data_1KLZ # _model_server_result.job_id QBDfoMBTp4-DHD8PJx_gWg _model_server_result.datetime_utc '2024-11-13 04:28:09' _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 1klz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2001}' # _entry.id 1KLZ # _exptl.entry_id 1KLZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 1KLZ _cell.length_a 58.225 _cell.length_b 103.295 _cell.length_c 74.582 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KLZ _symmetry.cell_setting orthorhombic _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 ? dimeric 2 author_defined_assembly 1 PISA,PQS dimeric 2 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,E 1 1,2 A,B,C,D,E 2 1,3 # 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' 3_656 -x+1,y,-z+3/2 -1 0 0 0 1 0 0 0 -1 58.225 0 111.873 3 'crystal symmetry operation' 4_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 74.582 # _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 # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 C2 U5P sing 330 n n N1 C6 U5P sing 331 n n N1 C1' U5P sing 332 n n C2 N3 U5P sing 333 n n C2 O2 U5P doub 334 n n N3 C4 U5P sing 335 n n N3 HN3 U5P sing 336 n n C4 C5 U5P sing 337 n n C4 O4 U5P doub 338 n n C5 C6 U5P doub 339 n n C5 H5 U5P sing 340 n n C6 H6 U5P sing 341 n n C1' C2' U5P sing 342 n n C1' O4' U5P sing 343 n n C1' H1' U5P sing 344 n n C2' O2' U5P sing 345 n n C2' C3' U5P sing 346 n n C2' H2' U5P sing 347 n n O2' HO2' U5P sing 348 n n C3' C4' U5P sing 349 n n C3' O3' U5P sing 350 n n C3' H3' U5P sing 351 n n C4' O4' U5P sing 352 n n C4' C5' U5P sing 353 n n C4' H4' U5P sing 354 n n O3' HO3' U5P sing 355 n n C5' O5' U5P sing 356 n n C5' "H5'1" U5P sing 357 n n C5' "H5'2" U5P sing 358 n n O5' P U5P sing 359 n n P O1P U5P doub 360 n n P O2P U5P sing 361 n n P O3P U5P sing 362 n n O2P HOP2 U5P sing 363 n n O3P HOP3 U5P sing 364 n n # _atom_sites.entry_id 1KLZ _atom_sites.fract_transf_matrix[1][1] 0.017175 _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] 0.009681 _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] 0.013408 _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 CL A 1 5001 5001 CL CL . C 2 CL A 1 5002 5002 CL CL . D 3 U5P A 1 2001 2001 U5P U . E 4 HOH A 1 3001 3001 HOH HOH . E 4 HOH A 2 3003 3003 HOH HOH . E 4 HOH A 3 3004 3004 HOH HOH . E 4 HOH A 4 3005 3005 HOH HOH . E 4 HOH A 5 3006 3006 HOH HOH . E 4 HOH A 6 3007 3007 HOH HOH . E 4 HOH A 7 3008 3008 HOH HOH . E 4 HOH A 8 3009 3009 HOH HOH . E 4 HOH A 9 3010 3010 HOH HOH . E 4 HOH A 10 3011 3011 HOH HOH . E 4 HOH A 11 3012 3012 HOH HOH . E 4 HOH A 12 3013 3013 HOH HOH . E 4 HOH A 13 3014 3014 HOH HOH . E 4 HOH A 14 3015 3015 HOH HOH . E 4 HOH A 15 3016 3016 HOH HOH . E 4 HOH A 16 3017 3017 HOH HOH . E 4 HOH A 17 3018 3018 HOH HOH . E 4 HOH A 18 3019 3019 HOH HOH . E 4 HOH A 19 3020 3020 HOH HOH . E 4 HOH A 20 3021 3021 HOH HOH . E 4 HOH A 21 3022 3022 HOH HOH . E 4 HOH A 22 3023 3023 HOH HOH . E 4 HOH A 23 3024 3024 HOH HOH . E 4 HOH A 24 3025 3025 HOH HOH . E 4 HOH A 25 3026 3026 HOH HOH . E 4 HOH A 26 3027 3027 HOH HOH . E 4 HOH A 27 3028 3028 HOH HOH . E 4 HOH A 28 3029 3029 HOH HOH . E 4 HOH A 29 3030 3030 HOH HOH . E 4 HOH A 30 3031 3031 HOH HOH . E 4 HOH A 31 3032 3032 HOH HOH . E 4 HOH A 32 3033 3033 HOH HOH . E 4 HOH A 33 3034 3034 HOH HOH . E 4 HOH A 34 3035 3035 HOH HOH . E 4 HOH A 35 3036 3036 HOH HOH . E 4 HOH A 36 3037 3037 HOH HOH . E 4 HOH A 37 3038 3038 HOH HOH . E 4 HOH A 38 3039 3039 HOH HOH . E 4 HOH A 39 3040 3040 HOH HOH . E 4 HOH A 40 3041 3041 HOH HOH . E 4 HOH A 41 3042 3042 HOH HOH . E 4 HOH A 42 3043 3043 HOH HOH . E 4 HOH A 43 3044 3044 HOH HOH . E 4 HOH A 44 3045 3045 HOH HOH . E 4 HOH A 45 3046 3046 HOH HOH . E 4 HOH A 46 3047 3047 HOH HOH . E 4 HOH A 47 3048 3048 HOH HOH . E 4 HOH A 48 3049 3049 HOH HOH . E 4 HOH A 49 3050 3050 HOH HOH . E 4 HOH A 50 3051 3051 HOH HOH . E 4 HOH A 51 3052 3052 HOH HOH . E 4 HOH A 52 3053 3053 HOH HOH . E 4 HOH A 53 3054 3054 HOH HOH . E 4 HOH A 54 3055 3055 HOH HOH . E 4 HOH A 55 3056 3056 HOH HOH . E 4 HOH A 56 3057 3057 HOH HOH . E 4 HOH A 57 3058 3058 HOH HOH . E 4 HOH A 58 3059 3059 HOH HOH . E 4 HOH A 59 3060 3060 HOH HOH . E 4 HOH A 60 3061 3061 HOH HOH . E 4 HOH A 61 3062 3062 HOH HOH . E 4 HOH A 62 3063 3063 HOH HOH . E 4 HOH A 63 3064 3064 HOH HOH . E 4 HOH A 64 3065 3065 HOH HOH . E 4 HOH A 65 3066 3066 HOH HOH . E 4 HOH A 66 3067 3067 HOH HOH . E 4 HOH A 67 3068 3068 HOH HOH . E 4 HOH A 68 3069 3069 HOH HOH . E 4 HOH A 69 3070 3070 HOH HOH . E 4 HOH A 70 3071 3071 HOH HOH . E 4 HOH A 71 3072 3072 HOH HOH . E 4 HOH A 72 3073 3073 HOH HOH . E 4 HOH A 73 3074 3074 HOH HOH . E 4 HOH A 74 3075 3075 HOH HOH . E 4 HOH A 75 3076 3076 HOH HOH . E 4 HOH A 76 3077 3077 HOH HOH . E 4 HOH A 77 3078 3078 HOH HOH . E 4 HOH A 78 3079 3079 HOH HOH . E 4 HOH A 79 3080 3080 HOH HOH . E 4 HOH A 80 3081 3081 HOH HOH . E 4 HOH A 81 3082 3082 HOH HOH . E 4 HOH A 82 3083 3083 HOH HOH . E 4 HOH A 83 3084 3084 HOH HOH . E 4 HOH A 84 3085 3085 HOH HOH . E 4 HOH A 85 3086 3086 HOH HOH . E 4 HOH A 86 3087 3087 HOH HOH . E 4 HOH A 87 3088 3088 HOH HOH . E 4 HOH A 88 3089 3089 HOH HOH . E 4 HOH A 89 3090 3090 HOH HOH . E 4 HOH A 90 3091 3091 HOH HOH . E 4 HOH A 91 3092 3092 HOH HOH . E 4 HOH A 92 3093 3093 HOH HOH . E 4 HOH A 93 3094 3094 HOH HOH . E 4 HOH A 94 3095 3095 HOH HOH . E 4 HOH A 95 3096 3096 HOH HOH . E 4 HOH A 96 3097 3097 HOH HOH . E 4 HOH A 97 3098 3098 HOH HOH . E 4 HOH A 98 3099 3099 HOH HOH . E 4 HOH A 99 3100 3100 HOH HOH . E 4 HOH A 100 3101 3101 HOH HOH . E 4 HOH A 101 3102 3102 HOH HOH . E 4 HOH A 102 3103 3103 HOH HOH . E 4 HOH A 103 3104 3104 HOH HOH . E 4 HOH A 104 3105 3105 HOH HOH . E 4 HOH A 105 3106 3106 HOH HOH . E 4 HOH A 106 3107 3107 HOH HOH . E 4 HOH A 107 3108 3108 HOH HOH . E 4 HOH A 108 3109 3109 HOH HOH . E 4 HOH A 109 3110 3110 HOH HOH . E 4 HOH A 110 3111 3111 HOH HOH . E 4 HOH A 111 3112 3112 HOH HOH . E 4 HOH A 112 3113 3113 HOH HOH . E 4 HOH A 113 3114 3114 HOH HOH . E 4 HOH A 114 3115 3115 HOH HOH . E 4 HOH A 115 3116 3116 HOH HOH . E 4 HOH A 116 3117 3117 HOH HOH . E 4 HOH A 117 3118 3118 HOH HOH . E 4 HOH A 118 3119 3119 HOH HOH . E 4 HOH A 119 3120 3120 HOH HOH . E 4 HOH A 120 3121 3121 HOH HOH . E 4 HOH A 121 3122 3122 HOH HOH . E 4 HOH A 122 3123 3123 HOH HOH . E 4 HOH A 123 3124 3124 HOH HOH . E 4 HOH A 124 3125 3125 HOH HOH . E 4 HOH A 125 3126 3126 HOH HOH . E 4 HOH A 126 3127 3127 HOH HOH . E 4 HOH A 127 3128 3128 HOH HOH . E 4 HOH A 128 3129 3129 HOH HOH . E 4 HOH A 129 3130 3130 HOH HOH . E 4 HOH A 130 3131 3131 HOH HOH . E 4 HOH A 131 3132 3132 HOH HOH . E 4 HOH A 132 3133 3133 HOH HOH . E 4 HOH A 133 3134 3134 HOH HOH . E 4 HOH A 134 3135 3135 HOH HOH . E 4 HOH A 135 3136 3136 HOH HOH . E 4 HOH A 136 3137 3137 HOH HOH . E 4 HOH A 137 3138 3138 HOH HOH . E 4 HOH A 138 3139 3139 HOH HOH . E 4 HOH A 139 3140 3140 HOH HOH . E 4 HOH A 140 3141 3141 HOH HOH . E 4 HOH A 141 3142 3142 HOH HOH . E 4 HOH A 142 3143 3143 HOH HOH . E 4 HOH A 143 3144 3144 HOH HOH . E 4 HOH A 144 3145 3145 HOH HOH . E 4 HOH A 145 3146 3146 HOH HOH . E 4 HOH A 146 3147 3147 HOH HOH . E 4 HOH A 147 3148 3148 HOH HOH . E 4 HOH A 148 3149 3149 HOH HOH . E 4 HOH A 149 3150 3150 HOH HOH . E 4 HOH A 150 3151 3151 HOH HOH . E 4 HOH A 151 3152 3152 HOH HOH . E 4 HOH A 152 3153 3153 HOH HOH . E 4 HOH A 153 3154 3154 HOH HOH . E 4 HOH A 154 3155 3155 HOH HOH . E 4 HOH A 155 3156 3156 HOH HOH . E 4 HOH A 156 3157 3157 HOH HOH . E 4 HOH A 157 3158 3158 HOH HOH . E 4 HOH A 158 3159 3159 HOH HOH . E 4 HOH A 159 3160 3160 HOH HOH . E 4 HOH A 160 3161 3161 HOH HOH . E 4 HOH A 161 3162 3162 HOH HOH . E 4 HOH A 162 3163 3163 HOH HOH . E 4 HOH A 163 3164 3164 HOH HOH . E 4 HOH A 164 3165 3165 HOH HOH . E 4 HOH A 165 3166 3166 HOH HOH . E 4 HOH A 166 3167 3167 HOH HOH . E 4 HOH A 167 3168 3168 HOH HOH . E 4 HOH A 168 3169 3169 HOH HOH . E 4 HOH A 169 3170 3170 HOH HOH . E 4 HOH A 170 3171 3171 HOH HOH . E 4 HOH A 171 3172 3172 HOH HOH . E 4 HOH A 172 3173 3173 HOH HOH . E 4 HOH A 173 3174 3174 HOH HOH . E 4 HOH A 174 3175 3175 HOH HOH . E 4 HOH A 175 3176 3176 HOH HOH . E 4 HOH A 176 3177 3177 HOH HOH . E 4 HOH A 177 3178 3178 HOH HOH . E 4 HOH A 178 3179 3179 HOH HOH . E 4 HOH A 179 3180 3180 HOH HOH . E 4 HOH A 180 3181 3181 HOH HOH . E 4 HOH A 181 3182 3182 HOH HOH . E 4 HOH A 182 3183 3183 HOH HOH . E 4 HOH A 183 3184 3184 HOH HOH . E 4 HOH A 184 3185 3185 HOH HOH . E 4 HOH A 185 3186 3186 HOH HOH . E 4 HOH A 186 3187 3187 HOH HOH . E 4 HOH A 187 3188 3188 HOH HOH . E 4 HOH A 188 3189 3189 HOH HOH . E 4 HOH A 189 3190 3190 HOH HOH . E 4 HOH A 190 3191 3191 HOH HOH . E 4 HOH A 191 3192 3192 HOH HOH . E 4 HOH A 192 3193 3193 HOH HOH . E 4 HOH A 193 3194 3194 HOH HOH . E 4 HOH A 194 3195 3195 HOH HOH . E 4 HOH A 195 3196 3196 HOH HOH . E 4 HOH A 196 3197 3197 HOH HOH . E 4 HOH A 197 3198 3198 HOH HOH . E 4 HOH A 198 3199 3199 HOH HOH . E 4 HOH A 199 3200 3200 HOH HOH . E 4 HOH A 200 3201 3201 HOH HOH . E 4 HOH A 201 3202 3202 HOH HOH . E 4 HOH A 202 3203 3203 HOH HOH . E 4 HOH A 203 3204 3204 HOH HOH . E 4 HOH A 204 3205 3205 HOH HOH . E 4 HOH A 205 3206 3206 HOH HOH . E 4 HOH A 206 3207 3207 HOH HOH . E 4 HOH A 207 3208 3208 HOH HOH . E 4 HOH A 208 3209 3209 HOH HOH . E 4 HOH A 209 3210 3210 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 U5P . . . D 3 41.757 -11.408 38.13 1 5.76 ? N1 U5P 2001 A 1 HETATM 2 C C2 U5P . . . D 3 42.692 -12.222 37.488 1 5.99 ? C2 U5P 2001 A 1 HETATM 3 N N3 U5P . . . D 3 44.01 -11.862 37.67 1 5.95 ? N3 U5P 2001 A 1 HETATM 4 C C4 U5P . . . D 3 44.495 -10.786 38.412 1 6.88 ? C4 U5P 2001 A 1 HETATM 5 C C5 U5P . . . D 3 43.474 -9.987 39.032 1 6.72 ? C5 U5P 2001 A 1 HETATM 6 C C6 U5P . . . D 3 42.187 -10.301 38.887 1 7.19 ? C6 U5P 2001 A 1 HETATM 7 O O2 U5P . . . D 3 42.337 -13.174 36.834 1 5.77 ? O2 U5P 2001 A 1 HETATM 8 O O4 U5P . . . D 3 45.691 -10.623 38.472 1 7.64 ? O4 U5P 2001 A 1 HETATM 9 C C1' U5P . . . D 3 40.333 -11.709 38.045 1 6.36 ? C1' U5P 2001 A 1 HETATM 10 C C2' U5P . . . D 3 39.624 -11.771 36.706 1 6.67 ? C2' U5P 2001 A 1 HETATM 11 O O2' U5P . . . D 3 39.193 -10.494 36.241 1 8.11 ? O2' U5P 2001 A 1 HETATM 12 C C3' U5P . . . D 3 38.482 -12.716 36.98 1 5.82 ? C3' U5P 2001 A 1 HETATM 13 C C4' U5P . . . D 3 39.099 -13.7 37.959 1 5.35 ? C4' U5P 2001 A 1 HETATM 14 O O3' U5P . . . D 3 37.391 -12.004 37.565 1 6.76 ? O3' U5P 2001 A 1 HETATM 15 O O4' U5P . . . D 3 40.05 -12.916 38.711 1 6.02 ? O4' U5P 2001 A 1 HETATM 16 C C5' U5P . . . D 3 39.752 -14.963 37.428 1 8.01 ? C5' U5P 2001 A 1 HETATM 17 O O5' U5P . . . D 3 38.783 -15.618 36.581 1 6.72 ? O5' U5P 2001 A 1 HETATM 18 P P U5P . . . D 3 39.105 -16.951 35.769 1 7.18 ? P U5P 2001 A 1 HETATM 19 O O1P U5P . . . D 3 40.371 -16.831 34.965 1 7.04 ? O1P U5P 2001 A 1 HETATM 20 O O2P U5P . . . D 3 37.924 -17.166 34.874 1 6.58 ? O2P U5P 2001 A 1 HETATM 21 O O3P U5P . . . D 3 39.134 -18.167 36.822 1 7.87 ? O3P U5P 2001 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #