data_4VGC
#
_model_server_result.job_id            00D16CLcuAze_AoQ2y-5YA 
_model_server_result.datetime_utc      '2025-03-03 13:16:29' 
_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          4vgc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":358}' 
#
_entry.id    4VGC 
#
_exptl.entry_id    4VGC 
_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            'D-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            4VGC 
_cell.length_a            69.89 
_cell.length_b            69.89 
_cell.length_c            96.14 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4VGC 
_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 1 1 
A,B,C,D,E,F,G,H,I 2 1,2 
A,G 3 3,4 
B,C,D,E,F,H,I 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 69.89 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 34.945 -34.945 48.07 
4 'crystal symmetry operation' 6_555 x+1/2,-y+1/2,-z+1/2 1 0 0 0 -1 0 0 0 -1 34.945 34.945 48.07 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             F 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf2 B SG CYS 27 B CYS 42 1_555 B SG CYS 43 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
disulf ? disulf3 B SG CYS 121 B CYS 136 1_555 C SG CYS 53 C CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
disulf ? disulf4 C SG CYS 20 C CYS 168 1_555 C SG CYS 34 C CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
disulf ? disulf5 C SG CYS 43 C CYS 191 1_555 C SG CYS 72 C CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? 
covale ? covale1 B NE2 HIS 42 B HIS 57 1_555 F B SRD . C SRD 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? 
covale ? covale2 C OG SER 47 C SER 195 1_555 F B SRD . C SRD 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? 
#
_chem_comp.formula           'C14 H17 B N O4 -1' 
_chem_comp.formula_weight    274.1 
_chem_comp.id                SRD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'D-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 SRD doub 294 n y 
C1 C6 SRD sing 295 n y 
C1 C7' SRD sing 296 n n 
C2 C3 SRD sing 297 n y 
C2 C7 SRD sing 298 n y 
C3 C4 SRD doub 299 n y 
C3 C10 SRD sing 300 n y 
C4 C5 SRD sing 301 n y 
C4 H4 SRD sing 302 n n 
C5 C6 SRD doub 303 n y 
C5 H5 SRD sing 304 n n 
C6 H6 SRD sing 305 n n 
C7 C8 SRD doub 306 n y 
C7 H7 SRD sing 307 n n 
C8 C9 SRD sing 308 n y 
C8 H8 SRD sing 309 n n 
C9 C10 SRD doub 310 n y 
C9 H9 SRD sing 311 n n 
C10 H10 SRD sing 312 n n 
C7' C8' SRD sing 313 n n 
C7' "H7'1" SRD sing 314 n n 
C7' "H7'2" SRD sing 315 n n 
C8' N SRD sing 316 n n 
C8' B SRD sing 317 n n 
C8' H8' SRD sing 318 n n 
C9' C SRD sing 319 n n 
C9' "H9'1" SRD sing 320 n n 
C9' "H9'2" SRD sing 321 n n 
C9' "H9'3" SRD sing 322 n n 
C N SRD sing 323 n n 
C O SRD doub 324 n n 
N HN SRD sing 325 n n 
O1B B SRD sing 326 n n 
O1B HOB1 SRD sing 327 n n 
O2B B SRD sing 328 n n 
O2B HOB2 SRD sing 329 n n 
O3B B SRD sing 330 n n 
O3B HOB3 SRD sing 331 n n 
#
_atom_sites.entry_id                     4VGC 
_atom_sites.fract_transf_matrix[1][1]    0.014308 
_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]    0.014308 
_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]    0.010401 
_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 1 358 358 SO4 SO4 . 
E 4 SO4 C 1 357 357 SO4 SO4 . 
F 5 SRD C 1 358 195 SRD SRD . 
G 6 HOH A 1 255 255 HOH HOH . 
G 6 HOH A 2 284 284 HOH HOH . 
G 6 HOH A 3 287 287 HOH HOH . 
G 6 HOH A 4 303 303 HOH HOH . 
G 6 HOH A 5 311 311 HOH HOH . 
G 6 HOH A 6 314 314 HOH HOH . 
H 6 HOH B 1 248 248 HOH HOH . 
H 6 HOH B 2 249 249 HOH HOH . 
H 6 HOH B 3 250 250 HOH HOH . 
H 6 HOH B 4 252 252 HOH HOH . 
H 6 HOH B 5 254 254 HOH HOH . 
H 6 HOH B 6 257 257 HOH HOH . 
H 6 HOH B 7 261 261 HOH HOH . 
H 6 HOH B 8 263 263 HOH HOH . 
H 6 HOH B 9 264 264 HOH HOH . 
H 6 HOH B 10 266 266 HOH HOH . 
H 6 HOH B 11 267 267 HOH HOH . 
H 6 HOH B 12 268 268 HOH HOH . 
H 6 HOH B 13 274 274 HOH HOH . 
H 6 HOH B 14 275 275 HOH HOH . 
H 6 HOH B 15 276 276 HOH HOH . 
H 6 HOH B 16 277 277 HOH HOH . 
H 6 HOH B 17 278 278 HOH HOH . 
H 6 HOH B 18 281 281 HOH HOH . 
H 6 HOH B 19 283 283 HOH HOH . 
H 6 HOH B 20 285 285 HOH HOH . 
H 6 HOH B 21 288 288 HOH HOH . 
H 6 HOH B 22 291 291 HOH HOH . 
H 6 HOH B 23 292 292 HOH HOH . 
H 6 HOH B 24 296 296 HOH HOH . 
H 6 HOH B 25 297 297 HOH HOH . 
H 6 HOH B 26 299 299 HOH HOH . 
H 6 HOH B 27 300 300 HOH HOH . 
H 6 HOH B 28 301 301 HOH HOH . 
H 6 HOH B 29 304 304 HOH HOH . 
H 6 HOH B 30 307 307 HOH HOH . 
H 6 HOH B 31 308 308 HOH HOH . 
H 6 HOH B 32 310 310 HOH HOH . 
H 6 HOH B 33 313 313 HOH HOH . 
H 6 HOH B 34 315 315 HOH HOH . 
H 6 HOH B 35 316 316 HOH HOH . 
H 6 HOH B 36 318 318 HOH HOH . 
H 6 HOH B 37 324 324 HOH HOH . 
H 6 HOH B 38 327 327 HOH HOH . 
H 6 HOH B 39 329 329 HOH HOH . 
I 6 HOH C 1 247 247 HOH HOH . 
I 6 HOH C 2 251 251 HOH HOH . 
I 6 HOH C 3 253 253 HOH HOH . 
I 6 HOH C 4 256 256 HOH HOH . 
I 6 HOH C 5 258 258 HOH HOH . 
I 6 HOH C 6 259 259 HOH HOH . 
I 6 HOH C 7 260 260 HOH HOH . 
I 6 HOH C 8 262 262 HOH HOH . 
I 6 HOH C 9 265 265 HOH HOH . 
I 6 HOH C 10 269 269 HOH HOH . 
I 6 HOH C 11 270 270 HOH HOH . 
I 6 HOH C 12 271 271 HOH HOH . 
I 6 HOH C 13 272 272 HOH HOH . 
I 6 HOH C 14 273 273 HOH HOH . 
I 6 HOH C 15 279 279 HOH HOH . 
I 6 HOH C 16 280 280 HOH HOH . 
I 6 HOH C 17 282 282 HOH HOH . 
I 6 HOH C 18 286 286 HOH HOH . 
I 6 HOH C 19 289 289 HOH HOH . 
I 6 HOH C 20 290 290 HOH HOH . 
I 6 HOH C 21 293 293 HOH HOH . 
I 6 HOH C 22 294 294 HOH HOH . 
I 6 HOH C 23 295 295 HOH HOH . 
I 6 HOH C 24 298 298 HOH HOH . 
I 6 HOH C 25 302 302 HOH HOH . 
I 6 HOH C 26 305 305 HOH HOH . 
I 6 HOH C 27 306 306 HOH HOH . 
I 6 HOH C 28 309 309 HOH HOH . 
I 6 HOH C 29 312 312 HOH HOH . 
I 6 HOH C 30 317 317 HOH HOH . 
I 6 HOH C 31 319 319 HOH HOH . 
I 6 HOH C 32 320 320 HOH HOH . 
I 6 HOH C 33 321 321 HOH HOH . 
I 6 HOH C 34 322 322 HOH HOH . 
I 6 HOH C 35 323 323 HOH HOH . 
I 6 HOH C 36 325 325 HOH HOH . 
I 6 HOH C 37 326 326 HOH HOH . 
I 6 HOH C 38 328 328 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 SRD . . . F 5 28.364 1.861 39.965 1 11.85 ? C1 SRD 358 C 1 
HETATM 2 C C2 SRD . . . F 5 27.835 2.915 40.69 1 10.75 ? C2 SRD 358 C 1 
HETATM 3 C C3 SRD . . . F 5 27.921 2.931 42.11 1 12.96 ? C3 SRD 358 C 1 
HETATM 4 C C4 SRD . . . F 5 28.548 1.894 42.783 1 13.15 ? C4 SRD 358 C 1 
HETATM 5 C C5 SRD . . . F 5 29.086 0.838 42.065 1 14.51 ? C5 SRD 358 C 1 
HETATM 6 C C6 SRD . . . F 5 28.991 0.827 40.661 1 14.2 ? C6 SRD 358 C 1 
HETATM 7 C C7 SRD . . . F 5 27.231 3.972 40.038 1 9.69 ? C7 SRD 358 C 1 
HETATM 8 C C8 SRD . . . F 5 26.711 5.033 40.766 1 10.01 ? C8 SRD 358 C 1 
HETATM 9 C C9 SRD . . . F 5 26.791 5.041 42.167 1 10.62 ? C9 SRD 358 C 1 
HETATM 10 C C10 SRD . . . F 5 27.391 4 42.835 1 10.72 ? C10 SRD 358 C 1 
HETATM 11 C C7' SRD . . . F 5 28.245 1.819 38.466 1 11.15 ? C7' SRD 358 C 1 
HETATM 12 C C8' SRD . . . F 5 29.525 2.206 37.734 1 12.34 ? C8' SRD 358 C 1 
HETATM 13 C C9' SRD . . . F 5 32.875 0.484 38.194 1 19.26 ? C9' SRD 358 C 1 
HETATM 14 C C SRD . . . F 5 31.84 1.581 38.058 1 19.33 ? C SRD 358 C 1 
HETATM 15 N N SRD . . . F 5 30.612 1.252 37.682 1 14.5 ? N SRD 358 C 1 
HETATM 16 O O SRD . . . F 5 32.155 2.752 38.339 1 27.38 ? O SRD 358 C 1 
HETATM 17 O O1B SRD . . . F 5 29.009 1.305 35.453 1 14.58 ? O1B SRD 358 C 1 
HETATM 18 B B SRD . . . F 5 29.074 2.546 36.254 1 10.52 ? B SRD 358 C 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           18 
#