data_8K77 # _model_server_result.job_id JlF-tOPW3xcEDcRXTVFMdw _model_server_result.datetime_utc '2025-04-23 14:26:19' _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 8k77 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":803}' # _entry.id 8K77 # _exptl.entry_id 8K77 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 212.289 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide _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 8K77 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8K77 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? _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 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 1 FUC NAG C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG A 902 NAG 3 n C NAG 2 C 2 NAG A 903 NAG 3 n C FUC 3 C 3 FUC A 904 FUC # 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 ND2 ASN 506 A ASN 498 1_555 D C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 A ND2 ASN 556 A ASN 548 1_555 E C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 581 A ASN 573 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _chem_comp.formula 'C11 H20 N2 O2' _chem_comp.formula_weight 212.289 _chem_comp.id VLX _chem_comp.mon_nstd_flag . _chem_comp.name (2S)-2-[(4R)-2-oxidanylidene-4-propyl-pyrrolidin-1-yl]butanamide _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 O2 C9 VLX doub 427 n n C11 C8 VLX sing 428 n n C8 C5 VLX sing 429 n n C9 N2 VLX sing 430 n n C9 C5 VLX sing 431 n n C5 N1 VLX sing 432 n n C7 C10 VLX sing 433 n n C7 C4 VLX sing 434 n n C2 N1 VLX sing 435 n n C2 C1 VLX sing 436 n n N1 C6 VLX sing 437 n n C4 C1 VLX sing 438 n n C1 C3 VLX sing 439 n n C6 C3 VLX sing 440 n n C6 O1 VLX doub 441 n n C10 H1 VLX sing 442 n n C10 H2 VLX sing 443 n n C10 H3 VLX sing 444 n n C7 H4 VLX sing 445 n n C7 H5 VLX sing 446 n n C5 H6 VLX sing 447 n n C4 H7 VLX sing 448 n n C4 H8 VLX sing 449 n n C3 H9 VLX sing 450 n n C3 H10 VLX sing 451 n n C2 H11 VLX sing 452 n n C2 H12 VLX sing 453 n n C1 H13 VLX sing 454 n n C11 H14 VLX sing 455 n n C11 H15 VLX sing 456 n n C11 H16 VLX sing 457 n n C8 H17 VLX sing 458 n n C8 H18 VLX sing 459 n n N2 H19 VLX sing 460 n n N2 H20 VLX sing 461 n n # _atom_sites.entry_id 8K77 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 NAG A 1 801 900 NAG NAG . E 4 NAG A 1 802 901 NAG NAG . F 5 VLX A 1 803 905 VLX BRV . # 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 C10 VLX . . . F 5 124.036 117.584 107.802 1 80 ? C10 VLX 803 A 1 HETATM 2 C C7 VLX . . . F 5 122.88 118.356 107.173 1 80 ? C7 VLX 803 A 1 HETATM 3 C C5 VLX . . . F 5 120.354 123.205 107.047 1 80 ? C5 VLX 803 A 1 HETATM 4 C C4 VLX . . . F 5 121.793 118.598 108.215 1 80 ? C4 VLX 803 A 1 HETATM 5 C C3 VLX . . . F 5 120.614 120.298 109.53 1 80 ? C3 VLX 803 A 1 HETATM 6 C C2 VLX . . . F 5 121.758 121.012 107.483 1 80 ? C2 VLX 803 A 1 HETATM 7 C C1 VLX . . . F 5 121.808 120.073 108.687 1 80 ? C1 VLX 803 A 1 HETATM 8 C C6 VLX . . . F 5 119.981 121.572 109.055 1 80 ? C6 VLX 803 A 1 HETATM 9 C C11 VLX . . . F 5 121.608 125.114 106.059 1 80 ? C11 VLX 803 A 1 HETATM 10 C C8 VLX . . . F 5 121.524 123.591 106.147 1 80 ? C8 VLX 803 A 1 HETATM 11 C C9 VLX . . . F 5 119.133 122.923 106.186 1 80 ? C9 VLX 803 A 1 HETATM 12 N N1 VLX . . . F 5 120.68 122.012 107.803 1 80 ? N1 VLX 803 A 1 HETATM 13 N N2 VLX . . . F 5 117.864 123.552 106.489 1 80 ? N2 VLX 803 A 1 HETATM 14 O O1 VLX . . . F 5 119.084 122.137 109.577 1 80 ? O1 VLX 803 A 1 HETATM 15 O O2 VLX . . . F 5 119.225 122.183 105.271 1 80 ? O2 VLX 803 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #