data_6YM4 # _model_server_result.job_id fqrXvvCoJmxQypuTq4durw _model_server_result.datetime_utc '2024-10-19 22:19:21' _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 6ym4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 6YM4 # _exptl.entry_id 6YM4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 93.37 _cell.angle_gamma 90 _cell.entry_id 6YM4 _cell.length_a 43.984 _cell.length_b 99.26 _cell.length_c 104.191 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YM4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 D N N ? 3 E N N ? 3 G 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 C ILE 347 A ILE 358 1_555 A N PHD 348 A PHD 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C PHD 348 A PHD 359 1_555 A N ILE 349 A ILE 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 B C ILE 347 B ILE 358 1_555 B N PHD 348 B PHD 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale4 B C PHD 348 B PHD 359 1_555 B N ILE 349 B ILE 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 6YM4 _atom_sites.fract_transf_matrix[1][1] 0.022736 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001338 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010075 _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] 0.009614 _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 P4Z A 1 501 501 P4Z LIG . D 3 GOL A 1 502 601 GOL GOL . E 3 GOL A 1 503 701 GOL GOL . F 2 P4Z B 1 501 501 P4Z LIG . G 3 GOL B 1 502 601 GOL GOL . H 4 HOH A 1 601 112 HOH HOH . H 4 HOH A 2 602 158 HOH HOH . H 4 HOH A 3 603 168 HOH HOH . H 4 HOH A 4 604 35 HOH HOH . H 4 HOH A 5 605 74 HOH HOH . H 4 HOH A 6 606 163 HOH HOH . H 4 HOH A 7 607 80 HOH HOH . H 4 HOH A 8 608 27 HOH HOH . H 4 HOH A 9 609 11 HOH HOH . H 4 HOH A 10 610 136 HOH HOH . H 4 HOH A 11 611 130 HOH HOH . H 4 HOH A 12 612 87 HOH HOH . H 4 HOH A 13 613 64 HOH HOH . H 4 HOH A 14 614 83 HOH HOH . H 4 HOH A 15 615 12 HOH HOH . H 4 HOH A 16 616 63 HOH HOH . H 4 HOH A 17 617 161 HOH HOH . H 4 HOH A 18 618 20 HOH HOH . H 4 HOH A 19 619 21 HOH HOH . H 4 HOH A 20 620 8 HOH HOH . H 4 HOH A 21 621 9 HOH HOH . H 4 HOH A 22 622 99 HOH HOH . H 4 HOH A 23 623 9 HOH HOH . H 4 HOH A 24 624 79 HOH HOH . H 4 HOH A 25 625 82 HOH HOH . H 4 HOH A 26 626 109 HOH HOH . H 4 HOH A 27 627 59 HOH HOH . H 4 HOH A 28 628 89 HOH HOH . H 4 HOH A 29 629 97 HOH HOH . H 4 HOH A 30 630 122 HOH HOH . H 4 HOH A 31 631 144 HOH HOH . H 4 HOH A 32 632 58 HOH HOH . H 4 HOH A 33 633 152 HOH HOH . H 4 HOH A 34 634 100 HOH HOH . H 4 HOH A 35 635 166 HOH HOH . H 4 HOH A 36 636 167 HOH HOH . H 4 HOH A 37 637 76 HOH HOH . H 4 HOH A 38 638 162 HOH HOH . H 4 HOH A 39 639 90 HOH HOH . H 4 HOH A 40 640 16 HOH HOH . H 4 HOH A 41 641 127 HOH HOH . H 4 HOH A 42 642 73 HOH HOH . H 4 HOH A 43 643 110 HOH HOH . H 4 HOH A 44 644 140 HOH HOH . H 4 HOH A 45 645 17 HOH HOH . H 4 HOH A 46 646 104 HOH HOH . H 4 HOH A 47 647 13 HOH HOH . H 4 HOH A 48 648 95 HOH HOH . H 4 HOH A 49 649 78 HOH HOH . H 4 HOH A 50 650 16 HOH HOH . H 4 HOH A 51 651 19 HOH HOH . H 4 HOH A 52 652 24 HOH HOH . H 4 HOH A 53 653 70 HOH HOH . H 4 HOH A 54 654 6 HOH HOH . H 4 HOH A 55 655 77 HOH HOH . H 4 HOH A 56 656 157 HOH HOH . H 4 HOH A 57 657 94 HOH HOH . H 4 HOH A 58 658 23 HOH HOH . H 4 HOH A 59 659 126 HOH HOH . H 4 HOH A 60 660 147 HOH HOH . H 4 HOH A 61 661 26 HOH HOH . H 4 HOH A 62 662 150 HOH HOH . H 4 HOH A 63 663 156 HOH HOH . H 4 HOH A 64 664 160 HOH HOH . H 4 HOH A 65 665 18 HOH HOH . H 4 HOH A 66 666 65 HOH HOH . H 4 HOH A 67 667 124 HOH HOH . H 4 HOH A 68 668 7 HOH HOH . H 4 HOH A 69 669 116 HOH HOH . H 4 HOH A 70 670 15 HOH HOH . H 4 HOH A 71 671 81 HOH HOH . H 4 HOH A 72 672 10 HOH HOH . H 4 HOH A 73 673 135 HOH HOH . H 4 HOH A 74 674 1 HOH HOH . H 4 HOH A 75 675 32 HOH HOH . H 4 HOH A 76 676 31 HOH HOH . H 4 HOH A 77 677 85 HOH HOH . H 4 HOH A 78 678 25 HOH HOH . H 4 HOH A 79 679 7 HOH HOH . H 4 HOH A 80 680 155 HOH HOH . H 4 HOH A 81 681 125 HOH HOH . H 4 HOH A 82 682 29 HOH HOH . H 4 HOH A 83 683 119 HOH HOH . H 4 HOH A 84 684 17 HOH HOH . H 4 HOH A 85 685 165 HOH HOH . H 4 HOH A 86 686 164 HOH HOH . H 4 HOH A 87 687 117 HOH HOH . H 4 HOH A 88 688 6 HOH HOH . H 4 HOH A 89 689 159 HOH HOH . H 4 HOH A 90 690 142 HOH HOH . H 4 HOH A 91 691 118 HOH HOH . H 4 HOH A 92 692 18 HOH HOH . H 4 HOH A 93 693 115 HOH HOH . H 4 HOH A 94 694 120 HOH HOH . I 4 HOH B 1 601 15 HOH HOH . I 4 HOH B 2 602 88 HOH HOH . I 4 HOH B 3 603 102 HOH HOH . I 4 HOH B 4 604 111 HOH HOH . I 4 HOH B 5 605 21 HOH HOH . I 4 HOH B 6 606 12 HOH HOH . I 4 HOH B 7 607 51 HOH HOH . I 4 HOH B 8 608 72 HOH HOH . I 4 HOH B 9 609 61 HOH HOH . I 4 HOH B 10 610 131 HOH HOH . I 4 HOH B 11 611 5 HOH HOH . I 4 HOH B 12 612 56 HOH HOH . I 4 HOH B 13 613 114 HOH HOH . I 4 HOH B 14 614 103 HOH HOH . I 4 HOH B 15 615 123 HOH HOH . I 4 HOH B 16 616 86 HOH HOH . I 4 HOH B 17 617 69 HOH HOH . I 4 HOH B 18 618 60 HOH HOH . I 4 HOH B 19 619 3 HOH HOH . I 4 HOH B 20 620 4 HOH HOH . I 4 HOH B 21 621 67 HOH HOH . I 4 HOH B 22 622 96 HOH HOH . I 4 HOH B 23 623 84 HOH HOH . I 4 HOH B 24 624 55 HOH HOH . I 4 HOH B 25 625 129 HOH HOH . I 4 HOH B 26 626 75 HOH HOH . I 4 HOH B 27 627 2 HOH HOH . I 4 HOH B 28 628 5 HOH HOH . I 4 HOH B 29 629 132 HOH HOH . I 4 HOH B 30 630 134 HOH HOH . I 4 HOH B 31 631 101 HOH HOH . I 4 HOH B 32 632 151 HOH HOH . I 4 HOH B 33 633 66 HOH HOH . I 4 HOH B 34 634 13 HOH HOH . I 4 HOH B 35 635 171 HOH HOH . I 4 HOH B 36 636 8 HOH HOH . I 4 HOH B 37 637 146 HOH HOH . I 4 HOH B 38 638 44 HOH HOH . I 4 HOH B 39 639 24 HOH HOH . I 4 HOH B 40 640 68 HOH HOH . I 4 HOH B 41 641 52 HOH HOH . I 4 HOH B 42 642 47 HOH HOH . I 4 HOH B 43 643 143 HOH HOH . I 4 HOH B 44 644 49 HOH HOH . I 4 HOH B 45 645 71 HOH HOH . I 4 HOH B 46 646 92 HOH HOH . I 4 HOH B 47 647 107 HOH HOH . I 4 HOH B 48 648 91 HOH HOH . I 4 HOH B 49 649 11 HOH HOH . I 4 HOH B 50 650 170 HOH HOH . I 4 HOH B 51 651 128 HOH HOH . I 4 HOH B 52 652 45 HOH HOH . I 4 HOH B 53 653 20 HOH HOH . I 4 HOH B 54 654 98 HOH HOH . I 4 HOH B 55 655 138 HOH HOH . I 4 HOH B 56 656 57 HOH HOH . I 4 HOH B 57 657 62 HOH HOH . I 4 HOH B 58 658 149 HOH HOH . I 4 HOH B 59 659 22 HOH HOH . I 4 HOH B 60 660 106 HOH HOH . I 4 HOH B 61 661 139 HOH HOH . I 4 HOH B 62 662 14 HOH HOH . I 4 HOH B 63 663 113 HOH HOH . I 4 HOH B 64 664 154 HOH HOH . I 4 HOH B 65 665 10 HOH HOH . I 4 HOH B 66 666 48 HOH HOH . I 4 HOH B 67 667 141 HOH HOH . I 4 HOH B 68 668 133 HOH HOH . I 4 HOH B 69 669 46 HOH HOH . I 4 HOH B 70 670 145 HOH HOH . I 4 HOH B 71 671 4 HOH HOH . I 4 HOH B 72 672 105 HOH HOH . I 4 HOH B 73 673 14 HOH HOH . I 4 HOH B 74 674 3 HOH HOH . I 4 HOH B 75 675 1 HOH HOH . I 4 HOH B 76 676 153 HOH HOH . I 4 HOH B 77 677 93 HOH HOH . I 4 HOH B 78 678 22 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 GOL . . . D 3 -0.43 -4.588 -0.239 1 38.41 ? C1 GOL 502 A 1 HETATM 2 O O1 GOL . . . D 3 -1.601 -5.285 -0.656 1 39.02 ? O1 GOL 502 A 1 HETATM 3 C C2 GOL . . . D 3 0.636 -4.66 -1.327 1 37.91 ? C2 GOL 502 A 1 HETATM 4 O O2 GOL . . . D 3 0.014 -4.251 -2.535 1 37.53 ? O2 GOL 502 A 1 HETATM 5 C C3 GOL . . . D 3 1.829 -3.767 -1.095 1 39.23 ? C3 GOL 502 A 1 HETATM 6 O O3 GOL . . . D 3 2.725 -3.759 -2.218 1 40.2 ? O3 GOL 502 A 1 # _model_server_stats.io_time_ms 83 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #