data_2GBG # _model_server_result.job_id k9BggIZhCdAvDyOomTU3eQ _model_server_result.datetime_utc '2025-01-10 19:59:04' _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 2gbg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":768}' # _entry.id 2GBG # _exptl.entry_id 2GBG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 263.378 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1S)-2-[(2S,5R)-2-(AMINOMETHYL)-5-PROP-1-YN-1-YLPYRROLIDIN-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 2GBG _cell.length_a 207.5 _cell.length_b 207.5 _cell.length_c 207.5 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GBG _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,D 1 1 A,B,C,D 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 -103.75 0 -103.75 3 'crystal symmetry operation' 10_554 -y,z+1/2,-x-1/2 0 -1 0 0 0 1 -1 0 0 0 103.75 -103.75 # _struct_asym.details ? _struct_asym.entity_id 3 _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 disulf ? disulf1 A SG CYS 289 A CYS 326 1_555 A SG CYS 300 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 A SG CYS 418 A CYS 455 1_555 A SG CYS 436 A CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 A SG CYS 613 A CYS 650 1_555 A SG CYS 726 A CYS 763 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 B SG CYS 289 B CYS 326 1_555 B SG CYS 300 B CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 B SG CYS 346 B CYS 383 1_555 B SG CYS 358 B CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 613 B CYS 650 1_555 B SG CYS 726 B CYS 763 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A OG SER 594 A SER 631 1_555 D C8 1AD . A 1AD 768 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? # _chem_comp.formula 'C15 H25 N3 O' _chem_comp.formula_weight 263.378 _chem_comp.id 1AD _chem_comp.mon_nstd_flag . _chem_comp.name (1S)-2-[(2S,5R)-2-(AMINOMETHYL)-5-PROP-1-YN-1-YLPYRROLIDIN-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 1AD sing 1 n n C2 C6 1AD sing 2 n n C2 N1 1AD sing 3 n n C2 H2 1AD sing 4 n n C3 C7 1AD sing 5 n n C3 C8 1AD sing 6 n n C3 N1 1AD sing 7 n n C3 H3 1AD sing 8 n n C4 C9 1AD sing 9 n n C4 N1 1AD sing 10 n n C4 O10 1AD doub 11 n n C5 C7 1AD sing 12 n n C5 H51 1AD sing 13 n n C5 H52 1AD sing 14 n n C6 C11 1AD trip 15 n n C7 H71 1AD sing 16 n n C7 H72 1AD sing 17 n n C8 N12 1AD sing 18 n n C8 H81 1AD sing 19 n n C8 H82 1AD sing 20 n n C9 C13 1AD sing 21 n n C9 N14 1AD sing 22 n n C9 H9 1AD sing 23 n n C11 C15 1AD sing 24 n n N12 H121 1AD sing 25 n n N12 H122 1AD sing 26 n n C13 C16 1AD sing 27 n n C13 C17 1AD sing 28 n n C13 H13 1AD sing 29 n n N14 H141 1AD sing 30 n n N14 H142 1AD sing 31 n n C15 H151 1AD sing 32 n n C15 H152 1AD sing 33 n n C15 H153 1AD sing 34 n n C16 C18 1AD sing 35 n n C16 H161 1AD sing 36 n n C16 H162 1AD sing 37 n n C17 C19 1AD sing 38 n n C17 H171 1AD sing 39 n n C17 H172 1AD sing 40 n n C18 C19 1AD sing 41 n n C18 H181 1AD sing 42 n n C18 H182 1AD sing 43 n n C19 H191 1AD sing 44 n n C19 H192 1AD sing 45 n n # _atom_sites.entry_id 2GBG _atom_sites.fract_transf_matrix[1][1] 0.004819 _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] 0.004819 _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] 0.004819 _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 SO4 A 1 900 900 SO4 SO4 . D 3 1AD A 1 768 768 1AD 1AD . # 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 1AD . . . D 3 14.361 39 -83.114 1 50.59 ? C2 1AD 768 A 1 HETATM 2 C C3 1AD . . . D 3 16.411 37.745 -83.518 1 50.59 ? C3 1AD 768 A 1 HETATM 3 C C4 1AD . . . D 3 14.883 36.914 -81.677 1 50.59 ? C4 1AD 768 A 1 HETATM 4 C C5 1AD . . . D 3 14.847 39.299 -84.543 1 50.59 ? C5 1AD 768 A 1 HETATM 5 C C6 1AD . . . D 3 14.668 40.112 -82.196 1 50.59 ? C6 1AD 768 A 1 HETATM 6 C C7 1AD . . . D 3 16.315 38.884 -84.539 1 50.59 ? C7 1AD 768 A 1 HETATM 7 C C8 1AD . . . D 3 17.742 37.993 -82.794 1 50.59 ? C8 1AD 768 A 1 HETATM 8 C C9 1AD . . . D 3 13.559 37.033 -80.855 1 50.59 ? C9 1AD 768 A 1 HETATM 9 N N1 1AD . . . D 3 15.182 37.84 -82.697 1 50.59 ? N1 1AD 768 A 1 HETATM 10 O O10 1AD . . . D 3 15.614 35.962 -81.379 1 50.59 ? O10 1AD 768 A 1 HETATM 11 C C11 1AD . . . D 3 14.876 40.977 -81.408 1 50.59 ? C11 1AD 768 A 1 HETATM 12 N N12 1AD . . . D 3 17.763 38.294 -81.499 1 50.59 ? N12 1AD 768 A 1 HETATM 13 C C13 1AD . . . D 3 13.598 37.868 -79.557 1 50.59 ? C13 1AD 768 A 1 HETATM 14 N N14 1AD . . . D 3 13.149 35.658 -80.603 1 50.59 ? N14 1AD 768 A 1 HETATM 15 C C15 1AD . . . D 3 15.073 42.028 -80.427 1 50.59 ? C15 1AD 768 A 1 HETATM 16 C C16 1AD . . . D 3 12.39 37.764 -78.634 1 50.59 ? C16 1AD 768 A 1 HETATM 17 C C17 1AD . . . D 3 14.716 37.612 -78.557 1 50.59 ? C17 1AD 768 A 1 HETATM 18 C C18 1AD . . . D 3 12.803 38.688 -77.493 1 50.59 ? C18 1AD 768 A 1 HETATM 19 C C19 1AD . . . D 3 14.34 38.588 -77.438 1 50.59 ? C19 1AD 768 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #