data_5VD4 # _model_server_result.job_id S-nmCxxfuJ16ob01YA1QYg _model_server_result.datetime_utc '2024-11-21 11:52:31' _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 5vd4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":604}' # _entry.id 5VD4 # _exptl.entry_id 5VD4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _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 103.04 _cell.angle_gamma 90 _cell.entry_id 5VD4 _cell.length_a 50.31 _cell.length_b 43.78 _cell.length_c 64.86 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VD4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 ? 4 E N N ? 4 F N N ? 4 G N N # _chem_comp.formula 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # 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 EDO sing 153 n n C1 C2 EDO sing 154 n n C1 H11 EDO sing 155 n n C1 H12 EDO sing 156 n n O1 HO1 EDO sing 157 n n C2 O2 EDO sing 158 n n C2 H21 EDO sing 159 n n C2 H22 EDO sing 160 n n O2 HO2 EDO sing 161 n n # _atom_sites.entry_id 5VD4 _atom_sites.fract_transf_matrix[1][1] 0.019877 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004605 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022841 _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] 0.015826 _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 99J A 1 601 1 99J LIG . C 3 PO4 A 1 602 1 PO4 PO4 . D 3 PO4 A 1 603 2 PO4 PO4 . E 4 EDO A 1 604 1 EDO EDO . F 4 EDO A 1 605 2 EDO EDO . G 4 EDO A 1 606 3 EDO EDO . H 5 CL A 1 607 1 CL CL . I 6 HOH A 1 701 28 HOH HOH . I 6 HOH A 2 702 51 HOH HOH . I 6 HOH A 3 703 5 HOH HOH . I 6 HOH A 4 704 15 HOH HOH . I 6 HOH A 5 705 21 HOH HOH . I 6 HOH A 6 706 43 HOH HOH . I 6 HOH A 7 707 17 HOH HOH . I 6 HOH A 8 708 9 HOH HOH . I 6 HOH A 9 709 1 HOH HOH . I 6 HOH A 10 710 23 HOH HOH . I 6 HOH A 11 711 4 HOH HOH . I 6 HOH A 12 712 18 HOH HOH . I 6 HOH A 13 713 6 HOH HOH . I 6 HOH A 14 714 49 HOH HOH . I 6 HOH A 15 715 39 HOH HOH . I 6 HOH A 16 716 8 HOH HOH . I 6 HOH A 17 717 22 HOH HOH . I 6 HOH A 18 718 45 HOH HOH . I 6 HOH A 19 719 29 HOH HOH . I 6 HOH A 20 720 2 HOH HOH . I 6 HOH A 21 721 31 HOH HOH . I 6 HOH A 22 722 10 HOH HOH . I 6 HOH A 23 723 3 HOH HOH . I 6 HOH A 24 724 52 HOH HOH . I 6 HOH A 25 725 13 HOH HOH . I 6 HOH A 26 726 26 HOH HOH . I 6 HOH A 27 727 44 HOH HOH . I 6 HOH A 28 728 48 HOH HOH . I 6 HOH A 29 729 30 HOH HOH . I 6 HOH A 30 730 32 HOH HOH . I 6 HOH A 31 731 7 HOH HOH . I 6 HOH A 32 732 14 HOH HOH . I 6 HOH A 33 733 25 HOH HOH . I 6 HOH A 34 734 12 HOH HOH . I 6 HOH A 35 735 46 HOH HOH . I 6 HOH A 36 736 24 HOH HOH . I 6 HOH A 37 737 11 HOH HOH . I 6 HOH A 38 738 36 HOH HOH . I 6 HOH A 39 739 16 HOH HOH . I 6 HOH A 40 740 40 HOH HOH . I 6 HOH A 41 741 47 HOH HOH . I 6 HOH A 42 742 34 HOH HOH . I 6 HOH A 43 743 38 HOH HOH . I 6 HOH A 44 744 27 HOH HOH . I 6 HOH A 45 745 50 HOH HOH . I 6 HOH A 46 746 41 HOH HOH . I 6 HOH A 47 747 19 HOH HOH . I 6 HOH A 48 748 42 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 EDO . . . E 4 6.048 11.784 8.971 1 41.21 ? C1 EDO 604 A 1 HETATM 2 O O1 EDO . . . E 4 5.864 10.69 9.876 1 26.39 ? O1 EDO 604 A 1 HETATM 3 C C2 EDO . . . E 4 5.648 11.352 7.564 1 58.09 ? C2 EDO 604 A 1 HETATM 4 O O2 EDO . . . E 4 4.262 11.635 7.339 1 71.17 ? O2 EDO 604 A 1 HETATM 5 H H11 EDO . . . E 4 5.436 12.632 9.286 1 49.46 ? H11 EDO 604 A 1 HETATM 6 H H12 EDO . . . E 4 7.094 12.098 8.978 1 49.46 ? H12 EDO 604 A 1 HETATM 7 H HO1 EDO . . . E 4 6.118 10.964 10.768 1 31.67 ? HO1 EDO 604 A 1 HETATM 8 H H21 EDO . . . E 4 6.256 11.885 6.83 1 69.71 ? H21 EDO 604 A 1 HETATM 9 H H22 EDO . . . E 4 5.829 10.282 7.443 1 69.71 ? H22 EDO 604 A 1 HETATM 10 H HO2 EDO . . . E 4 4.018 11.358 6.445 1 85.4 ? HO2 EDO 604 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #