data_3VGC # _model_server_result.job_id hk06R1j1IT_bzZXXF8OwKg _model_server_result.datetime_utc '2025-07-08 10:05:12' _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 3vgc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":358}' # _entry.id 3VGC # _exptl.entry_id 3VGC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 274.1 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'L-1-NAPHTHYL-2-ACETAMIDO-ETHANE BORONIC ACID' _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 3VGC _cell.length_a 69.895 _cell.length_b 69.895 _cell.length_c 97.142 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VGC _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 42 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 PISA hexameric 6 software_defined_assembly 3 # 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,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 2 1,2 A,H 3 3,4 B,C,D,E,F,G,I,J 3 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' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 69.895 0 0 3 'crystal symmetry operation' 5_545 -x+1/2,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 34.9475 -34.9475 48.571 4 'crystal symmetry operation' 6_555 x+1/2,-y+1/2,-z+1/2 1 0 0 0 -1 0 0 0 -1 34.9475 34.9475 48.571 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _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 disulf ? disulf1 A SG CYS 1 A CYS 1 1_555 B SG CYS 107 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 B SG CYS 27 B CYS 42 1_555 B SG CYS 43 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? disulf ? disulf3 B SG CYS 121 B CYS 136 1_555 C SG CYS 53 C CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? disulf ? disulf4 C SG CYS 20 C CYS 168 1_555 C SG CYS 34 C CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? disulf ? disulf5 C SG CYS 43 C CYS 191 1_555 C SG CYS 72 C CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? covale ? covale1 C OG SER 47 C SER 195 1_555 G B SRB . C SRB 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _chem_comp.formula 'C14 H17 B N O4 -1' _chem_comp.formula_weight 274.1 _chem_comp.id SRB _chem_comp.mon_nstd_flag . _chem_comp.name 'L-1-NAPHTHYL-2-ACETAMIDO-ETHANE BORONIC ACID' _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 C1 C2 SRB doub 294 n y C1 C6 SRB sing 295 n y C1 C7' SRB sing 296 n n C2 C3 SRB sing 297 n y C2 C7 SRB sing 298 n y C3 C4 SRB doub 299 n y C3 C10 SRB sing 300 n y C4 C5 SRB sing 301 n y C4 H4 SRB sing 302 n n C5 C6 SRB doub 303 n y C5 H5 SRB sing 304 n n C6 H6 SRB sing 305 n n C7 C8 SRB doub 306 n y C7 H7 SRB sing 307 n n C8 C9 SRB sing 308 n y C8 H8 SRB sing 309 n n C9 C10 SRB doub 310 n y C9 H9 SRB sing 311 n n C10 H10 SRB sing 312 n n C7' C8' SRB sing 313 n n C7' "H7'1" SRB sing 314 n n C7' "H7'2" SRB sing 315 n n C8' N SRB sing 316 n n C8' B SRB sing 317 n n C8' H8' SRB sing 318 n n C9' C SRB sing 319 n n C9' "H9'1" SRB sing 320 n n C9' "H9'2" SRB sing 321 n n C9' "H9'3" SRB sing 322 n n C N SRB sing 323 n n C O SRB doub 324 n n N HN SRB sing 325 n n O1B B SRB sing 326 n n O1B HOB1 SRB sing 327 n n O2B B SRB sing 328 n n O2B HOB2 SRB sing 329 n n O3B B SRB sing 330 n n O3B HOB3 SRB sing 331 n n # _atom_sites.entry_id 3VGC _atom_sites.fract_transf_matrix[1][1] 0.014307 _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] 0.014307 _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] 0.010294 _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 D 4 SO4 B 1 356 356 SO4 SO4 . E 4 SO4 B 1 358 358 SO4 SO4 . F 4 SO4 C 1 357 357 SO4 SO4 . G 5 SRB C 1 358 195 SRB SRB . H 6 HOH A 1 246 246 HOH HOH . H 6 HOH A 2 286 286 HOH HOH . H 6 HOH A 3 289 289 HOH HOH . H 6 HOH A 4 300 300 HOH HOH . H 6 HOH A 5 323 323 HOH HOH . H 6 HOH A 6 330 330 HOH HOH . H 6 HOH A 7 334 334 HOH HOH . H 6 HOH A 8 335 335 HOH HOH . H 6 HOH A 9 336 336 HOH HOH . I 6 HOH B 1 247 247 HOH HOH . I 6 HOH B 2 248 248 HOH HOH . I 6 HOH B 3 254 254 HOH HOH . I 6 HOH B 4 255 255 HOH HOH . I 6 HOH B 5 257 257 HOH HOH . I 6 HOH B 6 260 260 HOH HOH . I 6 HOH B 7 261 261 HOH HOH . I 6 HOH B 8 262 262 HOH HOH . I 6 HOH B 9 263 263 HOH HOH . I 6 HOH B 10 265 265 HOH HOH . I 6 HOH B 11 266 266 HOH HOH . I 6 HOH B 12 268 268 HOH HOH . I 6 HOH B 13 273 273 HOH HOH . I 6 HOH B 14 276 276 HOH HOH . I 6 HOH B 15 277 277 HOH HOH . I 6 HOH B 16 279 279 HOH HOH . I 6 HOH B 17 280 280 HOH HOH . I 6 HOH B 18 282 282 HOH HOH . I 6 HOH B 19 283 283 HOH HOH . I 6 HOH B 20 285 285 HOH HOH . I 6 HOH B 21 287 287 HOH HOH . I 6 HOH B 22 288 288 HOH HOH . I 6 HOH B 23 294 294 HOH HOH . I 6 HOH B 24 295 295 HOH HOH . I 6 HOH B 25 296 296 HOH HOH . I 6 HOH B 26 297 297 HOH HOH . I 6 HOH B 27 298 298 HOH HOH . I 6 HOH B 28 299 299 HOH HOH . I 6 HOH B 29 301 301 HOH HOH . I 6 HOH B 30 302 302 HOH HOH . I 6 HOH B 31 303 303 HOH HOH . I 6 HOH B 32 304 304 HOH HOH . I 6 HOH B 33 306 306 HOH HOH . I 6 HOH B 34 307 307 HOH HOH . I 6 HOH B 35 312 312 HOH HOH . I 6 HOH B 36 313 313 HOH HOH . I 6 HOH B 37 317 317 HOH HOH . I 6 HOH B 38 318 318 HOH HOH . I 6 HOH B 39 319 319 HOH HOH . I 6 HOH B 40 324 324 HOH HOH . I 6 HOH B 41 325 325 HOH HOH . I 6 HOH B 42 329 329 HOH HOH . I 6 HOH B 43 331 331 HOH HOH . I 6 HOH B 44 332 332 HOH HOH . I 6 HOH B 45 338 338 HOH HOH . I 6 HOH B 46 339 339 HOH HOH . I 6 HOH B 47 340 340 HOH HOH . I 6 HOH B 48 341 341 HOH HOH . J 6 HOH C 1 249 249 HOH HOH . J 6 HOH C 2 250 250 HOH HOH . J 6 HOH C 3 251 251 HOH HOH . J 6 HOH C 4 252 252 HOH HOH . J 6 HOH C 5 253 253 HOH HOH . J 6 HOH C 6 256 256 HOH HOH . J 6 HOH C 7 258 258 HOH HOH . J 6 HOH C 8 259 259 HOH HOH . J 6 HOH C 9 264 264 HOH HOH . J 6 HOH C 10 267 267 HOH HOH . J 6 HOH C 11 269 269 HOH HOH . J 6 HOH C 12 270 270 HOH HOH . J 6 HOH C 13 271 271 HOH HOH . J 6 HOH C 14 272 272 HOH HOH . J 6 HOH C 15 274 274 HOH HOH . J 6 HOH C 16 275 275 HOH HOH . J 6 HOH C 17 278 278 HOH HOH . J 6 HOH C 18 281 281 HOH HOH . J 6 HOH C 19 284 284 HOH HOH . J 6 HOH C 20 290 290 HOH HOH . J 6 HOH C 21 291 291 HOH HOH . J 6 HOH C 22 292 292 HOH HOH . J 6 HOH C 23 293 293 HOH HOH . J 6 HOH C 24 305 305 HOH HOH . J 6 HOH C 25 308 308 HOH HOH . J 6 HOH C 26 309 309 HOH HOH . J 6 HOH C 27 310 310 HOH HOH . J 6 HOH C 28 311 311 HOH HOH . J 6 HOH C 29 314 314 HOH HOH . J 6 HOH C 30 315 315 HOH HOH . J 6 HOH C 31 316 316 HOH HOH . J 6 HOH C 32 320 320 HOH HOH . J 6 HOH C 33 321 321 HOH HOH . J 6 HOH C 34 322 322 HOH HOH . J 6 HOH C 35 326 326 HOH HOH . J 6 HOH C 36 327 327 HOH HOH . J 6 HOH C 37 328 328 HOH HOH . J 6 HOH C 38 333 333 HOH HOH . J 6 HOH C 39 337 337 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 C1 SRB . . . G 5 27.505 3.022 40.42 1 21.79 ? C1 SRB 358 C 1 HETATM 2 C C2 SRB . . . G 5 27.011 4.16 41.078 1 22.23 ? C2 SRB 358 C 1 HETATM 3 C C3 SRB . . . G 5 26.986 4.215 42.493 1 22.23 ? C3 SRB 358 C 1 HETATM 4 C C4 SRB . . . G 5 27.464 3.15 43.236 1 21.02 ? C4 SRB 358 C 1 HETATM 5 C C5 SRB . . . G 5 27.979 2.036 42.599 1 20.39 ? C5 SRB 358 C 1 HETATM 6 C C6 SRB . . . G 5 27.999 1.976 41.202 1 23.91 ? C6 SRB 358 C 1 HETATM 7 C C7 SRB . . . G 5 26.608 5.275 40.357 1 21.21 ? C7 SRB 358 C 1 HETATM 8 C C8 SRB . . . G 5 26.19 6.418 41.014 1 23.81 ? C8 SRB 358 C 1 HETATM 9 C C9 SRB . . . G 5 26.161 6.456 42.409 1 23.53 ? C9 SRB 358 C 1 HETATM 10 C C10 SRB . . . G 5 26.557 5.354 43.14 1 22.56 ? C10 SRB 358 C 1 HETATM 11 C C7' SRB . . . G 5 27.344 2.864 38.921 1 22.45 ? C7' SRB 358 C 1 HETATM 12 C C8' SRB . . . G 5 28.422 2.061 38.199 1 21.85 ? C8' SRB 358 C 1 HETATM 13 C C9' SRB . . . G 5 32.194 2.737 38.324 1 29.42 ? C9' SRB 358 C 1 HETATM 14 C C SRB . . . G 5 30.856 1.998 38.399 1 29.2 ? C SRB 358 C 1 HETATM 15 N N SRB . . . G 5 29.748 2.642 38.049 1 26.66 ? N SRB 358 C 1 HETATM 16 O O SRB . . . G 5 30.833 0.821 38.773 1 31.1 ? O SRB 358 C 1 HETATM 17 O O1B SRB . . . G 5 28.884 0.977 35.994 1 22.13 ? O1B SRB 358 C 1 HETATM 18 O O2B SRB . . . G 5 26.599 1.059 36.746 1 23.24 ? O2B SRB 358 C 1 HETATM 19 B B SRB . . . G 5 27.903 1.779 36.741 1 20.88 ? B SRB 358 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 19 #