data_1YNR # _model_server_result.job_id rmZL8ht6Vc5rQ7xdjzNcZg _model_server_result.datetime_utc '2025-03-04 21:59:11' _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 1ynr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":608}' # _entry.id 1YNR # _exptl.entry_id 1YNR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 4 _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 1YNR _cell.length_a 56.712 _cell.length_b 56.712 _cell.length_c 220.179 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YNR _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 2 2' # _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,R,S,T,U,V,W _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 ? 4 G N N ? 4 H N N ? 4 I N N ? 4 L N N ? 4 M N N ? 4 P N N ? 4 Q N N ? 4 S 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 covale ? covale1 A SG CYS 10 A CYS 10 1_555 F CAB HEC . A HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? covale ? covale2 A SG CYS 13 A CYS 13 1_555 F CAC HEC . A HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? covale ? covale3 B SG CYS 10 B CYS 10 1_555 K CAB HEC . B HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.827 ? covale ? covale4 B SG CYS 13 B CYS 13 1_555 K CAC HEC . B HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? covale ? covale5 C SG CYS 10 C CYS 10 1_555 O CAB HEC . C HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? covale ? covale6 C SG CYS 13 C CYS 13 1_555 O CAC HEC . C HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? covale ? covale7 D SG CYS 10 D CYS 10 1_555 R CAB HEC . D HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? covale ? covale8 D SG CYS 13 D CYS 13 1_555 R CAC HEC . D HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc1 A NE2 HIS 14 A HIS 14 1_555 F FE HEC . A HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc2 A SD MET 59 A MET 59 1_555 F FE HEC . A HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc3 B NE2 HIS 14 B HIS 14 1_555 K FE HEC . B HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc4 B SD MET 59 B MET 59 1_555 K FE HEC . B HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc5 C NE2 HIS 14 C HIS 14 1_555 O FE HEC . C HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc6 C SD MET 59 C MET 59 1_555 O FE HEC . C HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc7 D NE2 HIS 14 D HIS 14 1_555 R FE HEC . D HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc8 D SD MET 59 D MET 59 1_555 R FE HEC . D HEC 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? # _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 321 n n C1 H11 MPD sing 322 n n C1 H12 MPD sing 323 n n C1 H13 MPD sing 324 n n C2 O2 MPD sing 325 n n C2 CM MPD sing 326 n n C2 C3 MPD sing 327 n n O2 HO2 MPD sing 328 n n CM HM1 MPD sing 329 n n CM HM2 MPD sing 330 n n CM HM3 MPD sing 331 n n C3 C4 MPD sing 332 n n C3 H31 MPD sing 333 n n C3 H32 MPD sing 334 n n C4 O4 MPD sing 335 n n C4 C5 MPD sing 336 n n C4 H4 MPD sing 337 n n O4 HO4 MPD sing 338 n n C5 H51 MPD sing 339 n n C5 H52 MPD sing 340 n n C5 H53 MPD sing 341 n n # _atom_sites.entry_id 1YNR _atom_sites.fract_transf_matrix[1][1] 0.017633 _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] 0.017633 _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] 0.004542 _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 E 2 SO4 A 1 502 2 SO4 SO4 . F 3 HEC A 1 81 81 HEC HEC . G 4 MPD A 1 601 1 MPD MPD . H 4 MPD A 1 603 3 MPD MPD . I 4 MPD A 1 606 6 MPD MPD . J 2 SO4 B 1 501 1 SO4 SO4 . K 3 HEC B 1 81 80 HEC HEC . L 4 MPD B 1 602 2 MPD MPD . M 4 MPD B 1 607 7 MPD MPD . N 2 SO4 C 1 503 3 SO4 SO4 . O 3 HEC C 1 81 81 HEC HEC . P 4 MPD C 1 604 4 MPD MPD . Q 4 MPD C 1 608 8 MPD MPD . R 3 HEC D 1 81 80 HEC HEC . S 4 MPD D 1 605 5 MPD MPD . T 5 HOH A 1 607 4 HOH HOH . T 5 HOH A 2 608 7 HOH HOH . T 5 HOH A 3 609 12 HOH HOH . T 5 HOH A 4 610 14 HOH HOH . T 5 HOH A 5 611 15 HOH HOH . T 5 HOH A 6 612 17 HOH HOH . T 5 HOH A 7 613 27 HOH HOH . T 5 HOH A 8 614 28 HOH HOH . T 5 HOH A 9 615 31 HOH HOH . T 5 HOH A 10 616 35 HOH HOH . T 5 HOH A 11 617 40 HOH HOH . T 5 HOH A 12 618 43 HOH HOH . T 5 HOH A 13 619 44 HOH HOH . T 5 HOH A 14 620 45 HOH HOH . T 5 HOH A 15 621 51 HOH HOH . T 5 HOH A 16 622 58 HOH HOH . T 5 HOH A 17 623 64 HOH HOH . T 5 HOH A 18 624 67 HOH HOH . T 5 HOH A 19 625 68 HOH HOH . T 5 HOH A 20 626 70 HOH HOH . T 5 HOH A 21 627 71 HOH HOH . T 5 HOH A 22 628 74 HOH HOH . T 5 HOH A 23 629 79 HOH HOH . T 5 HOH A 24 630 95 HOH HOH . T 5 HOH A 25 631 98 HOH HOH . T 5 HOH A 26 632 99 HOH HOH . T 5 HOH A 27 633 100 HOH HOH . T 5 HOH A 28 634 103 HOH HOH . T 5 HOH A 29 635 105 HOH HOH . T 5 HOH A 30 636 109 HOH HOH . T 5 HOH A 31 637 110 HOH HOH . T 5 HOH A 32 638 113 HOH HOH . T 5 HOH A 33 639 114 HOH HOH . T 5 HOH A 34 640 117 HOH HOH . T 5 HOH A 35 641 118 HOH HOH . T 5 HOH A 36 642 138 HOH HOH . T 5 HOH A 37 643 158 HOH HOH . T 5 HOH A 38 644 159 HOH HOH . T 5 HOH A 39 645 163 HOH HOH . T 5 HOH A 40 646 181 HOH HOH . T 5 HOH A 41 647 186 HOH HOH . T 5 HOH A 42 648 189 HOH HOH . T 5 HOH A 43 649 197 HOH HOH . T 5 HOH A 44 650 198 HOH HOH . T 5 HOH A 45 651 199 HOH HOH . T 5 HOH A 46 652 200 HOH HOH . T 5 HOH A 47 653 206 HOH HOH . T 5 HOH A 48 654 207 HOH HOH . U 5 HOH B 1 608 3 HOH HOH . U 5 HOH B 2 609 5 HOH HOH . U 5 HOH B 3 610 13 HOH HOH . U 5 HOH B 4 611 16 HOH HOH . U 5 HOH B 5 612 23 HOH HOH . U 5 HOH B 6 613 29 HOH HOH . U 5 HOH B 7 614 32 HOH HOH . U 5 HOH B 8 615 34 HOH HOH . U 5 HOH B 9 616 36 HOH HOH . U 5 HOH B 10 617 41 HOH HOH . U 5 HOH B 11 618 46 HOH HOH . U 5 HOH B 12 619 48 HOH HOH . U 5 HOH B 13 620 49 HOH HOH . U 5 HOH B 14 621 50 HOH HOH . U 5 HOH B 15 622 52 HOH HOH . U 5 HOH B 16 623 65 HOH HOH . U 5 HOH B 17 624 77 HOH HOH . U 5 HOH B 18 625 78 HOH HOH . U 5 HOH B 19 626 80 HOH HOH . U 5 HOH B 20 627 83 HOH HOH . U 5 HOH B 21 628 86 HOH HOH . U 5 HOH B 22 629 87 HOH HOH . U 5 HOH B 23 630 88 HOH HOH . U 5 HOH B 24 631 91 HOH HOH . U 5 HOH B 25 632 96 HOH HOH . U 5 HOH B 26 633 101 HOH HOH . U 5 HOH B 27 634 102 HOH HOH . U 5 HOH B 28 635 112 HOH HOH . U 5 HOH B 29 636 121 HOH HOH . U 5 HOH B 30 637 127 HOH HOH . U 5 HOH B 31 638 130 HOH HOH . U 5 HOH B 32 639 136 HOH HOH . U 5 HOH B 33 640 141 HOH HOH . U 5 HOH B 34 641 144 HOH HOH . U 5 HOH B 35 642 145 HOH HOH . U 5 HOH B 36 643 148 HOH HOH . U 5 HOH B 37 644 149 HOH HOH . U 5 HOH B 38 645 151 HOH HOH . U 5 HOH B 39 646 153 HOH HOH . U 5 HOH B 40 647 160 HOH HOH . U 5 HOH B 41 648 161 HOH HOH . U 5 HOH B 42 649 165 HOH HOH . U 5 HOH B 43 650 169 HOH HOH . U 5 HOH B 44 651 172 HOH HOH . U 5 HOH B 45 652 175 HOH HOH . U 5 HOH B 46 653 176 HOH HOH . U 5 HOH B 47 654 177 HOH HOH . U 5 HOH B 48 655 180 HOH HOH . U 5 HOH B 49 656 182 HOH HOH . U 5 HOH B 50 657 185 HOH HOH . U 5 HOH B 51 658 187 HOH HOH . U 5 HOH B 52 659 192 HOH HOH . U 5 HOH B 53 660 193 HOH HOH . U 5 HOH B 54 661 195 HOH HOH . U 5 HOH B 55 662 204 HOH HOH . U 5 HOH B 56 663 205 HOH HOH . V 5 HOH C 1 609 1 HOH HOH . V 5 HOH C 2 610 6 HOH HOH . V 5 HOH C 3 611 9 HOH HOH . V 5 HOH C 4 612 10 HOH HOH . V 5 HOH C 5 613 11 HOH HOH . V 5 HOH C 6 614 18 HOH HOH . V 5 HOH C 7 615 21 HOH HOH . V 5 HOH C 8 616 22 HOH HOH . V 5 HOH C 9 617 24 HOH HOH . V 5 HOH C 10 618 26 HOH HOH . V 5 HOH C 11 619 30 HOH HOH . V 5 HOH C 12 620 38 HOH HOH . V 5 HOH C 13 621 39 HOH HOH . V 5 HOH C 14 622 42 HOH HOH . V 5 HOH C 15 623 53 HOH HOH . V 5 HOH C 16 624 55 HOH HOH . V 5 HOH C 17 625 61 HOH HOH . V 5 HOH C 18 626 62 HOH HOH . V 5 HOH C 19 627 63 HOH HOH . V 5 HOH C 20 628 66 HOH HOH . V 5 HOH C 21 629 72 HOH HOH . V 5 HOH C 22 630 73 HOH HOH . V 5 HOH C 23 631 81 HOH HOH . V 5 HOH C 24 632 82 HOH HOH . V 5 HOH C 25 633 84 HOH HOH . V 5 HOH C 26 634 90 HOH HOH . V 5 HOH C 27 635 92 HOH HOH . V 5 HOH C 28 636 97 HOH HOH . V 5 HOH C 29 637 119 HOH HOH . V 5 HOH C 30 638 120 HOH HOH . V 5 HOH C 31 639 122 HOH HOH . V 5 HOH C 32 640 124 HOH HOH . V 5 HOH C 33 641 125 HOH HOH . V 5 HOH C 34 642 126 HOH HOH . V 5 HOH C 35 643 129 HOH HOH . V 5 HOH C 36 644 137 HOH HOH . V 5 HOH C 37 645 139 HOH HOH . V 5 HOH C 38 646 142 HOH HOH . V 5 HOH C 39 647 143 HOH HOH . V 5 HOH C 40 648 147 HOH HOH . V 5 HOH C 41 649 150 HOH HOH . V 5 HOH C 42 650 152 HOH HOH . V 5 HOH C 43 651 154 HOH HOH . V 5 HOH C 44 652 156 HOH HOH . V 5 HOH C 45 653 157 HOH HOH . V 5 HOH C 46 654 166 HOH HOH . V 5 HOH C 47 655 167 HOH HOH . V 5 HOH C 48 656 173 HOH HOH . V 5 HOH C 49 657 179 HOH HOH . V 5 HOH C 50 658 183 HOH HOH . V 5 HOH C 51 659 188 HOH HOH . V 5 HOH C 52 660 194 HOH HOH . V 5 HOH C 53 661 201 HOH HOH . V 5 HOH C 54 662 203 HOH HOH . V 5 HOH C 55 663 208 HOH HOH . W 5 HOH D 1 606 2 HOH HOH . W 5 HOH D 2 607 8 HOH HOH . W 5 HOH D 3 608 19 HOH HOH . W 5 HOH D 4 609 20 HOH HOH . W 5 HOH D 5 610 25 HOH HOH . W 5 HOH D 6 611 33 HOH HOH . W 5 HOH D 7 612 37 HOH HOH . W 5 HOH D 8 613 47 HOH HOH . W 5 HOH D 9 614 54 HOH HOH . W 5 HOH D 10 615 56 HOH HOH . W 5 HOH D 11 616 57 HOH HOH . W 5 HOH D 12 617 59 HOH HOH . W 5 HOH D 13 618 60 HOH HOH . W 5 HOH D 14 619 69 HOH HOH . W 5 HOH D 15 620 75 HOH HOH . W 5 HOH D 16 621 76 HOH HOH . W 5 HOH D 17 622 85 HOH HOH . W 5 HOH D 18 623 89 HOH HOH . W 5 HOH D 19 624 93 HOH HOH . W 5 HOH D 20 625 94 HOH HOH . W 5 HOH D 21 626 104 HOH HOH . W 5 HOH D 22 627 106 HOH HOH . W 5 HOH D 23 628 107 HOH HOH . W 5 HOH D 24 629 108 HOH HOH . W 5 HOH D 25 630 111 HOH HOH . W 5 HOH D 26 631 115 HOH HOH . W 5 HOH D 27 632 116 HOH HOH . W 5 HOH D 28 633 123 HOH HOH . W 5 HOH D 29 634 128 HOH HOH . W 5 HOH D 30 635 131 HOH HOH . W 5 HOH D 31 636 132 HOH HOH . W 5 HOH D 32 637 133 HOH HOH . W 5 HOH D 33 638 134 HOH HOH . W 5 HOH D 34 639 135 HOH HOH . W 5 HOH D 35 640 140 HOH HOH . W 5 HOH D 36 641 155 HOH HOH . W 5 HOH D 37 642 162 HOH HOH . W 5 HOH D 38 643 168 HOH HOH . W 5 HOH D 39 644 170 HOH HOH . W 5 HOH D 40 645 171 HOH HOH . W 5 HOH D 41 646 174 HOH HOH . W 5 HOH D 42 647 178 HOH HOH . W 5 HOH D 43 648 184 HOH HOH . W 5 HOH D 44 649 190 HOH HOH . W 5 HOH D 45 650 191 HOH HOH . W 5 HOH D 46 651 196 HOH HOH . W 5 HOH D 47 652 202 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 . . . Q 4 34.971 60.039 104.881 1 41.15 ? C1 MPD 608 C 1 HETATM 2 C C2 MPD . . . Q 4 33.882 59.009 105.157 1 40.99 ? C2 MPD 608 C 1 HETATM 3 O O2 MPD . . . Q 4 32.759 59.667 105.797 1 41.41 ? O2 MPD 608 C 1 HETATM 4 C CM MPD . . . Q 4 33.344 58.428 103.858 1 40.53 ? CM MPD 608 C 1 HETATM 5 C C3 MPD . . . Q 4 34.445 57.896 106.037 1 41.65 ? C3 MPD 608 C 1 HETATM 6 C C4 MPD . . . Q 4 34.36 58.151 107.541 1 43.74 ? C4 MPD 608 C 1 HETATM 7 O O4 MPD . . . Q 4 33.683 57.059 108.121 1 45.38 ? O4 MPD 608 C 1 HETATM 8 C C5 MPD . . . Q 4 35.733 58.271 108.199 1 44.1 ? C5 MPD 608 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #