data_3ND7 # _model_server_result.job_id F-0Q5_5NsD9sg5sn6KqkcQ _model_server_result.datetime_utc '2024-10-19 03:53:14' _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 3nd7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":504}' # _entry.id 3ND7 # _exptl.entry_id 3ND7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 278.368 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide _entity.pdbx_number_of_molecules 6 _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 3ND7 _cell.length_a 109.64 _cell.length_b 125.791 _cell.length_c 125.804 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ND7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R _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 ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N # _chem_comp.formula 'C11 H22 N2 O4 S' _chem_comp.formula_weight 278.368 _chem_comp.id PNY _chem_comp.mon_nstd_flag . _chem_comp.name (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms pantetheine;(R)-2,4-Dihydroxy-N-(3-((2-mercaptoethyl)amino)-3-oxopropyl)-3,3-dimethylbutanamide # 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 CAA OAE PNY sing 247 n n CAA CAF PNY sing 248 n n CAB CAF PNY sing 249 n n OAC CAO PNY doub 250 n n OAD CAP PNY doub 251 n n CAF CAI PNY sing 252 n n CAF CAQ PNY sing 253 n n SAG CAH PNY sing 254 n n CAH CAJ PNY sing 255 n n CAJ NAM PNY sing 256 n n CAK CAL PNY sing 257 n n CAK NAN PNY sing 258 n n CAL CAO PNY sing 259 n n NAM CAO PNY sing 260 n n NAN CAP PNY sing 261 n n CAP CAQ PNY sing 262 n n CAQ OAR PNY sing 263 n n CAA HAA PNY sing 264 n n CAA HAAA PNY sing 265 n n CAB HAB PNY sing 266 n n CAB HABA PNY sing 267 n n CAB HABB PNY sing 268 n n OAE HOAE PNY sing 269 n n SAG HSAG PNY sing 270 n n CAH HAH PNY sing 271 n n CAH HAHA PNY sing 272 n n CAI HAI PNY sing 273 n n CAI HAIA PNY sing 274 n n CAI HAIB PNY sing 275 n n CAJ HAJ PNY sing 276 n n CAJ HAJA PNY sing 277 n n CAK HAK PNY sing 278 n n CAK HAKA PNY sing 279 n n CAL HAL PNY sing 280 n n CAL HALA PNY sing 281 n n NAM HNAM PNY sing 282 n n NAN HNAN PNY sing 283 n n CAQ HAQ PNY sing 284 n n OAR HOAR PNY sing 285 n n # _atom_sites.entry_id 3ND7 _atom_sites.fract_transf_matrix[1][1] 0.009121 _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] 0.00795 _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] 0.007949 _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 G 2 PNY A 1 501 501 PNY PNY . H 2 PNY B 1 502 502 PNY PNY . I 2 PNY C 1 503 503 PNY PNY . J 2 PNY D 1 504 504 PNY PNY . K 2 PNY E 1 505 505 PNY PNY . L 2 PNY F 1 506 506 PNY PNY . M 3 HOH A 1 172 1 HOH HOH . M 3 HOH A 2 173 173 HOH HOH . M 3 HOH A 3 174 174 HOH HOH . M 3 HOH A 4 175 3 HOH HOH . M 3 HOH A 5 176 9 HOH HOH . M 3 HOH A 6 177 177 HOH HOH . M 3 HOH A 7 178 13 HOH HOH . M 3 HOH A 8 179 18 HOH HOH . M 3 HOH A 9 180 27 HOH HOH . M 3 HOH A 10 181 181 HOH HOH . M 3 HOH A 11 182 39 HOH HOH . M 3 HOH A 12 183 52 HOH HOH . M 3 HOH A 13 184 184 HOH HOH . M 3 HOH A 14 185 60 HOH HOH . M 3 HOH A 15 186 61 HOH HOH . M 3 HOH A 16 187 187 HOH HOH . M 3 HOH A 17 188 62 HOH HOH . M 3 HOH A 18 189 79 HOH HOH . M 3 HOH A 19 190 190 HOH HOH . M 3 HOH A 20 191 191 HOH HOH . M 3 HOH A 21 192 90 HOH HOH . M 3 HOH A 22 193 94 HOH HOH . M 3 HOH A 23 194 194 HOH HOH . M 3 HOH A 24 195 112 HOH HOH . M 3 HOH A 25 196 115 HOH HOH . M 3 HOH A 26 197 122 HOH HOH . M 3 HOH A 27 198 125 HOH HOH . M 3 HOH A 28 199 127 HOH HOH . M 3 HOH A 29 200 129 HOH HOH . M 3 HOH A 30 201 201 HOH HOH . M 3 HOH A 31 202 131 HOH HOH . M 3 HOH A 32 203 132 HOH HOH . M 3 HOH A 33 204 147 HOH HOH . M 3 HOH A 34 205 205 HOH HOH . M 3 HOH A 35 206 206 HOH HOH . M 3 HOH A 36 207 149 HOH HOH . M 3 HOH A 37 208 150 HOH HOH . M 3 HOH A 38 209 155 HOH HOH . M 3 HOH A 39 210 158 HOH HOH . M 3 HOH A 40 213 213 HOH HOH . M 3 HOH A 41 218 218 HOH HOH . M 3 HOH A 42 220 220 HOH HOH . M 3 HOH A 43 221 221 HOH HOH . M 3 HOH A 44 223 223 HOH HOH . M 3 HOH A 45 227 227 HOH HOH . M 3 HOH A 46 233 233 HOH HOH . M 3 HOH A 47 243 243 HOH HOH . M 3 HOH A 48 251 251 HOH HOH . N 3 HOH B 1 172 5 HOH HOH . N 3 HOH B 2 173 6 HOH HOH . N 3 HOH B 3 174 7 HOH HOH . N 3 HOH B 4 175 10 HOH HOH . N 3 HOH B 5 176 15 HOH HOH . N 3 HOH B 6 177 19 HOH HOH . N 3 HOH B 7 178 31 HOH HOH . N 3 HOH B 8 179 179 HOH HOH . N 3 HOH B 9 180 34 HOH HOH . N 3 HOH B 10 181 53 HOH HOH . N 3 HOH B 11 182 55 HOH HOH . N 3 HOH B 12 183 57 HOH HOH . N 3 HOH B 13 184 65 HOH HOH . N 3 HOH B 14 185 67 HOH HOH . N 3 HOH B 15 186 69 HOH HOH . N 3 HOH B 16 187 72 HOH HOH . N 3 HOH B 17 188 78 HOH HOH . N 3 HOH B 18 189 82 HOH HOH . N 3 HOH B 19 190 83 HOH HOH . N 3 HOH B 20 191 92 HOH HOH . N 3 HOH B 21 192 192 HOH HOH . N 3 HOH B 22 193 93 HOH HOH . N 3 HOH B 23 194 98 HOH HOH . N 3 HOH B 24 195 100 HOH HOH . N 3 HOH B 25 196 102 HOH HOH . N 3 HOH B 26 197 108 HOH HOH . N 3 HOH B 27 198 109 HOH HOH . N 3 HOH B 28 199 128 HOH HOH . N 3 HOH B 29 200 145 HOH HOH . N 3 HOH B 30 201 168 HOH HOH . N 3 HOH B 31 202 171 HOH HOH . N 3 HOH B 32 204 204 HOH HOH . N 3 HOH B 33 208 208 HOH HOH . N 3 HOH B 34 209 209 HOH HOH . N 3 HOH B 35 214 214 HOH HOH . N 3 HOH B 36 222 222 HOH HOH . N 3 HOH B 37 224 224 HOH HOH . N 3 HOH B 38 226 226 HOH HOH . N 3 HOH B 39 230 230 HOH HOH . N 3 HOH B 40 234 234 HOH HOH . N 3 HOH B 41 237 237 HOH HOH . N 3 HOH B 42 246 246 HOH HOH . O 3 HOH C 1 172 17 HOH HOH . O 3 HOH C 2 173 28 HOH HOH . O 3 HOH C 3 174 30 HOH HOH . O 3 HOH C 4 175 175 HOH HOH . O 3 HOH C 5 176 47 HOH HOH . O 3 HOH C 6 177 48 HOH HOH . O 3 HOH C 7 178 178 HOH HOH . O 3 HOH C 8 179 58 HOH HOH . O 3 HOH C 9 180 59 HOH HOH . O 3 HOH C 10 181 77 HOH HOH . O 3 HOH C 11 182 81 HOH HOH . O 3 HOH C 12 183 86 HOH HOH . O 3 HOH C 13 184 88 HOH HOH . O 3 HOH C 14 185 89 HOH HOH . O 3 HOH C 15 186 103 HOH HOH . O 3 HOH C 16 187 104 HOH HOH . O 3 HOH C 17 188 188 HOH HOH . O 3 HOH C 18 189 105 HOH HOH . O 3 HOH C 19 190 110 HOH HOH . O 3 HOH C 20 191 113 HOH HOH . O 3 HOH C 21 192 123 HOH HOH . O 3 HOH C 22 193 134 HOH HOH . O 3 HOH C 23 194 136 HOH HOH . O 3 HOH C 24 195 139 HOH HOH . O 3 HOH C 25 196 140 HOH HOH . O 3 HOH C 26 197 197 HOH HOH . O 3 HOH C 27 198 142 HOH HOH . O 3 HOH C 28 199 146 HOH HOH . O 3 HOH C 29 200 200 HOH HOH . O 3 HOH C 30 201 148 HOH HOH . O 3 HOH C 31 202 152 HOH HOH . O 3 HOH C 32 203 154 HOH HOH . O 3 HOH C 33 204 156 HOH HOH . O 3 HOH C 34 205 157 HOH HOH . O 3 HOH C 35 217 217 HOH HOH . O 3 HOH C 36 229 229 HOH HOH . O 3 HOH C 37 239 239 HOH HOH . O 3 HOH C 38 242 242 HOH HOH . O 3 HOH C 39 252 252 HOH HOH . O 3 HOH C 40 254 254 HOH HOH . P 3 HOH D 1 172 172 HOH HOH . P 3 HOH D 2 173 2 HOH HOH . P 3 HOH D 3 174 14 HOH HOH . P 3 HOH D 4 175 21 HOH HOH . P 3 HOH D 5 176 176 HOH HOH . P 3 HOH D 6 177 22 HOH HOH . P 3 HOH D 7 178 24 HOH HOH . P 3 HOH D 8 179 29 HOH HOH . P 3 HOH D 9 180 32 HOH HOH . P 3 HOH D 10 181 43 HOH HOH . P 3 HOH D 11 182 46 HOH HOH . P 3 HOH D 12 183 49 HOH HOH . P 3 HOH D 13 184 51 HOH HOH . P 3 HOH D 14 185 54 HOH HOH . P 3 HOH D 15 186 71 HOH HOH . P 3 HOH D 16 187 76 HOH HOH . P 3 HOH D 17 188 80 HOH HOH . P 3 HOH D 18 189 91 HOH HOH . P 3 HOH D 19 190 97 HOH HOH . P 3 HOH D 20 191 106 HOH HOH . P 3 HOH D 21 192 120 HOH HOH . P 3 HOH D 22 193 135 HOH HOH . P 3 HOH D 23 194 143 HOH HOH . P 3 HOH D 24 195 151 HOH HOH . P 3 HOH D 25 196 162 HOH HOH . P 3 HOH D 26 197 165 HOH HOH . P 3 HOH D 27 199 199 HOH HOH . P 3 HOH D 28 210 210 HOH HOH . P 3 HOH D 29 211 211 HOH HOH . P 3 HOH D 30 216 216 HOH HOH . P 3 HOH D 31 235 235 HOH HOH . P 3 HOH D 32 236 236 HOH HOH . P 3 HOH D 33 240 240 HOH HOH . P 3 HOH D 34 241 241 HOH HOH . P 3 HOH D 35 250 250 HOH HOH . P 3 HOH D 36 253 253 HOH HOH . Q 3 HOH E 1 172 4 HOH HOH . Q 3 HOH E 2 173 8 HOH HOH . Q 3 HOH E 3 174 11 HOH HOH . Q 3 HOH E 4 175 16 HOH HOH . Q 3 HOH E 5 176 25 HOH HOH . Q 3 HOH E 6 177 26 HOH HOH . Q 3 HOH E 7 178 36 HOH HOH . Q 3 HOH E 8 179 40 HOH HOH . Q 3 HOH E 9 180 180 HOH HOH . Q 3 HOH E 10 181 45 HOH HOH . Q 3 HOH E 11 182 182 HOH HOH . Q 3 HOH E 12 183 63 HOH HOH . Q 3 HOH E 13 184 66 HOH HOH . Q 3 HOH E 14 185 185 HOH HOH . Q 3 HOH E 15 186 186 HOH HOH . Q 3 HOH E 16 187 73 HOH HOH . Q 3 HOH E 17 188 75 HOH HOH . Q 3 HOH E 18 189 85 HOH HOH . Q 3 HOH E 19 190 95 HOH HOH . Q 3 HOH E 20 191 96 HOH HOH . Q 3 HOH E 21 192 99 HOH HOH . Q 3 HOH E 22 193 101 HOH HOH . Q 3 HOH E 23 194 111 HOH HOH . Q 3 HOH E 24 195 117 HOH HOH . Q 3 HOH E 25 196 196 HOH HOH . Q 3 HOH E 26 197 118 HOH HOH . Q 3 HOH E 27 198 198 HOH HOH . Q 3 HOH E 28 199 121 HOH HOH . Q 3 HOH E 29 200 124 HOH HOH . Q 3 HOH E 30 201 126 HOH HOH . Q 3 HOH E 31 202 130 HOH HOH . Q 3 HOH E 32 203 203 HOH HOH . Q 3 HOH E 33 204 133 HOH HOH . Q 3 HOH E 34 205 138 HOH HOH . Q 3 HOH E 35 206 159 HOH HOH . Q 3 HOH E 36 207 207 HOH HOH . Q 3 HOH E 37 208 160 HOH HOH . Q 3 HOH E 38 209 161 HOH HOH . Q 3 HOH E 39 210 166 HOH HOH . Q 3 HOH E 40 211 167 HOH HOH . Q 3 HOH E 41 212 169 HOH HOH . Q 3 HOH E 42 215 215 HOH HOH . Q 3 HOH E 43 219 219 HOH HOH . Q 3 HOH E 44 225 225 HOH HOH . Q 3 HOH E 45 228 228 HOH HOH . Q 3 HOH E 46 231 231 HOH HOH . Q 3 HOH E 47 232 232 HOH HOH . Q 3 HOH E 48 244 244 HOH HOH . Q 3 HOH E 49 245 245 HOH HOH . Q 3 HOH E 50 248 248 HOH HOH . R 3 HOH F 1 172 12 HOH HOH . R 3 HOH F 2 173 20 HOH HOH . R 3 HOH F 3 174 23 HOH HOH . R 3 HOH F 4 175 33 HOH HOH . R 3 HOH F 5 176 35 HOH HOH . R 3 HOH F 6 177 37 HOH HOH . R 3 HOH F 7 178 38 HOH HOH . R 3 HOH F 8 179 41 HOH HOH . R 3 HOH F 9 180 42 HOH HOH . R 3 HOH F 10 181 44 HOH HOH . R 3 HOH F 11 182 50 HOH HOH . R 3 HOH F 12 183 183 HOH HOH . R 3 HOH F 13 184 56 HOH HOH . R 3 HOH F 14 185 64 HOH HOH . R 3 HOH F 15 186 68 HOH HOH . R 3 HOH F 16 187 70 HOH HOH . R 3 HOH F 17 188 74 HOH HOH . R 3 HOH F 18 189 189 HOH HOH . R 3 HOH F 19 190 84 HOH HOH . R 3 HOH F 20 191 87 HOH HOH . R 3 HOH F 21 192 107 HOH HOH . R 3 HOH F 22 193 193 HOH HOH . R 3 HOH F 23 194 114 HOH HOH . R 3 HOH F 24 195 195 HOH HOH . R 3 HOH F 25 196 116 HOH HOH . R 3 HOH F 26 197 119 HOH HOH . R 3 HOH F 27 198 137 HOH HOH . R 3 HOH F 28 199 141 HOH HOH . R 3 HOH F 29 200 144 HOH HOH . R 3 HOH F 30 201 153 HOH HOH . R 3 HOH F 31 202 202 HOH HOH . R 3 HOH F 32 203 163 HOH HOH . R 3 HOH F 33 204 164 HOH HOH . R 3 HOH F 34 205 170 HOH HOH . R 3 HOH F 35 212 212 HOH HOH . R 3 HOH F 36 238 238 HOH HOH . R 3 HOH F 37 247 247 HOH HOH . R 3 HOH F 38 249 249 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 CAA PNY . . . J 2 10.296 3.883 -5.248 1 56.66 ? CAA PNY 504 D 1 HETATM 2 C CAB PNY . . . J 2 9.892 2.868 -7.554 1 57.2 ? CAB PNY 504 D 1 HETATM 3 O OAC PNY . . . J 2 14.414 -2.149 -7.27 1 44.2 ? OAC PNY 504 D 1 HETATM 4 O OAD PNY . . . J 2 13.108 0.578 -6.775 1 51.47 ? OAD PNY 504 D 1 HETATM 5 O OAE PNY . . . J 2 10.927 3.595 -3.971 1 52.32 ? OAE PNY 504 D 1 HETATM 6 C CAF PNY . . . J 2 10.88 2.992 -6.38 1 56.28 ? CAF PNY 504 D 1 HETATM 7 S SAG PNY . . . J 2 15.846 -2.048 -2.406 1 44.37 ? SAG PNY 504 D 1 HETATM 8 C CAH PNY . . . J 2 14.255 -2.142 -3.255 1 44.09 ? CAH PNY 504 D 1 HETATM 9 C CAI PNY . . . J 2 12.174 3.628 -6.88 1 55.37 ? CAI PNY 504 D 1 HETATM 10 C CAJ PNY . . . J 2 14.462 -2.651 -4.66 1 47.36 ? CAJ PNY 504 D 1 HETATM 11 C CAK PNY . . . J 2 11.581 -1.244 -8.359 1 45.75 ? CAK PNY 504 D 1 HETATM 12 C CAL PNY . . . J 2 11.975 -2.494 -7.581 1 45.25 ? CAL PNY 504 D 1 HETATM 13 N NAM PNY . . . J 2 13.204 -2.641 -5.469 1 47.57 ? NAM PNY 504 D 1 HETATM 14 N NAN PNY . . . J 2 11.054 -0.206 -7.447 1 48.41 ? NAN PNY 504 D 1 HETATM 15 C CAO PNY . . . J 2 13.311 -2.41 -6.769 1 45.75 ? CAO PNY 504 D 1 HETATM 16 C CAP PNY . . . J 2 11.859 0.597 -6.722 1 52.83 ? CAP PNY 504 D 1 HETATM 17 C CAQ PNY . . . J 2 11.141 1.591 -5.749 1 54.41 ? CAQ PNY 504 D 1 HETATM 18 O OAR PNY . . . J 2 9.886 1.086 -5.183 1 56.19 ? OAR PNY 504 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 18 #