data_5K5E # _model_server_result.job_id dlj5Kur1-V0t4izPidv2vQ _model_server_result.datetime_utc '2024-11-25 14:13:47' _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 5k5e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":613}' # _entry.id 5K5E # _exptl.entry_id 5K5E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 2 _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 5K5E _cell.length_a 75.81 _cell.length_b 80.07 _cell.length_c 230.63 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K5E _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,F,G,H,I,J,K,W 1 1 B,E,L,M,N,O,P,Q,R,S,T,U,V,X 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+1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 40.035 115.315 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 U N N ? 6 V N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 NAG 1 C 1 NAG C 3 NAG 2 n C NAG 2 C 2 NAG C 8 NAG 2 n D NAG 1 D 1 NAG C 6 NAG 2 n D NAG 2 D 2 NAG C 7 NAG 2 n E NAG 1 E 1 NAG C 14 NAG 2 n E NAG 2 E 2 NAG C 16 NAG # 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 disulf ? disulf1 A SG CYS 65 A CYS 65 1_555 A SG CYS 92 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 252 A CYS 252 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf3 A SG CYS 400 A CYS 400 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf4 B SG CYS 65 B CYS 65 1_555 B SG CYS 92 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 252 B CYS 252 1_555 B SG CYS 263 B CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 B SG CYS 400 B CYS 400 1_555 B SG CYS 519 B CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? covale ? covale1 A ND2 ASN 17 A ASN 17 1_555 F C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 106 A ASN 106 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale3 A ND2 ASN 241 A ASN 241 1_555 H C1 NAG . A NAG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 A ND2 ASN 341 A ASN 341 1_555 I C1 NAG . A NAG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale5 A ND2 ASN 481 A ASN 481 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 B ND2 ASN 17 B ASN 17 1_555 L C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 B ND2 ASN 106 B ASN 106 1_555 N C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale8 B ND2 ASN 241 B ASN 241 1_555 O C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale9 B ND2 ASN 256 B ASN 256 1_555 P C1 NAG . B NAG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale10 B ND2 ASN 341 B ASN 341 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale11 B ND2 ASN 481 B ASN 481 1_555 Q C1 NAG . B NAG 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale12 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _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 211 n n C1 C2 GOL sing 212 n n C1 H11 GOL sing 213 n n C1 H12 GOL sing 214 n n O1 HO1 GOL sing 215 n n C2 O2 GOL sing 216 n n C2 C3 GOL sing 217 n n C2 H2 GOL sing 218 n n O2 HO2 GOL sing 219 n n C3 O3 GOL sing 220 n n C3 H31 GOL sing 221 n n C3 H32 GOL sing 222 n n O3 HO3 GOL sing 223 n n # _atom_sites.entry_id 5K5E _atom_sites.fract_transf_matrix[1][1] 0.013191 _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] 0.012489 _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] 0.004336 _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 F 3 NAG A 1 601 1 NAG NAG . G 3 NAG A 1 602 2 NAG NAG . H 3 NAG A 1 605 4 NAG NAG . I 3 NAG A 1 606 5 NAG NAG . J 4 6QS A 1 609 1 6QS 9SX . K 5 EDO A 1 610 1 EDO EDO . L 3 NAG B 1 601 9 NAG NAG . M 3 NAG B 1 602 10 NAG NAG . N 3 NAG B 1 603 11 NAG NAG . O 3 NAG B 1 604 12 NAG NAG . P 3 NAG B 1 605 13 NAG NAG . Q 3 NAG B 1 608 15 NAG NAG . R 4 6QS B 1 609 2 6QS 9SX . S 5 EDO B 1 610 2 EDO EDO . T 5 EDO B 1 611 3 EDO EDO . U 6 GOL B 1 612 4 GOL GOL . V 6 GOL B 1 613 5 GOL GOL . W 7 HOH A 1 701 36 HOH HOH . W 7 HOH A 2 702 33 HOH HOH . W 7 HOH A 3 703 108 HOH HOH . W 7 HOH A 4 704 7 HOH HOH . W 7 HOH A 5 705 50 HOH HOH . W 7 HOH A 6 706 32 HOH HOH . W 7 HOH A 7 707 10 HOH HOH . W 7 HOH A 8 708 8 HOH HOH . W 7 HOH A 9 709 129 HOH HOH . W 7 HOH A 10 710 47 HOH HOH . W 7 HOH A 11 711 96 HOH HOH . W 7 HOH A 12 712 79 HOH HOH . W 7 HOH A 13 713 20 HOH HOH . W 7 HOH A 14 714 17 HOH HOH . W 7 HOH A 15 715 34 HOH HOH . W 7 HOH A 16 716 84 HOH HOH . W 7 HOH A 17 717 102 HOH HOH . W 7 HOH A 18 718 25 HOH HOH . W 7 HOH A 19 719 39 HOH HOH . W 7 HOH A 20 720 43 HOH HOH . W 7 HOH A 21 721 18 HOH HOH . W 7 HOH A 22 722 16 HOH HOH . W 7 HOH A 23 723 85 HOH HOH . W 7 HOH A 24 724 6 HOH HOH . W 7 HOH A 25 725 122 HOH HOH . W 7 HOH A 26 726 35 HOH HOH . W 7 HOH A 27 727 119 HOH HOH . W 7 HOH A 28 728 24 HOH HOH . W 7 HOH A 29 729 128 HOH HOH . W 7 HOH A 30 730 23 HOH HOH . W 7 HOH A 31 731 123 HOH HOH . W 7 HOH A 32 732 27 HOH HOH . W 7 HOH A 33 733 48 HOH HOH . W 7 HOH A 34 734 49 HOH HOH . W 7 HOH A 35 735 95 HOH HOH . W 7 HOH A 36 736 104 HOH HOH . W 7 HOH A 37 737 15 HOH HOH . W 7 HOH A 38 738 46 HOH HOH . W 7 HOH A 39 739 29 HOH HOH . W 7 HOH A 40 740 22 HOH HOH . W 7 HOH A 41 741 21 HOH HOH . W 7 HOH A 42 742 42 HOH HOH . W 7 HOH A 43 743 37 HOH HOH . W 7 HOH A 44 744 14 HOH HOH . W 7 HOH A 45 745 120 HOH HOH . W 7 HOH A 46 746 121 HOH HOH . W 7 HOH A 47 747 45 HOH HOH . W 7 HOH A 48 748 41 HOH HOH . W 7 HOH A 49 749 124 HOH HOH . W 7 HOH A 50 750 44 HOH HOH . W 7 HOH A 51 751 106 HOH HOH . W 7 HOH A 52 752 100 HOH HOH . W 7 HOH A 53 753 97 HOH HOH . W 7 HOH A 54 754 51 HOH HOH . W 7 HOH A 55 755 19 HOH HOH . W 7 HOH A 56 756 31 HOH HOH . W 7 HOH A 57 757 40 HOH HOH . W 7 HOH A 58 758 11 HOH HOH . W 7 HOH A 59 759 105 HOH HOH . W 7 HOH A 60 760 30 HOH HOH . W 7 HOH A 61 761 26 HOH HOH . W 7 HOH A 62 762 38 HOH HOH . W 7 HOH A 63 763 28 HOH HOH . W 7 HOH A 64 764 99 HOH HOH . W 7 HOH A 65 765 107 HOH HOH . W 7 HOH A 66 766 86 HOH HOH . W 7 HOH A 67 767 103 HOH HOH . X 7 HOH B 1 701 66 HOH HOH . X 7 HOH B 2 702 61 HOH HOH . X 7 HOH B 3 703 75 HOH HOH . X 7 HOH B 4 704 72 HOH HOH . X 7 HOH B 5 705 80 HOH HOH . X 7 HOH B 6 706 69 HOH HOH . X 7 HOH B 7 707 63 HOH HOH . X 7 HOH B 8 708 64 HOH HOH . X 7 HOH B 9 709 114 HOH HOH . X 7 HOH B 10 710 71 HOH HOH . X 7 HOH B 11 711 78 HOH HOH . X 7 HOH B 12 712 94 HOH HOH . X 7 HOH B 13 713 87 HOH HOH . X 7 HOH B 14 714 9 HOH HOH . X 7 HOH B 15 715 62 HOH HOH . X 7 HOH B 16 716 88 HOH HOH . X 7 HOH B 17 717 13 HOH HOH . X 7 HOH B 18 718 74 HOH HOH . X 7 HOH B 19 719 93 HOH HOH . X 7 HOH B 20 720 83 HOH HOH . X 7 HOH B 21 721 3 HOH HOH . X 7 HOH B 22 722 59 HOH HOH . X 7 HOH B 23 723 77 HOH HOH . X 7 HOH B 24 724 58 HOH HOH . X 7 HOH B 25 725 73 HOH HOH . X 7 HOH B 26 726 67 HOH HOH . X 7 HOH B 27 727 82 HOH HOH . X 7 HOH B 28 728 91 HOH HOH . X 7 HOH B 29 729 1 HOH HOH . X 7 HOH B 30 730 5 HOH HOH . X 7 HOH B 31 731 76 HOH HOH . X 7 HOH B 32 732 56 HOH HOH . X 7 HOH B 33 733 57 HOH HOH . X 7 HOH B 34 734 98 HOH HOH . X 7 HOH B 35 735 53 HOH HOH . X 7 HOH B 36 736 127 HOH HOH . X 7 HOH B 37 737 70 HOH HOH . X 7 HOH B 38 738 126 HOH HOH . X 7 HOH B 39 739 125 HOH HOH . X 7 HOH B 40 740 55 HOH HOH . X 7 HOH B 41 741 90 HOH HOH . X 7 HOH B 42 742 109 HOH HOH . X 7 HOH B 43 743 54 HOH HOH . X 7 HOH B 44 744 92 HOH HOH . X 7 HOH B 45 745 2 HOH HOH . X 7 HOH B 46 746 101 HOH HOH . X 7 HOH B 47 747 68 HOH HOH . X 7 HOH B 48 748 60 HOH HOH . X 7 HOH B 49 749 12 HOH HOH . X 7 HOH B 50 750 111 HOH HOH . X 7 HOH B 51 751 89 HOH HOH . X 7 HOH B 52 752 113 HOH HOH . X 7 HOH B 53 753 65 HOH HOH . X 7 HOH B 54 754 112 HOH HOH . X 7 HOH B 55 755 110 HOH HOH . X 7 HOH B 56 756 81 HOH HOH . X 7 HOH B 57 757 115 HOH HOH . X 7 HOH B 58 758 118 HOH HOH . X 7 HOH B 59 759 117 HOH HOH . X 7 HOH B 60 760 116 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 . . . V 6 -21.216 3.902 41.406 1 94.13 ? C1 GOL 613 B 1 HETATM 2 O O1 GOL . . . V 6 -22.583 3.638 41.077 1 88.11 ? O1 GOL 613 B 1 HETATM 3 C C2 GOL . . . V 6 -20.663 5.137 40.671 1 100.21 ? C2 GOL 613 B 1 HETATM 4 O O2 GOL . . . V 6 -21.697 5.779 39.951 1 108.52 ? O2 GOL 613 B 1 HETATM 5 C C3 GOL . . . V 6 -20.052 6.147 41.655 1 92.41 ? C3 GOL 613 B 1 HETATM 6 O O3 GOL . . . V 6 -19.601 7.318 40.985 1 79.71 ? O3 GOL 613 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #