data_4K7T # _model_server_result.job_id QDLc0DWdrABTopI6HJBrgQ _model_server_result.datetime_utc '2025-02-18 00:35:04' _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 4k7t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":101}' # _entry.id 4K7T # _exptl.entry_id 4K7T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.209 _entity.id 2 _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 120 _cell.entry_id 4K7T _cell.length_a 35.98 _cell.length_b 35.98 _cell.length_c 16.12 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K7T _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 covale ? covale1 A C ILE 1 A ILE 1 1_555 A SG CYS 2 A CYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 sing covale ? covale2 A C ILE 1 A ILE 1 1_555 A N CYS 2 A CYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? covale ? covale3 A C LEU 3 A LEU 3 1_555 A N DGL 4 A DGL 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 sing covale ? covale4 A C DGL 4 A DGL 4 1_555 A N ILE 5 A ILE 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 sing covale ? covale5 A C LYS 6 A LYS 6 1_555 A N ORD 7 A ORD 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 sing covale ? covale6 A NZ LYS 6 A LYS 6 1_555 A C ASN 12 A ASN 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 sing covale ? covale7 A C ORD 7 A ORD 7 1_555 A N ILE 8 A ILE 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 sing covale ? covale8 A C ILE 8 A ILE 8 1_555 A N DPN 9 A DPN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 sing covale ? covale9 A C DPN 9 A DPN 9 1_555 A N HIS 10 A HIS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 sing covale ? covale10 A C HIS 10 A HIS 10 1_555 A N DAS 11 A DAS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 sing covale ? covale11 A C DAS 11 A DAS 11 1_555 A N ASN 12 A ASN 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 sing metalc ? metalc1 A N ILE 1 A ILE 1 1_555 C ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 A N CYS 2 A CYS 2 1_555 C ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc3 A OE1 DGL 4 A DGL 4 1_555 C ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 A O ILE 5 A ILE 5 1_555 D NA NA . A NA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc5 A O ILE 8 A ILE 8 1_555 D NA NA . A NA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc6 A OD2 DAS 11 A DAS 11 1_555 D NA NA . A NA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc7 B O1B GPP . A GPP 101 1_555 C ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc8 B O1A GPP . A GPP 101 1_555 C ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc9 B O2B GPP . A GPP 101 1_555 D NA NA . A NA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc10 B O2A GPP . A GPP 101 1_555 D NA NA . A NA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc11 B O3A GPP . A GPP 101 1_555 D NA NA . A NA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.1 ? metalc ? metalc12 C ZN ZN . A ZN 102 1_555 E O HOH . A HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? # _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 86 n n C1 C2 GPP sing 87 n n C1 H11 GPP sing 88 n n C1 H12 GPP sing 89 n n O1 PA GPP sing 90 n n C2 C3 GPP doub 91 e n C2 H2 GPP sing 92 n n C3 C4 GPP sing 93 n n C3 C5 GPP sing 94 n n C4 H41 GPP sing 95 n n C4 H42 GPP sing 96 n n C4 H43 GPP sing 97 n n C5 C6 GPP sing 98 n n C5 H51 GPP sing 99 n n C5 H52 GPP sing 100 n n C6 C7 GPP sing 101 n n C6 H61 GPP sing 102 n n C6 H62 GPP sing 103 n n C7 C8 GPP doub 104 n n C7 H7 GPP sing 105 n n C8 C9 GPP sing 106 n n C8 C10 GPP sing 107 n n C9 H91 GPP sing 108 n n C9 H92 GPP sing 109 n n C9 H93 GPP sing 110 n n C10 H101 GPP sing 111 n n C10 H102 GPP sing 112 n n C10 H103 GPP sing 113 n n PA O1A GPP doub 114 n n PA O2A GPP sing 115 n n PA O3A GPP sing 116 n n O2A HOA2 GPP sing 117 n n O3A PB GPP sing 118 n n PB O1B GPP doub 119 n n PB O2B GPP sing 120 n n PB O3B GPP sing 121 n n O2B HOB2 GPP sing 122 n n O3B HOB3 GPP sing 123 n n # _atom_sites.entry_id 4K7T _atom_sites.fract_transf_matrix[1][1] 0.027793 _atom_sites.fract_transf_matrix[1][2] 0.016046 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.032093 _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] 0.062035 _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 GPP A 1 101 101 GPP GPP . C 3 ZN A 1 102 102 ZN ZN . D 4 NA A 1 103 103 NA NA . E 5 HOH A 1 201 201 HOH HOH . E 5 HOH A 2 202 202 HOH HOH . E 5 HOH A 3 203 203 HOH HOH . E 5 HOH A 4 204 204 HOH HOH . E 5 HOH A 5 205 205 HOH HOH . E 5 HOH A 6 206 206 HOH HOH . E 5 HOH A 7 207 207 HOH HOH . E 5 HOH A 8 208 208 HOH HOH . E 5 HOH A 9 209 209 HOH HOH . E 5 HOH A 10 210 210 HOH HOH . E 5 HOH A 11 211 211 HOH HOH . E 5 HOH A 12 212 212 HOH HOH . E 5 HOH A 13 213 213 HOH HOH . E 5 HOH A 14 214 214 HOH HOH . E 5 HOH A 15 215 215 HOH HOH . E 5 HOH A 16 216 216 HOH HOH . E 5 HOH A 17 217 217 HOH HOH . E 5 HOH A 18 218 218 HOH HOH . E 5 HOH A 19 219 219 HOH HOH . E 5 HOH A 20 220 220 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 . . . B 2 -0.622 9.818 8.239 1 10.8 ? C1 GPP 101 A 1 HETATM 2 O O1 GPP . . . B 2 -0.563 10.085 9.643 1 8.37 ? O1 GPP 101 A 1 HETATM 3 C C2 GPP . . . B 2 -0.853 8.344 7.962 1 13.62 ? C2 GPP 101 A 1 HETATM 4 C C3 GPP . . . B 2 -0.016 7.561 7.251 1 16.32 ? C3 GPP 101 A 1 HETATM 5 C C4 GPP . . . B 2 1.255 8.096 6.668 1 17.05 ? C4 GPP 101 A 1 HETATM 6 C C5 GPP . . . B 2 -0.34 6.095 7.029 1 19.17 ? C5 GPP 101 A 1 HETATM 7 C C6 GPP . . . B 2 -1.701 5.914 6.349 1 21.84 ? C6 GPP 101 A 1 HETATM 8 C C7 GPP . . . B 2 -1.823 4.561 5.657 1 23.33 ? C7 GPP 101 A 1 HETATM 9 C C8 GPP . . . B 2 -2.982 4.141 5.097 1 23.93 ? C8 GPP 101 A 1 HETATM 10 C C9 GPP . . . B 2 -3.06 2.803 4.42 1 24.39 ? C9 GPP 101 A 1 HETATM 11 C C10 GPP . . . B 2 -4.21 4.998 5.135 1 23.89 ? C10 GPP 101 A 1 HETATM 12 P PA GPP . . . B 2 -0.367 11.588 10.178 1 6.97 ? PA GPP 101 A 1 HETATM 13 O O1A GPP . . . B 2 0.029 11.443 11.616 1 6.54 ? O1A GPP 101 A 1 HETATM 14 O O2A GPP . . . B 2 0.459 12.423 9.236 1 7.13 ? O2A GPP 101 A 1 HETATM 15 O O3A GPP . . . B 2 -1.88 12.155 10.124 1 6.08 ? O3A GPP 101 A 1 HETATM 16 P PB GPP . . . B 2 -2.431 13.596 10.607 1 6.34 ? PB GPP 101 A 1 HETATM 17 O O1B GPP . . . B 2 -1.693 13.921 11.857 1 5.91 ? O1B GPP 101 A 1 HETATM 18 O O2B GPP . . . B 2 -2.175 14.58 9.496 1 5.78 ? O2B GPP 101 A 1 HETATM 19 O O3B GPP . . . B 2 -3.911 13.327 10.846 1 6.48 ? O3B GPP 101 A 1 HETATM 20 H H11 GPP . . . B 2 0.313 10.133 7.771 1 12.96 ? H11 GPP 101 A 1 HETATM 21 H H12 GPP . . . B 2 -1.431 10.402 7.793 1 12.96 ? H12 GPP 101 A 1 HETATM 22 H H2 GPP . . . B 2 -1.75 7.894 8.353 1 16.35 ? H2 GPP 101 A 1 HETATM 23 H H41 GPP . . . B 2 1.84 8.53 7.435 1 20.46 ? H41 GPP 101 A 1 HETATM 24 H H42 GPP . . . B 2 1.027 8.83 5.939 1 20.46 ? H42 GPP 101 A 1 HETATM 25 H H43 GPP . . . B 2 1.795 7.305 6.216 1 20.46 ? H43 GPP 101 A 1 HETATM 26 H H51 GPP . . . B 2 -0.344 5.576 7.99 1 23.01 ? H51 GPP 101 A 1 HETATM 27 H H52 GPP . . . B 2 0.437 5.643 6.409 1 23.01 ? H52 GPP 101 A 1 HETATM 28 H H61 GPP . . . B 2 -1.844 6.708 5.612 1 26.2 ? H61 GPP 101 A 1 HETATM 29 H H62 GPP . . . B 2 -2.492 6.009 7.096 1 26.2 ? H62 GPP 101 A 1 HETATM 30 H H7 GPP . . . B 2 -0.958 3.92 5.61 1 27.99 ? H7 GPP 101 A 1 HETATM 31 H H91 GPP . . . B 2 -4.042 2.649 4.056 1 29.27 ? H91 GPP 101 A 1 HETATM 32 H H92 GPP . . . B 2 -2.817 2.041 5.114 1 29.27 ? H92 GPP 101 A 1 HETATM 33 H H93 GPP . . . B 2 -2.376 2.775 3.612 1 29.27 ? H93 GPP 101 A 1 HETATM 34 H H101 GPP . . . B 2 -3.993 5.945 4.714 1 28.66 ? H101 GPP 101 A 1 HETATM 35 H H102 GPP . . . B 2 -4.523 5.122 6.139 1 28.66 ? H102 GPP 101 A 1 HETATM 36 H H103 GPP . . . B 2 -4.982 4.533 4.579 1 28.66 ? H103 GPP 101 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #