data_7AMZ # _model_server_result.job_id k9ja6fKeWFCod0ygTDHwtg _model_server_result.datetime_utc '2024-11-24 11:06:26' _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 7amz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":605}' # _entry.id 7AMZ # _exptl.entry_id 7AMZ _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 3 _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 7AMZ _cell.length_a 154.35 _cell.length_b 154.35 _cell.length_c 128.06 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7AMZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall 'I 4 2' _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 5 H N N ? 5 I N N ? 5 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 FUC NAG C1 O1 . O6 HO6 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 1 FUC NAG 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 B NAG 1 B 1 NAG A 530 NAG 2 n B FUC 2 B 2 FUC A 1302 FUC 3 n C NAG 1 C 1 NAG A 531 NAG 3 n C NAG 2 C 2 NAG A 532 NAG 3 n C FUC 3 C 3 FUC A 533 FUC 3 n D NAG 1 D 1 NAG A 534 NAG 3 n D NAG 2 D 2 NAG A 1002 NAG 3 n D FUC 3 D 3 FUC A 1003 FUC 3 n E NAG 1 E 1 NAG A 537 NAG 3 n E NAG 2 E 2 NAG A 538 NAG 3 n E FUC 3 E 3 FUC A 539 FUC # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 252 A CYS 252 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 400 A CYS 400 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? covale ? covale1 A ND2 ASN 57 A ASN 57 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale2 A ND2 ASN 106 A ASN 106 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 241 A ASN 241 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 A ND2 ASN 256 A ASN 256 1_555 F C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale5 A ND2 ASN 341 A ASN 341 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 A ND2 ASN 485 A ASN 485 1_555 G C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale13 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 152 n n C1 C2 GOL sing 153 n n C1 H11 GOL sing 154 n n C1 H12 GOL sing 155 n n O1 HO1 GOL sing 156 n n C2 O2 GOL sing 157 n n C2 C3 GOL sing 158 n n C2 H2 GOL sing 159 n n O2 HO2 GOL sing 160 n n C3 O3 GOL sing 161 n n C3 H31 GOL sing 162 n n C3 H32 GOL sing 163 n n O3 HO3 GOL sing 164 n n # _atom_sites.entry_id 7AMZ _atom_sites.fract_transf_matrix[1][1] 0.006479 _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] 0.006479 _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] 0.007809 _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 4 NAG A 1 601 536 NAG NAG . G 4 NAG A 1 602 540 NAG NAG . H 5 GOL A 1 603 601 GOL GOL . I 5 GOL A 1 604 701 GOL GOL . J 5 GOL A 1 605 901 GOL GOL . K 6 SIA A 1 606 1101 SIA SIA . L 7 RNZ A 1 607 1201 RNZ LIG . M 8 MES A 1 608 1401 MES MES . N 9 SO4 A 1 609 1 SO4 SO4 . O 9 SO4 A 1 610 4 SO4 SO4 . P 10 HOH A 1 701 90 HOH HOH . P 10 HOH A 2 702 134 HOH HOH . P 10 HOH A 3 703 95 HOH HOH . P 10 HOH A 4 704 131 HOH HOH . P 10 HOH A 5 705 52 HOH HOH . P 10 HOH A 6 706 17 HOH HOH . P 10 HOH A 7 707 107 HOH HOH . P 10 HOH A 8 708 84 HOH HOH . P 10 HOH A 9 709 145 HOH HOH . P 10 HOH A 10 710 125 HOH HOH . P 10 HOH A 11 711 78 HOH HOH . P 10 HOH A 12 712 128 HOH HOH . P 10 HOH A 13 713 42 HOH HOH . P 10 HOH A 14 714 46 HOH HOH . P 10 HOH A 15 715 115 HOH HOH . P 10 HOH A 16 716 5 HOH HOH . P 10 HOH A 17 717 62 HOH HOH . P 10 HOH A 18 718 8 HOH HOH . P 10 HOH A 19 719 23 HOH HOH . P 10 HOH A 20 720 113 HOH HOH . P 10 HOH A 21 721 31 HOH HOH . P 10 HOH A 22 722 27 HOH HOH . P 10 HOH A 23 723 99 HOH HOH . P 10 HOH A 24 724 108 HOH HOH . P 10 HOH A 25 725 67 HOH HOH . P 10 HOH A 26 726 6 HOH HOH . P 10 HOH A 27 727 85 HOH HOH . P 10 HOH A 28 728 124 HOH HOH . P 10 HOH A 29 729 76 HOH HOH . P 10 HOH A 30 730 109 HOH HOH . P 10 HOH A 31 731 18 HOH HOH . P 10 HOH A 32 732 121 HOH HOH . P 10 HOH A 33 733 3 HOH HOH . P 10 HOH A 34 734 19 HOH HOH . P 10 HOH A 35 735 72 HOH HOH . P 10 HOH A 36 736 38 HOH HOH . P 10 HOH A 37 737 106 HOH HOH . P 10 HOH A 38 738 34 HOH HOH . P 10 HOH A 39 739 126 HOH HOH . P 10 HOH A 40 740 127 HOH HOH . P 10 HOH A 41 741 123 HOH HOH . P 10 HOH A 42 742 94 HOH HOH . P 10 HOH A 43 743 13 HOH HOH . P 10 HOH A 44 744 91 HOH HOH . P 10 HOH A 45 745 24 HOH HOH . P 10 HOH A 46 746 87 HOH HOH . P 10 HOH A 47 747 92 HOH HOH . P 10 HOH A 48 748 28 HOH HOH . P 10 HOH A 49 749 39 HOH HOH . P 10 HOH A 50 750 56 HOH HOH . P 10 HOH A 51 751 138 HOH HOH . P 10 HOH A 52 752 35 HOH HOH . P 10 HOH A 53 753 9 HOH HOH . P 10 HOH A 54 754 29 HOH HOH . P 10 HOH A 55 755 26 HOH HOH . P 10 HOH A 56 756 7 HOH HOH . P 10 HOH A 57 757 150 HOH HOH . P 10 HOH A 58 758 44 HOH HOH . P 10 HOH A 59 759 20 HOH HOH . P 10 HOH A 60 760 70 HOH HOH . P 10 HOH A 61 761 4 HOH HOH . P 10 HOH A 62 762 65 HOH HOH . P 10 HOH A 63 763 41 HOH HOH . P 10 HOH A 64 764 51 HOH HOH . P 10 HOH A 65 765 1 HOH HOH . P 10 HOH A 66 766 122 HOH HOH . P 10 HOH A 67 767 40 HOH HOH . P 10 HOH A 68 768 45 HOH HOH . P 10 HOH A 69 769 32 HOH HOH . P 10 HOH A 70 770 16 HOH HOH . P 10 HOH A 71 771 141 HOH HOH . P 10 HOH A 72 772 21 HOH HOH . P 10 HOH A 73 773 100 HOH HOH . P 10 HOH A 74 774 63 HOH HOH . P 10 HOH A 75 775 147 HOH HOH . P 10 HOH A 76 776 15 HOH HOH . P 10 HOH A 77 777 96 HOH HOH . P 10 HOH A 78 778 120 HOH HOH . P 10 HOH A 79 779 103 HOH HOH . P 10 HOH A 80 780 43 HOH HOH . P 10 HOH A 81 781 112 HOH HOH . P 10 HOH A 82 782 48 HOH HOH . P 10 HOH A 83 783 110 HOH HOH . P 10 HOH A 84 784 102 HOH HOH . P 10 HOH A 85 785 58 HOH HOH . P 10 HOH A 86 786 71 HOH HOH . P 10 HOH A 87 787 111 HOH HOH . P 10 HOH A 88 788 83 HOH HOH . P 10 HOH A 89 789 11 HOH HOH . P 10 HOH A 90 790 14 HOH HOH . P 10 HOH A 91 791 30 HOH HOH . P 10 HOH A 92 792 68 HOH HOH . P 10 HOH A 93 793 25 HOH HOH . P 10 HOH A 94 794 89 HOH HOH . P 10 HOH A 95 795 82 HOH HOH . P 10 HOH A 96 796 22 HOH HOH . P 10 HOH A 97 797 88 HOH HOH . P 10 HOH A 98 798 47 HOH HOH . P 10 HOH A 99 799 10 HOH HOH . P 10 HOH A 100 800 36 HOH HOH . P 10 HOH A 101 801 114 HOH HOH . P 10 HOH A 102 802 55 HOH HOH . P 10 HOH A 103 803 50 HOH HOH . P 10 HOH A 104 804 105 HOH HOH . P 10 HOH A 105 805 151 HOH HOH . P 10 HOH A 106 806 80 HOH HOH . P 10 HOH A 107 807 148 HOH HOH . P 10 HOH A 108 808 81 HOH HOH . P 10 HOH A 109 809 59 HOH HOH . P 10 HOH A 110 810 33 HOH HOH . P 10 HOH A 111 811 97 HOH HOH . P 10 HOH A 112 812 2 HOH HOH . P 10 HOH A 113 813 57 HOH HOH . P 10 HOH A 114 814 119 HOH HOH . P 10 HOH A 115 815 116 HOH HOH . P 10 HOH A 116 816 101 HOH HOH . P 10 HOH A 117 817 86 HOH HOH . P 10 HOH A 118 818 64 HOH HOH . P 10 HOH A 119 819 54 HOH HOH . P 10 HOH A 120 820 143 HOH HOH . P 10 HOH A 121 821 12 HOH HOH . P 10 HOH A 122 822 137 HOH HOH . P 10 HOH A 123 823 132 HOH HOH . P 10 HOH A 124 824 93 HOH HOH . P 10 HOH A 125 825 149 HOH HOH . P 10 HOH A 126 826 146 HOH HOH . P 10 HOH A 127 827 37 HOH HOH . P 10 HOH A 128 828 104 HOH HOH . P 10 HOH A 129 829 142 HOH HOH . P 10 HOH A 130 830 152 HOH HOH . P 10 HOH A 131 831 117 HOH HOH . P 10 HOH A 132 832 77 HOH HOH . P 10 HOH A 133 833 144 HOH HOH . P 10 HOH A 134 834 49 HOH HOH . P 10 HOH A 135 835 53 HOH HOH . P 10 HOH A 136 836 130 HOH HOH . P 10 HOH A 137 837 135 HOH HOH . P 10 HOH A 138 838 136 HOH HOH . P 10 HOH A 139 839 133 HOH HOH . P 10 HOH A 140 840 129 HOH HOH . P 10 HOH A 141 841 69 HOH HOH . P 10 HOH A 142 842 74 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 . . . J 5 5.933 41.466 40.442 1 64.57 ? C1 GOL 605 A 1 HETATM 2 O O1 GOL . . . J 5 5.648 41.277 39.062 1 56.97 ? O1 GOL 605 A 1 HETATM 3 C C2 GOL . . . J 5 5.431 42.92 40.868 1 70.59 ? C2 GOL 605 A 1 HETATM 4 O O2 GOL . . . J 5 4.59 42.882 41.984 1 77.21 ? O2 GOL 605 A 1 HETATM 5 C C3 GOL . . . J 5 6.728 43.787 41.132 1 67.85 ? C3 GOL 605 A 1 HETATM 6 O O3 GOL . . . J 5 7.675 42.935 41.764 1 61.57 ? O3 GOL 605 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #