data_3KBR
#
_model_server_result.job_id            90u1TYy156TjTmXoUtUozQ 
_model_server_result.datetime_utc      '2024-11-29 09:16:40' 
_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          3kbr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":263}' 
#
_entry.id    3KBR 
#
_exptl.entry_id    3KBR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    5 
_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         120 
_cell.entry_id            3KBR 
_cell.length_a            126.39 
_cell.length_b            126.39 
_cell.length_c            88.981 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KBR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4,5,6 
#
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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 88.981 
5 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 88.981 
6 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 88.981 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 E N N 
? 4 F N N 
? 4 H N N 
? 4 I N 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 109 A CYS 131 1_555 A SG CYS 188 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
covale ? covale1 A C ASP 43 A ASP 65 1_555 A N MSE 44 A MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 A C MSE 44 A MSE 66 1_555 A N ALA 45 A ALA 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale3 A C LEU 66 A LEU 88 1_555 A N MSE 67 A MSE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale4 A C MSE 67 A MSE 89 1_555 A N ARG 68 A ARG 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale5 A C ALA 78 A ALA 100 1_555 A N MSE 79 A MSE 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale6 A C MSE 79 A MSE 101 1_555 A N SER 80 A SER 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale7 A C LEU 169 A LEU 191 1_555 A N MSE 170 A MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale8 A C MSE 170 A MSE 192 1_555 A N MSE 171 A MSE 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale9 A C MSE 171 A MSE 193 1_555 A N THR 172 A THR 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale10 A C ARG 231 A ARG 253 1_555 A N MSE 232 A MSE 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale11 A C MSE 232 A MSE 254 1_555 A N GLU 233 A GLU 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
metalc ? metalc1 B NI NI . A NI 1 1_555 A OE1 GLU 112 A GLU 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? 
metalc ? metalc2 B NI NI . A NI 1 1_555 A OE2 GLU 112 A GLU 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc3 B NI NI . A NI 1 1_555 A NE2 HIS 191 A HIS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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 O1 GOL sing 166 n n 
C1 C2 GOL sing 167 n n 
C1 H11 GOL sing 168 n n 
C1 H12 GOL sing 169 n n 
O1 HO1 GOL sing 170 n n 
C2 O2 GOL sing 171 n n 
C2 C3 GOL sing 172 n n 
C2 H2 GOL sing 173 n n 
O2 HO2 GOL sing 174 n n 
C3 O3 GOL sing 175 n n 
C3 H31 GOL sing 176 n n 
C3 H32 GOL sing 177 n n 
O3 HO3 GOL sing 178 n n 
#
_atom_sites.entry_id                     3KBR 
_atom_sites.fract_transf_matrix[1][1]    0.007912 
_atom_sites.fract_transf_matrix[1][2]    0.004568 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009136 
_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]    0.011238 
_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 NI A 1 1 1 NI NI . 
C 3 CL A 1 262 1 CL CL . 
D 4 GOL A 1 263 1 GOL GOL . 
E 4 GOL A 1 2 2 GOL GOL . 
F 4 GOL A 1 3 3 GOL GOL . 
G 5 FMT A 1 265 2 FMT FMT . 
H 4 GOL A 1 4 4 GOL GOL . 
I 4 GOL A 1 5 5 GOL GOL . 
J 5 FMT A 1 264 1 FMT FMT . 
K 6 EPE A 1 266 1 EPE EPE . 
L 7 HOH A 1 6 6 HOH HOH . 
L 7 HOH A 2 7 7 HOH HOH . 
L 7 HOH A 3 8 8 HOH HOH . 
L 7 HOH A 4 9 9 HOH HOH . 
L 7 HOH A 5 10 10 HOH HOH . 
L 7 HOH A 6 11 11 HOH HOH . 
L 7 HOH A 7 12 12 HOH HOH . 
L 7 HOH A 8 13 13 HOH HOH . 
L 7 HOH A 9 14 14 HOH HOH . 
L 7 HOH A 10 15 15 HOH HOH . 
L 7 HOH A 11 16 16 HOH HOH . 
L 7 HOH A 12 17 17 HOH HOH . 
L 7 HOH A 13 18 18 HOH HOH . 
L 7 HOH A 14 19 19 HOH HOH . 
L 7 HOH A 15 20 20 HOH HOH . 
L 7 HOH A 16 21 21 HOH HOH . 
L 7 HOH A 17 22 22 HOH HOH . 
L 7 HOH A 18 267 1 HOH HOH . 
L 7 HOH A 19 268 2 HOH HOH . 
L 7 HOH A 20 269 3 HOH HOH . 
L 7 HOH A 21 270 4 HOH HOH . 
L 7 HOH A 22 271 5 HOH HOH . 
L 7 HOH A 23 272 23 HOH HOH . 
L 7 HOH A 24 273 24 HOH HOH . 
L 7 HOH A 25 274 25 HOH HOH . 
L 7 HOH A 26 275 26 HOH HOH . 
L 7 HOH A 27 276 27 HOH HOH . 
L 7 HOH A 28 277 28 HOH HOH . 
L 7 HOH A 29 278 29 HOH HOH . 
L 7 HOH A 30 279 30 HOH HOH . 
L 7 HOH A 31 280 31 HOH HOH . 
L 7 HOH A 32 281 32 HOH HOH . 
L 7 HOH A 33 282 33 HOH HOH . 
L 7 HOH A 34 283 34 HOH HOH . 
L 7 HOH A 35 284 35 HOH HOH . 
L 7 HOH A 36 285 36 HOH HOH . 
L 7 HOH A 37 286 37 HOH HOH . 
L 7 HOH A 38 287 38 HOH HOH . 
L 7 HOH A 39 288 39 HOH HOH . 
L 7 HOH A 40 289 40 HOH HOH . 
L 7 HOH A 41 290 41 HOH HOH . 
L 7 HOH A 42 291 42 HOH HOH . 
L 7 HOH A 43 292 43 HOH HOH . 
L 7 HOH A 44 293 44 HOH HOH . 
L 7 HOH A 45 294 45 HOH HOH . 
L 7 HOH A 46 295 46 HOH HOH . 
L 7 HOH A 47 296 47 HOH HOH . 
L 7 HOH A 48 297 48 HOH HOH . 
L 7 HOH A 49 298 49 HOH HOH . 
L 7 HOH A 50 299 50 HOH HOH . 
L 7 HOH A 51 300 51 HOH HOH . 
L 7 HOH A 52 301 52 HOH HOH . 
L 7 HOH A 53 302 53 HOH HOH . 
L 7 HOH A 54 303 54 HOH HOH . 
L 7 HOH A 55 304 55 HOH HOH . 
L 7 HOH A 56 305 56 HOH HOH . 
L 7 HOH A 57 306 57 HOH HOH . 
L 7 HOH A 58 307 58 HOH HOH . 
L 7 HOH A 59 308 59 HOH HOH . 
L 7 HOH A 60 309 60 HOH HOH . 
L 7 HOH A 61 310 61 HOH HOH . 
L 7 HOH A 62 311 62 HOH HOH . 
L 7 HOH A 63 312 63 HOH HOH . 
L 7 HOH A 64 313 64 HOH HOH . 
L 7 HOH A 65 314 65 HOH HOH . 
L 7 HOH A 66 315 66 HOH HOH . 
L 7 HOH A 67 316 67 HOH HOH . 
L 7 HOH A 68 317 68 HOH HOH . 
L 7 HOH A 69 318 69 HOH HOH . 
L 7 HOH A 70 319 70 HOH HOH . 
L 7 HOH A 71 320 71 HOH HOH . 
L 7 HOH A 72 321 72 HOH HOH . 
L 7 HOH A 73 322 73 HOH HOH . 
L 7 HOH A 74 323 74 HOH HOH . 
L 7 HOH A 75 324 75 HOH HOH . 
L 7 HOH A 76 325 76 HOH HOH . 
L 7 HOH A 77 326 77 HOH HOH . 
L 7 HOH A 78 327 78 HOH HOH . 
L 7 HOH A 79 328 79 HOH HOH . 
L 7 HOH A 80 329 80 HOH HOH . 
L 7 HOH A 81 330 81 HOH HOH . 
L 7 HOH A 82 331 82 HOH HOH . 
L 7 HOH A 83 332 83 HOH HOH . 
L 7 HOH A 84 333 84 HOH HOH . 
L 7 HOH A 85 334 85 HOH HOH . 
L 7 HOH A 86 335 86 HOH HOH . 
L 7 HOH A 87 336 87 HOH HOH . 
L 7 HOH A 88 337 88 HOH HOH . 
L 7 HOH A 89 338 89 HOH HOH . 
L 7 HOH A 90 339 90 HOH HOH . 
L 7 HOH A 91 340 91 HOH HOH . 
L 7 HOH A 92 341 92 HOH HOH . 
L 7 HOH A 93 342 93 HOH HOH . 
L 7 HOH A 94 343 94 HOH HOH . 
L 7 HOH A 95 344 95 HOH HOH . 
L 7 HOH A 96 345 96 HOH HOH . 
L 7 HOH A 97 346 97 HOH HOH . 
L 7 HOH A 98 347 98 HOH HOH . 
L 7 HOH A 99 348 99 HOH HOH . 
L 7 HOH A 100 349 100 HOH HOH . 
L 7 HOH A 101 350 101 HOH HOH . 
L 7 HOH A 102 351 102 HOH HOH . 
L 7 HOH A 103 352 103 HOH HOH . 
L 7 HOH A 104 353 104 HOH HOH . 
L 7 HOH A 105 354 105 HOH HOH . 
L 7 HOH A 106 355 106 HOH HOH . 
L 7 HOH A 107 356 107 HOH HOH . 
L 7 HOH A 108 357 108 HOH HOH . 
L 7 HOH A 109 358 109 HOH HOH . 
L 7 HOH A 110 359 110 HOH HOH . 
L 7 HOH A 111 360 111 HOH HOH . 
L 7 HOH A 112 361 112 HOH HOH . 
L 7 HOH A 113 362 113 HOH HOH . 
L 7 HOH A 114 363 114 HOH HOH . 
L 7 HOH A 115 364 115 HOH HOH . 
L 7 HOH A 116 365 116 HOH HOH . 
L 7 HOH A 117 366 117 HOH HOH . 
L 7 HOH A 118 367 118 HOH HOH . 
L 7 HOH A 119 368 119 HOH HOH . 
L 7 HOH A 120 369 120 HOH HOH . 
L 7 HOH A 121 370 121 HOH HOH . 
L 7 HOH A 122 371 122 HOH HOH . 
L 7 HOH A 123 372 123 HOH HOH . 
L 7 HOH A 124 373 124 HOH HOH . 
L 7 HOH A 125 374 125 HOH HOH . 
L 7 HOH A 126 375 126 HOH HOH . 
L 7 HOH A 127 376 127 HOH HOH . 
L 7 HOH A 128 377 128 HOH HOH . 
L 7 HOH A 129 378 129 HOH HOH . 
L 7 HOH A 130 379 130 HOH HOH . 
L 7 HOH A 131 380 131 HOH HOH . 
L 7 HOH A 132 381 132 HOH HOH . 
L 7 HOH A 133 382 133 HOH HOH . 
L 7 HOH A 134 383 134 HOH HOH . 
L 7 HOH A 135 384 135 HOH HOH . 
L 7 HOH A 136 385 136 HOH HOH . 
L 7 HOH A 137 386 137 HOH HOH . 
L 7 HOH A 138 387 138 HOH HOH . 
L 7 HOH A 139 388 139 HOH HOH . 
L 7 HOH A 140 389 140 HOH HOH . 
L 7 HOH A 141 390 141 HOH HOH . 
L 7 HOH A 142 391 142 HOH HOH . 
L 7 HOH A 143 392 143 HOH HOH . 
L 7 HOH A 144 393 144 HOH HOH . 
L 7 HOH A 145 394 145 HOH HOH . 
L 7 HOH A 146 395 146 HOH HOH . 
L 7 HOH A 147 396 147 HOH HOH . 
L 7 HOH A 148 397 148 HOH HOH . 
L 7 HOH A 149 398 149 HOH HOH . 
L 7 HOH A 150 399 150 HOH HOH . 
L 7 HOH A 151 400 151 HOH HOH . 
L 7 HOH A 152 401 152 HOH HOH . 
L 7 HOH A 153 402 153 HOH HOH . 
L 7 HOH A 154 403 154 HOH HOH . 
L 7 HOH A 155 404 155 HOH HOH . 
L 7 HOH A 156 405 156 HOH HOH . 
L 7 HOH A 157 406 157 HOH HOH . 
L 7 HOH A 158 407 158 HOH HOH . 
L 7 HOH A 159 408 159 HOH HOH . 
L 7 HOH A 160 409 160 HOH HOH . 
L 7 HOH A 161 410 161 HOH HOH . 
L 7 HOH A 162 411 162 HOH HOH . 
L 7 HOH A 163 412 163 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 GOL . . . D 4 14.346 14.926 27.97 1 72.62 ? C1 GOL 263 A 1 
HETATM 2 O O1 GOL . . . D 4 15.429 15.606 27.379 1 79.42 ? O1 GOL 263 A 1 
HETATM 3 C C2 GOL . . . D 4 14.591 14.817 29.469 1 60.29 ? C2 GOL 263 A 1 
HETATM 4 O O2 GOL . . . D 4 14.317 16.05 30.102 1 55.46 ? O2 GOL 263 A 1 
HETATM 5 C C3 GOL . . . D 4 16.046 14.425 29.699 1 43.38 ? C3 GOL 263 A 1 
HETATM 6 O O3 GOL . . . D 4 16.052 13.275 30.511 1 35.41 ? O3 GOL 263 A 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           6 
#