data_5CKR # _model_server_result.job_id o0YkpvvBL_3A3quX0AxjNg _model_server_result.datetime_utc '2024-11-12 21:29:16' _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 5ckr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5CKR # _exptl.entry_id 5CKR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 915.944 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Muraymycin D2' _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 5CKR _cell.length_a 94.48 _cell.length_b 102.05 _cell.length_c 135.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CKR _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 PISA _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 _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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C37 H61 N11 O16' _chem_comp.formula_weight 915.944 _chem_comp.id 57M _chem_comp.mon_nstd_flag . _chem_comp.name 'Muraymycin D2' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'N-({(1S)-2-{[(2S)-1-{[3-({(1S,2S)-2-[(5-amino-5-deoxy-beta-D-ribofuranosyl)oxy]-1-carboxy-2-[(2S,3S,4R,5R)-5-(2,4-dioxo -3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]ethyl}amino)propyl]amino}-4-methyl-1-oxopentan-2-yl]am ino}-1-[(4S)-2-amino-3,4,5,6-tetrahydropyrimidin-4-yl]-2-oxoethyl}carbamoyl)-L-valine' # 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 O56 C55 57M doub 1 n n O57 C55 57M sing 2 n n C55 C51 57M sing 3 n n C54 C52 57M sing 4 n n C51 C52 57M sing 5 n n C51 N50 57M sing 6 n n C52 C53 57M sing 7 n n N50 C48 57M sing 8 n n C48 N47 57M sing 9 n n C48 O49 57M doub 10 n n N47 C46 57M sing 11 n n C64 C63 57M sing 12 n n C64 N61 57M sing 13 n n C63 C58 57M sing 14 n n C03 C02 57M sing 15 n n C46 C58 57M sing 16 n n C46 C44 57M sing 17 n n C58 N59 57M sing 18 n n N61 C60 57M doub 19 n n C44 O45 57M doub 20 n n C44 N43 57M sing 21 n n C01 C02 57M sing 22 n n C02 C04 57M sing 23 n n N43 C05 57M sing 24 n n N59 C60 57M sing 25 n n C60 N62 57M sing 26 n n C05 C04 57M sing 27 n n C05 C06 57M sing 28 n n C06 O07 57M doub 29 n n C06 N08 57M sing 30 n n O42 C40 57M doub 31 n n N08 C09 57M sing 32 n n O33 C29 57M doub 33 n n C40 O41 57M sing 34 n n C40 C13 57M sing 35 n n C11 C10 57M sing 36 n n C11 N12 57M sing 37 n n C09 C10 57M sing 38 n n C29 N30 57M sing 39 n n C29 N28 57M sing 40 n n O26 C27 57M sing 41 n n O26 C25 57M sing 42 n n N30 C31 57M sing 43 n n C27 N28 57M sing 44 n n C27 C37 57M sing 45 n n C13 N12 57M sing 46 n n C13 C14 57M sing 47 n n N28 C34 57M sing 48 n n C31 O32 57M doub 49 n n C31 C35 57M sing 50 n n O38 C37 57M sing 51 n n C25 C14 57M sing 52 n n C25 C36 57M sing 53 n n C34 C35 57M doub 54 n n C37 C36 57M sing 55 n n C14 O15 57M sing 56 n n C36 O39 57M sing 57 n n O15 C16 57M sing 58 n n C19 N20 57M sing 59 n n C19 C18 57M sing 60 n n C16 O17 57M sing 61 n n C16 C21 57M sing 62 n n C22 C21 57M sing 63 n n C22 C18 57M sing 64 n n C22 O23 57M sing 65 n n O17 C18 57M sing 66 n n C21 O24 57M sing 67 n n C10 H1 57M sing 68 n n C10 H2 57M sing 69 n n N12 H3 57M sing 70 n n C13 H5 57M sing 71 n n C21 H6 57M sing 72 n n C22 H7 57M sing 73 n n C01 H8 57M sing 74 n n C01 H9 57M sing 75 n n C01 H10 57M sing 76 n n C02 H11 57M sing 77 n n C03 H12 57M sing 78 n n C03 H13 57M sing 79 n n C03 H14 57M sing 80 n n C04 H15 57M sing 81 n n C04 H16 57M sing 82 n n C05 H17 57M sing 83 n n N08 H18 57M sing 84 n n C09 H19 57M sing 85 n n C09 H20 57M sing 86 n n C11 H21 57M sing 87 n n C11 H22 57M sing 88 n n C14 H23 57M sing 89 n n C16 H24 57M sing 90 n n C18 H25 57M sing 91 n n C19 H26 57M sing 92 n n C19 H27 57M sing 93 n n N20 H28 57M sing 94 n n N20 H29 57M sing 95 n n O23 H31 57M sing 96 n n O24 H32 57M sing 97 n n C25 H33 57M sing 98 n n C27 H34 57M sing 99 n n N30 H35 57M sing 100 n n C34 H36 57M sing 101 n n C35 H37 57M sing 102 n n C36 H38 57M sing 103 n n C37 H39 57M sing 104 n n O38 H40 57M sing 105 n n O39 H41 57M sing 106 n n O41 H42 57M sing 107 n n N43 H43 57M sing 108 n n C46 H44 57M sing 109 n n N47 H45 57M sing 110 n n N50 H46 57M sing 111 n n C51 H47 57M sing 112 n n C52 H48 57M sing 113 n n C53 H49 57M sing 114 n n C53 H50 57M sing 115 n n C53 H51 57M sing 116 n n C54 H52 57M sing 117 n n C54 H53 57M sing 118 n n C54 H54 57M sing 119 n n O57 H55 57M sing 120 n n C58 H56 57M sing 121 n n N59 H57 57M sing 122 n n N62 H58 57M sing 123 n n N62 H59 57M sing 124 n n C63 H60 57M sing 125 n n C63 H61 57M sing 126 n n C64 H62 57M sing 127 n n C64 H63 57M sing 128 n n # _atom_sites.entry_id 5CKR _atom_sites.fract_transf_matrix[1][1] 0.010584 _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] 0.009799 _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] 0.007364 _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 57M A 1 401 360 57M LIG . C 3 HOH A 1 501 6 HOH HOH . C 3 HOH A 2 502 5 HOH HOH . C 3 HOH A 3 503 8 HOH HOH . C 3 HOH A 4 504 2 HOH HOH . C 3 HOH A 5 505 9 HOH HOH . C 3 HOH A 6 506 7 HOH HOH . C 3 HOH A 7 507 3 HOH HOH . C 3 HOH A 8 508 1 HOH HOH . C 3 HOH A 9 509 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 C C10 57M . . . B 2 13.508 19.618 6.979 1 55.62 ? C10 57M 401 A 1 HETATM 2 N N12 57M . . . B 2 11.994 17.625 7.747 1 55.15 ? N12 57M 401 A 1 HETATM 3 C C13 57M . . . B 2 11.128 16.568 7.28 1 63.69 ? C13 57M 401 A 1 HETATM 4 C C21 57M . . . B 2 11.984 13.998 11.198 1 62.4 ? C21 57M 401 A 1 HETATM 5 C C22 57M . . . B 2 13.428 14.061 11.021 1 64.58 ? C22 57M 401 A 1 HETATM 6 C C01 57M . . . B 2 11.957 26.372 2.232 1 44.79 ? C01 57M 401 A 1 HETATM 7 C C02 57M . . . B 2 12.992 25.245 2.246 1 47.74 ? C02 57M 401 A 1 HETATM 8 C C03 57M . . . B 2 13.042 24.504 0.901 1 45.43 ? C03 57M 401 A 1 HETATM 9 C C04 57M . . . B 2 12.945 24.343 3.52 1 54.59 ? C04 57M 401 A 1 HETATM 10 C C05 57M . . . B 2 12.36 22.954 3.36 1 57.76 ? C05 57M 401 A 1 HETATM 11 C C06 57M . . . B 2 12.167 22.173 4.664 1 64.81 ? C06 57M 401 A 1 HETATM 12 O O07 57M . . . B 2 11.044 21.801 4.959 1 84.4 ? O07 57M 401 A 1 HETATM 13 N N08 57M . . . B 2 13.247 21.814 5.555 1 58.09 ? N08 57M 401 A 1 HETATM 14 C C09 57M . . . B 2 12.877 21.044 6.763 1 46.39 ? C09 57M 401 A 1 HETATM 15 C C11 57M . . . B 2 12.683 18.316 6.658 1 50.82 ? C11 57M 401 A 1 HETATM 16 C C14 57M . . . B 2 10.432 15.897 8.483 1 67.59 ? C14 57M 401 A 1 HETATM 17 O O15 57M . . . B 2 11.411 15.211 9.278 1 64.74 ? O15 57M 401 A 1 HETATM 18 C C16 57M . . . B 2 11.488 15.279 10.67 1 60 ? C16 57M 401 A 1 HETATM 19 O O17 57M . . . B 2 12.531 16.265 11.062 1 59.87 ? O17 57M 401 A 1 HETATM 20 C C18 57M . . . B 2 13.78 15.464 11.27 1 63.28 ? C18 57M 401 A 1 HETATM 21 C C19 57M . . . B 2 14.815 15.919 10.302 1 72.41 ? C19 57M 401 A 1 HETATM 22 N N20 57M . . . B 2 16.179 15.953 10.759 1 79.34 ? N20 57M 401 A 1 HETATM 23 O O23 57M . . . B 2 14.064 13.205 11.993 1 63.32 ? O23 57M 401 A 1 HETATM 24 O O24 57M . . . B 2 11.695 13.886 12.616 1 68.17 ? O24 57M 401 A 1 HETATM 25 C C25 57M . . . B 2 9.332 14.955 8.062 1 65.26 ? C25 57M 401 A 1 HETATM 26 O O26 57M . . . B 2 9.668 14.135 6.856 1 62.62 ? O26 57M 401 A 1 HETATM 27 C C27 57M . . . B 2 9.289 12.717 7.174 1 56.24 ? C27 57M 401 A 1 HETATM 28 N N28 57M . . . B 2 10.408 11.857 7.387 1 54.99 ? N28 57M 401 A 1 HETATM 29 C C29 57M . . . B 2 10.476 10.606 6.799 1 50.7 ? C29 57M 401 A 1 HETATM 30 N N30 57M . . . B 2 11.583 9.802 7.012 1 43.08 ? N30 57M 401 A 1 HETATM 31 C C31 57M . . . B 2 12.614 10.21 7.793 1 51.22 ? C31 57M 401 A 1 HETATM 32 O O32 57M . . . B 2 13.579 9.486 7.979 1 57.93 ? O32 57M 401 A 1 HETATM 33 O O33 57M . . . B 2 9.571 10.188 6.087 1 50.96 ? O33 57M 401 A 1 HETATM 34 C C34 57M . . . B 2 11.455 12.25 8.176 1 51.31 ? C34 57M 401 A 1 HETATM 35 C C35 57M . . . B 2 12.564 11.452 8.381 1 57.36 ? C35 57M 401 A 1 HETATM 36 C C36 57M . . . B 2 9.024 13.964 9.111 1 56.12 ? C36 57M 401 A 1 HETATM 37 C C37 57M . . . B 2 8.439 12.853 8.361 1 55.72 ? C37 57M 401 A 1 HETATM 38 O O38 57M . . . B 2 7.119 13.249 7.911 1 61.83 ? O38 57M 401 A 1 HETATM 39 O O39 57M . . . B 2 8.107 14.473 10.12 1 58.15 ? O39 57M 401 A 1 HETATM 40 C C40 57M . . . B 2 10.148 17.076 6.232 1 64.7 ? C40 57M 401 A 1 HETATM 41 O O41 57M . . . B 2 9.626 18.233 6.301 1 65.78 ? O41 57M 401 A 1 HETATM 42 O O42 57M . . . B 2 9.844 16.338 5.247 1 61.98 ? O42 57M 401 A 1 HETATM 43 N N43 57M . . . B 2 11.074 23.084 2.741 1 56.48 ? N43 57M 401 A 1 HETATM 44 C C44 57M . . . B 2 10.483 21.902 2.117 1 57.54 ? C44 57M 401 A 1 HETATM 45 O O45 57M . . . B 2 11.09 20.845 2.149 1 62.65 ? O45 57M 401 A 1 HETATM 46 C C46 57M . . . B 2 9.15 21.985 1.451 1 56.64 ? C46 57M 401 A 1 HETATM 47 N N47 57M . . . B 2 9.358 22.294 0.118 1 64.47 ? N47 57M 401 A 1 HETATM 48 C C48 57M . . . B 2 8.921 23.581 -0.388 1 70.59 ? C48 57M 401 A 1 HETATM 49 O O49 57M . . . B 2 8.385 24.362 0.375 1 80.03 ? O49 57M 401 A 1 HETATM 50 N N50 57M . . . B 2 9.116 23.94 -1.777 1 68.28 ? N50 57M 401 A 1 HETATM 51 C C51 57M . . . B 2 8.65 25.223 -2.184 1 74.89 ? C51 57M 401 A 1 HETATM 52 C C52 57M . . . B 2 9.808 26.219 -2.121 1 54.16 ? C52 57M 401 A 1 HETATM 53 C C53 57M . . . B 2 9.948 26.919 -0.755 1 45.34 ? C53 57M 401 A 1 HETATM 54 C C54 57M . . . B 2 11.147 25.663 -2.616 1 52.19 ? C54 57M 401 A 1 HETATM 55 C C55 57M . . . B 2 8.029 25.111 -3.559 1 93.46 ? C55 57M 401 A 1 HETATM 56 O O56 57M . . . B 2 8.597 24.4 -4.44 1 95.41 ? O56 57M 401 A 1 HETATM 57 O O57 57M . . . B 2 6.934 25.709 -3.823 1 98.27 ? O57 57M 401 A 1 HETATM 58 C C58 57M . . . B 2 8.444 20.543 1.505 1 62.31 ? C58 57M 401 A 1 HETATM 59 N N59 57M . . . B 2 8.495 20.055 2.777 1 64.56 ? N59 57M 401 A 1 HETATM 60 C C60 57M . . . B 2 7.425 19.001 3.103 1 61.87 ? C60 57M 401 A 1 HETATM 61 N N61 57M . . . B 2 6.433 18.654 1.977 1 64.87 ? N61 57M 401 A 1 HETATM 62 N N62 57M . . . B 2 7.354 18.426 4.279 1 62.36 ? N62 57M 401 A 1 HETATM 63 C C63 57M . . . B 2 7.107 20.622 0.795 1 62.35 ? C63 57M 401 A 1 HETATM 64 C C64 57M . . . B 2 6.635 19.408 0.648 1 63.65 ? C64 57M 401 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 64 #