data_2GBF # _model_server_result.job_id WGNN5qSXcU550R7v3Pk4rg _model_server_result.datetime_utc '2024-11-04 23:30:52' _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 2gbf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":768}' # _entry.id 2GBF # _exptl.entry_id 2GBF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 249.352 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1S)-2-[(2S,5R)-2-(AMINOMETHYL)-5-ETHYNYLPYRROLIDIN-1-YL]-1-CYCLOPENTYL-2-OXOETHANAMINE _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 2GBF _cell.length_a 208.171 _cell.length_b 208.171 _cell.length_c 208.171 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GBF _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # 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 hexameric 6 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 1 1 A,B,C 2 1,2,3 # 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' 7_454 -z-1/2,-x,y-1/2 0 0 -1 -1 0 0 0 1 0 -104.0855 0 -104.0855 3 'crystal symmetry operation' 10_554 -y,z+1/2,-x-1/2 0 -1 0 0 0 1 -1 0 0 0 104.0855 -104.0855 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 289 A CYS 326 1_555 A SG CYS 300 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 346 A CYS 383 1_555 A SG CYS 358 A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 408 A CYS 445 1_555 A SG CYS 411 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 A SG CYS 418 A CYS 455 1_555 A SG CYS 436 A CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 613 A CYS 650 1_555 A SG CYS 726 A CYS 763 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 289 B CYS 326 1_555 B SG CYS 300 B CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 B SG CYS 346 B CYS 383 1_555 B SG CYS 358 B CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf8 B SG CYS 408 B CYS 445 1_555 B SG CYS 411 B CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf9 B SG CYS 418 B CYS 455 1_555 B SG CYS 436 B CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf10 B SG CYS 613 B CYS 650 1_555 B SG CYS 726 B CYS 763 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A OG SER 594 A SER 631 1_555 C C8 AIA . A AIA 768 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? # _chem_comp.formula 'C14 H23 N3 O' _chem_comp.formula_weight 249.352 _chem_comp.id AIA _chem_comp.mon_nstd_flag . _chem_comp.name (1S)-2-[(2S,5R)-2-(AMINOMETHYL)-5-ETHYNYLPYRROLIDIN-1-YL]-1-CYCLOPENTYL-2-OXOETHANAMINE _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 C2 C5 AIA sing 1 n n C2 C6 AIA sing 2 n n C2 N1 AIA sing 3 n n C2 H2 AIA sing 4 n n C3 C7 AIA sing 5 n n C3 C8 AIA sing 6 n n C3 N1 AIA sing 7 n n C3 H3 AIA sing 8 n n C4 C9 AIA sing 9 n n C4 N1 AIA sing 10 n n C4 O10 AIA doub 11 n n C5 C7 AIA sing 12 n n C5 H51 AIA sing 13 n n C5 H52 AIA sing 14 n n C6 C11 AIA trip 15 n n C7 H71 AIA sing 16 n n C7 H72 AIA sing 17 n n C8 N12 AIA sing 18 n n C8 H81 AIA sing 19 n n C8 H82 AIA sing 20 n n C9 C13 AIA sing 21 n n C9 N14 AIA sing 22 n n C9 H9 AIA sing 23 n n C11 H11 AIA sing 24 n n N12 H121 AIA sing 25 n n N12 H122 AIA sing 26 n n C13 C16 AIA sing 27 n n C13 C17 AIA sing 28 n n C13 H13 AIA sing 29 n n N14 H141 AIA sing 30 n n N14 H142 AIA sing 31 n n C16 C18 AIA sing 32 n n C16 H161 AIA sing 33 n n C16 H162 AIA sing 34 n n C17 C19 AIA sing 35 n n C17 H171 AIA sing 36 n n C17 H172 AIA sing 37 n n C18 C19 AIA sing 38 n n C18 H181 AIA sing 39 n n C18 H182 AIA sing 40 n n C19 H191 AIA sing 41 n n C19 H192 AIA sing 42 n n # _atom_sites.entry_id 2GBF _atom_sites.fract_transf_matrix[1][1] 0.004804 _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] 0.004804 _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] 0.004804 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id AIA _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 768 _pdbx_nonpoly_scheme.auth_seq_num 768 _pdbx_nonpoly_scheme.pdb_mon_id AIA _pdbx_nonpoly_scheme.auth_mon_id AIA _pdbx_nonpoly_scheme.pdb_ins_code . # 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 C2 AIA . . . C 2 14.277 39.318 -83.274 1 65.23 ? C2 AIA 768 A 1 HETATM 2 C C3 AIA . . . C 2 16.303 38.039 -83.799 1 65.23 ? C3 AIA 768 A 1 HETATM 3 C C4 AIA . . . C 2 14.808 37.193 -81.951 1 65.23 ? C4 AIA 768 A 1 HETATM 4 C C5 AIA . . . C 2 14.705 39.653 -84.705 1 65.23 ? C5 AIA 768 A 1 HETATM 5 C C6 AIA . . . C 2 14.643 40.417 -82.337 1 65.23 ? C6 AIA 768 A 1 HETATM 6 C C7 AIA . . . C 2 16.17 39.24 -84.762 1 65.23 ? C7 AIA 768 A 1 HETATM 7 C C8 AIA . . . C 2 17.642 38.286 -83.087 1 65.23 ? C8 AIA 768 A 1 HETATM 8 C C9 AIA . . . C 2 13.514 37.361 -81.106 1 65.23 ? C9 AIA 768 A 1 HETATM 9 N N1 AIA . . . C 2 15.097 38.124 -82.937 1 65.23 ? N1 AIA 768 A 1 HETATM 10 O O10 AIA . . . C 2 15.513 36.221 -81.698 1 65.23 ? O10 AIA 768 A 1 HETATM 11 C C11 AIA . . . C 2 14.962 41.257 -81.554 1 65.23 ? C11 AIA 768 A 1 HETATM 12 N N12 AIA . . . C 2 17.688 38.586 -81.772 1 65.23 ? N12 AIA 768 A 1 HETATM 13 C C13 AIA . . . C 2 13.663 38.085 -79.754 1 65.23 ? C13 AIA 768 A 1 HETATM 14 N N14 AIA . . . C 2 12.976 36.028 -80.93 1 65.23 ? N14 AIA 768 A 1 HETATM 15 C C16 AIA . . . C 2 12.342 38.54 -79.132 1 65.23 ? C16 AIA 768 A 1 HETATM 16 C C17 AIA . . . C 2 14.301 37.3 -78.614 1 65.23 ? C17 AIA 768 A 1 HETATM 17 C C18 AIA . . . C 2 12.73 38.959 -77.714 1 65.23 ? C18 AIA 768 A 1 HETATM 18 C C19 AIA . . . C 2 13.997 38.156 -77.379 1 65.23 ? C19 AIA 768 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 18 #