD 402 A 1 HETATM 19 H HO4 MPD . . . D 2 24.541 23.376 27.535 1 44.93 ? HO4 MPD 402 A 1 HETATM 20 H H51 MPD . . . D 2 22.381 20.547 25.688 1 33.62 ? H51 MPD 402 A 1 HETATM 21 H H52 MPD . . . D 2 22.99 20.542 27.361 1 33.62 ? H52 MPD 402 A 1 HETATM 22 H H53 MPD . . . D 2 24.117 20.31 26.003 1 33.62 ? H53 MPD 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #