data_8IKT # _model_server_result.job_id CP0rxIdWuJaiLH6H3IFpFg _model_server_result.datetime_utc '2025-01-03 01:27:08' _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 8ikt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":508}' # _entry.id 8IKT # _exptl.entry_id 8IKT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 6 _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 120 _cell.entry_id 8IKT _cell.length_a 82.764 _cell.length_b 82.764 _cell.length_c 103.494 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8IKT _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,J,K,L,M,N,O,P _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 6 _struct_asym.id K _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 SG CYS 272 A CYS 347 1_555 L CA 3CN . B 3CN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.66 ? covale ? covale2 B C GLU 64 B GLU 64 1_555 B N SEP 65 B SEP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale3 B C SEP 65 B SEP 65 1_555 B N THR 66 B THR 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 B C GLY 75 B GLY 75 1_555 L ND 3CN . B 3CN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale5 C C GLN 64 C GLN 64 1_555 C N SEP 65 C SEP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale6 C C SEP 65 C SEP 65 1_555 C N ILE 66 C ILE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? metalc ? metalc1 A SG CYS 75 A CYS 150 1_555 I ZN ZN . A ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc2 A SG CYS 79 A CYS 154 1_555 I ZN ZN . A ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc3 A SG CYS 91 A CYS 166 1_555 F ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc4 A SG CYS 94 A CYS 169 1_555 F ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc5 A SG CYS 121 A CYS 196 1_555 F ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc6 A SG CYS 126 A CYS 201 1_555 F ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc7 A SG CYS 137 A CYS 212 1_555 I ZN ZN . A ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc8 A NE2 HIS 140 A HIS 215 1_555 I ZN ZN . A ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc9 A SG CYS 163 A CYS 238 1_555 G ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc10 A SG CYS 166 A CYS 241 1_555 G ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc11 A SG CYS 178 A CYS 253 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc12 A ND1 HIS 182 A HIS 257 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc13 A SG CYS 185 A CYS 260 1_555 G ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc14 A SG CYS 188 A CYS 263 1_555 G ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc15 A SG CYS 214 A CYS 289 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc16 A SG CYS 218 A CYS 293 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc17 A SG CYS 257 A CYS 332 1_555 H ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc18 A SG CYS 262 A CYS 337 1_555 H ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc19 A SG CYS 277 A CYS 352 1_555 H ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc20 A SG CYS 285 A CYS 360 1_555 H ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc21 A SG CYS 290 A CYS 365 1_555 E ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc22 A SG CYS 293 A CYS 368 1_555 E ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc23 A NE2 HIS 298 A HIS 373 1_555 E ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc24 A SG CYS 302 A CYS 377 1_555 E ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? # _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 262 n n C1 H11 MPD sing 263 n n C1 H12 MPD sing 264 n n C1 H13 MPD sing 265 n n C2 O2 MPD sing 266 n n C2 CM MPD sing 267 n n C2 C3 MPD sing 268 n n O2 HO2 MPD sing 269 n n CM HM1 MPD sing 270 n n CM HM2 MPD sing 271 n n CM HM3 MPD sing 272 n n C3 C4 MPD sing 273 n n C3 H31 MPD sing 274 n n C3 H32 MPD sing 275 n n C4 O4 MPD sing 276 n n C4 C5 MPD sing 277 n n C4 H4 MPD sing 278 n n O4 HO4 MPD sing 279 n n C5 H51 MPD sing 280 n n C5 H52 MPD sing 281 n n C5 H53 MPD sing 282 n n # _atom_sites.entry_id 8IKT _atom_sites.fract_transf_matrix[1][1] 0.012083 _atom_sites.fract_transf_matrix[1][2] 0.006976 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013952 _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] 0.009662 _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 D 4 ZN A 1 501 501 ZN ZN . E 4 ZN A 1 502 502 ZN ZN . F 4 ZN A 1 503 503 ZN ZN . G 4 ZN A 1 504 504 ZN ZN . H 4 ZN A 1 505 505 ZN ZN . I 4 ZN A 1 506 506 ZN ZN . J 5 GOL A 1 507 509 GOL GOL . K 6 MPD A 1 508 510 MPD MPD . L 7 3CN B 1 101 76 3CN 3CN . M 5 GOL C 1 101 507 GOL GOL . N 8 HOH A 1 601 636 HOH HOH . N 8 HOH A 2 602 627 HOH HOH . N 8 HOH A 3 603 619 HOH HOH . N 8 HOH A 4 604 603 HOH HOH . N 8 HOH A 5 605 644 HOH HOH . N 8 HOH A 6 606 620 HOH HOH . N 8 HOH A 7 607 641 HOH HOH . N 8 HOH A 8 608 616 HOH HOH . N 8 HOH A 9 609 624 HOH HOH . N 8 HOH A 10 610 671 HOH HOH . N 8 HOH A 11 611 633 HOH HOH . N 8 HOH A 12 612 696 HOH HOH . N 8 HOH A 13 613 697 HOH HOH . N 8 HOH A 14 614 652 HOH HOH . N 8 HOH A 15 615 712 HOH HOH . N 8 HOH A 16 616 684 HOH HOH . N 8 HOH A 17 617 662 HOH HOH . N 8 HOH A 18 618 683 HOH HOH . N 8 HOH A 19 619 673 HOH HOH . N 8 HOH A 20 620 695 HOH HOH . N 8 HOH A 21 621 667 HOH HOH . N 8 HOH A 22 622 705 HOH HOH . N 8 HOH A 23 623 613 HOH HOH . N 8 HOH A 24 624 663 HOH HOH . N 8 HOH A 25 625 661 HOH HOH . N 8 HOH A 26 626 672 HOH HOH . N 8 HOH A 27 627 630 HOH HOH . N 8 HOH A 28 628 690 HOH HOH . N 8 HOH A 29 629 715 HOH HOH . N 8 HOH A 30 630 660 HOH HOH . N 8 HOH A 31 631 709 HOH HOH . N 8 HOH A 32 632 626 HOH HOH . N 8 HOH A 33 633 724 HOH HOH . O 8 HOH B 1 201 220 HOH HOH . O 8 HOH B 2 202 203 HOH HOH . O 8 HOH B 3 203 224 HOH HOH . O 8 HOH B 4 204 205 HOH HOH . O 8 HOH B 5 205 209 HOH HOH . O 8 HOH B 6 206 207 HOH HOH . O 8 HOH B 7 207 622 HOH HOH . O 8 HOH B 8 208 228 HOH HOH . O 8 HOH B 9 209 234 HOH HOH . O 8 HOH B 10 210 227 HOH HOH . O 8 HOH B 11 211 212 HOH HOH . O 8 HOH B 12 212 232 HOH HOH . O 8 HOH B 13 213 215 HOH HOH . O 8 HOH B 14 214 211 HOH HOH . O 8 HOH B 15 215 226 HOH HOH . O 8 HOH B 16 216 230 HOH HOH . O 8 HOH B 17 217 238 HOH HOH . P 8 HOH C 1 201 617 HOH HOH . P 8 HOH C 2 202 688 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 . . . K 6 0.476 -28.818 -13.302 1 68.22 ? C1 MPD 508 A 1 HETATM 2 C C2 MPD . . . K 6 -0.614 -29.523 -14.094 1 67.36 ? C2 MPD 508 A 1 HETATM 3 O O2 MPD . . . K 6 -0.329 -30.931 -14.063 1 68.66 ? O2 MPD 508 A 1 HETATM 4 C CM MPD . . . K 6 -1.968 -29.333 -13.432 1 63.9 ? CM MPD 508 A 1 HETATM 5 C C3 MPD . . . K 6 -0.64 -29.053 -15.553 1 67.84 ? C3 MPD 508 A 1 HETATM 6 C C4 MPD . . . K 6 0.354 -29.753 -16.447 1 67.31 ? C4 MPD 508 A 1 HETATM 7 O O4 MPD . . . K 6 -0.186 -31.011 -16.837 1 68.72 ? O4 MPD 508 A 1 HETATM 8 C C5 MPD . . . K 6 0.726 -28.971 -17.673 1 66.11 ? C5 MPD 508 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #