data_2GZL # _model_server_result.job_id 9kKoKkNrBFBkW0VR-PcazQ _model_server_result.datetime_utc '2024-11-08 01:47:06' _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 2gzl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":903}' # _entry.id 2GZL # _exptl.entry_id 2GZL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.209 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYL DIPHOSPHATE' _entity.pdbx_number_of_molecules 1 _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 2GZL _cell.length_a 145.098 _cell.length_b 145.098 _cell.length_c 145.098 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GZL _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD2 ASP 10 A ASP 8 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A NE2 HIS 12 A HIS 10 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc3 A ND1 HIS 44 A HIS 42 1_555 B ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc4 B ZN ZN . A ZN 900 1_555 C O1' 2AA . A 2AA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? # _chem_comp.formula 'C10 H20 O7 P2' _chem_comp.formula_weight 314.209 _chem_comp.id GPP _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYL DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 GPP sing 207 n n C1 C2 GPP sing 208 n n C1 H11 GPP sing 209 n n C1 H12 GPP sing 210 n n O1 PA GPP sing 211 n n C2 C3 GPP doub 212 e n C2 H2 GPP sing 213 n n C3 C4 GPP sing 214 n n C3 C5 GPP sing 215 n n C4 H41 GPP sing 216 n n C4 H42 GPP sing 217 n n C4 H43 GPP sing 218 n n C5 C6 GPP sing 219 n n C5 H51 GPP sing 220 n n C5 H52 GPP sing 221 n n C6 C7 GPP sing 222 n n C6 H61 GPP sing 223 n n C6 H62 GPP sing 224 n n C7 C8 GPP doub 225 n n C7 H7 GPP sing 226 n n C8 C9 GPP sing 227 n n C8 C10 GPP sing 228 n n C9 H91 GPP sing 229 n n C9 H92 GPP sing 230 n n C9 H93 GPP sing 231 n n C10 H101 GPP sing 232 n n C10 H102 GPP sing 233 n n C10 H103 GPP sing 234 n n PA O1A GPP doub 235 n n PA O2A GPP sing 236 n n PA O3A GPP sing 237 n n O2A HOA2 GPP sing 238 n n O3A PB GPP sing 239 n n PB O1B GPP doub 240 n n PB O2B GPP sing 241 n n PB O3B GPP sing 242 n n O2B HOB2 GPP sing 243 n n O3B HOB3 GPP sing 244 n n # _atom_sites.entry_id 2GZL _atom_sites.fract_transf_matrix[1][1] 0.006892 _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] 0.006892 _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] 0.006892 _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 ZN A 1 900 900 ZN ZN . C 3 2AA A 1 901 901 2AA 2AA . D 4 GPP A 1 903 903 GPP GPP . E 5 HOH A 1 904 1 HOH HOH . E 5 HOH A 2 905 2 HOH HOH . E 5 HOH A 3 906 4 HOH HOH . E 5 HOH A 4 907 5 HOH HOH . E 5 HOH A 5 908 6 HOH HOH . E 5 HOH A 6 909 7 HOH HOH . E 5 HOH A 7 910 8 HOH HOH . E 5 HOH A 8 911 9 HOH HOH . E 5 HOH A 9 912 10 HOH HOH . E 5 HOH A 10 913 11 HOH HOH . E 5 HOH A 11 914 12 HOH HOH . E 5 HOH A 12 915 13 HOH HOH . E 5 HOH A 13 916 14 HOH HOH . E 5 HOH A 14 917 15 HOH HOH . E 5 HOH A 15 918 16 HOH HOH . E 5 HOH A 16 919 17 HOH HOH . E 5 HOH A 17 920 18 HOH HOH . E 5 HOH A 18 921 19 HOH HOH . E 5 HOH A 19 922 20 HOH HOH . E 5 HOH A 20 923 21 HOH HOH . E 5 HOH A 21 924 22 HOH HOH . E 5 HOH A 22 925 23 HOH HOH . E 5 HOH A 23 926 24 HOH HOH . E 5 HOH A 24 927 25 HOH HOH . E 5 HOH A 25 928 26 HOH HOH . E 5 HOH A 26 929 27 HOH HOH . E 5 HOH A 27 930 28 HOH HOH . E 5 HOH A 28 931 29 HOH HOH . E 5 HOH A 29 932 30 HOH HOH . E 5 HOH A 30 933 31 HOH HOH . E 5 HOH A 31 934 32 HOH HOH . E 5 HOH A 32 935 33 HOH HOH . E 5 HOH A 33 936 34 HOH HOH . E 5 HOH A 34 937 35 HOH HOH . E 5 HOH A 35 938 36 HOH HOH . E 5 HOH A 36 939 37 HOH HOH . E 5 HOH A 37 940 38 HOH HOH . E 5 HOH A 38 941 39 HOH HOH . E 5 HOH A 39 942 40 HOH HOH . E 5 HOH A 40 943 41 HOH HOH . E 5 HOH A 41 944 43 HOH HOH . E 5 HOH A 42 945 44 HOH HOH . E 5 HOH A 43 946 45 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 GPP . . . D 4 11.697 14.225 12.769 0.33 57.46 ? C1 GPP 903 A 1 HETATM 2 O O1 GPP . . . D 4 11.327 12.909 12.663 0.33 58.21 ? O1 GPP 903 A 1 HETATM 3 C C2 GPP . . . D 4 12.779 14.667 13.529 0.33 56.5 ? C2 GPP 903 A 1 HETATM 4 C C3 GPP . . . D 4 13.081 16.023 13.587 0.33 55.98 ? C3 GPP 903 A 1 HETATM 5 C C4 GPP . . . D 4 12.227 17.045 12.836 0.33 56.29 ? C4 GPP 903 A 1 HETATM 6 C C5 GPP . . . D 4 14.267 16.508 14.407 0.33 55.23 ? C5 GPP 903 A 1 HETATM 7 C C6 GPP . . . D 4 13.864 16.711 15.868 0.33 54.94 ? C6 GPP 903 A 1 HETATM 8 C C7 GPP . . . D 4 14.688 15.975 16.713 0.33 54.53 ? C7 GPP 903 A 1 HETATM 9 C C8 GPP . . . D 4 15.913 16.357 17.265 0.33 54.28 ? C8 GPP 903 A 1 HETATM 10 C C9 GPP . . . D 4 16.653 15.382 18.178 0.33 54.2 ? C9 GPP 903 A 1 HETATM 11 C C10 GPP . . . D 4 16.539 17.73 16.986 0.33 54.01 ? C10 GPP 903 A 1 HETATM 12 P PA GPP . . . D 4 12.558 11.893 12.308 0.33 58.76 ? PA GPP 903 A 1 HETATM 13 O O1A GPP . . . D 4 13.262 12.352 11.083 0.33 58.48 ? O1A GPP 903 A 1 HETATM 14 O O2A GPP . . . D 4 13.328 11.671 13.556 0.33 58.15 ? O2A GPP 903 A 1 HETATM 15 O O3A GPP . . . D 4 11.77 10.515 11.956 0.33 55.53 ? O3A GPP 903 A 1 HETATM 16 P PB GPP . . . D 4 10.686 10.368 10.755 0.33 52.68 ? PB GPP 903 A 1 HETATM 17 O O1B GPP . . . D 4 9.287 10.321 11.225 0.33 52.61 ? O1B GPP 903 A 1 HETATM 18 O O2B GPP . . . D 4 10.962 11.498 9.658 0.33 52.69 ? O2B GPP 903 A 1 HETATM 19 O O3B GPP . . . D 4 11.147 9.02 10.014 0.33 52.72 ? O3B GPP 903 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 19 #