data_4DZW # _model_server_result.job_id gwjfsmDhKjdIDaQzi22l0g _model_server_result.datetime_utc '2024-10-20 22:29:01' _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 4dzw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 4DZW # _exptl.entry_id 4DZW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 246.092 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-METHYLBUT-3-ENYL TRIHYDROGEN 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 4DZW _cell.length_a 57.975 _cell.length_b 57.975 _cell.length_c 395.026 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DZW _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 10_444 -y-1,-x-1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -28.9875 -50.207823 -65.837667 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 FME 1 A FME 1 1_555 A N ALA 2 A ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 A OD2 ASP 102 A ASP 102 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc2 A OD2 ASP 250 A ASP 250 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc3 B O5 0MQ . A 0MQ 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc4 B O6 0MQ . A 0MQ 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc5 B O2 0MQ . A 0MQ 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? # _chem_comp.formula 'C5 H12 O7 P2' _chem_comp.formula_weight 246.092 _chem_comp.id IPE _chem_comp.mon_nstd_flag . _chem_comp.name '3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ISOPENTENYL PYROPHOSPHATE' # 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 IPE sing 230 n n C1 C2 IPE sing 231 n n C1 H11 IPE sing 232 n n C1 H12 IPE sing 233 n n O1 PA IPE sing 234 n n C2 C3 IPE sing 235 n n C2 H21 IPE sing 236 n n C2 H22 IPE sing 237 n n C3 C4 IPE doub 238 n n C3 C5 IPE sing 239 n n C4 H41 IPE sing 240 n n C4 H42 IPE sing 241 n n C5 H51 IPE sing 242 n n C5 H52 IPE sing 243 n n C5 H53 IPE sing 244 n n PA O1A IPE doub 245 n n PA O2A IPE sing 246 n n PA O3A IPE sing 247 n n O2A H2A IPE sing 248 n n O3A PB IPE sing 249 n n PB O1B IPE sing 250 n n PB O2B IPE doub 251 n n PB O3B IPE sing 252 n n O1B H1B IPE sing 253 n n O3B H3B IPE sing 254 n n # _atom_sites.entry_id 4DZW _atom_sites.fract_transf_matrix[1][1] 0.017249 _atom_sites.fract_transf_matrix[1][2] 0.009959 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019917 _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] 0.002531 _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 0MQ A 1 401 500 0MQ 0MQ . C 3 MG A 1 402 401 MG MG . D 3 MG A 1 403 402 MG MG . E 4 IPE A 1 404 501 IPE IPR . F 5 SO4 A 1 405 1 SO4 SO4 . G 5 SO4 A 1 406 2 SO4 SO4 . H 6 HOH A 1 501 1 HOH HOH . H 6 HOH A 2 502 4 HOH HOH . H 6 HOH A 3 503 6 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 IPE . . . E 4 -8.717 -11.925 -20.052 0.6 48.45 ? C1 IPE 404 A 1 HETATM 2 O O1 IPE . . . E 4 -8.262 -12.203 -21.378 0.6 49.2 ? O1 IPE 404 A 1 HETATM 3 C C2 IPE . . . E 4 -10.172 -12.362 -19.914 0.6 48.47 ? C2 IPE 404 A 1 HETATM 4 C C3 IPE . . . E 4 -10.32 -13.86 -19.739 0.6 48.63 ? C3 IPE 404 A 1 HETATM 5 C C4 IPE . . . E 4 -10.16 -14.676 -20.76 0.6 48.84 ? C4 IPE 404 A 1 HETATM 6 C C5 IPE . . . E 4 -10.672 -14.449 -18.405 0.6 49.2 ? C5 IPE 404 A 1 HETATM 7 P PA IPE . . . E 4 -7.114 -11.336 -22.121 0.6 49.47 ? PA IPE 404 A 1 HETATM 8 O O1A IPE . . . E 4 -6.621 -12.108 -23.32 0.6 49.19 ? O1A IPE 404 A 1 HETATM 9 O O2A IPE . . . E 4 -7.658 -9.944 -22.344 0.6 49.81 ? O2A IPE 404 A 1 HETATM 10 O O3A IPE . . . E 4 -5.9 -11.273 -21.061 0.6 49.02 ? O3A IPE 404 A 1 HETATM 11 P PB IPE . . . E 4 -4.502 -10.612 -21.502 0.6 49.12 ? PB IPE 404 A 1 HETATM 12 O O1B IPE . . . E 4 -4.917 -9.27 -22.037 0.6 49 ? O1B IPE 404 A 1 HETATM 13 O O2B IPE . . . E 4 -3.943 -11.564 -22.534 0.6 49.36 ? O2B IPE 404 A 1 HETATM 14 O O3B IPE . . . E 4 -3.7 -10.537 -20.228 0.6 49.43 ? O3B IPE 404 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #