data_8Z2U # _model_server_result.job_id hVMHp2T92z3W7VSjqnWhrg _model_server_result.datetime_utc '2025-01-08 11:48:05' _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 8z2u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":603}' # _entry.id 8Z2U # _exptl.entry_id 8Z2U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 335.35 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL _entity.pdbx_number_of_molecules 4 _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 8Z2U _cell.length_a 134.731 _cell.length_b 152.031 _cell.length_c 153.213 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Z2U _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' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,G,K,L,M 1 1 B,D,H,I,J,N,O,P 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 ? 4 G N N ? 4 J N N ? 4 M N N ? 4 P N 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 metalc ? metalc1 A OD1 ASP 26 A ASP 24 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? metalc ? metalc2 A OD1 ASN 28 A ASN 26 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc3 A OD1 ASP 30 A ASP 28 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc4 A O LYS 32 A LYS 30 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc5 A OD1 ASN 107 A ASN 105 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc6 A OD2 ASP 181 A ASP 179 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? metalc ? metalc7 A O TYR 215 A TYR 213 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc8 A O LEU 216 A LEU 214 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc9 A OE2 GLU 218 A GLU 216 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc10 B OD1 ASN 28 B ASN 26 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc11 B OD1 ASP 30 B ASP 28 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc12 B O LYS 32 B LYS 30 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc13 B OD1 ASN 107 B ASN 105 1_555 H CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc14 B OD2 ASP 181 B ASP 179 1_555 H CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc15 B O TYR 215 B TYR 213 1_555 H CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc16 B O LEU 216 B LEU 214 1_555 H CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc17 B OE2 GLU 218 B GLU 216 1_555 H CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc18 C OD1 ASN 28 C ASN 26 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc19 C OD1 ASP 30 C ASP 28 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc20 C OD2 ASP 30 C ASP 28 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc21 C O LYS 32 C LYS 30 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc22 C O ASP 79 C ASP 77 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc23 C OD1 ASN 107 C ASN 105 1_555 K CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc24 C OD2 ASP 181 C ASP 179 1_555 K CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc25 C O TYR 215 C TYR 213 1_555 K CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc26 C O LEU 216 C LEU 214 1_555 K CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc27 C OE2 GLU 218 C GLU 216 1_555 K CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc28 D OD1 ASN 28 D ASN 26 1_555 O MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc29 D OD1 ASP 30 D ASP 28 1_555 O MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc30 D OD2 ASP 30 D ASP 28 1_555 O MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc31 D O LYS 32 D LYS 30 1_555 O MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc32 D OD1 ASP 34 D ASP 32 1_555 O MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc33 D OD1 ASN 107 D ASN 105 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc34 D OD2 ASP 181 D ASP 179 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc35 D O TYR 215 D TYR 213 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc36 D O LEU 216 D LEU 214 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc37 D OE2 GLU 218 D GLU 216 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? # _chem_comp.formula 'C14 H25 N O8' _chem_comp.formula_weight 335.35 _chem_comp.id VDM _chem_comp.mon_nstd_flag . _chem_comp.name (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms VALIDOXYLAMINE # 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 O7 C7 VDM sing 374 n n O7 H7 VDM sing 375 n n C7 C5 VDM sing 376 n n C7 H7C1 VDM sing 377 n n C7 H7C2 VDM sing 378 n n C5 C6 VDM doub 379 n n C5 C4 VDM sing 380 n n C6 C1 VDM sing 381 n n C6 H6 VDM sing 382 n n C4 O4 VDM sing 383 n n C4 C3 VDM sing 384 n n C4 H4 VDM sing 385 n n O4 HA VDM sing 386 n n C3 O3 VDM sing 387 n n C3 C2 VDM sing 388 n n C3 H3 VDM sing 389 n n O3 HB VDM sing 390 n n C2 O2 VDM sing 391 n n C2 C1 VDM sing 392 n n C2 H2 VDM sing 393 n n O2 HC VDM sing 394 n n C1 N1' VDM sing 395 n n C1 H1 VDM sing 396 n n N1' C1' VDM sing 397 n n N1' H1' VDM sing 398 n n C1' HD VDM sing 399 n n C1' C2' VDM sing 400 n n C1' C6' VDM sing 401 n n C2' H2' VDM sing 402 n n C2' O2' VDM sing 403 n n C2' C3' VDM sing 404 n n O2' HE VDM sing 405 n n C6' "H6'1" VDM sing 406 n n C6' "H6'2" VDM sing 407 n n C6' C5' VDM sing 408 n n C5' H5' VDM sing 409 n n C5' C7' VDM sing 410 n n C5' C4' VDM sing 411 n n C7' "H7'1" VDM sing 412 n n C7' "H7'2" VDM sing 413 n n C7' O7' VDM sing 414 n n O7' H7' VDM sing 415 n n C4' H4' VDM sing 416 n n C4' O4' VDM sing 417 n n C4' C3' VDM sing 418 n n O4' HF VDM sing 419 n n C3' H3' VDM sing 420 n n C3' O3' VDM sing 421 n n O3' HG VDM sing 422 n n # _atom_sites.entry_id 8Z2U _atom_sites.fract_transf_matrix[1][1] 0.007422 _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] 0.006578 _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] 0.006527 _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 2 CA A 1 601 600 CA CA . F 3 MG A 1 602 601 MG MG . G 4 VDM A 1 603 700 VDM VDM . H 2 CA B 1 601 600 CA CA . I 3 MG B 1 602 601 MG MG . J 4 VDM B 1 603 700 VDM VDM . K 2 CA C 1 601 600 CA CA . L 3 MG C 1 602 601 MG MG . M 4 VDM C 1 603 700 VDM VDM . N 2 CA D 1 601 600 CA CA . O 3 MG D 1 602 601 MG MG . P 4 VDM D 1 603 700 VDM VDM . # 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 O O7 VDM . . . G 4 2.326 33.983 -33.916 1 27.71 ? O7 VDM 603 A 1 HETATM 2 C C7 VDM . . . G 4 0.975 33.678 -33.599 1 27.56 ? C7 VDM 603 A 1 HETATM 3 C C5 VDM . . . G 4 0.834 32.463 -32.726 1 30.49 ? C5 VDM 603 A 1 HETATM 4 C C6 VDM . . . G 4 -0.047 31.511 -33.009 1 36.8 ? C6 VDM 603 A 1 HETATM 5 C C4 VDM . . . G 4 1.742 32.409 -31.517 1 29.94 ? C4 VDM 603 A 1 HETATM 6 O O4 VDM . . . G 4 1.608 33.591 -30.75 1 41.04 ? O4 VDM 603 A 1 HETATM 7 C C3 VDM . . . G 4 1.434 31.208 -30.631 1 28.46 ? C3 VDM 603 A 1 HETATM 8 O O3 VDM . . . G 4 2.51 31.001 -29.722 1 27.45 ? O3 VDM 603 A 1 HETATM 9 C C2 VDM . . . G 4 1.192 29.984 -31.499 1 30.51 ? C2 VDM 603 A 1 HETATM 10 O O2 VDM . . . G 4 1.148 28.8 -30.706 1 31.24 ? O2 VDM 603 A 1 HETATM 11 C C1 VDM . . . G 4 -0.11 30.184 -32.291 1 38.03 ? C1 VDM 603 A 1 HETATM 12 N N1' VDM . . . G 4 -1.377 30.042 -31.475 1 38.03 ? N1' VDM 603 A 1 HETATM 13 C C1' VDM . . . G 4 -2.225 28.807 -31.711 1 28.88 ? C1' VDM 603 A 1 HETATM 14 C C2' VDM . . . G 4 -3.003 28.558 -30.439 1 30.59 ? C2' VDM 603 A 1 HETATM 15 O O2' VDM . . . G 4 -3.42 29.771 -29.817 1 31.82 ? O2' VDM 603 A 1 HETATM 16 C C6' VDM . . . G 4 -1.297 27.649 -32.102 1 30.94 ? C6' VDM 603 A 1 HETATM 17 C C5' VDM . . . G 4 -1.701 26.293 -31.504 1 24.36 ? C5' VDM 603 A 1 HETATM 18 C C7' VDM . . . G 4 -2.832 25.606 -32.243 1 30.33 ? C7' VDM 603 A 1 HETATM 19 O O7' VDM . . . G 4 -2.772 24.194 -32.122 1 40.49 ? O7' VDM 603 A 1 HETATM 20 C C4' VDM . . . G 4 -1.901 26.381 -29.984 1 20.25 ? C4' VDM 603 A 1 HETATM 21 O O4' VDM . . . G 4 -0.781 25.818 -29.316 1 25.42 ? O4' VDM 603 A 1 HETATM 22 C C3' VDM . . . G 4 -2.097 27.8 -29.491 1 26.12 ? C3' VDM 603 A 1 HETATM 23 O O3' VDM . . . G 4 -2.636 27.805 -28.174 1 26.26 ? O3' VDM 603 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #