data_1YFY # _model_server_result.job_id oNjKZDdqAJvvbUULtI_4iQ _model_server_result.datetime_utc '2024-10-10 18:27:50' _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 1yfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 1YFY # _exptl.entry_id 1YFY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 122.143 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL _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 120 _cell.entry_id 1YFY _cell.length_a 58.5 _cell.length_b 58.5 _cell.length_c 230.7 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YFY _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 10_665 -y+1,-x+1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 29.25 50.662486 38.45 # _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 metalc ? metalc1 A ND1 HIS 51 A HIS 51 1_555 B FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc2 A OE2 GLU 57 A GLU 57 1_555 B FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc3 A OE1 GLU 57 A GLU 57 1_555 B FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc4 A NE2 HIS 95 A HIS 95 1_555 B FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc5 A SG CYS 125 A CYS 125 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc6 A SG CYS 128 A CYS 128 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc7 A SG CYS 162 A CYS 162 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc8 A SG CYS 165 A CYS 165 1_555 C FE FE . A FE 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc9 B FE FE . A FE 300 1_555 E N10 3HA . A 3HA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc10 B FE FE . A FE 300 1_555 E O11 3HA . A 3HA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? # _chem_comp.formula 'C4 H12 N O3 1' _chem_comp.formula_weight 122.143 _chem_comp.id TRS _chem_comp.mon_nstd_flag . _chem_comp.name 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'TRIS BUFFER' # 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 C C1 TRS sing 350 n n C C2 TRS sing 351 n n C C3 TRS sing 352 n n C N TRS sing 353 n n C1 O1 TRS sing 354 n n C1 H11 TRS sing 355 n n C1 H12 TRS sing 356 n n C2 O2 TRS sing 357 n n C2 H21 TRS sing 358 n n C2 H22 TRS sing 359 n n C3 O3 TRS sing 360 n n C3 H31 TRS sing 361 n n C3 H32 TRS sing 362 n n N HN1 TRS sing 363 n n N HN2 TRS sing 364 n n N HN3 TRS sing 365 n n O1 HO1 TRS sing 366 n n O2 HO2 TRS sing 367 n n O3 HO3 TRS sing 368 n n # _atom_sites.entry_id 1YFY _atom_sites.fract_transf_matrix[1][1] 0.017094 _atom_sites.fract_transf_matrix[1][2] 0.009869 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019738 _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] 0.004335 _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 FE A 1 300 300 FE FE . C 2 FE A 1 301 301 FE FE . D 3 TRS A 1 400 400 TRS TRS . E 4 3HA A 1 401 401 3HA 3HA . # 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 C TRS . . . D 3 17.141 9.111 -11.068 1 85.71 ? C TRS 400 A 1 HETATM 2 C C1 TRS . . . D 3 18.586 9.613 -11.093 1 86.13 ? C1 TRS 400 A 1 HETATM 3 C C2 TRS . . . D 3 17.01 7.998 -12.098 1 85.56 ? C2 TRS 400 A 1 HETATM 4 C C3 TRS . . . D 3 16.922 8.7 -9.599 1 85.39 ? C3 TRS 400 A 1 HETATM 5 N N TRS . . . D 3 16.116 10.096 -11.452 1 85.24 ? N TRS 400 A 1 HETATM 6 O O1 TRS . . . D 3 18.72 11.006 -10.606 1 86.42 ? O1 TRS 400 A 1 HETATM 7 O O2 TRS . . . D 3 17.133 8.507 -13.491 1 85.66 ? O2 TRS 400 A 1 HETATM 8 O O3 TRS . . . D 3 17.862 7.73 -9.102 1 83.84 ? O3 TRS 400 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 8 #