data_3T4V # _model_server_result.job_id h1w1CyaA73nxvvMOM1L0tg _model_server_result.datetime_utc '2024-12-07 09:36:05' _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 3t4v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 3T4V # _exptl.entry_id 3T4V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 333.359 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-(carboxycarbonyl)-S-(naphthalen-2-ylmethyl)-L-cysteine _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 76.33 _cell.angle_beta 74.56 _cell.angle_gamma 65.28 _cell.entry_id 3T4V _cell.length_a 37.07 _cell.length_b 39.234 _cell.length_c 40.261 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3T4V _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A NE2 HIS 121 A HIS 131 1_555 B FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc2 A OD1 ASP 123 A ASP 133 1_555 B FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc3 A NE2 HIS 177 A HIS 187 1_555 B FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc4 B FE FE . A FE 300 1_555 C O04 MD3 . A MD3 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc5 B FE FE . A FE 300 1_555 C O03 MD3 . A MD3 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? # _chem_comp.formula 'C16 H15 N O5 S' _chem_comp.formula_weight 333.359 _chem_comp.id MD3 _chem_comp.mon_nstd_flag n _chem_comp.name N-(carboxycarbonyl)-S-(naphthalen-2-ylmethyl)-L-cysteine _chem_comp.type 'l-peptide linking' _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 C12 C16 MD3 doub 231 n y C16 C15 MD3 sing 232 n y C16 H16 MD3 sing 233 n n CA N MD3 sing 234 n n N C02 MD3 sing 235 n n N H2 MD3 sing 236 n n O05 C01 MD3 doub 237 n n SG CB MD3 sing 238 n n SG C06 MD3 sing 239 n n C02 C01 MD3 sing 240 n n C01 O04 MD3 sing 241 n n OXT C MD3 sing 242 n n OXT HXT MD3 sing 243 n n C02 O03 MD3 doub 244 n n O C MD3 doub 245 n n C CA MD3 sing 246 n n CA CB MD3 sing 247 n n CA HA MD3 sing 248 n n O04 HO04 MD3 sing 249 n n CB HB2 MD3 sing 250 n n CB HB3 MD3 sing 251 n n C06 C07 MD3 sing 252 n n C06 H06 MD3 sing 253 n n C06 H06A MD3 sing 254 n n C08 C07 MD3 sing 255 n y C07 C11 MD3 doub 256 n y C08 C09 MD3 doub 257 n y C08 H08 MD3 sing 258 n n C09 C10 MD3 sing 259 n y C09 H09 MD3 sing 260 n n C10 C12 MD3 sing 261 n y C10 C13 MD3 doub 262 n y C11 C12 MD3 sing 263 n y C11 H11 MD3 sing 264 n n C13 C14 MD3 sing 265 n y C13 H13 MD3 sing 266 n n C14 C15 MD3 doub 267 n y C14 H14 MD3 sing 268 n n C15 H15 MD3 sing 269 n n # _atom_sites.entry_id 3T4V _atom_sites.fract_transf_matrix[1][1] 0.026976 _atom_sites.fract_transf_matrix[1][2] -0.012418 _atom_sites.fract_transf_matrix[1][3] -0.005736 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028059 _atom_sites.fract_transf_matrix[2][3] -0.004048 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.026035 _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 FE A 1 300 300 FE FE . C 3 MD3 A 1 401 401 MD3 MD3 . D 4 GOL A 1 2000 2000 GOL GOL . E 5 HOH A 1 1 1 HOH HOH . E 5 HOH A 2 2 2 HOH HOH . E 5 HOH A 3 3 3 HOH HOH . E 5 HOH A 4 4 4 HOH HOH . E 5 HOH A 5 5 5 HOH HOH . E 5 HOH A 6 6 6 HOH HOH . E 5 HOH A 7 7 7 HOH HOH . E 5 HOH A 8 8 8 HOH HOH . E 5 HOH A 9 9 9 HOH HOH . E 5 HOH A 10 10 10 HOH HOH . E 5 HOH A 11 217 11 HOH HOH . E 5 HOH A 12 218 12 HOH HOH . E 5 HOH A 13 219 219 HOH HOH . E 5 HOH A 14 220 220 HOH HOH . E 5 HOH A 15 221 221 HOH HOH . E 5 HOH A 16 222 222 HOH HOH . E 5 HOH A 17 223 13 HOH HOH . E 5 HOH A 18 224 224 HOH HOH . E 5 HOH A 19 225 14 HOH HOH . E 5 HOH A 20 226 226 HOH HOH . E 5 HOH A 21 227 227 HOH HOH . E 5 HOH A 22 228 228 HOH HOH . E 5 HOH A 23 229 229 HOH HOH . E 5 HOH A 24 230 230 HOH HOH . E 5 HOH A 25 231 15 HOH HOH . E 5 HOH A 26 232 232 HOH HOH . E 5 HOH A 27 233 233 HOH HOH . E 5 HOH A 28 234 234 HOH HOH . E 5 HOH A 29 235 235 HOH HOH . E 5 HOH A 30 236 236 HOH HOH . E 5 HOH A 31 237 237 HOH HOH . E 5 HOH A 32 238 16 HOH HOH . E 5 HOH A 33 239 239 HOH HOH . E 5 HOH A 34 240 240 HOH HOH . E 5 HOH A 35 241 241 HOH HOH . E 5 HOH A 36 242 242 HOH HOH . E 5 HOH A 37 243 243 HOH HOH . E 5 HOH A 38 244 244 HOH HOH . E 5 HOH A 39 245 17 HOH HOH . E 5 HOH A 40 246 18 HOH HOH . E 5 HOH A 41 247 247 HOH HOH . E 5 HOH A 42 248 248 HOH HOH . E 5 HOH A 43 249 249 HOH HOH . E 5 HOH A 44 250 19 HOH HOH . E 5 HOH A 45 251 251 HOH HOH . E 5 HOH A 46 252 20 HOH HOH . E 5 HOH A 47 253 253 HOH HOH . E 5 HOH A 48 254 21 HOH HOH . E 5 HOH A 49 255 255 HOH HOH . E 5 HOH A 50 256 22 HOH HOH . E 5 HOH A 51 257 257 HOH HOH . E 5 HOH A 52 258 23 HOH HOH . E 5 HOH A 53 259 24 HOH HOH . E 5 HOH A 54 260 260 HOH HOH . E 5 HOH A 55 261 261 HOH HOH . E 5 HOH A 56 262 262 HOH HOH . E 5 HOH A 57 263 25 HOH HOH . E 5 HOH A 58 264 26 HOH HOH . E 5 HOH A 59 265 265 HOH HOH . E 5 HOH A 60 266 266 HOH HOH . E 5 HOH A 61 267 267 HOH HOH . E 5 HOH A 62 268 268 HOH HOH . E 5 HOH A 63 269 27 HOH HOH . E 5 HOH A 64 270 28 HOH HOH . E 5 HOH A 65 271 271 HOH HOH . E 5 HOH A 66 272 29 HOH HOH . E 5 HOH A 67 273 30 HOH HOH . E 5 HOH A 68 274 274 HOH HOH . E 5 HOH A 69 275 275 HOH HOH . E 5 HOH A 70 276 31 HOH HOH . E 5 HOH A 71 277 32 HOH HOH . E 5 HOH A 72 278 278 HOH HOH . E 5 HOH A 73 279 279 HOH HOH . E 5 HOH A 74 280 280 HOH HOH . E 5 HOH A 75 281 281 HOH HOH . E 5 HOH A 76 282 282 HOH HOH . E 5 HOH A 77 283 33 HOH HOH . E 5 HOH A 78 284 34 HOH HOH . E 5 HOH A 79 285 35 HOH HOH . E 5 HOH A 80 286 36 HOH HOH . E 5 HOH A 81 287 37 HOH HOH . E 5 HOH A 82 288 38 HOH HOH . E 5 HOH A 83 289 39 HOH HOH . E 5 HOH A 84 290 40 HOH HOH . E 5 HOH A 85 291 41 HOH HOH . E 5 HOH A 86 292 42 HOH HOH . E 5 HOH A 87 293 43 HOH HOH . E 5 HOH A 88 294 44 HOH HOH . E 5 HOH A 89 295 45 HOH HOH . E 5 HOH A 90 296 46 HOH HOH . E 5 HOH A 91 297 47 HOH HOH . E 5 HOH A 92 298 48 HOH HOH . E 5 HOH A 93 299 49 HOH HOH . E 5 HOH A 94 301 50 HOH HOH . E 5 HOH A 95 302 51 HOH HOH . E 5 HOH A 96 303 52 HOH HOH . E 5 HOH A 97 304 53 HOH HOH . E 5 HOH A 98 305 54 HOH HOH . E 5 HOH A 99 306 55 HOH HOH . E 5 HOH A 100 307 56 HOH HOH . E 5 HOH A 101 308 57 HOH HOH . E 5 HOH A 102 309 58 HOH HOH . E 5 HOH A 103 310 59 HOH HOH . E 5 HOH A 104 311 60 HOH HOH . E 5 HOH A 105 312 61 HOH HOH . E 5 HOH A 106 313 62 HOH HOH . E 5 HOH A 107 314 63 HOH HOH . E 5 HOH A 108 315 64 HOH HOH . E 5 HOH A 109 316 65 HOH HOH . E 5 HOH A 110 317 66 HOH HOH . E 5 HOH A 111 318 67 HOH HOH . E 5 HOH A 112 319 68 HOH HOH . E 5 HOH A 113 320 69 HOH HOH . E 5 HOH A 114 321 70 HOH HOH . E 5 HOH A 115 322 71 HOH HOH . E 5 HOH A 116 323 72 HOH HOH . E 5 HOH A 117 324 73 HOH HOH . E 5 HOH A 118 325 74 HOH HOH . E 5 HOH A 119 326 75 HOH HOH . E 5 HOH A 120 327 76 HOH HOH . E 5 HOH A 121 328 77 HOH HOH . E 5 HOH A 122 329 79 HOH HOH . E 5 HOH A 123 330 80 HOH HOH . E 5 HOH A 124 331 81 HOH HOH . E 5 HOH A 125 332 82 HOH HOH . E 5 HOH A 126 333 83 HOH HOH . E 5 HOH A 127 334 84 HOH HOH . E 5 HOH A 128 335 85 HOH HOH . E 5 HOH A 129 336 86 HOH HOH . E 5 HOH A 130 337 87 HOH HOH . E 5 HOH A 131 338 88 HOH HOH . E 5 HOH A 132 339 89 HOH HOH . E 5 HOH A 133 340 90 HOH HOH . E 5 HOH A 134 341 91 HOH HOH . E 5 HOH A 135 342 92 HOH HOH . E 5 HOH A 136 343 93 HOH HOH . E 5 HOH A 137 344 94 HOH HOH . E 5 HOH A 138 345 95 HOH HOH . E 5 HOH A 139 346 96 HOH HOH . E 5 HOH A 140 347 97 HOH HOH . E 5 HOH A 141 348 98 HOH HOH . E 5 HOH A 142 349 100 HOH HOH . E 5 HOH A 143 350 101 HOH HOH . E 5 HOH A 144 351 102 HOH HOH . E 5 HOH A 145 352 103 HOH HOH . E 5 HOH A 146 353 104 HOH HOH . E 5 HOH A 147 354 105 HOH HOH . E 5 HOH A 148 355 106 HOH HOH . E 5 HOH A 149 356 107 HOH HOH . E 5 HOH A 150 357 108 HOH HOH . E 5 HOH A 151 358 109 HOH HOH . E 5 HOH A 152 359 110 HOH HOH . E 5 HOH A 153 360 111 HOH HOH . E 5 HOH A 154 361 112 HOH HOH . E 5 HOH A 155 362 113 HOH HOH . E 5 HOH A 156 363 114 HOH HOH . E 5 HOH A 157 364 115 HOH HOH . E 5 HOH A 158 365 116 HOH HOH . E 5 HOH A 159 366 117 HOH HOH . E 5 HOH A 160 367 118 HOH HOH . E 5 HOH A 161 368 119 HOH HOH . E 5 HOH A 162 369 120 HOH HOH . E 5 HOH A 163 370 121 HOH HOH . E 5 HOH A 164 371 122 HOH HOH . E 5 HOH A 165 372 123 HOH HOH . E 5 HOH A 166 373 124 HOH HOH . E 5 HOH A 167 374 125 HOH HOH . E 5 HOH A 168 375 126 HOH HOH . E 5 HOH A 169 376 127 HOH HOH . E 5 HOH A 170 377 128 HOH HOH . E 5 HOH A 171 378 129 HOH HOH . E 5 HOH A 172 379 130 HOH HOH . E 5 HOH A 173 380 132 HOH HOH . E 5 HOH A 174 381 133 HOH HOH . E 5 HOH A 175 382 134 HOH HOH . E 5 HOH A 176 383 137 HOH HOH . E 5 HOH A 177 384 138 HOH HOH . E 5 HOH A 178 385 139 HOH HOH . E 5 HOH A 179 386 141 HOH HOH . E 5 HOH A 180 387 142 HOH HOH . E 5 HOH A 181 388 143 HOH HOH . E 5 HOH A 182 389 144 HOH HOH . E 5 HOH A 183 390 145 HOH HOH . E 5 HOH A 184 391 148 HOH HOH . E 5 HOH A 185 392 150 HOH HOH . E 5 HOH A 186 393 153 HOH HOH . E 5 HOH A 187 394 155 HOH HOH . E 5 HOH A 188 395 156 HOH HOH . E 5 HOH A 189 396 158 HOH HOH . E 5 HOH A 190 397 161 HOH HOH . E 5 HOH A 191 398 162 HOH HOH . E 5 HOH A 192 399 164 HOH HOH . E 5 HOH A 193 400 170 HOH HOH . E 5 HOH A 194 402 171 HOH HOH . E 5 HOH A 195 403 172 HOH HOH . E 5 HOH A 196 404 173 HOH HOH . E 5 HOH A 197 405 175 HOH HOH . E 5 HOH A 198 406 177 HOH HOH . E 5 HOH A 199 407 178 HOH HOH . E 5 HOH A 200 408 179 HOH HOH . E 5 HOH A 201 409 180 HOH HOH . E 5 HOH A 202 410 181 HOH HOH . E 5 HOH A 203 411 184 HOH HOH . E 5 HOH A 204 412 185 HOH HOH . E 5 HOH A 205 413 188 HOH HOH . E 5 HOH A 206 414 192 HOH HOH . E 5 HOH A 207 415 204 HOH HOH . E 5 HOH A 208 416 209 HOH HOH . E 5 HOH A 209 417 210 HOH HOH . E 5 HOH A 210 418 212 HOH HOH . E 5 HOH A 211 419 213 HOH HOH . E 5 HOH A 212 420 215 HOH HOH . E 5 HOH A 213 421 216 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 C16 MD3 . . . C 3 -1.734 5.205 6.36 1 23.42 ? C16 MD3 401 A 1 HETATM 2 N N MD3 . . . C 3 -3.365 0.585 1.033 1 19.7 ? N MD3 401 A 1 HETATM 3 O O05 MD3 . . . C 3 -1.5 -1.209 1.832 1 22.53 ? O05 MD3 401 A 1 HETATM 4 S SG MD3 . . . C 3 -3.086 3.908 0.14 1 22.81 ? SG MD3 401 A 1 HETATM 5 C C01 MD3 . . . C 3 -2.151 -0.686 2.779 1 24.52 ? C01 MD3 401 A 1 HETATM 6 O OXT MD3 . . . C 3 -4.127 0.062 -1.43 1 22.05 ? OXT MD3 401 A 1 HETATM 7 C C02 MD3 . . . C 3 -3.246 0.23 2.401 1 21.22 ? C02 MD3 401 A 1 HETATM 8 O O MD3 . . . C 3 -4.706 2.122 -1.77 1 20.47 ? O MD3 401 A 1 HETATM 9 C CA MD3 . . . C 3 -4.395 1.406 0.496 1 17.82 ? CA MD3 401 A 1 HETATM 10 O O03 MD3 . . . C 3 -4.012 0.634 3.228 1 22.69 ? O03 MD3 401 A 1 HETATM 11 C C MD3 . . . C 3 -4.407 1.196 -0.984 1 19.22 ? C MD3 401 A 1 HETATM 12 O O04 MD3 . . . C 3 -1.918 -0.955 3.997 1 27.2 ? O04 MD3 401 A 1 HETATM 13 C CB MD3 . . . C 3 -4.341 2.865 0.849 1 19.01 ? CB MD3 401 A 1 HETATM 14 C C06 MD3 . . . C 3 -2.668 4.944 1.522 1 23.29 ? C06 MD3 401 A 1 HETATM 15 C C07 MD3 . . . C 3 -2.063 4.364 2.762 1 24.11 ? C07 MD3 401 A 1 HETATM 16 C C08 MD3 . . . C 3 -1.328 3.183 2.708 1 24.39 ? C08 MD3 401 A 1 HETATM 17 C C09 MD3 . . . C 3 -0.74 2.694 3.868 1 23.57 ? C09 MD3 401 A 1 HETATM 18 C C10 MD3 . . . C 3 -0.874 3.353 5.091 1 23.17 ? C10 MD3 401 A 1 HETATM 19 C C11 MD3 . . . C 3 -2.191 5.038 3.97 1 25.01 ? C11 MD3 401 A 1 HETATM 20 C C12 MD3 . . . C 3 -1.594 4.539 5.139 1 25.07 ? C12 MD3 401 A 1 HETATM 21 C C13 MD3 . . . C 3 -0.289 2.832 6.263 1 21.62 ? C13 MD3 401 A 1 HETATM 22 C C14 MD3 . . . C 3 -0.414 3.512 7.473 1 21.83 ? C14 MD3 401 A 1 HETATM 23 C C15 MD3 . . . C 3 -1.155 4.701 7.518 1 21.96 ? C15 MD3 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #