data_5Z44 # _model_server_result.job_id nxlbIq31IoqBb56oUPeohg _model_server_result.datetime_utc '2024-11-25 04:29:25' _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 5z44 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 5Z44 # _exptl.entry_id 5Z44 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 330.275 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYL S-THIOLODIPHOSPHATE' _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 90 _cell.entry_id 5Z44 _cell.length_a 115.717 _cell.length_b 115.717 _cell.length_c 48.431 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z44 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,G 1 1 B,E,F,H 2 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 ? 2 C N N ? 2 E 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 covale ? covale1 B NZ LYS 278 B LYS 278 1_555 E O3A GST . B GST 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? metalc ? metalc1 A OD1 ASN 41 A ASN 41 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc2 A OE2 GLU 63 A GLU 63 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc3 B OE1 GLU 63 B GLU 63 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc4 B OD1 ASP 65 B ASP 65 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? # _chem_comp.formula 'C10 H20 O6 P2 S' _chem_comp.formula_weight 330.275 _chem_comp.id GST _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYL S-THIOLODIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE' # 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 PA O1A GST sing 129 n n PA O2A GST doub 130 n n PA O3A GST sing 131 n n PA O1B GST sing 132 n n O1A H1A GST sing 133 n n O3A H3A GST sing 134 n n O1B PB GST sing 135 n n PB O2B GST doub 136 n n PB O3B GST sing 137 n n PB S1 GST sing 138 n n O3B H3B GST sing 139 n n S1 C1 GST sing 140 n n C1 C2 GST sing 141 n n C1 H11 GST sing 142 n n C1 H12 GST sing 143 n n C2 C3 GST doub 144 e n C2 H2 GST sing 145 n n C3 C10 GST sing 146 n n C3 C4 GST sing 147 n n C10 H101 GST sing 148 n n C10 H102 GST sing 149 n n C10 H103 GST sing 150 n n C4 C5 GST sing 151 n n C4 H41 GST sing 152 n n C4 H42 GST sing 153 n n C5 C6 GST sing 154 n n C5 H51 GST sing 155 n n C5 H52 GST sing 156 n n C6 C7 GST doub 157 n n C6 H6 GST sing 158 n n C7 C9 GST sing 159 n n C7 C8 GST sing 160 n n C9 H91 GST sing 161 n n C9 H92 GST sing 162 n n C9 H93 GST sing 163 n n C8 H81 GST sing 164 n n C8 H82 GST sing 165 n n C8 H83 GST sing 166 n n # _atom_sites.entry_id 5Z44 _atom_sites.fract_transf_matrix[1][1] 0.008642 _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] 0.008642 _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] 0.020648 _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 C 2 GST A 1 401 1 GST GST . D 3 MG A 1 402 2 MG MG . E 2 GST B 1 401 2 GST GST . F 3 MG B 1 402 1 MG MG . G 4 HOH A 1 501 39 HOH HOH . G 4 HOH A 2 502 19 HOH HOH . G 4 HOH A 3 503 7 HOH HOH . G 4 HOH A 4 504 24 HOH HOH . G 4 HOH A 5 505 10 HOH HOH . G 4 HOH A 6 506 44 HOH HOH . G 4 HOH A 7 507 45 HOH HOH . G 4 HOH A 8 508 3 HOH HOH . G 4 HOH A 9 509 34 HOH HOH . G 4 HOH A 10 510 4 HOH HOH . G 4 HOH A 11 511 40 HOH HOH . G 4 HOH A 12 512 18 HOH HOH . G 4 HOH A 13 513 26 HOH HOH . G 4 HOH A 14 514 36 HOH HOH . G 4 HOH A 15 515 28 HOH HOH . G 4 HOH A 16 516 43 HOH HOH . H 4 HOH B 1 501 47 HOH HOH . H 4 HOH B 2 502 32 HOH HOH . H 4 HOH B 3 503 13 HOH HOH . H 4 HOH B 4 504 1 HOH HOH . H 4 HOH B 5 505 12 HOH HOH . H 4 HOH B 6 506 9 HOH HOH . H 4 HOH B 7 507 21 HOH HOH . H 4 HOH B 8 508 20 HOH HOH . H 4 HOH B 9 509 33 HOH HOH . H 4 HOH B 10 510 23 HOH HOH . H 4 HOH B 11 511 48 HOH HOH . H 4 HOH B 12 512 17 HOH HOH . H 4 HOH B 13 513 16 HOH HOH . H 4 HOH B 14 514 6 HOH HOH . H 4 HOH B 15 515 42 HOH HOH . H 4 HOH B 16 516 15 HOH HOH . H 4 HOH B 17 517 37 HOH HOH . H 4 HOH B 18 518 38 HOH HOH . H 4 HOH B 19 519 2 HOH HOH . H 4 HOH B 20 520 30 HOH HOH . H 4 HOH B 21 521 31 HOH HOH . H 4 HOH B 22 522 27 HOH HOH . H 4 HOH B 23 523 46 HOH HOH . H 4 HOH B 24 524 25 HOH HOH . H 4 HOH B 25 525 35 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 P PA GST . . . E 2 -7.615 -28.169 -22.117 1 58.97 ? PA GST 401 B 1 HETATM 2 O O1A GST . . . E 2 -8.63 -29.164 -22.611 1 74.27 ? O1A GST 401 B 1 HETATM 3 O O2A GST . . . E 2 -7.397 -27.035 -23.065 1 58.03 ? O2A GST 401 B 1 HETATM 4 O O3A GST . . . E 2 -7.808 -27.82 -20.649 1 65.55 ? O3A GST 401 B 1 HETATM 5 O O1B GST . . . E 2 -6.227 -28.977 -22.196 1 72.5 ? O1B GST 401 B 1 HETATM 6 P PB GST . . . E 2 -4.905 -28.54 -21.382 1 71.19 ? PB GST 401 B 1 HETATM 7 O O2B GST . . . E 2 -4.406 -27.282 -21.972 1 74.94 ? O2B GST 401 B 1 HETATM 8 O O3B GST . . . E 2 -5.23 -28.376 -19.818 1 61.98 ? O3B GST 401 B 1 HETATM 9 S S1 GST . . . E 2 -3.441 -29.935 -21.613 1 84.11 ? S1 GST 401 B 1 HETATM 10 C C1 GST . . . E 2 -2.367 -29.707 -20.217 1 86.7 ? C1 GST 401 B 1 HETATM 11 C C2 GST . . . E 2 -1.154 -30.624 -20.307 1 86.03 ? C2 GST 401 B 1 HETATM 12 C C3 GST . . . E 2 -0.769 -31.467 -19.328 1 84.66 ? C3 GST 401 B 1 HETATM 13 C C10 GST . . . E 2 -1.564 -31.559 -18.059 1 79.69 ? C10 GST 401 B 1 HETATM 14 C C4 GST . . . E 2 0.47 -32.33 -19.509 1 92.53 ? C4 GST 401 B 1 HETATM 15 C C5 GST . . . E 2 1.539 -31.947 -18.47 1 98.54 ? C5 GST 401 B 1 HETATM 16 C C6 GST . . . E 2 2.919 -31.665 -19.054 1 96.73 ? C6 GST 401 B 1 HETATM 17 C C7 GST . . . E 2 3.602 -30.525 -18.788 1 90.76 ? C7 GST 401 B 1 HETATM 18 C C9 GST . . . E 2 3.013 -29.47 -17.893 1 85.82 ? C9 GST 401 B 1 HETATM 19 C C8 GST . . . E 2 4.963 -30.3 -19.385 1 86.85 ? C8 GST 401 B 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #