data_1KM6 # _model_server_result.job_id eUY4BqAvj2OccjezaSmrIg _model_server_result.datetime_utc '2024-11-23 07:50:04' _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 1km6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2001}' # _entry.id 1KM6 # _exptl.entry_id 1KM6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 368.191 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "OROTIDINE-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 1KM6 _cell.length_a 58.32 _cell.length_b 103.387 _cell.length_c 73.713 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KM6 _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 1 1,2 A,B,C 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 58.32 0 110.5695 3 'crystal symmetry operation' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 103.387 73.713 # _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 'C10 H13 N2 O11 P' _chem_comp.formula_weight 368.191 _chem_comp.id OMP _chem_comp.mon_nstd_flag . _chem_comp.name "OROTIDINE-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 P O1P OMP doub 237 n n P O2P OMP sing 238 n n P O3P OMP sing 239 n n P O5' OMP sing 240 n n O2P HOP2 OMP sing 241 n n O3P HOP3 OMP sing 242 n n O5' C5' OMP sing 243 n n C5' C4' OMP sing 244 n n C5' "H5'1" OMP sing 245 n n C5' "H5'2" OMP sing 246 n n C4' O4' OMP sing 247 n n C4' C3' OMP sing 248 n n C4' H4' OMP sing 249 n n O4' C1' OMP sing 250 n n C3' C2' OMP sing 251 n n C3' O3' OMP sing 252 n n C3' H3' OMP sing 253 n n O3' HO3' OMP sing 254 n n C2' C1' OMP sing 255 n n C2' O2' OMP sing 256 n n C2' H2' OMP sing 257 n n O2' HO2' OMP sing 258 n n C1' N1 OMP sing 259 n n C1' H1' OMP sing 260 n n N1 C2 OMP sing 261 n n N1 C6 OMP sing 262 n n C2 N3 OMP sing 263 n n C2 O2 OMP doub 264 n n N3 C4 OMP sing 265 n n N3 HN3 OMP sing 266 n n C4 C5 OMP sing 267 n n C4 O4 OMP doub 268 n n C5 C6 OMP doub 269 n n C5 H5 OMP sing 270 n n C6 C7 OMP sing 271 n n C7 O71 OMP doub 272 n n C7 O72 OMP sing 273 n n O72 HO7 OMP sing 274 n n # _atom_sites.entry_id 1KM6 _atom_sites.fract_transf_matrix[1][1] 0.017147 _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] 0.009672 _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] 0.013566 _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 OMP A 1 2001 2001 OMP OMP . C 3 HOH A 1 3001 3001 HOH HOH . C 3 HOH A 2 3002 3002 HOH HOH . C 3 HOH A 3 3003 3003 HOH HOH . C 3 HOH A 4 3004 3004 HOH HOH . C 3 HOH A 5 3005 3005 HOH HOH . C 3 HOH A 6 3006 3006 HOH HOH . C 3 HOH A 7 3007 3007 HOH HOH . C 3 HOH A 8 3008 3008 HOH HOH . C 3 HOH A 9 3009 3009 HOH HOH . C 3 HOH A 10 3010 3010 HOH HOH . C 3 HOH A 11 3011 3011 HOH HOH . C 3 HOH A 12 3012 3012 HOH HOH . C 3 HOH A 13 3013 3013 HOH HOH . C 3 HOH A 14 3014 3014 HOH HOH . C 3 HOH A 15 3015 3015 HOH HOH . C 3 HOH A 16 3016 3016 HOH HOH . C 3 HOH A 17 3017 3017 HOH HOH . C 3 HOH A 18 3018 3018 HOH HOH . C 3 HOH A 19 3019 3019 HOH HOH . C 3 HOH A 20 3020 3020 HOH HOH . C 3 HOH A 21 3021 3021 HOH HOH . C 3 HOH A 22 3022 3022 HOH HOH . C 3 HOH A 23 3023 3023 HOH HOH . C 3 HOH A 24 3024 3024 HOH HOH . C 3 HOH A 25 3025 3025 HOH HOH . C 3 HOH A 26 3026 3026 HOH HOH . C 3 HOH A 27 3027 3027 HOH HOH . C 3 HOH A 28 3028 3028 HOH HOH . C 3 HOH A 29 3029 3029 HOH HOH . C 3 HOH A 30 3030 3030 HOH HOH . C 3 HOH A 31 3031 3031 HOH HOH . C 3 HOH A 32 3032 3032 HOH HOH . C 3 HOH A 33 3033 3033 HOH HOH . C 3 HOH A 34 3034 3034 HOH HOH . C 3 HOH A 35 3035 3035 HOH HOH . C 3 HOH A 36 3036 3036 HOH HOH . C 3 HOH A 37 3037 3037 HOH HOH . C 3 HOH A 38 3038 3038 HOH HOH . C 3 HOH A 39 3039 3039 HOH HOH . C 3 HOH A 40 3040 3040 HOH HOH . C 3 HOH A 41 3041 3041 HOH HOH . C 3 HOH A 42 3042 3042 HOH HOH . C 3 HOH A 43 3043 3043 HOH HOH . C 3 HOH A 44 3044 3044 HOH HOH . C 3 HOH A 45 3046 3046 HOH HOH . C 3 HOH A 46 3047 3047 HOH HOH . C 3 HOH A 47 3048 3048 HOH HOH . C 3 HOH A 48 3049 3049 HOH HOH . C 3 HOH A 49 3050 3050 HOH HOH . C 3 HOH A 50 3051 3051 HOH HOH . C 3 HOH A 51 3052 3052 HOH HOH . C 3 HOH A 52 3053 3053 HOH HOH . C 3 HOH A 53 3054 3054 HOH HOH . C 3 HOH A 54 3055 3055 HOH HOH . C 3 HOH A 55 3056 3056 HOH HOH . C 3 HOH A 56 3057 3057 HOH HOH . C 3 HOH A 57 3058 3058 HOH HOH . C 3 HOH A 58 3059 3059 HOH HOH . C 3 HOH A 59 3060 3060 HOH HOH . C 3 HOH A 60 3061 3061 HOH HOH . C 3 HOH A 61 3062 3062 HOH HOH . C 3 HOH A 62 3063 3063 HOH HOH . C 3 HOH A 63 3064 3064 HOH HOH . C 3 HOH A 64 3065 3065 HOH HOH . C 3 HOH A 65 3066 3066 HOH HOH . C 3 HOH A 66 3067 3067 HOH HOH . C 3 HOH A 67 3068 3068 HOH HOH . C 3 HOH A 68 3069 3069 HOH HOH . C 3 HOH A 69 3070 3070 HOH HOH . C 3 HOH A 70 3071 3071 HOH HOH . C 3 HOH A 71 3072 3072 HOH HOH . C 3 HOH A 72 3073 3073 HOH HOH . C 3 HOH A 73 3074 3074 HOH HOH . C 3 HOH A 74 3075 3075 HOH HOH . C 3 HOH A 75 3076 3076 HOH HOH . C 3 HOH A 76 3077 3077 HOH HOH . C 3 HOH A 77 3078 3078 HOH HOH . C 3 HOH A 78 3079 3079 HOH HOH . C 3 HOH A 79 3080 3080 HOH HOH . C 3 HOH A 80 3081 3081 HOH HOH . C 3 HOH A 81 3082 3082 HOH HOH . C 3 HOH A 82 3083 3083 HOH HOH . C 3 HOH A 83 3084 3084 HOH HOH . C 3 HOH A 84 3085 3085 HOH HOH . C 3 HOH A 85 3086 3086 HOH HOH . C 3 HOH A 86 3087 3087 HOH HOH . C 3 HOH A 87 3088 3088 HOH HOH . C 3 HOH A 88 3089 3089 HOH HOH . C 3 HOH A 89 3090 3090 HOH HOH . C 3 HOH A 90 3091 3091 HOH HOH . C 3 HOH A 91 3092 3092 HOH HOH . C 3 HOH A 92 3093 3093 HOH HOH . C 3 HOH A 93 3094 3094 HOH HOH . C 3 HOH A 94 3095 3095 HOH HOH . C 3 HOH A 95 3096 3096 HOH HOH . C 3 HOH A 96 3097 3097 HOH HOH . C 3 HOH A 97 3098 3098 HOH HOH . C 3 HOH A 98 3099 3099 HOH HOH . C 3 HOH A 99 3100 3100 HOH HOH . C 3 HOH A 100 3101 3101 HOH HOH . C 3 HOH A 101 3102 3102 HOH HOH . C 3 HOH A 102 3103 3103 HOH HOH . C 3 HOH A 103 3104 3104 HOH HOH . C 3 HOH A 104 3105 3105 HOH HOH . C 3 HOH A 105 3106 3106 HOH HOH . C 3 HOH A 106 3107 3107 HOH HOH . C 3 HOH A 107 3108 3108 HOH HOH . C 3 HOH A 108 3109 3109 HOH HOH . C 3 HOH A 109 3110 3110 HOH HOH . C 3 HOH A 110 3111 3111 HOH HOH . C 3 HOH A 111 3112 3112 HOH HOH . C 3 HOH A 112 3113 3113 HOH HOH . C 3 HOH A 113 3114 3114 HOH HOH . C 3 HOH A 114 3115 3115 HOH HOH . C 3 HOH A 115 3116 3116 HOH HOH . C 3 HOH A 116 3117 3117 HOH HOH . C 3 HOH A 117 3118 3118 HOH HOH . C 3 HOH A 118 3119 3119 HOH HOH . C 3 HOH A 119 3120 3120 HOH HOH . C 3 HOH A 120 3121 3121 HOH HOH . C 3 HOH A 121 3122 3122 HOH HOH . C 3 HOH A 122 3123 3123 HOH HOH . C 3 HOH A 123 3124 3124 HOH HOH . C 3 HOH A 124 3125 3125 HOH HOH . C 3 HOH A 125 3126 3126 HOH HOH . C 3 HOH A 126 3127 3127 HOH HOH . C 3 HOH A 127 3128 3128 HOH HOH . C 3 HOH A 128 3129 3129 HOH HOH . C 3 HOH A 129 3130 3130 HOH HOH . C 3 HOH A 130 3131 3131 HOH HOH . C 3 HOH A 131 3132 3132 HOH HOH . C 3 HOH A 132 3133 3133 HOH HOH . C 3 HOH A 133 3134 3134 HOH HOH . C 3 HOH A 134 3135 3135 HOH HOH . C 3 HOH A 135 3136 3136 HOH HOH . C 3 HOH A 136 3137 3137 HOH HOH . C 3 HOH A 137 3138 3138 HOH HOH . C 3 HOH A 138 3139 3139 HOH HOH . C 3 HOH A 139 3140 3140 HOH HOH . C 3 HOH A 140 3141 3141 HOH HOH . C 3 HOH A 141 3142 3142 HOH HOH . C 3 HOH A 142 3143 3143 HOH HOH . C 3 HOH A 143 3144 3144 HOH HOH . C 3 HOH A 144 3145 3145 HOH HOH . C 3 HOH A 145 3146 3146 HOH HOH . C 3 HOH A 146 3147 3147 HOH HOH . C 3 HOH A 147 3148 3148 HOH HOH . C 3 HOH A 148 3149 3149 HOH HOH . C 3 HOH A 149 3150 3150 HOH HOH . C 3 HOH A 150 3151 3151 HOH HOH . C 3 HOH A 151 3152 3152 HOH HOH . C 3 HOH A 152 3153 3153 HOH HOH . C 3 HOH A 153 3154 3154 HOH HOH . C 3 HOH A 154 3155 3155 HOH HOH . C 3 HOH A 155 3156 3156 HOH HOH . C 3 HOH A 156 3157 3157 HOH HOH . C 3 HOH A 157 3158 3158 HOH HOH . C 3 HOH A 158 3159 3159 HOH HOH . C 3 HOH A 159 3160 3160 HOH HOH . C 3 HOH A 160 3161 3161 HOH HOH . C 3 HOH A 161 3162 3162 HOH HOH . C 3 HOH A 162 3163 3163 HOH HOH . C 3 HOH A 163 3164 3164 HOH HOH . C 3 HOH A 164 3165 3165 HOH HOH . C 3 HOH A 165 3166 3166 HOH HOH . C 3 HOH A 166 3167 3167 HOH HOH . C 3 HOH A 167 3168 3168 HOH HOH . C 3 HOH A 168 3169 3169 HOH HOH . C 3 HOH A 169 3170 3170 HOH HOH . C 3 HOH A 170 3171 3171 HOH HOH . C 3 HOH A 171 3172 3172 HOH HOH . C 3 HOH A 172 3173 3173 HOH HOH . C 3 HOH A 173 3174 3174 HOH HOH . C 3 HOH A 174 3175 3175 HOH HOH . C 3 HOH A 175 3176 3176 HOH HOH . C 3 HOH A 176 3177 3177 HOH HOH . C 3 HOH A 177 3178 3178 HOH HOH . C 3 HOH A 178 3179 3179 HOH HOH . C 3 HOH A 179 3180 3180 HOH HOH . C 3 HOH A 180 3181 3181 HOH HOH . C 3 HOH A 181 3182 3182 HOH HOH . C 3 HOH A 182 3183 3183 HOH HOH . C 3 HOH A 183 3184 3184 HOH HOH . C 3 HOH A 184 3185 3185 HOH HOH . C 3 HOH A 185 3186 3186 HOH HOH . C 3 HOH A 186 3187 3187 HOH HOH . C 3 HOH A 187 3188 3188 HOH HOH . C 3 HOH A 188 3189 3189 HOH HOH . C 3 HOH A 189 3190 3190 HOH HOH . C 3 HOH A 190 3191 3191 HOH HOH . C 3 HOH A 191 3192 3192 HOH HOH . C 3 HOH A 192 3193 3193 HOH HOH . C 3 HOH A 193 3194 3194 HOH HOH . C 3 HOH A 194 3195 3195 HOH HOH . C 3 HOH A 195 3196 3196 HOH HOH . C 3 HOH A 196 3197 3197 HOH HOH . C 3 HOH A 197 3198 3198 HOH HOH . C 3 HOH A 198 3199 3199 HOH HOH . C 3 HOH A 199 3200 3200 HOH HOH . C 3 HOH A 200 3201 3201 HOH HOH . C 3 HOH A 201 3202 3202 HOH HOH . C 3 HOH A 202 3203 3203 HOH HOH . C 3 HOH A 203 3204 3204 HOH HOH . C 3 HOH A 204 3205 3205 HOH HOH . C 3 HOH A 205 3206 3206 HOH HOH . C 3 HOH A 206 3207 3207 HOH HOH . C 3 HOH A 207 3208 3208 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 P P OMP . . . B 2 39.208 34.69 35.291 1 9.19 ? P OMP 2001 A 1 HETATM 2 O O1P OMP . . . B 2 40.481 34.85 34.502 1 9.43 ? O1P OMP 2001 A 1 HETATM 3 O O2P OMP . . . B 2 38.049 34.464 34.393 1 8.67 ? O2P OMP 2001 A 1 HETATM 4 O O3P OMP . . . B 2 39.276 33.473 36.349 1 9.06 ? O3P OMP 2001 A 1 HETATM 5 O O5' OMP . . . B 2 38.837 36.023 36.112 1 7.5 ? O5' OMP 2001 A 1 HETATM 6 C C5' OMP . . . B 2 39.768 36.678 36.979 1 11.29 ? C5' OMP 2001 A 1 HETATM 7 C C4' OMP . . . B 2 39.085 37.93 37.476 1 7.41 ? C4' OMP 2001 A 1 HETATM 8 O O4' OMP . . . B 2 39.997 38.678 38.28 1 7.7 ? O4' OMP 2001 A 1 HETATM 9 C C3' OMP . . . B 2 38.535 38.921 36.476 1 8.21 ? C3' OMP 2001 A 1 HETATM 10 O O3' OMP . . . B 2 37.404 39.627 36.99 1 9.5 ? O3' OMP 2001 A 1 HETATM 11 C C2' OMP . . . B 2 39.701 39.873 36.295 1 6.66 ? C2' OMP 2001 A 1 HETATM 12 O O2' OMP . . . B 2 39.337 41.169 35.814 1 9.06 ? O2' OMP 2001 A 1 HETATM 13 C C1' OMP . . . B 2 40.311 39.898 37.681 1 7.56 ? C1' OMP 2001 A 1 HETATM 14 N N1 OMP . . . B 2 41.714 40.267 37.858 1 7.45 ? N1 OMP 2001 A 1 HETATM 15 C C2 OMP . . . B 2 42.673 39.497 37.213 1 8.79 ? C2 OMP 2001 A 1 HETATM 16 O O2 OMP . . . B 2 42.354 38.547 36.531 1 9.06 ? O2 OMP 2001 A 1 HETATM 17 N N3 OMP . . . B 2 43.982 39.882 37.395 1 8.59 ? N3 OMP 2001 A 1 HETATM 18 C C4 OMP . . . B 2 44.433 40.964 38.164 1 10.1 ? C4 OMP 2001 A 1 HETATM 19 O O4 OMP . . . B 2 45.632 41.16 38.215 1 11.15 ? O4 OMP 2001 A 1 HETATM 20 C C5 OMP . . . B 2 43.39 41.722 38.813 1 9.8 ? C5 OMP 2001 A 1 HETATM 21 C C6 OMP . . . B 2 42.097 41.388 38.665 1 8.7 ? C6 OMP 2001 A 1 HETATM 22 C C7 OMP . . . B 2 41.205 42.042 39.637 1 15.88 ? C7 OMP 2001 A 1 HETATM 23 O O71 OMP . . . B 2 41.41 43.235 39.947 1 18.28 ? O71 OMP 2001 A 1 HETATM 24 O O72 OMP . . . B 2 40.25 41.418 40.17 1 15.64 ? O72 OMP 2001 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #