data_5YG5 # _model_server_result.job_id 1HeGE7gPJ03IdQ7cAUW7uA _model_server_result.datetime_utc '2024-11-16 18:35:42' _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 5yg5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 5YG5 # _exptl.entry_id 5YG5 _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 1 _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 120 _cell.entry_id 5YG5 _cell.length_a 98.99 _cell.length_b 98.99 _cell.length_c 257.091 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YG5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,R,S _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' 5_655 -x+y+1,y,-z+1/3 -1 0 0 0 1 0 0 0 -1 98.99 0 85.697 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 MET 193 A MET 193 1_555 F K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.243 ? metalc ? metalc2 A O LYS 194 A LYS 194 1_555 F K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc3 A O THR 196 A THR 196 1_555 F K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc4 F K K . A K 403 1_555 Q O HOH . A HOH 540 5_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.365 ? metalc ? metalc5 B O MET 193 B MET 193 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.224 ? metalc ? metalc6 B O LYS 194 B LYS 194 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.062 ? metalc ? metalc7 B O THR 196 B THR 196 1_555 H K K . B K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc8 H K K . B K 402 1_555 S O HOH . C HOH 516 5_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.444 ? metalc ? metalc9 C O MET 193 C MET 193 1_555 N K K . C K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.252 ? metalc ? metalc10 C O LYS 194 C LYS 194 1_555 N K K . C K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? metalc ? metalc11 C O THR 196 C THR 196 1_555 N K K . C K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc12 N K K . C K 402 1_555 S O HOH . C HOH 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.105 ? # _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 277 n n C1 H11 MPD sing 278 n n C1 H12 MPD sing 279 n n C1 H13 MPD sing 280 n n C2 O2 MPD sing 281 n n C2 CM MPD sing 282 n n C2 C3 MPD sing 283 n n O2 HO2 MPD sing 284 n n CM HM1 MPD sing 285 n n CM HM2 MPD sing 286 n n CM HM3 MPD sing 287 n n C3 C4 MPD sing 288 n n C3 H31 MPD sing 289 n n C3 H32 MPD sing 290 n n C4 O4 MPD sing 291 n n C4 C5 MPD sing 292 n n C4 H4 MPD sing 293 n n O4 HO4 MPD sing 294 n n C5 H51 MPD sing 295 n n C5 H52 MPD sing 296 n n C5 H53 MPD sing 297 n n # _atom_sites.entry_id 5YG5 _atom_sites.fract_transf_matrix[1][1] 0.010102 _atom_sites.fract_transf_matrix[1][2] 0.005832 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011665 _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] 0.00389 _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 D 2 RUB A 1 401 1 RUB RUB . E 3 MPD A 1 402 4 MPD MPD . F 4 K A 1 403 8 K K . G 2 RUB B 1 401 2 RUB RUB . H 4 K B 1 402 9 K K . I 5 PEG B 1 403 11 PEG PEG . J 6 5GP B 1 404 31 5GP G . K 6 5GP B 1 405 41 5GP G . L 6 5GP B 1 406 51 5GP G . M 2 RUB C 1 401 3 RUB RUB . N 4 K C 1 402 10 K K . O 6 5GP C 1 403 21 5GP G . P 6 5GP C 1 404 61 5GP G . Q 7 HOH A 1 501 77 HOH HOH . Q 7 HOH A 2 502 105 HOH HOH . Q 7 HOH A 3 503 112 HOH HOH . Q 7 HOH A 4 504 78 HOH HOH . Q 7 HOH A 5 505 135 HOH HOH . Q 7 HOH A 6 506 132 HOH HOH . Q 7 HOH A 7 507 139 HOH HOH . Q 7 HOH A 8 508 60 HOH HOH . Q 7 HOH A 9 509 175 HOH HOH . Q 7 HOH A 10 510 22 HOH HOH . Q 7 HOH A 11 511 67 HOH HOH . Q 7 HOH A 12 512 192 HOH HOH . Q 7 HOH A 13 513 93 HOH HOH . Q 7 HOH A 14 514 9 HOH HOH . Q 7 HOH A 15 515 7 HOH HOH . Q 7 HOH A 16 516 109 HOH HOH . Q 7 HOH A 17 517 80 HOH HOH . Q 7 HOH A 18 518 90 HOH HOH . Q 7 HOH A 19 519 88 HOH HOH . Q 7 HOH A 20 520 176 HOH HOH . Q 7 HOH A 21 521 69 HOH HOH . Q 7 HOH A 22 522 25 HOH HOH . Q 7 HOH A 23 523 76 HOH HOH . Q 7 HOH A 24 524 95 HOH HOH . Q 7 HOH A 25 525 131 HOH HOH . Q 7 HOH A 26 526 75 HOH HOH . Q 7 HOH A 27 527 79 HOH HOH . Q 7 HOH A 28 528 66 HOH HOH . Q 7 HOH A 29 529 138 HOH HOH . Q 7 HOH A 30 530 58 HOH HOH . Q 7 HOH A 31 531 53 HOH HOH . Q 7 HOH A 32 532 137 HOH HOH . Q 7 HOH A 33 533 89 HOH HOH . Q 7 HOH A 34 534 127 HOH HOH . Q 7 HOH A 35 535 5 HOH HOH . Q 7 HOH A 36 536 177 HOH HOH . Q 7 HOH A 37 537 106 HOH HOH . Q 7 HOH A 38 538 18 HOH HOH . Q 7 HOH A 39 539 56 HOH HOH . Q 7 HOH A 40 540 108 HOH HOH . Q 7 HOH A 41 541 8 HOH HOH . Q 7 HOH A 42 542 104 HOH HOH . Q 7 HOH A 43 543 15 HOH HOH . Q 7 HOH A 44 544 14 HOH HOH . Q 7 HOH A 45 545 6 HOH HOH . Q 7 HOH A 46 546 16 HOH HOH . Q 7 HOH A 47 547 120 HOH HOH . Q 7 HOH A 48 548 121 HOH HOH . Q 7 HOH A 49 549 23 HOH HOH . Q 7 HOH A 50 550 126 HOH HOH . Q 7 HOH A 51 551 10 HOH HOH . Q 7 HOH A 52 552 61 HOH HOH . Q 7 HOH A 53 553 20 HOH HOH . Q 7 HOH A 54 554 124 HOH HOH . Q 7 HOH A 55 555 134 HOH HOH . Q 7 HOH A 56 556 103 HOH HOH . Q 7 HOH A 57 557 136 HOH HOH . Q 7 HOH A 58 558 125 HOH HOH . Q 7 HOH A 59 559 140 HOH HOH . Q 7 HOH A 60 560 68 HOH HOH . Q 7 HOH A 61 561 128 HOH HOH . Q 7 HOH A 62 562 57 HOH HOH . Q 7 HOH A 63 563 129 HOH HOH . Q 7 HOH A 64 564 122 HOH HOH . Q 7 HOH A 65 565 21 HOH HOH . Q 7 HOH A 66 566 133 HOH HOH . Q 7 HOH A 67 567 52 HOH HOH . Q 7 HOH A 68 568 59 HOH HOH . Q 7 HOH A 69 569 123 HOH HOH . R 7 HOH B 1 501 98 HOH HOH . R 7 HOH B 2 502 72 HOH HOH . R 7 HOH B 3 503 39 HOH HOH . R 7 HOH B 4 504 158 HOH HOH . R 7 HOH B 5 505 110 HOH HOH . R 7 HOH B 6 506 82 HOH HOH . R 7 HOH B 7 507 148 HOH HOH . R 7 HOH B 8 508 26 HOH HOH . R 7 HOH B 9 509 92 HOH HOH . R 7 HOH B 10 510 83 HOH HOH . R 7 HOH B 11 511 42 HOH HOH . R 7 HOH B 12 512 118 HOH HOH . R 7 HOH B 13 513 81 HOH HOH . R 7 HOH B 14 514 30 HOH HOH . R 7 HOH B 15 515 160 HOH HOH . R 7 HOH B 16 516 34 HOH HOH . R 7 HOH B 17 517 156 HOH HOH . R 7 HOH B 18 518 28 HOH HOH . R 7 HOH B 19 519 17 HOH HOH . R 7 HOH B 20 520 184 HOH HOH . R 7 HOH B 21 521 146 HOH HOH . R 7 HOH B 22 522 70 HOH HOH . R 7 HOH B 23 523 19 HOH HOH . R 7 HOH B 24 524 151 HOH HOH . R 7 HOH B 25 525 41 HOH HOH . R 7 HOH B 26 526 159 HOH HOH . R 7 HOH B 27 527 1 HOH HOH . R 7 HOH B 28 528 43 HOH HOH . R 7 HOH B 29 529 33 HOH HOH . R 7 HOH B 30 530 161 HOH HOH . R 7 HOH B 31 531 31 HOH HOH . R 7 HOH B 32 532 155 HOH HOH . R 7 HOH B 33 533 130 HOH HOH . R 7 HOH B 34 534 29 HOH HOH . R 7 HOH B 35 535 24 HOH HOH . R 7 HOH B 36 536 40 HOH HOH . R 7 HOH B 37 537 86 HOH HOH . R 7 HOH B 38 538 73 HOH HOH . R 7 HOH B 39 539 116 HOH HOH . R 7 HOH B 40 540 71 HOH HOH . R 7 HOH B 41 541 87 HOH HOH . R 7 HOH B 42 542 3 HOH HOH . R 7 HOH B 43 543 142 HOH HOH . R 7 HOH B 44 544 150 HOH HOH . R 7 HOH B 45 545 153 HOH HOH . R 7 HOH B 46 546 4 HOH HOH . R 7 HOH B 47 547 107 HOH HOH . R 7 HOH B 48 548 91 HOH HOH . R 7 HOH B 49 549 97 HOH HOH . R 7 HOH B 50 550 85 HOH HOH . R 7 HOH B 51 551 54 HOH HOH . R 7 HOH B 52 552 36 HOH HOH . R 7 HOH B 53 553 183 HOH HOH . R 7 HOH B 54 554 32 HOH HOH . R 7 HOH B 55 555 74 HOH HOH . R 7 HOH B 56 556 27 HOH HOH . R 7 HOH B 57 557 144 HOH HOH . R 7 HOH B 58 558 96 HOH HOH . R 7 HOH B 59 559 178 HOH HOH . R 7 HOH B 60 560 147 HOH HOH . R 7 HOH B 61 561 35 HOH HOH . R 7 HOH B 62 562 152 HOH HOH . R 7 HOH B 63 563 193 HOH HOH . R 7 HOH B 64 564 38 HOH HOH . R 7 HOH B 65 565 157 HOH HOH . R 7 HOH B 66 566 117 HOH HOH . R 7 HOH B 67 567 37 HOH HOH . R 7 HOH B 68 568 84 HOH HOH . R 7 HOH B 69 569 182 HOH HOH . R 7 HOH B 70 570 179 HOH HOH . R 7 HOH B 71 571 180 HOH HOH . R 7 HOH B 72 572 185 HOH HOH . R 7 HOH B 73 573 181 HOH HOH . R 7 HOH B 74 574 143 HOH HOH . R 7 HOH B 75 575 119 HOH HOH . R 7 HOH B 76 576 145 HOH HOH . R 7 HOH B 77 577 149 HOH HOH . R 7 HOH B 78 578 51 HOH HOH . R 7 HOH B 79 579 154 HOH HOH . S 7 HOH C 1 501 65 HOH HOH . S 7 HOH C 2 502 162 HOH HOH . S 7 HOH C 3 503 188 HOH HOH . S 7 HOH C 4 504 114 HOH HOH . S 7 HOH C 5 505 100 HOH HOH . S 7 HOH C 6 506 44 HOH HOH . S 7 HOH C 7 507 47 HOH HOH . S 7 HOH C 8 508 11 HOH HOH . S 7 HOH C 9 509 172 HOH HOH . S 7 HOH C 10 510 113 HOH HOH . S 7 HOH C 11 511 99 HOH HOH . S 7 HOH C 12 512 50 HOH HOH . S 7 HOH C 13 513 169 HOH HOH . S 7 HOH C 14 514 165 HOH HOH . S 7 HOH C 15 515 55 HOH HOH . S 7 HOH C 16 516 94 HOH HOH . S 7 HOH C 17 517 186 HOH HOH . S 7 HOH C 18 518 167 HOH HOH . S 7 HOH C 19 519 12 HOH HOH . S 7 HOH C 20 520 2 HOH HOH . S 7 HOH C 21 521 141 HOH HOH . S 7 HOH C 22 522 48 HOH HOH . S 7 HOH C 23 523 62 HOH HOH . S 7 HOH C 24 524 173 HOH HOH . S 7 HOH C 25 525 45 HOH HOH . S 7 HOH C 26 526 46 HOH HOH . S 7 HOH C 27 527 101 HOH HOH . S 7 HOH C 28 528 115 HOH HOH . S 7 HOH C 29 529 190 HOH HOH . S 7 HOH C 30 530 164 HOH HOH . S 7 HOH C 31 531 13 HOH HOH . S 7 HOH C 32 532 49 HOH HOH . S 7 HOH C 33 533 111 HOH HOH . S 7 HOH C 34 534 170 HOH HOH . S 7 HOH C 35 535 174 HOH HOH . S 7 HOH C 36 536 166 HOH HOH . S 7 HOH C 37 537 189 HOH HOH . S 7 HOH C 38 538 64 HOH HOH . S 7 HOH C 39 539 163 HOH HOH . S 7 HOH C 40 540 191 HOH HOH . S 7 HOH C 41 541 102 HOH HOH . S 7 HOH C 42 542 168 HOH HOH . S 7 HOH C 43 543 171 HOH HOH . S 7 HOH C 44 544 63 HOH HOH . S 7 HOH C 45 545 187 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 . . . E 3 51.585 -24.811 36.869 1 46.67 ? C1 MPD 402 A 1 HETATM 2 C C2 MPD . . . E 3 50.739 -24.825 38.11 1 46.12 ? C2 MPD 402 A 1 HETATM 3 O O2 MPD . . . E 3 51.187 -23.697 38.864 1 43.21 ? O2 MPD 402 A 1 HETATM 4 C CM MPD . . . E 3 50.86 -26.192 38.826 1 46.76 ? CM MPD 402 A 1 HETATM 5 C C3 MPD . . . E 3 49.33 -24.541 37.651 1 49.67 ? C3 MPD 402 A 1 HETATM 6 C C4 MPD . . . E 3 48.389 -24.183 38.784 1 48.86 ? C4 MPD 402 A 1 HETATM 7 O O4 MPD . . . E 3 48.061 -22.814 38.557 1 44.67 ? O4 MPD 402 A 1 HETATM 8 C C5 MPD . . . E 3 47.212 -25.156 38.7 1 50.8 ? C5 MPD 402 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 8 #