data_8DRD # _model_server_result.job_id owRlSr9r6R2m4n0-i2l3ow _model_server_result.datetime_utc '2024-11-15 09:56:21' _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 8drd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 8DRD # _exptl.entry_id 8DRD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _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 8DRD _cell.length_a 42.09 _cell.length_b 55.43 _cell.length_c 101.97 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DRD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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,I _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 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 disulf ? disulf1 A SG CYS 96 A CYS 96 1_555 B SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? covale ? covale1 A SG CYS 98 A CYS 98 1_555 C CAB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.768 ? covale ? covale2 A SG CYS 101 A CYS 101 1_555 C CAC HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.773 ? covale ? covale3 B SG CYS 98 B CYS 98 1_555 F CAB HEC . B HEC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.773 ? covale ? covale4 B SG CYS 101 B CYS 101 1_555 F CAC HEC . B HEC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? metalc ? metalc1 A SD MET 7 A MET 7 1_555 C FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc2 A NE2 HIS 60 A HIS 60 1_555 D NI NI . A NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc3 A NE2 HIS 102 A HIS 102 1_555 C FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc4 A NE2 HIS 104 A HIS 104 1_555 D NI NI . A NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc5 D NI NI . A NI 202 1_555 H O HOH . A HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc6 D NI NI . A NI 202 1_555 B NE2 HIS 100 B HIS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc7 D NI NI . A NI 202 1_555 B NE2 HIS 104 B HIS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc8 D NI NI . A NI 202 1_555 I O HOH . B HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc9 B OD2 ASP 2 B ASP 2 1_555 G NI NI . B NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc10 B SD MET 7 B MET 7 1_555 F FE HEC . B HEC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc11 B NE2 HIS 102 B HIS 102 1_555 F FE HEC . B HEC 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _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 C2 MPD sing 321 n n C1 H11 MPD sing 322 n n C1 H12 MPD sing 323 n n C1 H13 MPD sing 324 n n C2 O2 MPD sing 325 n n C2 CM MPD sing 326 n n C2 C3 MPD sing 327 n n O2 HO2 MPD sing 328 n n CM HM1 MPD sing 329 n n CM HM2 MPD sing 330 n n CM HM3 MPD sing 331 n n C3 C4 MPD sing 332 n n C3 H31 MPD sing 333 n n C3 H32 MPD sing 334 n n C4 O4 MPD sing 335 n n C4 C5 MPD sing 336 n n C4 H4 MPD sing 337 n n O4 HO4 MPD sing 338 n n C5 H51 MPD sing 339 n n C5 H52 MPD sing 340 n n C5 H53 MPD sing 341 n n # _atom_sites.entry_id 8DRD _atom_sites.fract_transf_matrix[1][1] 0.023759 _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] 0.018041 _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] 0.009807 _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 HEC A 1 201 150 HEC HEM . D 3 NI A 1 202 1 NI NI . E 4 MPD B 1 201 201 MPD MPD . F 2 HEC B 1 202 150 HEC HEM . G 3 NI B 1 203 2 NI NI . H 5 HOH A 1 301 32 HOH HOH . H 5 HOH A 2 302 11 HOH HOH . H 5 HOH A 3 303 12 HOH HOH . H 5 HOH A 4 304 60 HOH HOH . H 5 HOH A 5 305 54 HOH HOH . H 5 HOH A 6 306 41 HOH HOH . H 5 HOH A 7 307 16 HOH HOH . H 5 HOH A 8 308 38 HOH HOH . H 5 HOH A 9 309 51 HOH HOH . H 5 HOH A 10 310 30 HOH HOH . H 5 HOH A 11 311 56 HOH HOH . H 5 HOH A 12 312 17 HOH HOH . H 5 HOH A 13 313 14 HOH HOH . H 5 HOH A 14 314 39 HOH HOH . H 5 HOH A 15 315 42 HOH HOH . H 5 HOH A 16 316 59 HOH HOH . H 5 HOH A 17 317 47 HOH HOH . H 5 HOH A 18 318 3 HOH HOH . H 5 HOH A 19 319 22 HOH HOH . H 5 HOH A 20 320 18 HOH HOH . H 5 HOH A 21 321 44 HOH HOH . H 5 HOH A 22 322 65 HOH HOH . H 5 HOH A 23 323 23 HOH HOH . H 5 HOH A 24 324 71 HOH HOH . H 5 HOH A 25 325 72 HOH HOH . H 5 HOH A 26 326 34 HOH HOH . H 5 HOH A 27 327 63 HOH HOH . H 5 HOH A 28 328 28 HOH HOH . H 5 HOH A 29 329 76 HOH HOH . H 5 HOH A 30 330 50 HOH HOH . H 5 HOH A 31 331 9 HOH HOH . H 5 HOH A 32 332 45 HOH HOH . H 5 HOH A 33 333 25 HOH HOH . H 5 HOH A 34 334 5 HOH HOH . H 5 HOH A 35 335 24 HOH HOH . H 5 HOH A 36 336 4 HOH HOH . H 5 HOH A 37 337 2 HOH HOH . H 5 HOH A 38 338 57 HOH HOH . H 5 HOH A 39 339 20 HOH HOH . H 5 HOH A 40 340 13 HOH HOH . H 5 HOH A 41 341 79 HOH HOH . H 5 HOH A 42 342 37 HOH HOH . H 5 HOH A 43 343 33 HOH HOH . H 5 HOH A 44 344 46 HOH HOH . H 5 HOH A 45 345 70 HOH HOH . H 5 HOH A 46 346 43 HOH HOH . H 5 HOH A 47 347 35 HOH HOH . H 5 HOH A 48 348 61 HOH HOH . H 5 HOH A 49 349 1 HOH HOH . H 5 HOH A 50 350 36 HOH HOH . I 5 HOH B 1 301 66 HOH HOH . I 5 HOH B 2 302 55 HOH HOH . I 5 HOH B 3 303 10 HOH HOH . I 5 HOH B 4 304 48 HOH HOH . I 5 HOH B 5 305 29 HOH HOH . I 5 HOH B 6 306 31 HOH HOH . I 5 HOH B 7 307 75 HOH HOH . I 5 HOH B 8 308 68 HOH HOH . I 5 HOH B 9 309 67 HOH HOH . I 5 HOH B 10 310 15 HOH HOH . I 5 HOH B 11 311 6 HOH HOH . I 5 HOH B 12 312 74 HOH HOH . I 5 HOH B 13 313 27 HOH HOH . I 5 HOH B 14 314 73 HOH HOH . I 5 HOH B 15 315 58 HOH HOH . I 5 HOH B 16 316 49 HOH HOH . I 5 HOH B 17 317 19 HOH HOH . I 5 HOH B 18 318 40 HOH HOH . I 5 HOH B 19 319 7 HOH HOH . I 5 HOH B 20 320 21 HOH HOH . I 5 HOH B 21 321 52 HOH HOH . I 5 HOH B 22 322 78 HOH HOH . I 5 HOH B 23 323 77 HOH HOH . I 5 HOH B 24 324 8 HOH HOH . I 5 HOH B 25 325 69 HOH HOH . I 5 HOH B 26 326 53 HOH HOH . I 5 HOH B 27 327 26 HOH HOH . I 5 HOH B 28 328 62 HOH HOH . I 5 HOH B 29 329 64 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 MPD . . . E 4 1.648 -6.17 -11.556 1 10.64 ? C1 MPD 201 B 1 HETATM 2 C C2 MPD . . . E 4 1.498 -5.764 -10.112 1 18.05 ? C2 MPD 201 B 1 HETATM 3 O O2 MPD . . . E 4 2.766 -6.073 -9.454 1 22.87 ? O2 MPD 201 B 1 HETATM 4 C CM MPD . . . E 4 0.375 -6.574 -9.47 1 14.38 ? CM MPD 201 B 1 HETATM 5 C C3 MPD . . . E 4 1.168 -4.282 -10.002 1 16.51 ? C3 MPD 201 B 1 HETATM 6 C C4 MPD . . . E 4 2.317 -3.347 -10.364 1 17.2 ? C4 MPD 201 B 1 HETATM 7 O O4 MPD . . . E 4 2.658 -3.419 -11.727 1 17 ? O4 MPD 201 B 1 HETATM 8 C C5 MPD . . . E 4 1.895 -1.908 -10.129 1 14.56 ? C5 MPD 201 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 66 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 636 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 8 #