data_5VCD # _model_server_result.job_id aPeOJ0RlUOMeRYIgyhgn4A _model_server_result.datetime_utc '2024-11-08 04:40:43' _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 5vcd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":613}' # _entry.id 5VCD # _exptl.entry_id 5VCD _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 12 _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 5VCD _cell.length_a 76.46 _cell.length_b 99.66 _cell.length_c 132.89 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VCD _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 1 1,2 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 2 1,2,3,4 # 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_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -76.46 0 0 3 'crystal symmetry operation' 3_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -76.46 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N 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 metalc ? metalc1 A SG CYS 422 A CYS 442 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 O O HOH . A HOH 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? # _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 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 5VCD _atom_sites.fract_transf_matrix[1][1] 0.013079 _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] 0.010034 _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] 0.007525 _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 B 2 HEM A 1 601 500 HEM HEM . C 3 GOL A 1 602 600 GOL GOL . D 3 GOL A 1 603 601 GOL GOL . E 3 GOL A 1 604 602 GOL GOL . F 3 GOL A 1 605 603 GOL GOL . G 3 GOL A 1 606 604 GOL GOL . H 3 GOL A 1 607 605 GOL GOL . I 3 GOL A 1 608 606 GOL GOL . J 3 GOL A 1 609 607 GOL GOL . K 3 GOL A 1 610 608 GOL GOL . L 3 GOL A 1 611 609 GOL GOL . M 3 GOL A 1 612 610 GOL GOL . N 3 GOL A 1 613 611 GOL GOL . O 4 HOH A 1 701 103 HOH HOH . O 4 HOH A 2 702 96 HOH HOH . O 4 HOH A 3 703 68 HOH HOH . O 4 HOH A 4 704 11 HOH HOH . O 4 HOH A 5 705 102 HOH HOH . O 4 HOH A 6 706 45 HOH HOH . O 4 HOH A 7 707 32 HOH HOH . O 4 HOH A 8 708 73 HOH HOH . O 4 HOH A 9 709 20 HOH HOH . O 4 HOH A 10 710 50 HOH HOH . O 4 HOH A 11 711 81 HOH HOH . O 4 HOH A 12 712 58 HOH HOH . O 4 HOH A 13 713 92 HOH HOH . O 4 HOH A 14 714 9 HOH HOH . O 4 HOH A 15 715 30 HOH HOH . O 4 HOH A 16 716 95 HOH HOH . O 4 HOH A 17 717 74 HOH HOH . O 4 HOH A 18 718 29 HOH HOH . O 4 HOH A 19 719 17 HOH HOH . O 4 HOH A 20 720 14 HOH HOH . O 4 HOH A 21 721 7 HOH HOH . O 4 HOH A 22 722 72 HOH HOH . O 4 HOH A 23 723 15 HOH HOH . O 4 HOH A 24 724 34 HOH HOH . O 4 HOH A 25 725 36 HOH HOH . O 4 HOH A 26 726 93 HOH HOH . O 4 HOH A 27 727 70 HOH HOH . O 4 HOH A 28 728 5 HOH HOH . O 4 HOH A 29 729 61 HOH HOH . O 4 HOH A 30 730 31 HOH HOH . O 4 HOH A 31 731 22 HOH HOH . O 4 HOH A 32 732 52 HOH HOH . O 4 HOH A 33 733 82 HOH HOH . O 4 HOH A 34 734 27 HOH HOH . O 4 HOH A 35 735 47 HOH HOH . O 4 HOH A 36 736 71 HOH HOH . O 4 HOH A 37 737 39 HOH HOH . O 4 HOH A 38 738 12 HOH HOH . O 4 HOH A 39 739 25 HOH HOH . O 4 HOH A 40 740 19 HOH HOH . O 4 HOH A 41 741 62 HOH HOH . O 4 HOH A 42 742 91 HOH HOH . O 4 HOH A 43 743 10 HOH HOH . O 4 HOH A 44 744 88 HOH HOH . O 4 HOH A 45 745 101 HOH HOH . O 4 HOH A 46 746 106 HOH HOH . O 4 HOH A 47 747 53 HOH HOH . O 4 HOH A 48 748 89 HOH HOH . O 4 HOH A 49 749 46 HOH HOH . O 4 HOH A 50 750 51 HOH HOH . O 4 HOH A 51 751 35 HOH HOH . O 4 HOH A 52 752 42 HOH HOH . O 4 HOH A 53 753 67 HOH HOH . O 4 HOH A 54 754 80 HOH HOH . O 4 HOH A 55 755 78 HOH HOH . O 4 HOH A 56 756 2 HOH HOH . O 4 HOH A 57 757 65 HOH HOH . O 4 HOH A 58 758 86 HOH HOH . O 4 HOH A 59 759 28 HOH HOH . O 4 HOH A 60 760 49 HOH HOH . O 4 HOH A 61 761 38 HOH HOH . O 4 HOH A 62 762 54 HOH HOH . O 4 HOH A 63 763 56 HOH HOH . O 4 HOH A 64 764 33 HOH HOH . O 4 HOH A 65 765 23 HOH HOH . O 4 HOH A 66 766 90 HOH HOH . O 4 HOH A 67 767 4 HOH HOH . O 4 HOH A 68 768 6 HOH HOH . O 4 HOH A 69 769 18 HOH HOH . O 4 HOH A 70 770 24 HOH HOH . O 4 HOH A 71 771 64 HOH HOH . O 4 HOH A 72 772 79 HOH HOH . O 4 HOH A 73 773 13 HOH HOH . O 4 HOH A 74 774 41 HOH HOH . O 4 HOH A 75 775 40 HOH HOH . O 4 HOH A 76 776 3 HOH HOH . O 4 HOH A 77 777 37 HOH HOH . O 4 HOH A 78 778 26 HOH HOH . O 4 HOH A 79 779 98 HOH HOH . O 4 HOH A 80 780 43 HOH HOH . O 4 HOH A 81 781 83 HOH HOH . O 4 HOH A 82 782 44 HOH HOH . O 4 HOH A 83 783 84 HOH HOH . O 4 HOH A 84 784 63 HOH HOH . O 4 HOH A 85 785 85 HOH HOH . O 4 HOH A 86 786 21 HOH HOH . O 4 HOH A 87 787 94 HOH HOH . O 4 HOH A 88 788 75 HOH HOH . O 4 HOH A 89 789 97 HOH HOH . O 4 HOH A 90 790 104 HOH HOH . O 4 HOH A 91 791 76 HOH HOH . O 4 HOH A 92 792 59 HOH HOH . O 4 HOH A 93 793 57 HOH HOH . O 4 HOH A 94 794 55 HOH HOH . O 4 HOH A 95 795 8 HOH HOH . O 4 HOH A 96 796 77 HOH HOH . O 4 HOH A 97 797 87 HOH HOH . O 4 HOH A 98 798 60 HOH HOH . O 4 HOH A 99 799 99 HOH HOH . O 4 HOH A 100 800 16 HOH HOH . O 4 HOH A 101 801 48 HOH HOH . O 4 HOH A 102 802 100 HOH HOH . O 4 HOH A 103 803 69 HOH HOH . O 4 HOH A 104 804 1 HOH HOH . O 4 HOH A 105 805 66 HOH HOH . O 4 HOH A 106 806 105 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 . . . N 3 -29.117 -29.197 -18.953 1 96.44 ? C1 GOL 613 A 1 HETATM 2 O O1 GOL . . . N 3 -27.895 -28.653 -19.395 1 95.3 ? O1 GOL 613 A 1 HETATM 3 C C2 GOL . . . N 3 -28.93 -29.835 -17.581 1 92.39 ? C2 GOL 613 A 1 HETATM 4 O O2 GOL . . . N 3 -29.512 -28.995 -16.61 1 86.28 ? O2 GOL 613 A 1 HETATM 5 C C3 GOL . . . N 3 -27.444 -29.995 -17.275 1 90.85 ? C3 GOL 613 A 1 HETATM 6 O O3 GOL . . . N 3 -27.241 -30.932 -16.238 1 91.78 ? O3 GOL 613 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #