data_5Y6K # _model_server_result.job_id q8k5pVG6ZczW_izCHWa6GQ _model_server_result.datetime_utc '2025-01-11 20:44:25' _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 5y6k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":705}' # _entry.id 5Y6K # _exptl.entry_id 5Y6K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 503.462 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-6-[2-(7-azido-4-methyl-2-oxidanylidene-chromen-3-yl)ethanoylamino]-2-[bis(2-hydroxy-2-oxoethyl)amino]hexanoic acid' _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 5Y6K _cell.length_a 138.012 _cell.length_b 155.752 _cell.length_c 107.554 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y6K _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,G _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 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 ? 4 E N N ? 4 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 9 A CYS 9 1_555 A SG CYS 48 A CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? disulf ? disulf2 A SG CYS 19 A CYS 19 1_555 A SG CYS 39 A CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? disulf ? disulf3 A SG CYS 118 A CYS 118 1_555 A SG CYS 194 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 137 A CYS 137 1_555 A SG CYS 331 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? disulf ? disulf5 A SG CYS 158 A CYS 158 1_555 A SG CYS 174 A CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf6 A SG CYS 161 A CYS 161 1_555 A SG CYS 179 A CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? disulf ? disulf7 A SG CYS 171 A CYS 171 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 A SG CYS 227 A CYS 227 1_555 A SG CYS 241 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf9 A SG CYS 339 A CYS 339 1_555 A SG CYS 596 A CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf10 A SG CYS 345 A CYS 345 1_555 A SG CYS 377 A CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf11 A SG CYS 355 A CYS 355 1_555 A SG CYS 368 A CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf12 A SG CYS 402 A CYS 402 1_555 A SG CYS 674 A CYS 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf13 A SG CYS 450 A CYS 450 1_555 A SG CYS 523 A CYS 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf14 A SG CYS 474 A CYS 474 1_555 A SG CYS 665 A CYS 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf15 A SG CYS 484 A CYS 484 1_555 A SG CYS 498 A CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf16 A SG CYS 495 A CYS 495 1_555 A SG CYS 506 A CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf17 A SG CYS 563 A CYS 563 1_555 A SG CYS 577 A CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc1 A OH TYR 188 A TYR 188 1_555 D FE FE . A FE 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc2 A OD1 ASP 392 A ASP 392 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc3 A OH TYR 426 A TYR 426 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc4 A OH TYR 517 A TYR 517 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc5 A NE2 HIS 585 A HIS 585 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc6 B O7 MLI . A MLI 701 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc7 B O9 MLI . A MLI 701 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? metalc ? metalc8 D FE FE . A FE 703 1_555 E N1 8R6 . A 8R6 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc9 D FE FE . A FE 703 1_555 E O5 8R6 . A 8R6 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc10 D FE FE . A FE 703 1_555 E O13 8R6 . A 8R6 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? # _chem_comp.formula 'C22 H25 N5 O9' _chem_comp.formula_weight 503.462 _chem_comp.id 8R6 _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-6-[2-(7-azido-4-methyl-2-oxidanylidene-chromen-3-yl)ethanoylamino]-2-[bis(2-hydroxy-2-oxoethyl)amino]hexanoic acid' _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 C21 C22 8R6 sing 1 n n C21 C19 8R6 sing 2 n n C28 C23 8R6 sing 3 n n C22 C23 8R6 doub 4 n n C22 C27 8R6 sing 5 n n O29 C27 8R6 doub 6 n n C23 C24 8R6 sing 7 n n C27 O26 8R6 sing 8 n n C24 C30 8R6 doub 9 n y C24 C25 8R6 sing 10 n y C19 O20 8R6 doub 11 n n C19 N18 8R6 sing 12 n n O26 C25 8R6 sing 13 n n C30 C31 8R6 sing 14 n y C25 C33 8R6 doub 15 n y C31 C32 8R6 doub 16 n y C33 C32 8R6 sing 17 n y N18 C17 8R6 sing 18 n n C17 C16 8R6 sing 19 n n C32 N34 8R6 sing 20 n n C16 C15 8R6 sing 21 n n O4 C3 8R6 doub 22 n n C3 C2 8R6 sing 23 n n C3 O5 8R6 sing 24 n n C2 N1 8R6 sing 25 n n O8 C7 8R6 doub 26 n n C15 C14 8R6 sing 27 n n O13 C11 8R6 doub 28 n n C7 O9 8R6 sing 29 n n C7 C6 8R6 sing 30 n n O12 C11 8R6 sing 31 n n C11 C10 8R6 sing 32 n n N1 C6 8R6 sing 33 n n N1 C10 8R6 sing 34 n n C14 C6 8R6 sing 35 n n C33 H1 8R6 sing 36 n n C31 H4 8R6 sing 37 n n C30 H5 8R6 sing 38 n n C28 H6 8R6 sing 39 n n C28 H7 8R6 sing 40 n n C28 H8 8R6 sing 41 n n C21 H9 8R6 sing 42 n n C21 H10 8R6 sing 43 n n N18 H11 8R6 sing 44 n n C17 H12 8R6 sing 45 n n C17 H13 8R6 sing 46 n n C16 H14 8R6 sing 47 n n C16 H15 8R6 sing 48 n n C15 H16 8R6 sing 49 n n C15 H17 8R6 sing 50 n n C14 H18 8R6 sing 51 n n C14 H19 8R6 sing 52 n n C6 H20 8R6 sing 53 n n O9 H21 8R6 sing 54 n n C2 H23 8R6 sing 55 n n C2 H24 8R6 sing 56 n n O5 H25 8R6 sing 57 n n C10 H26 8R6 sing 58 n n C10 H27 8R6 sing 59 n n O12 H28 8R6 sing 60 n n N34 N2 8R6 doub 61 n n N2 N3 8R6 doub 62 n n # _atom_sites.entry_id 5Y6K _atom_sites.fract_transf_matrix[1][1] 0.007246 _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] 0.00642 _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] 0.009298 _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 MLI A 1 701 702 MLI MLI . C 3 FE A 1 702 1 FE FE . D 3 FE A 1 703 2 FE FE . E 4 8R6 A 1 704 3 8R6 NAC . F 4 8R6 A 1 705 4 8R6 NAC . G 5 HOH A 1 801 5 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 O O29 8R6 . . . F 4 50.755 39.287 23.172 1 102.2 ? O29 8R6 705 A 1 HETATM 2 C C27 8R6 . . . F 4 49.85 39.783 22.479 1 99.99 ? C27 8R6 705 A 1 HETATM 3 O O26 8R6 . . . F 4 49.314 40.992 22.816 1 98.51 ? O26 8R6 705 A 1 HETATM 4 C C25 8R6 . . . F 4 48.326 41.58 22.12 1 89.09 ? C25 8R6 705 A 1 HETATM 5 C C33 8R6 . . . F 4 47.84 42.8 22.524 1 81.88 ? C33 8R6 705 A 1 HETATM 6 C C32 8R6 . . . F 4 46.839 43.41 21.787 1 81.6 ? C32 8R6 705 A 1 HETATM 7 N N34 8R6 . . . F 4 46.363 44.594 22.162 1 80.93 ? N34 8R6 705 A 1 HETATM 8 C C31 8R6 . . . F 4 46.311 42.815 20.666 1 90.39 ? C31 8R6 705 A 1 HETATM 9 C C30 8R6 . . . F 4 46.765 41.571 20.23 1 96.35 ? C30 8R6 705 A 1 HETATM 10 C C24 8R6 . . . F 4 47.763 40.92 20.926 1 95.89 ? C24 8R6 705 A 1 HETATM 11 C C23 8R6 . . . F 4 48.288 39.629 20.509 1 92.81 ? C23 8R6 705 A 1 HETATM 12 C C28 8R6 . . . F 4 47.781 38.917 19.292 1 87.35 ? C28 8R6 705 A 1 HETATM 13 C C22 8R6 . . . F 4 49.37 39.036 21.312 1 96.07 ? C22 8R6 705 A 1 HETATM 14 C C21 8R6 . . . F 4 49.98 37.701 21.004 1 95.66 ? C21 8R6 705 A 1 HETATM 15 C C19 8R6 . . . F 4 49.007 36.668 21.482 1 107.16 ? C19 8R6 705 A 1 HETATM 16 O O20 8R6 . . . F 4 49.358 35.81 22.28 1 103.53 ? O20 8R6 705 A 1 HETATM 17 N N18 8R6 . . . F 4 47.752 36.738 21.077 1 114.57 ? N18 8R6 705 A 1 HETATM 18 C C17 8R6 . . . F 4 46.699 36.014 21.661 1 101.35 ? C17 8R6 705 A 1 HETATM 19 C C16 8R6 . . . F 4 46.241 36.794 22.874 1 107.51 ? C16 8R6 705 A 1 HETATM 20 C C15 8R6 . . . F 4 44.8 36.421 23.237 1 107.23 ? C15 8R6 705 A 1 HETATM 21 C C14 8R6 . . . F 4 44.234 37.527 24.098 1 118.21 ? C14 8R6 705 A 1 HETATM 22 C C6 8R6 . . . F 4 44.046 38.785 23.246 1 130.83 ? C6 8R6 705 A 1 HETATM 23 C C7 8R6 . . . F 4 42.604 39.172 23.317 1 125.23 ? C7 8R6 705 A 1 HETATM 24 O O8 8R6 . . . F 4 42.228 40.15 23.96 1 131.54 ? O8 8R6 705 A 1 HETATM 25 O O9 8R6 . . . F 4 41.823 38.442 22.7 1 100.28 ? O9 8R6 705 A 1 HETATM 26 N N1 8R6 . . . F 4 45.043 39.828 23.597 1 133.76 ? N1 8R6 705 A 1 HETATM 27 C C2 8R6 . . . F 4 44.748 40.516 24.881 1 115.4 ? C2 8R6 705 A 1 HETATM 28 C C3 8R6 . . . F 4 46.008 41.11 25.438 1 96.74 ? C3 8R6 705 A 1 HETATM 29 O O4 8R6 . . . F 4 47.075 40.42 25.423 1 80.86 ? O4 8R6 705 A 1 HETATM 30 O O5 8R6 . . . F 4 45.915 42.256 25.92 1 75.24 ? O5 8R6 705 A 1 HETATM 31 C C10 8R6 . . . F 4 45.2 40.772 22.499 1 116.93 ? C10 8R6 705 A 1 HETATM 32 C C11 8R6 . . . F 4 44.004 41.647 22.246 1 105.14 ? C11 8R6 705 A 1 HETATM 33 O O12 8R6 . . . F 4 43.488 42.243 23.18 1 102.98 ? O12 8R6 705 A 1 HETATM 34 O O13 8R6 . . . F 4 43.579 41.781 21.111 1 90.02 ? O13 8R6 705 A 1 # _model_server_stats.io_time_ms 85 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 534 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 34 #