data_1YED # _model_server_result.job_id vzSu95K-X_IF_IC0dAR0gw _model_server_result.datetime_utc '2024-12-01 09:17:53' _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 1yed # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":552}' # _entry.id 1YED # _exptl.entry_id 1YED _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 360.256 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE _entity.pdbx_number_of_molecules 2 _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 1YED _cell.length_a 99.25 _cell.length_b 104.79 _cell.length_c 223.75 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YED _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # 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 dimeric 2 author_and_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,C,E,G,I 1 1 B,D,F,H,J 2 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 x,y,z _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N 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 23 L CYS 23 1_555 A SG CYS 93 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 139 L CYS 137 1_555 A SG CYS 199 L CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf3 B SG CYS 23 A CYS 23 1_555 B SG CYS 93 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 139 A CYS 137 1_555 B SG CYS 199 A CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf5 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf6 C SG CYS 151 H CYS 142 1_555 C SG CYS 206 H CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf7 D SG CYS 22 B CYS 22 1_555 D SG CYS 96 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 D SG CYS 151 B CYS 142 1_555 D SG CYS 206 B CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? # _chem_comp.formula 'C13 H17 N2 O8 P' _chem_comp.formula_weight 360.256 _chem_comp.id PNB _chem_comp.mon_nstd_flag . _chem_comp.name 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE _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 N1 O4 PNB doub 260 n n N1 O5 PNB sing 261 n n N1 C4 PNB sing 262 n n C1 C2 PNB doub 263 n y C1 C6 PNB sing 264 n y C1 C7 PNB sing 265 n n C2 C3 PNB sing 266 n y C2 H2 PNB sing 267 n n C3 C4 PNB doub 268 n y C3 H3 PNB sing 269 n n C4 C5 PNB sing 270 n y C5 C6 PNB doub 271 n y C5 H5 PNB sing 272 n n C6 H6 PNB sing 273 n n C7 O1 PNB sing 274 n n C7 H71 PNB sing 275 n n C7 H72 PNB sing 276 n n O1 P1 PNB sing 277 n n P1 O2 PNB doub 278 n n P1 O3 PNB sing 279 n n P1 C8 PNB sing 280 n n O3 HO3 PNB sing 281 n n C8 C9 PNB sing 282 n n C8 H81 PNB sing 283 n n C8 H82 PNB sing 284 n n C9 C10 PNB sing 285 n n C9 H91 PNB sing 286 n n C9 H92 PNB sing 287 n n C10 C11 PNB sing 288 n n C10 H101 PNB sing 289 n n C10 H102 PNB sing 290 n n C11 O6 PNB doub 291 n n C11 N2 PNB sing 292 n n N2 C12 PNB sing 293 n n N2 HN2 PNB sing 294 n n C12 C13 PNB sing 295 n n C12 H121 PNB sing 296 n n C12 H122 PNB sing 297 n n C13 O7 PNB doub 298 n n C13 O8 PNB sing 299 n n O8 HO8 PNB sing 300 n n # _atom_sites.entry_id 1YED _atom_sites.fract_transf_matrix[1][1] 0.010076 _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] 0.009543 _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] 0.004469 _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 E 3 PNB L 1 551 551 PNB PNB . F 3 PNB A 1 552 552 PNB PNB . G 4 HOH L 1 552 1 HOH HOH . H 4 HOH A 1 553 3 HOH HOH . I 4 HOH H 1 218 2 HOH HOH . J 4 HOH B 1 218 4 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 N N1 PNB . . . F 3 19.293 67.212 35.245 1 38.6 ? N1 PNB 552 A 1 HETATM 2 O O4 PNB . . . F 3 20.187 66.689 34.545 1 38.6 ? O4 PNB 552 A 1 HETATM 3 O O5 PNB . . . F 3 19.565 67.612 36.391 1 38.6 ? O5 PNB 552 A 1 HETATM 4 C C1 PNB . . . F 3 15.282 67.656 33.798 1 38.6 ? C1 PNB 552 A 1 HETATM 5 C C2 PNB . . . F 3 15.616 68.098 35.07 1 38.6 ? C2 PNB 552 A 1 HETATM 6 C C3 PNB . . . F 3 16.92 67.953 35.541 1 38.6 ? C3 PNB 552 A 1 HETATM 7 C C4 PNB . . . F 3 17.907 67.376 34.723 1 38.6 ? C4 PNB 552 A 1 HETATM 8 C C5 PNB . . . F 3 17.564 66.929 33.441 1 38.6 ? C5 PNB 552 A 1 HETATM 9 C C6 PNB . . . F 3 16.257 67.083 32.99 1 38.6 ? C6 PNB 552 A 1 HETATM 10 C C7 PNB . . . F 3 13.868 67.799 33.257 1 38.6 ? C7 PNB 552 A 1 HETATM 11 O O1 PNB . . . F 3 13.293 69.164 33.392 1 13.23 ? O1 PNB 552 A 1 HETATM 12 P P1 PNB . . . F 3 13.485 70.335 32.245 1 13.23 ? P1 PNB 552 A 1 HETATM 13 O O2 PNB . . . F 3 14.044 71.466 32.904 1 13.23 ? O2 PNB 552 A 1 HETATM 14 O O3 PNB . . . F 3 14.241 69.808 31.117 1 13.23 ? O3 PNB 552 A 1 HETATM 15 C C8 PNB . . . F 3 11.865 70.71 31.805 1 13.23 ? C8 PNB 552 A 1 HETATM 16 C C9 PNB . . . F 3 10.858 70.373 32.927 1 35.06 ? C9 PNB 552 A 1 HETATM 17 C C10 PNB . . . F 3 9.443 70.15 32.38 1 35.06 ? C10 PNB 552 A 1 HETATM 18 C C11 PNB . . . F 3 8.333 70.13 33.447 1 35.06 ? C11 PNB 552 A 1 HETATM 19 O O6 PNB . . . F 3 8.437 70.89 34.402 1 35.06 ? O6 PNB 552 A 1 HETATM 20 N N2 PNB . . . F 3 7.245 69.333 33.312 1 35.06 ? N2 PNB 552 A 1 HETATM 21 C C12 PNB . . . F 3 6.229 69.35 34.196 1 35.06 ? C12 PNB 552 A 1 HETATM 22 C C13 PNB . . . F 3 6.427 68.474 35.436 1 35.06 ? C13 PNB 552 A 1 HETATM 23 O O7 PNB . . . F 3 5.452 67.832 35.855 1 35.06 ? O7 PNB 552 A 1 HETATM 24 O O8 PNB . . . F 3 7.359 68.728 36.216 1 35.06 ? O8 PNB 552 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 497 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #