data_5HVM # _model_server_result.job_id I0z8v4HcbbzGKZLJ7FVnlA _model_server_result.datetime_utc '2024-11-24 19:48:45' _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 5hvm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":602}' # _entry.id 5HVM # _exptl.entry_id 5HVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 335.35 _entity.id 3 _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 2 _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 5HVM _cell.length_a 83.915 _cell.length_b 101.153 _cell.length_c 146.992 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 2 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 ? dimeric 2 author_defined_assembly 1 PISA tetrameric 4 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,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 # _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 416 n n O7 H7 VDM sing 417 n n C7 C5 VDM sing 418 n n C7 H7C1 VDM sing 419 n n C7 H7C2 VDM sing 420 n n C5 C6 VDM doub 421 n n C5 C4 VDM sing 422 n n C6 C1 VDM sing 423 n n C6 H6 VDM sing 424 n n C4 O4 VDM sing 425 n n C4 C3 VDM sing 426 n n C4 H4 VDM sing 427 n n O4 HA VDM sing 428 n n C3 O3 VDM sing 429 n n C3 C2 VDM sing 430 n n C3 H3 VDM sing 431 n n O3 HB VDM sing 432 n n C2 O2 VDM sing 433 n n C2 C1 VDM sing 434 n n C2 H2 VDM sing 435 n n O2 HC VDM sing 436 n n C1 N1' VDM sing 437 n n C1 H1 VDM sing 438 n n N1' C1' VDM sing 439 n n N1' H1' VDM sing 440 n n C1' HD VDM sing 441 n n C1' C2' VDM sing 442 n n C1' C6' VDM sing 443 n n C2' H2' VDM sing 444 n n C2' O2' VDM sing 445 n n C2' C3' VDM sing 446 n n O2' HE VDM sing 447 n n C6' "H6'1" VDM sing 448 n n C6' "H6'2" VDM sing 449 n n C6' C5' VDM sing 450 n n C5' H5' VDM sing 451 n n C5' C7' VDM sing 452 n n C5' C4' VDM sing 453 n n C7' "H7'1" VDM sing 454 n n C7' "H7'2" VDM sing 455 n n C7' O7' VDM sing 456 n n O7' H7' VDM sing 457 n n C4' H4' VDM sing 458 n n C4' O4' VDM sing 459 n n C4' C3' VDM sing 460 n n O4' HF VDM sing 461 n n C3' H3' VDM sing 462 n n C3' O3' VDM sing 463 n n O3' HG VDM sing 464 n n # _atom_sites.entry_id 5HVM _atom_sites.fract_transf_matrix[1][1] 0.011917 _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] 0.009886 _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] 0.006803 _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 UDP A 1 601 601 UDP UDP . D 3 VDM A 1 602 602 VDM VDM . E 2 UDP B 1 601 601 UDP UDP . F 3 VDM B 1 602 602 VDM VDM . G 4 HOH A 1 701 5 HOH HOH . G 4 HOH A 2 702 3 HOH HOH . G 4 HOH A 3 703 2 HOH HOH . G 4 HOH A 4 704 6 HOH HOH . G 4 HOH A 5 705 1 HOH HOH . G 4 HOH A 6 706 7 HOH HOH . H 4 HOH B 1 701 8 HOH HOH . H 4 HOH B 2 702 4 HOH HOH . H 4 HOH B 3 703 9 HOH HOH . H 4 HOH B 4 704 10 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 O O7 VDM . . . F 3 2.039 15.167 20.483 1 80.1 ? O7 VDM 602 B 1 HETATM 2 C C7 VDM . . . F 3 3.259 15.901 20.43 1 66.64 ? C7 VDM 602 B 1 HETATM 3 C C5 VDM . . . F 3 2.931 17.322 20.112 1 53.51 ? C5 VDM 602 B 1 HETATM 4 C C6 VDM . . . F 3 3.635 17.98 19.183 1 64.29 ? C6 VDM 602 B 1 HETATM 5 C C4 VDM . . . F 3 1.785 17.935 20.849 1 60.83 ? C4 VDM 602 B 1 HETATM 6 O O4 VDM . . . F 3 1.873 17.536 22.211 1 59.01 ? O4 VDM 602 B 1 HETATM 7 C C3 VDM . . . F 3 1.783 19.445 20.776 1 62.31 ? C3 VDM 602 B 1 HETATM 8 O O3 VDM . . . F 3 0.516 19.917 21.198 1 56.69 ? O3 VDM 602 B 1 HETATM 9 C C2 VDM . . . F 3 2.012 19.911 19.36 1 62.15 ? C2 VDM 602 B 1 HETATM 10 O O2 VDM . . . F 3 1.923 21.325 19.388 1 74.98 ? O2 VDM 602 B 1 HETATM 11 C C1 VDM . . . F 3 3.343 19.415 18.777 1 76.11 ? C1 VDM 602 B 1 HETATM 12 N N1' VDM . . . F 3 4.486 20.261 19.102 1 80 ? N1' VDM 602 B 1 HETATM 13 C C1' VDM . . . F 3 4.725 21.55 18.474 1 63.78 ? C1' VDM 602 B 1 HETATM 14 C C2' VDM . . . F 3 5.489 21.46 17.181 1 61.65 ? C2' VDM 602 B 1 HETATM 15 O O2' VDM . . . F 3 5.257 20.163 16.664 1 66.92 ? O2' VDM 602 B 1 HETATM 16 C C6' VDM . . . F 3 5.342 22.502 19.469 1 53.74 ? C6' VDM 602 B 1 HETATM 17 C C5' VDM . . . F 3 6.933 22.744 19.565 1 53.75 ? C5' VDM 602 B 1 HETATM 18 C C7' VDM . . . F 3 7.258 24.019 20.279 1 58.29 ? C7' VDM 602 B 1 HETATM 19 O O7' VDM . . . F 3 6.715 23.961 21.585 1 69.68 ? O7' VDM 602 B 1 HETATM 20 C C4' VDM . . . F 3 7.382 22.802 18.026 1 52.76 ? C4' VDM 602 B 1 HETATM 21 O O4' VDM . . . F 3 8.795 22.798 17.969 1 58.81 ? O4' VDM 602 B 1 HETATM 22 C C3' VDM . . . F 3 6.926 21.63 17.21 1 61.63 ? C3' VDM 602 B 1 HETATM 23 O O3' VDM . . . F 3 7.414 21.781 15.882 1 66.39 ? O3' VDM 602 B 1 HETATM 24 H H7 VDM . . . F 3 1.474 15.54 21.173 1 96.12 ? H7 VDM 602 B 1 HETATM 25 H H7C1 VDM . . . F 3 3.911 15.486 19.661 1 79.97 ? H7C1 VDM 602 B 1 HETATM 26 H H7C2 VDM . . . F 3 3.768 15.845 21.392 1 79.97 ? H7C2 VDM 602 B 1 HETATM 27 H H6 VDM . . . F 3 4.444 17.466 18.696 1 77.15 ? H6 VDM 602 B 1 HETATM 28 H H4 VDM . . . F 3 0.844 17.567 20.422 1 72.99 ? H4 VDM 602 B 1 HETATM 29 H H1 VDM . . . F 3 3.236 19.43 17.685 1 91.33 ? H1 VDM 602 B 1 HETATM 30 H HA VDM . . . F 3 1.799 16.575 22.266 1 70.82 ? HA VDM 602 B 1 HETATM 31 H H3 VDM . . . F 3 2.577 19.841 21.421 1 74.77 ? H3 VDM 602 B 1 HETATM 32 H HB VDM . . . F 3 0.241 19.435 21.988 1 68.03 ? HB VDM 602 B 1 HETATM 33 H H2 VDM . . . F 3 1.199 19.511 18.744 1 74.58 ? H2 VDM 602 B 1 HETATM 34 H HC VDM . . . F 3 1.062 21.588 19.739 1 89.98 ? HC VDM 602 B 1 HETATM 35 H H1' VDM . . . F 3 5.144 19.937 19.794 1 96 ? H1' VDM 602 B 1 HETATM 36 H HD VDM . . . F 3 3.757 21.974 18.195 1 76.54 ? HD VDM 602 B 1 HETATM 37 H H2' VDM . . . F 3 5.078 22.203 16.488 1 73.98 ? H2' VDM 602 B 1 HETATM 38 H "H6'1" VDM . . . F 3 4.883 23.477 19.303 1 64.49 ? "H6'1" VDM 602 B 1 HETATM 39 H "H6'2" VDM . . . F 3 5.013 22.18 20.457 1 64.49 ? "H6'2" VDM 602 B 1 HETATM 40 H HE VDM . . . F 3 5.672 20.095 15.795 1 80.31 ? HE VDM 602 B 1 HETATM 41 H H3' VDM . . . F 3 7.358 20.724 17.65 1 73.95 ? H3' VDM 602 B 1 HETATM 42 H H5' VDM . . . F 3 7.415 21.896 20.065 1 64.5 ? H5' VDM 602 B 1 HETATM 43 H "H7'1" VDM . . . F 3 6.833 24.864 19.739 1 69.95 ? "H7'1" VDM 602 B 1 HETATM 44 H "H7'2" VDM . . . F 3 8.338 24.15 20.329 1 69.95 ? "H7'2" VDM 602 B 1 HETATM 45 H H4' VDM . . . F 3 6.988 23.719 17.575 1 63.31 ? H4' VDM 602 B 1 HETATM 46 H H7' VDM . . . F 3 5.865 24.42 21.592 1 83.62 ? H7' VDM 602 B 1 HETATM 47 H HF VDM . . . F 3 9.138 22.217 18.659 1 70.57 ? HF VDM 602 B 1 HETATM 48 H HG VDM . . . F 3 6.859 22.412 15.407 1 79.67 ? HG VDM 602 B 1 # _model_server_stats.io_time_ms 85 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 727 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 48 #