data_5JQ3 # _model_server_result.job_id JLQcmSa5NJSL8zjerjcAeA _model_server_result.datetime_utc '2024-11-28 03:17:58' _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 5jq3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":606}' # _entry.id 5JQ3 # _exptl.entry_id 5JQ3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _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 120 _cell.entry_id 5JQ3 _cell.length_a 114.258 _cell.length_b 114.258 _cell.length_c 307.377 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JQ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -57.129 98.950331 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -114.258 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 H N N ? 5 I N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN BMA 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 3 n C NAG 1 C 1 NAG B 702 NAG 3 n C NAG 2 C 2 NAG B 703 NAG 3 n C BMA 3 C 3 BMA B 704 BMA 3 n C MAN 4 C 4 MAN B 706 MAN 3 n C MAN 5 C 5 MAN B 705 MAN # 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 26 A CYS 53 1_555 B SG CYS 108 B CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 81 A CYS 108 1_555 A SG CYS 108 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf3 A SG CYS 94 A CYS 121 1_555 A SG CYS 120 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 B SG CYS 10 B CYS 511 1_555 B SG CYS 55 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf5 B SG CYS 100 B CYS 601 1_555 B SG CYS 107 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? covale ? covale1 A ND2 ASN 201 A ASN 228 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 211 A ASN 238 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A ND2 ASN 230 A ASN 257 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 A ND2 ASN 241 A ASN 268 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 B ND2 ASN 62 B ASN 563 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale6 B ND2 ASN 117 B ASN 618 1_555 J C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _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 153 n n C1 C2 GOL sing 154 n n C1 H11 GOL sing 155 n n C1 H12 GOL sing 156 n n O1 HO1 GOL sing 157 n n C2 O2 GOL sing 158 n n C2 C3 GOL sing 159 n n C2 H2 GOL sing 160 n n O2 HO2 GOL sing 161 n n C3 O3 GOL sing 162 n n C3 H31 GOL sing 163 n n C3 H32 GOL sing 164 n n O3 HO3 GOL sing 165 n n # _atom_sites.entry_id 5JQ3 _atom_sites.fract_transf_matrix[1][1] 0.008752 _atom_sites.fract_transf_matrix[1][2] 0.005053 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010106 _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] 0.003253 _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 4 NAG A 1 601 601 NAG NAG . E 4 NAG A 1 602 602 NAG NAG . F 4 NAG A 1 603 603 NAG NAG . G 4 NAG A 1 604 604 NAG NAG . H 5 GOL A 1 605 605 GOL GOL . I 5 GOL A 1 606 606 GOL GOL . J 4 NAG B 1 701 701 NAG NAG . K 6 HOH A 1 701 701 HOH HOH . K 6 HOH A 2 702 702 HOH HOH . K 6 HOH A 3 703 703 HOH HOH . K 6 HOH A 4 704 704 HOH HOH . K 6 HOH A 5 705 705 HOH HOH . K 6 HOH A 6 706 706 HOH HOH . K 6 HOH A 7 707 707 HOH HOH . K 6 HOH A 8 708 708 HOH HOH . K 6 HOH A 9 709 709 HOH HOH . K 6 HOH A 10 710 710 HOH HOH . K 6 HOH A 11 711 711 HOH HOH . K 6 HOH A 12 712 712 HOH HOH . K 6 HOH A 13 713 713 HOH HOH . K 6 HOH A 14 714 714 HOH HOH . K 6 HOH A 15 715 715 HOH HOH . K 6 HOH A 16 716 716 HOH HOH . K 6 HOH A 17 717 717 HOH HOH . K 6 HOH A 18 718 718 HOH HOH . K 6 HOH A 19 719 719 HOH HOH . K 6 HOH A 20 720 720 HOH HOH . K 6 HOH A 21 721 721 HOH HOH . K 6 HOH A 22 722 722 HOH HOH . K 6 HOH A 23 723 723 HOH HOH . K 6 HOH A 24 724 724 HOH HOH . K 6 HOH A 25 725 725 HOH HOH . K 6 HOH A 26 726 726 HOH HOH . K 6 HOH A 27 727 727 HOH HOH . K 6 HOH A 28 728 728 HOH HOH . K 6 HOH A 29 729 729 HOH HOH . K 6 HOH A 30 730 730 HOH HOH . K 6 HOH A 31 731 731 HOH HOH . K 6 HOH A 32 732 732 HOH HOH . K 6 HOH A 33 733 733 HOH HOH . K 6 HOH A 34 734 734 HOH HOH . K 6 HOH A 35 735 735 HOH HOH . K 6 HOH A 36 736 736 HOH HOH . K 6 HOH A 37 737 737 HOH HOH . K 6 HOH A 38 738 738 HOH HOH . K 6 HOH A 39 739 739 HOH HOH . K 6 HOH A 40 740 740 HOH HOH . K 6 HOH A 41 741 741 HOH HOH . K 6 HOH A 42 742 742 HOH HOH . K 6 HOH A 43 743 743 HOH HOH . K 6 HOH A 44 744 744 HOH HOH . K 6 HOH A 45 745 745 HOH HOH . K 6 HOH A 46 746 746 HOH HOH . K 6 HOH A 47 747 747 HOH HOH . K 6 HOH A 48 748 748 HOH HOH . K 6 HOH A 49 749 749 HOH HOH . K 6 HOH A 50 750 750 HOH HOH . K 6 HOH A 51 751 751 HOH HOH . K 6 HOH A 52 752 752 HOH HOH . K 6 HOH A 53 753 753 HOH HOH . K 6 HOH A 54 754 754 HOH HOH . K 6 HOH A 55 755 755 HOH HOH . K 6 HOH A 56 756 756 HOH HOH . K 6 HOH A 57 757 757 HOH HOH . K 6 HOH A 58 758 758 HOH HOH . K 6 HOH A 59 759 759 HOH HOH . K 6 HOH A 60 760 760 HOH HOH . K 6 HOH A 61 761 761 HOH HOH . K 6 HOH A 62 762 762 HOH HOH . K 6 HOH A 63 763 763 HOH HOH . K 6 HOH A 64 764 764 HOH HOH . K 6 HOH A 65 765 765 HOH HOH . K 6 HOH A 66 766 766 HOH HOH . K 6 HOH A 67 767 767 HOH HOH . K 6 HOH A 68 768 768 HOH HOH . K 6 HOH A 69 769 769 HOH HOH . L 6 HOH B 1 801 801 HOH HOH . L 6 HOH B 2 802 802 HOH HOH . L 6 HOH B 3 803 803 HOH HOH . L 6 HOH B 4 804 804 HOH HOH . L 6 HOH B 5 805 805 HOH HOH . L 6 HOH B 6 806 806 HOH HOH . L 6 HOH B 7 807 807 HOH HOH . L 6 HOH B 8 808 808 HOH HOH . L 6 HOH B 9 809 809 HOH HOH . L 6 HOH B 10 810 810 HOH HOH . L 6 HOH B 11 811 811 HOH HOH . L 6 HOH B 12 812 812 HOH HOH . L 6 HOH B 13 813 813 HOH HOH . L 6 HOH B 14 814 814 HOH HOH . L 6 HOH B 15 815 815 HOH HOH . L 6 HOH B 16 816 816 HOH HOH . L 6 HOH B 17 817 817 HOH HOH . L 6 HOH B 18 818 818 HOH HOH . L 6 HOH B 19 819 819 HOH HOH . L 6 HOH B 20 820 820 HOH HOH . L 6 HOH B 21 821 821 HOH HOH . L 6 HOH B 22 822 822 HOH HOH . L 6 HOH B 23 823 823 HOH HOH . L 6 HOH B 24 824 824 HOH HOH . L 6 HOH B 25 825 825 HOH HOH . L 6 HOH B 26 826 826 HOH HOH . L 6 HOH B 27 827 827 HOH HOH . L 6 HOH B 28 828 828 HOH HOH . L 6 HOH B 29 829 829 HOH HOH . L 6 HOH B 30 830 830 HOH HOH . L 6 HOH B 31 831 831 HOH HOH . L 6 HOH B 32 832 832 HOH HOH . L 6 HOH B 33 833 833 HOH HOH . L 6 HOH B 34 834 834 HOH HOH . L 6 HOH B 35 835 835 HOH HOH . L 6 HOH B 36 836 836 HOH HOH . L 6 HOH B 37 837 837 HOH HOH . L 6 HOH B 38 838 838 HOH HOH . L 6 HOH B 39 839 839 HOH HOH . L 6 HOH B 40 840 840 HOH HOH . L 6 HOH B 41 841 841 HOH HOH . L 6 HOH B 42 842 842 HOH HOH . L 6 HOH B 43 843 843 HOH HOH . L 6 HOH B 44 844 844 HOH HOH . L 6 HOH B 45 845 845 HOH HOH . L 6 HOH B 46 846 846 HOH HOH . L 6 HOH B 47 847 847 HOH HOH . L 6 HOH B 48 848 848 HOH HOH . L 6 HOH B 49 849 849 HOH HOH . L 6 HOH B 50 850 850 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 . . . I 5 -64.95 19.544 -37.729 1 89.72 ? C1 GOL 606 A 1 HETATM 2 O O1 GOL . . . I 5 -64.56 20.356 -36.611 1 89.74 ? O1 GOL 606 A 1 HETATM 3 C C2 GOL . . . I 5 -63.886 19.543 -38.826 1 89.42 ? C2 GOL 606 A 1 HETATM 4 O O2 GOL . . . I 5 -64.047 20.704 -39.653 1 92.35 ? O2 GOL 606 A 1 HETATM 5 C C3 GOL . . . I 5 -62.474 19.501 -38.238 1 88.49 ? C3 GOL 606 A 1 HETATM 6 O O3 GOL . . . I 5 -62.055 20.815 -37.846 1 87.85 ? O3 GOL 606 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #