data_5OYD # _model_server_result.job_id Av4-vGjjw_bRcUwpDSBUFg _model_server_result.datetime_utc '2024-11-13 04:14:28' _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 5oyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":509}' # _entry.id 5OYD # _exptl.entry_id 5OYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 5 _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 5OYD _cell.length_a 55.455 _cell.length_b 97.598 _cell.length_c 157.196 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OYD _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,M 1 1 B,D,I,J,K,L,N 2 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 E N N ? 4 F N N ? 4 G N N ? 4 I N N ? 4 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 BGC NBG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 2 4 3 BGC BGC C1 O1 . O4 HO4 . sing 4 ? 2 5 3 XYS BGC C1 O1 . O6 HO6 . sing 5 ? 2 6 2 XYS BGC C1 O1 . O6 HO6 . sing 6 ? 3 2 1 BGC NBG C1 O1 . O4 HO4 . sing 7 ? 3 3 2 BGC BGC C1 O1 . O4 HO4 . sing 8 ? 3 4 3 BGC BGC C1 O1 . O4 HO4 . sing 9 ? 3 5 4 XYS BGC C1 O1 . O6 HO6 . sing 10 ? 3 6 3 XYS BGC C1 O1 . O6 HO6 . sing 11 ? 3 7 2 XYS BGC C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NBG 1 C 1 NBG C 1 NBG 2 n C BGC 2 C 2 BGC E 1 BGC 2 n C BGC 3 C 3 BGC E 2 BGC 2 n C BGC 4 C 4 BGC E 3 BGC 2 n C XYS 5 C 5 XYS F 2 XYS 2 n C XYS 6 C 6 XYS F 1 XYS 3 n D NBG 1 D 1 NBG C 2 NBG 3 n D BGC 2 D 2 BGC E 4 BGC 3 n D BGC 3 D 3 BGC E 5 BGC 3 n D BGC 4 D 4 BGC E 6 BGC 3 n D XYS 5 D 5 XYS F 5 XYS 3 n D XYS 6 D 6 XYS F 4 XYS 3 n D XYS 7 D 7 XYS F 3 XYS # 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 OE2 GLU 183 A GLU 255 1_555 C C8 NBG . C NBG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale2 B OE2 GLU 183 B GLU 255 1_555 D C8 NBG . D NBG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale3 C O4 NBG . C NBG 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale4 C O4 BGC . C BGC 2 1_555 C C1 BGC . C BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale5 C O6 BGC . C BGC 2 1_555 C C1 XYS . C XYS 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale6 C O4 BGC . C BGC 3 1_555 C C1 BGC . C BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale7 C O6 BGC . C BGC 3 1_555 C C1 XYS . C XYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale8 D O4 NBG . D NBG 1 1_555 D C1 BGC . D BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale9 D O4 BGC . D BGC 2 1_555 D C1 BGC . D BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 D O6 BGC . D BGC 2 1_555 D C1 XYS . D XYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale11 D O4 BGC . D BGC 3 1_555 D C1 BGC . D BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale12 D O6 BGC . D BGC 3 1_555 D C1 XYS . D XYS 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale13 D O6 BGC . D BGC 4 1_555 D C1 XYS . D XYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _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 140 n n C1 C2 GOL sing 141 n n C1 H11 GOL sing 142 n n C1 H12 GOL sing 143 n n O1 HO1 GOL sing 144 n n C2 O2 GOL sing 145 n n C2 C3 GOL sing 146 n n C2 H2 GOL sing 147 n n O2 HO2 GOL sing 148 n n C3 O3 GOL sing 149 n n C3 H31 GOL sing 150 n n C3 H32 GOL sing 151 n n O3 HO3 GOL sing 152 n n # _atom_sites.entry_id 5OYD _atom_sites.fract_transf_matrix[1][1] 0.018033 _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] 0.010246 _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] 0.006361 _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 4 GOL A 1 507 7 GOL GOL . F 4 GOL A 1 508 9 GOL GOL . G 4 GOL A 1 509 10 GOL GOL . H 5 CL A 1 510 2 CL CL . I 4 GOL B 1 508 4 GOL GOL . J 4 GOL B 1 509 8 GOL GOL . K 5 CL B 1 510 1 CL CL . L 6 SO4 B 1 511 1 SO4 SO4 . M 7 HOH A 1 601 28 HOH HOH . M 7 HOH A 2 602 60 HOH HOH . M 7 HOH A 3 603 93 HOH HOH . M 7 HOH A 4 604 160 HOH HOH . M 7 HOH A 5 605 184 HOH HOH . M 7 HOH A 6 606 12 HOH HOH . M 7 HOH A 7 607 113 HOH HOH . M 7 HOH A 8 608 121 HOH HOH . M 7 HOH A 9 609 57 HOH HOH . M 7 HOH A 10 610 112 HOH HOH . M 7 HOH A 11 611 188 HOH HOH . M 7 HOH A 12 612 145 HOH HOH . M 7 HOH A 13 613 179 HOH HOH . M 7 HOH A 14 614 181 HOH HOH . M 7 HOH A 15 615 85 HOH HOH . M 7 HOH A 16 616 75 HOH HOH . M 7 HOH A 17 617 76 HOH HOH . M 7 HOH A 18 618 72 HOH HOH . M 7 HOH A 19 619 18 HOH HOH . M 7 HOH A 20 620 95 HOH HOH . M 7 HOH A 21 621 97 HOH HOH . M 7 HOH A 22 622 61 HOH HOH . M 7 HOH A 23 623 194 HOH HOH . M 7 HOH A 24 624 16 HOH HOH . M 7 HOH A 25 625 120 HOH HOH . M 7 HOH A 26 626 47 HOH HOH . M 7 HOH A 27 627 134 HOH HOH . M 7 HOH A 28 628 167 HOH HOH . M 7 HOH A 29 629 192 HOH HOH . M 7 HOH A 30 630 119 HOH HOH . M 7 HOH A 31 631 103 HOH HOH . M 7 HOH A 32 632 90 HOH HOH . M 7 HOH A 33 633 136 HOH HOH . M 7 HOH A 34 634 102 HOH HOH . M 7 HOH A 35 635 20 HOH HOH . M 7 HOH A 36 636 45 HOH HOH . M 7 HOH A 37 637 174 HOH HOH . M 7 HOH A 38 638 122 HOH HOH . M 7 HOH A 39 639 77 HOH HOH . M 7 HOH A 40 640 8 HOH HOH . M 7 HOH A 41 641 13 HOH HOH . M 7 HOH A 42 642 21 HOH HOH . M 7 HOH A 43 643 62 HOH HOH . M 7 HOH A 44 644 1 HOH HOH . M 7 HOH A 45 645 83 HOH HOH . M 7 HOH A 46 646 138 HOH HOH . M 7 HOH A 47 647 187 HOH HOH . M 7 HOH A 48 648 73 HOH HOH . M 7 HOH A 49 649 4 HOH HOH . M 7 HOH A 50 650 80 HOH HOH . M 7 HOH A 51 651 197 HOH HOH . M 7 HOH A 52 652 123 HOH HOH . M 7 HOH A 53 653 94 HOH HOH . M 7 HOH A 54 654 190 HOH HOH . M 7 HOH A 55 655 143 HOH HOH . M 7 HOH A 56 656 58 HOH HOH . M 7 HOH A 57 657 23 HOH HOH . M 7 HOH A 58 658 203 HOH HOH . M 7 HOH A 59 659 84 HOH HOH . M 7 HOH A 60 660 59 HOH HOH . M 7 HOH A 61 661 92 HOH HOH . M 7 HOH A 62 662 162 HOH HOH . M 7 HOH A 63 663 74 HOH HOH . M 7 HOH A 64 664 15 HOH HOH . M 7 HOH A 65 665 79 HOH HOH . M 7 HOH A 66 666 87 HOH HOH . M 7 HOH A 67 667 33 HOH HOH . M 7 HOH A 68 668 49 HOH HOH . M 7 HOH A 69 669 78 HOH HOH . M 7 HOH A 70 670 154 HOH HOH . M 7 HOH A 71 671 155 HOH HOH . M 7 HOH A 72 672 132 HOH HOH . M 7 HOH A 73 673 126 HOH HOH . M 7 HOH A 74 674 117 HOH HOH . M 7 HOH A 75 675 110 HOH HOH . M 7 HOH A 76 676 140 HOH HOH . M 7 HOH A 77 677 156 HOH HOH . M 7 HOH A 78 678 163 HOH HOH . M 7 HOH A 79 679 178 HOH HOH . M 7 HOH A 80 680 88 HOH HOH . M 7 HOH A 81 681 89 HOH HOH . M 7 HOH A 82 682 19 HOH HOH . M 7 HOH A 83 683 133 HOH HOH . M 7 HOH A 84 684 17 HOH HOH . M 7 HOH A 85 685 14 HOH HOH . M 7 HOH A 86 686 127 HOH HOH . M 7 HOH A 87 687 124 HOH HOH . M 7 HOH A 88 688 196 HOH HOH . M 7 HOH A 89 689 108 HOH HOH . M 7 HOH A 90 690 98 HOH HOH . M 7 HOH A 91 691 159 HOH HOH . M 7 HOH A 92 692 173 HOH HOH . M 7 HOH A 93 693 130 HOH HOH . M 7 HOH A 94 694 153 HOH HOH . M 7 HOH A 95 695 115 HOH HOH . M 7 HOH A 96 696 195 HOH HOH . M 7 HOH A 97 697 46 HOH HOH . M 7 HOH A 98 698 109 HOH HOH . M 7 HOH A 99 699 135 HOH HOH . M 7 HOH A 100 700 125 HOH HOH . M 7 HOH A 101 701 131 HOH HOH . N 7 HOH B 1 601 139 HOH HOH . N 7 HOH B 2 602 41 HOH HOH . N 7 HOH B 3 603 172 HOH HOH . N 7 HOH B 4 604 114 HOH HOH . N 7 HOH B 5 605 128 HOH HOH . N 7 HOH B 6 606 157 HOH HOH . N 7 HOH B 7 607 171 HOH HOH . N 7 HOH B 8 608 26 HOH HOH . N 7 HOH B 9 609 169 HOH HOH . N 7 HOH B 10 610 205 HOH HOH . N 7 HOH B 11 611 50 HOH HOH . N 7 HOH B 12 612 147 HOH HOH . N 7 HOH B 13 613 22 HOH HOH . N 7 HOH B 14 614 101 HOH HOH . N 7 HOH B 15 615 42 HOH HOH . N 7 HOH B 16 616 158 HOH HOH . N 7 HOH B 17 617 111 HOH HOH . N 7 HOH B 18 618 39 HOH HOH . N 7 HOH B 19 619 199 HOH HOH . N 7 HOH B 20 620 36 HOH HOH . N 7 HOH B 21 621 175 HOH HOH . N 7 HOH B 22 622 24 HOH HOH . N 7 HOH B 23 623 180 HOH HOH . N 7 HOH B 24 624 53 HOH HOH . N 7 HOH B 25 625 151 HOH HOH . N 7 HOH B 26 626 30 HOH HOH . N 7 HOH B 27 627 182 HOH HOH . N 7 HOH B 28 628 191 HOH HOH . N 7 HOH B 29 629 63 HOH HOH . N 7 HOH B 30 630 142 HOH HOH . N 7 HOH B 31 631 177 HOH HOH . N 7 HOH B 32 632 27 HOH HOH . N 7 HOH B 33 633 176 HOH HOH . N 7 HOH B 34 634 55 HOH HOH . N 7 HOH B 35 635 64 HOH HOH . N 7 HOH B 36 636 25 HOH HOH . N 7 HOH B 37 637 186 HOH HOH . N 7 HOH B 38 638 82 HOH HOH . N 7 HOH B 39 639 31 HOH HOH . N 7 HOH B 40 640 185 HOH HOH . N 7 HOH B 41 641 44 HOH HOH . N 7 HOH B 42 642 54 HOH HOH . N 7 HOH B 43 643 170 HOH HOH . N 7 HOH B 44 644 141 HOH HOH . N 7 HOH B 45 645 200 HOH HOH . N 7 HOH B 46 646 129 HOH HOH . N 7 HOH B 47 647 65 HOH HOH . N 7 HOH B 48 648 9 HOH HOH . N 7 HOH B 49 649 29 HOH HOH . N 7 HOH B 50 650 91 HOH HOH . N 7 HOH B 51 651 52 HOH HOH . N 7 HOH B 52 652 68 HOH HOH . N 7 HOH B 53 653 3 HOH HOH . N 7 HOH B 54 654 164 HOH HOH . N 7 HOH B 55 655 51 HOH HOH . N 7 HOH B 56 656 6 HOH HOH . N 7 HOH B 57 657 7 HOH HOH . N 7 HOH B 58 658 86 HOH HOH . N 7 HOH B 59 659 69 HOH HOH . N 7 HOH B 60 660 81 HOH HOH . N 7 HOH B 61 661 34 HOH HOH . N 7 HOH B 62 662 99 HOH HOH . N 7 HOH B 63 663 43 HOH HOH . N 7 HOH B 64 664 66 HOH HOH . N 7 HOH B 65 665 144 HOH HOH . N 7 HOH B 66 666 32 HOH HOH . N 7 HOH B 67 667 118 HOH HOH . N 7 HOH B 68 668 38 HOH HOH . N 7 HOH B 69 669 165 HOH HOH . N 7 HOH B 70 670 107 HOH HOH . N 7 HOH B 71 671 201 HOH HOH . N 7 HOH B 72 672 71 HOH HOH . N 7 HOH B 73 673 137 HOH HOH . N 7 HOH B 74 674 35 HOH HOH . N 7 HOH B 75 675 10 HOH HOH . N 7 HOH B 76 676 150 HOH HOH . N 7 HOH B 77 677 168 HOH HOH . N 7 HOH B 78 678 116 HOH HOH . N 7 HOH B 79 679 148 HOH HOH . N 7 HOH B 80 680 146 HOH HOH . N 7 HOH B 81 681 193 HOH HOH . N 7 HOH B 82 682 149 HOH HOH . N 7 HOH B 83 683 67 HOH HOH . N 7 HOH B 84 684 152 HOH HOH . N 7 HOH B 85 685 56 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 . . . G 4 -5.088 100.775 41.987 0.5 46.15 ? C1 GOL 509 A 1 HETATM 2 O O1 GOL . . . G 4 -5.036 99.857 40.882 0.5 42.74 ? O1 GOL 509 A 1 HETATM 3 C C2 GOL . . . G 4 -3.726 101.405 42.288 0.5 43.64 ? C2 GOL 509 A 1 HETATM 4 O O2 GOL . . . G 4 -3.795 101.906 43.599 0.5 46.02 ? O2 GOL 509 A 1 HETATM 5 C C3 GOL . . . G 4 -2.541 100.468 42.243 0.5 45.85 ? C3 GOL 509 A 1 HETATM 6 O O3 GOL . . . G 4 -1.905 100.413 43.547 0.5 44.84 ? O3 GOL 509 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 393 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 6 #