data_4RKZ # _model_server_result.job_id YvJdFnkGsZlnJ3J57a34yA _model_server_result.datetime_utc '2024-11-14 17:36:01' _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 4rkz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 4RKZ # _exptl.entry_id 4RKZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.137 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3R)-5-hydroxy-3-methyl-3-(phosphonooxy)pentanoic acid' _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 122.95 _cell.angle_gamma 90 _cell.entry_id 4RKZ _cell.length_a 146.37 _cell.length_b 61.06 _cell.length_c 103.55 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RKZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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,E,J 1 1 B,F,G,H,I,K 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 ? 3 D N N ? 3 F N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 62 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 43 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 62 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 43 _struct_conn.ptnr2_symmetry 1_555 _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 2.036 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C6 H13 O7 P' _chem_comp.formula_weight 228.137 _chem_comp.id 3S4 _chem_comp.mon_nstd_flag . _chem_comp.name '(3R)-5-hydroxy-3-methyl-3-(phosphonooxy)pentanoic acid' _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 C C1 3S4 sing 1 n n C H 3S4 sing 2 n n C HA 3S4 sing 3 n n C HB 3S4 sing 4 n n O C3 3S4 sing 5 n n O HO 3S4 sing 6 n n O4 P 3S4 doub 7 n n O5 P 3S4 sing 8 n n O6 P 3S4 sing 9 n n P O3 3S4 sing 10 n n C2 C1 3S4 sing 11 n n O3 C1 3S4 sing 12 n n C1 C4 3S4 sing 13 n n C5 O1 3S4 sing 14 n n O1 HO1 3S4 sing 15 n n C3 C2 3S4 sing 16 n n C2 H2 3S4 sing 17 n n C2 H2A 3S4 sing 18 n n O2 C5 3S4 doub 19 n n C3 H3 3S4 sing 20 n n C3 H3A 3S4 sing 21 n n C4 C5 3S4 sing 22 n n C4 H4 3S4 sing 23 n n C4 H4A 3S4 sing 24 n n O5 HO5 3S4 sing 25 n n O6 HO6 3S4 sing 26 n n # _atom_sites.entry_id 4RKZ _atom_sites.fract_transf_matrix[1][1] 0.006832 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004428 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016377 _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] 0.011508 _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 ADP A 1 401 1 ADP ADP . D 3 3S4 A 1 402 1 3S4 M3P . E 4 SO4 A 1 403 4 SO4 SO4 . F 3 3S4 B 1 401 2 3S4 M3P . G 4 SO4 B 1 402 1 SO4 SO4 . H 4 SO4 B 1 403 2 SO4 SO4 . I 4 SO4 B 1 404 3 SO4 SO4 . J 5 HOH A 1 501 1 HOH HOH . J 5 HOH A 2 502 2 HOH HOH . J 5 HOH A 3 503 5 HOH HOH . J 5 HOH A 4 504 13 HOH HOH . J 5 HOH A 5 505 14 HOH HOH . J 5 HOH A 6 506 16 HOH HOH . J 5 HOH A 7 507 17 HOH HOH . J 5 HOH A 8 508 18 HOH HOH . J 5 HOH A 9 509 20 HOH HOH . J 5 HOH A 10 510 23 HOH HOH . J 5 HOH A 11 511 26 HOH HOH . J 5 HOH A 12 512 27 HOH HOH . J 5 HOH A 13 513 28 HOH HOH . J 5 HOH A 14 514 29 HOH HOH . J 5 HOH A 15 515 31 HOH HOH . J 5 HOH A 16 516 32 HOH HOH . J 5 HOH A 17 517 33 HOH HOH . J 5 HOH A 18 518 34 HOH HOH . J 5 HOH A 19 519 35 HOH HOH . J 5 HOH A 20 520 37 HOH HOH . J 5 HOH A 21 521 43 HOH HOH . J 5 HOH A 22 522 44 HOH HOH . J 5 HOH A 23 523 48 HOH HOH . J 5 HOH A 24 524 50 HOH HOH . J 5 HOH A 25 525 51 HOH HOH . K 5 HOH B 1 501 3 HOH HOH . K 5 HOH B 2 502 4 HOH HOH . K 5 HOH B 3 503 6 HOH HOH . K 5 HOH B 4 504 7 HOH HOH . K 5 HOH B 5 505 8 HOH HOH . K 5 HOH B 6 506 11 HOH HOH . K 5 HOH B 7 507 12 HOH HOH . K 5 HOH B 8 508 25 HOH HOH . K 5 HOH B 9 509 38 HOH HOH . K 5 HOH B 10 510 39 HOH HOH . K 5 HOH B 11 511 40 HOH HOH . K 5 HOH B 12 512 42 HOH HOH . K 5 HOH B 13 513 49 HOH HOH . K 5 HOH B 14 514 55 HOH HOH . K 5 HOH B 15 515 56 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 C 3S4 . . . F 3 12.512 2.425 34.717 1 78.86 ? C 3S4 401 B 1 HETATM 2 O O 3S4 . . . F 3 12.246 5.566 32.47 1 84.23 ? O 3S4 401 B 1 HETATM 3 P P 3S4 . . . F 3 15.397 3.077 33.146 1 99.58 ? P 3S4 401 B 1 HETATM 4 C C1 3S4 . . . F 3 13.649 3.367 35.056 1 81.02 ? C1 3S4 401 B 1 HETATM 5 O O1 3S4 . . . F 3 14.112 5.801 37.37 1 61.42 ? O1 3S4 401 B 1 HETATM 6 C C2 3S4 . . . F 3 13.413 4.7 34.378 1 75.79 ? C2 3S4 401 B 1 HETATM 7 O O2 3S4 . . . F 3 15.819 4.712 36.552 1 71.88 ? O2 3S4 401 B 1 HETATM 8 C C3 3S4 . . . F 3 12.185 4.598 33.497 1 83.18 ? C3 3S4 401 B 1 HETATM 9 O O3 3S4 . . . F 3 14.872 2.818 34.621 1 80.78 ? O3 3S4 401 B 1 HETATM 10 C C4 3S4 . . . F 3 13.703 3.575 36.557 1 70.84 ? C4 3S4 401 B 1 HETATM 11 O O4 3S4 . . . F 3 14.357 3.527 32.189 1 88.81 ? O4 3S4 401 B 1 HETATM 12 C C5 3S4 . . . F 3 14.594 4.762 36.846 1 65.76 ? C5 3S4 401 B 1 HETATM 13 O O5 3S4 . . . F 3 15.994 1.883 32.501 1 83.59 ? O5 3S4 401 B 1 HETATM 14 O O6 3S4 . . . F 3 16.452 4.116 33.057 1 91.06 ? O6 3S4 401 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #