data_5KJR # _model_server_result.job_id KfJ1qJ942bM12HWWoUukBw _model_server_result.datetime_utc '2025-07-21 13:05:39' _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 5kjr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":301}' # _entry.id 5KJR # _exptl.entry_id 5KJR _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 90 _cell.entry_id 5KJR _cell.length_a 95.191 _cell.length_b 101.944 _cell.length_c 108.747 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KJR _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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,Q,R _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 O _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 11 G CYS 54 1_555 A SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? disulf ? disulf2 A SG CYS 76 G CYS 119 1_555 A SG CYS 89 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf3 A SG CYS 102 G CYS 218 1_555 A SG CYS 131 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 112 G CYS 228 1_555 A SG CYS 123 G CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? disulf ? disulf5 A SG CYS 180 G CYS 296 1_555 A SG CYS 199 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf6 A SG CYS 245 G CYS 378 1_555 A SG CYS 306 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf7 A SG CYS 252 G CYS 385 1_555 A SG CYS 279 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? disulf ? disulf8 A SG CYS 262 G CYS 395 1_555 A SG CYS 271 G CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf9 B SG MPT 1 N MPT 1 1_555 B SG CYS 19 N CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf10 B SG CYS 6 N CYS 6 1_555 B SG CYS 24 N CYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf11 B SG CYS 10 N CYS 10 1_555 B SG CYS 26 N CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf12 C SG CYS 22 H CYS 22 1_555 C SG CYS 97 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf13 C SG CYS 149 H CYS 140 1_555 C SG CYS 205 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? disulf ? disulf14 D SG CYS 27 L CYS 23 1_555 D SG CYS 95 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? disulf ? disulf15 D SG CYS 143 L CYS 134 1_555 D SG CYS 202 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 118 G ASN 234 1_555 E C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 125 G ASN 241 1_555 F C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale3 A ND2 ASN 146 G ASN 262 1_555 G C1 NAG . G NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale4 A ND2 ASN 160 G ASN 276 1_555 H C1 NAG . G NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 A ND2 ASN 173 G ASN 289 1_555 I C1 NAG . G NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 A ND2 ASN 179 G ASN 295 1_555 J C1 NAG . G NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale7 A ND2 ASN 202 G ASN 334 1_555 K C1 NAG . G NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale8 A ND2 ASN 253 G ASN 386 1_555 L C1 NAG . G NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale9 A ND2 ASN 259 G ASN 392 1_555 M C1 NAG . G NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.51 ? covale ? covale10 A ND2 ASN 322 G ASN 461 1_555 N C1 NAG . G NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale11 B C MPT 1 N MPT 1 1_555 B N ASN 2 N ASN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.294 ? covale ? covale12 B C ALA 20 N ALA 20 1_555 B N DPR 21 N DPR 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale13 B C DPR 21 N DPR 21 1_555 B N THR 22 N THR 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale14 B C THR 22 N THR 22 1_555 B N U2X 23 N U2X 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.264 ? covale ? covale15 B C U2X 23 N U2X 23 1_555 B N CYS 24 N CYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale16 B C VAL 27 N VAL 27 1_555 B N NH2 28 N NH2 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.282 ? # _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 254 n n C1 H11 MPD sing 255 n n C1 H12 MPD sing 256 n n C1 H13 MPD sing 257 n n C2 O2 MPD sing 258 n n C2 CM MPD sing 259 n n C2 C3 MPD sing 260 n n O2 HO2 MPD sing 261 n n CM HM1 MPD sing 262 n n CM HM2 MPD sing 263 n n CM HM3 MPD sing 264 n n C3 C4 MPD sing 265 n n C3 H31 MPD sing 266 n n C3 H32 MPD sing 267 n n C4 O4 MPD sing 268 n n C4 C5 MPD sing 269 n n C4 H4 MPD sing 270 n n O4 HO4 MPD sing 271 n n C5 H51 MPD sing 272 n n C5 H52 MPD sing 273 n n C5 H53 MPD sing 274 n n # _atom_sites.entry_id 5KJR _atom_sites.fract_transf_matrix[1][1] 0.010505 _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] 0.009809 _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] 0.009196 _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 E 5 NAG G 1 501 502 NAG NAG . F 5 NAG G 1 502 503 NAG NAG . G 5 NAG G 1 503 504 NAG NAG . H 5 NAG G 1 504 505 NAG NAG . I 5 NAG G 1 505 506 NAG NAG . J 5 NAG G 1 506 507 NAG NAG . K 5 NAG G 1 507 508 NAG NAG . L 5 NAG G 1 508 509 NAG NAG . M 5 NAG G 1 509 510 NAG NAG . N 5 NAG G 1 510 511 NAG NAG . O 6 MPD L 1 301 1 MPD MPD . P 7 HOH G 1 601 2 HOH HOH . P 7 HOH G 2 602 3 HOH HOH . P 7 HOH G 3 603 9 HOH HOH . P 7 HOH G 4 604 4 HOH HOH . Q 7 HOH H 1 301 7 HOH HOH . Q 7 HOH H 2 302 8 HOH HOH . Q 7 HOH H 3 303 5 HOH HOH . R 7 HOH L 1 401 1 HOH HOH . R 7 HOH L 2 402 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 MPD . . . O 6 22.307 7.213 6.15 1 58.77 ? C1 MPD 301 L 1 HETATM 2 C C2 MPD . . . O 6 23.052 7.197 7.489 1 59.85 ? C2 MPD 301 L 1 HETATM 3 O O2 MPD . . . O 6 23.604 8.487 7.751 1 54.91 ? O2 MPD 301 L 1 HETATM 4 C CM MPD . . . O 6 22.095 6.86 8.615 1 58.02 ? CM MPD 301 L 1 HETATM 5 C C3 MPD . . . O 6 24.207 6.2 7.535 1 63.91 ? C3 MPD 301 L 1 HETATM 6 C C4 MPD . . . O 6 25.076 6.195 6.278 1 67.39 ? C4 MPD 301 L 1 HETATM 7 O O4 MPD . . . O 6 25.537 7.524 6.012 1 70.44 ? O4 MPD 301 L 1 HETATM 8 C C5 MPD . . . O 6 26.269 5.252 6.418 1 67.26 ? C5 MPD 301 L 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 8 #