data_5VP8 # _model_server_result.job_id 2WV6G7m61S-1LJY5Vic6_Q _model_server_result.datetime_utc '2024-11-15 02:28:45' _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 5vp8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 5VP8 # _exptl.entry_id 5VP8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 541.682 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[(3R,5S,7R)-1,5,7,9-tetrakis(2-oxopyrrolidin-1-yl)nonan-3-yl]-1,3-dihydro-2H-pyrrol-2-one _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 5VP8 _cell.length_a 90.098 _cell.length_b 90.098 _cell.length_c 134.108 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VP8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # 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 tetrameric 4 software_defined_assembly 1 PISA monomeric 1 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 1 1,2,3,4 A,B,C,D,E 2 1 # 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_685 -x+1,-y+3,z -1 0 0 0 -1 0 0 0 1 90.098 270.294 0 3 'crystal symmetry operation' 3_765 -y+2,x+1,z 0 -1 0 1 0 0 0 0 1 180.196 90.098 0 4 'crystal symmetry operation' 4_475 y-1,-x+2,z 0 1 0 -1 0 0 0 0 1 -90.098 180.196 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 metalc ? metalc1 A NE2 HIS 61 A HIS 41 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc2 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 A OE2 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc4 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc5 B MN MN . A MN 201 1_555 E O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc6 B MN MN . A MN 201 1_555 E O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? # _chem_comp.formula 'C29 H43 N5 O5' _chem_comp.formula_weight 541.682 _chem_comp.id 9HD _chem_comp.mon_nstd_flag . _chem_comp.name 1-[(3R,5S,7R)-1,5,7,9-tetrakis(2-oxopyrrolidin-1-yl)nonan-3-yl]-1,3-dihydro-2H-pyrrol-2-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Polyvinylpyrrolidone K15' # 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 C69 C66 9HD sing 1 n n C69 N61 9HD sing 2 n n C66 C63 9HD sing 3 n n C58 N61 9HD sing 4 n n C58 C55 9HD sing 5 n n N61 C62 9HD sing 6 n n C63 C62 9HD sing 7 n n C55 C41 9HD sing 8 n n C62 O72 9HD doub 9 n n C21 C18 9HD sing 10 n n C21 N24 9HD sing 11 n n C18 C13 9HD sing 12 n n O77 C76 9HD doub 13 n n C41 N43 9HD sing 14 n n C41 C38 9HD sing 15 n n N24 C25 9HD sing 16 n n N24 C32 9HD sing 17 n n O37 C25 9HD doub 18 n n O54 C44 9HD doub 19 n n C25 C26 9HD sing 20 n n C35 C38 9HD sing 21 n n C35 C15 9HD sing 22 n n C35 N78 9HD sing 23 n n C32 C29 9HD sing 24 n n N43 C44 9HD sing 25 n n N43 C51 9HD sing 26 n n C76 N78 9HD sing 27 n n C76 C73 9HD sing 28 n n C44 C45 9HD sing 29 n n O12 C08 9HD doub 30 n n C13 C15 9HD sing 31 n n C13 N07 9HD sing 32 n n N78 C79 9HD sing 33 n n C51 C48 9HD sing 34 n n C26 C29 9HD sing 35 n n C45 C48 9HD sing 36 n n C08 N07 9HD sing 37 n n C08 C09 9HD sing 38 n n C73 C82 9HD sing 39 n n N07 C04 9HD sing 40 n n C79 C82 9HD sing 41 n n C09 C01 9HD sing 42 n n C04 C01 9HD doub 43 n n C01 H1 9HD sing 44 n n C04 H2 9HD sing 45 n n C09 H3 9HD sing 46 n n C09 H4 9HD sing 47 n n C13 H5 9HD sing 48 n n C15 H6 9HD sing 49 n n C15 H7 9HD sing 50 n n C18 H8 9HD sing 51 n n C18 H9 9HD sing 52 n n C21 H10 9HD sing 53 n n C21 H11 9HD sing 54 n n C26 H12 9HD sing 55 n n C26 H13 9HD sing 56 n n C29 H14 9HD sing 57 n n C29 H15 9HD sing 58 n n C32 H16 9HD sing 59 n n C32 H17 9HD sing 60 n n C35 H18 9HD sing 61 n n C38 H19 9HD sing 62 n n C38 H20 9HD sing 63 n n C41 H21 9HD sing 64 n n C45 H22 9HD sing 65 n n C45 H23 9HD sing 66 n n C48 H24 9HD sing 67 n n C48 H25 9HD sing 68 n n C51 H26 9HD sing 69 n n C51 H27 9HD sing 70 n n C55 H28 9HD sing 71 n n C55 H29 9HD sing 72 n n C58 H30 9HD sing 73 n n C58 H31 9HD sing 74 n n C63 H32 9HD sing 75 n n C63 H33 9HD sing 76 n n C66 H34 9HD sing 77 n n C66 H35 9HD sing 78 n n C69 H36 9HD sing 79 n n C69 H37 9HD sing 80 n n C73 H38 9HD sing 81 n n C73 H39 9HD sing 82 n n C79 H40 9HD sing 83 n n C79 H41 9HD sing 84 n n C82 H42 9HD sing 85 n n C82 H43 9HD sing 86 n n # _atom_sites.entry_id 5VP8 _atom_sites.fract_transf_matrix[1][1] 0.011099 _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] 0.011099 _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] 0.007457 _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 B 2 MN A 1 201 201 MN MN . C 3 SO4 A 1 202 202 SO4 SO4 . D 4 9HD A 1 203 1 9HD 7GK . E 5 HOH A 1 301 18 HOH HOH . E 5 HOH A 2 302 1 HOH HOH . E 5 HOH A 3 303 13 HOH HOH . E 5 HOH A 4 304 7 HOH HOH . E 5 HOH A 5 305 5 HOH HOH . E 5 HOH A 6 306 17 HOH HOH . E 5 HOH A 7 307 15 HOH HOH . E 5 HOH A 8 308 10 HOH HOH . E 5 HOH A 9 309 9 HOH HOH . E 5 HOH A 10 310 6 HOH HOH . E 5 HOH A 11 311 8 HOH HOH . E 5 HOH A 12 312 2 HOH HOH . E 5 HOH A 13 313 21 HOH HOH . E 5 HOH A 14 314 16 HOH HOH . E 5 HOH A 15 315 19 HOH HOH . E 5 HOH A 16 316 3 HOH HOH . E 5 HOH A 17 317 20 HOH HOH . E 5 HOH A 18 318 4 HOH HOH . E 5 HOH A 19 319 14 HOH HOH . E 5 HOH A 20 320 11 HOH HOH . E 5 HOH A 21 321 12 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 C01 9HD . . . D 4 39.719 123.367 283.935 1 71.39 ? C01 9HD 203 A 1 HETATM 2 C C04 9HD . . . D 4 41.094 123.321 283.197 1 72.86 ? C04 9HD 203 A 1 HETATM 3 N N07 9HD . . . D 4 40.833 122.696 281.823 1 71.77 ? N07 9HD 203 A 1 HETATM 4 C C08 9HD . . . D 4 39.423 122.204 281.708 1 68.59 ? C08 9HD 203 A 1 HETATM 5 C C09 9HD . . . D 4 38.67 122.521 283.065 1 70.44 ? C09 9HD 203 A 1 HETATM 6 O O12 9HD . . . D 4 38.93 121.596 280.716 1 69.56 ? O12 9HD 203 A 1 HETATM 7 C C13 9HD . . . D 4 41.925 122.65 280.73 1 71.01 ? C13 9HD 203 A 1 HETATM 8 C C15 9HD . . . D 4 42.717 121.319 280.925 1 67.83 ? C15 9HD 203 A 1 HETATM 9 C C18 9HD . . . D 4 41.328 122.808 279.233 1 77.5 ? C18 9HD 203 A 1 HETATM 10 C C21 9HD . . . D 4 41.222 124.268 278.627 1 74.61 ? C21 9HD 203 A 1 HETATM 11 N N24 9HD . . . D 4 40.787 125.163 279.686 1 77.1 ? N24 9HD 203 A 1 HETATM 12 C C25 9HD . . . D 4 39.402 125.156 280.293 1 85.05 ? C25 9HD 203 A 1 HETATM 13 C C26 9HD . . . D 4 39.288 126.297 281.453 1 84.62 ? C26 9HD 203 A 1 HETATM 14 C C29 9HD . . . D 4 40.757 126.814 281.664 1 88.8 ? C29 9HD 203 A 1 HETATM 15 C C32 9HD . . . D 4 41.644 126.241 280.366 1 85.91 ? C32 9HD 203 A 1 HETATM 16 C C35 9HD . . . D 4 44.128 121.209 280.313 1 71.72 ? C35 9HD 203 A 1 HETATM 17 O O37 9HD . . . D 4 38.459 124.402 279.983 1 76.93 ? O37 9HD 203 A 1 HETATM 18 C C38 9HD . . . D 4 44.771 119.859 280.561 1 75.63 ? C38 9HD 203 A 1 HETATM 19 C C41 9HD . . . D 4 45.733 119.099 279.509 1 74.5 ? C41 9HD 203 A 1 HETATM 20 N N43 9HD . . . D 4 46.767 118.467 280.388 1 70.85 ? N43 9HD 203 A 1 HETATM 21 C C44 9HD . . . D 4 47.047 117.088 280.584 1 72.23 ? C44 9HD 203 A 1 HETATM 22 C C45 9HD . . . D 4 48.191 116.908 281.572 1 70.93 ? C45 9HD 203 A 1 HETATM 23 C C48 9HD . . . D 4 48.859 118.289 281.694 1 71.44 ? C48 9HD 203 A 1 HETATM 24 C C51 9HD . . . D 4 47.689 119.252 281.348 1 72.86 ? C51 9HD 203 A 1 HETATM 25 O O54 9HD . . . D 4 46.543 116.118 280.071 1 79.06 ? O54 9HD 203 A 1 HETATM 26 C C55 9HD . . . D 4 46.223 119.957 278.305 1 80.05 ? C55 9HD 203 A 1 HETATM 27 C C58 9HD . . . D 4 47.189 119.277 277.298 1 87.75 ? C58 9HD 203 A 1 HETATM 28 N N61 9HD . . . D 4 48.649 119.632 277.454 1 98.84 ? N61 9HD 203 A 1 HETATM 29 C C62 9HD . . . D 4 49.158 120.76 278.356 1 102.68 ? C62 9HD 203 A 1 HETATM 30 C C63 9HD . . . D 4 50.685 120.705 278.132 1 101.8 ? C63 9HD 203 A 1 HETATM 31 C C66 9HD . . . D 4 50.944 119.904 276.758 1 101.01 ? C66 9HD 203 A 1 HETATM 32 C C69 9HD . . . D 4 49.787 118.916 276.682 1 96.46 ? C69 9HD 203 A 1 HETATM 33 O O72 9HD . . . D 4 48.549 121.553 279.072 1 92.61 ? O72 9HD 203 A 1 HETATM 34 C C73 9HD . . . D 4 46.275 124.159 281.771 1 74.1 ? C73 9HD 203 A 1 HETATM 35 C C76 9HD . . . D 4 45.665 123.286 280.514 1 79.98 ? C76 9HD 203 A 1 HETATM 36 O O77 9HD . . . D 4 45.817 123.44 279.272 1 74.8 ? O77 9HD 203 A 1 HETATM 37 N N78 9HD . . . D 4 44.882 122.196 281.108 1 75.26 ? N78 9HD 203 A 1 HETATM 38 C C79 9HD . . . D 4 44.888 122.302 282.69 1 72.09 ? C79 9HD 203 A 1 HETATM 39 C C82 9HD . . . D 4 46.167 123.173 283.01 1 74.86 ? C82 9HD 203 A 1 # _model_server_stats.io_time_ms 138 _model_server_stats.parse_time_ms 48 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 1207 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 39 #