data_5NDU
#
_model_server_result.job_id            WkbOYTQvLTs0ugNAtIyj2g 
_model_server_result.datetime_utc      '2025-08-01 21:10:26' 
_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          5ndu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":205}' 
#
_entry.id    5NDU 
#
_exptl.entry_id    5NDU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          96.93 
_cell.angle_gamma         90 
_cell.entry_id            5NDU 
_cell.length_a            136.15 
_cell.length_b            34.57 
_cell.length_c            44.24 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NDU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,L 1 1 
B,G,H,I,J,K,M 2 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
? 5 F N N 
? 5 J N N 
? 5 K N N 
#
_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 226 n n 
C1 C2 GOL sing 227 n n 
C1 H11 GOL sing 228 n n 
C1 H12 GOL sing 229 n n 
O1 HO1 GOL sing 230 n n 
C2 O2 GOL sing 231 n n 
C2 C3 GOL sing 232 n n 
C2 H2 GOL sing 233 n n 
O2 HO2 GOL sing 234 n n 
C3 O3 GOL sing 235 n n 
C3 H31 GOL sing 236 n n 
C3 H32 GOL sing 237 n n 
O3 HO3 GOL sing 238 n n 
#
_atom_sites.entry_id                     5NDU 
_atom_sites.fract_transf_matrix[1][1]    0.007345 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000893 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.028927 
_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]    0.02277 
_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
C 2 8V2 A 1 201 1 8V2 212 . 
D 3 SO4 A 1 202 3 SO4 SO4 . 
E 4 NO3 A 1 203 1 NO3 NO3 . 
F 5 GOL A 1 204 1 GOL GOL . 
G 2 8V2 B 1 201 1 8V2 212 . 
H 2 8V2 B 1 202 2 8V2 212 . 
I 4 NO3 B 1 203 2 NO3 NO3 . 
J 5 GOL B 1 204 2 GOL GOL . 
K 5 GOL B 1 205 3 GOL GOL . 
L 6 HOH A 1 301 148 HOH HOH . 
L 6 HOH A 2 302 78 HOH HOH . 
L 6 HOH A 3 303 136 HOH HOH . 
L 6 HOH A 4 304 99 HOH HOH . 
L 6 HOH A 5 305 52 HOH HOH . 
L 6 HOH A 6 306 110 HOH HOH . 
L 6 HOH A 7 307 158 HOH HOH . 
L 6 HOH A 8 308 55 HOH HOH . 
L 6 HOH A 9 309 53 HOH HOH . 
L 6 HOH A 10 310 90 HOH HOH . 
L 6 HOH A 11 311 160 HOH HOH . 
L 6 HOH A 12 312 14 HOH HOH . 
L 6 HOH A 13 313 151 HOH HOH . 
L 6 HOH A 14 314 50 HOH HOH . 
L 6 HOH A 15 315 62 HOH HOH . 
L 6 HOH A 16 316 37 HOH HOH . 
L 6 HOH A 17 317 24 HOH HOH . 
L 6 HOH A 18 318 6 HOH HOH . 
L 6 HOH A 19 319 51 HOH HOH . 
L 6 HOH A 20 320 41 HOH HOH . 
L 6 HOH A 21 321 72 HOH HOH . 
L 6 HOH A 22 322 73 HOH HOH . 
L 6 HOH A 23 323 43 HOH HOH . 
L 6 HOH A 24 324 48 HOH HOH . 
L 6 HOH A 25 325 108 HOH HOH . 
L 6 HOH A 26 326 9 HOH HOH . 
L 6 HOH A 27 327 12 HOH HOH . 
L 6 HOH A 28 328 107 HOH HOH . 
L 6 HOH A 29 329 94 HOH HOH . 
L 6 HOH A 30 330 33 HOH HOH . 
L 6 HOH A 31 331 96 HOH HOH . 
L 6 HOH A 32 332 3 HOH HOH . 
L 6 HOH A 33 333 77 HOH HOH . 
L 6 HOH A 34 334 2 HOH HOH . 
L 6 HOH A 35 335 40 HOH HOH . 
L 6 HOH A 36 336 88 HOH HOH . 
L 6 HOH A 37 337 10 HOH HOH . 
L 6 HOH A 38 338 114 HOH HOH . 
L 6 HOH A 39 339 58 HOH HOH . 
L 6 HOH A 40 340 113 HOH HOH . 
L 6 HOH A 41 341 49 HOH HOH . 
L 6 HOH A 42 342 22 HOH HOH . 
L 6 HOH A 43 343 116 HOH HOH . 
L 6 HOH A 44 344 95 HOH HOH . 
L 6 HOH A 45 345 80 HOH HOH . 
L 6 HOH A 46 346 118 HOH HOH . 
L 6 HOH A 47 347 83 HOH HOH . 
L 6 HOH A 48 348 18 HOH HOH . 
L 6 HOH A 49 349 141 HOH HOH . 
L 6 HOH A 50 350 152 HOH HOH . 
L 6 HOH A 51 351 56 HOH HOH . 
L 6 HOH A 52 352 57 HOH HOH . 
L 6 HOH A 53 353 82 HOH HOH . 
L 6 HOH A 54 354 131 HOH HOH . 
L 6 HOH A 55 355 125 HOH HOH . 
L 6 HOH A 56 356 29 HOH HOH . 
L 6 HOH A 57 357 133 HOH HOH . 
L 6 HOH A 58 358 13 HOH HOH . 
L 6 HOH A 59 359 39 HOH HOH . 
L 6 HOH A 60 360 154 HOH HOH . 
L 6 HOH A 61 361 117 HOH HOH . 
L 6 HOH A 62 362 98 HOH HOH . 
L 6 HOH A 63 363 87 HOH HOH . 
L 6 HOH A 64 364 161 HOH HOH . 
L 6 HOH A 65 365 65 HOH HOH . 
L 6 HOH A 66 366 92 HOH HOH . 
L 6 HOH A 67 367 123 HOH HOH . 
L 6 HOH A 68 368 69 HOH HOH . 
L 6 HOH A 69 369 126 HOH HOH . 
L 6 HOH A 70 370 106 HOH HOH . 
L 6 HOH A 71 371 31 HOH HOH . 
L 6 HOH A 72 372 157 HOH HOH . 
L 6 HOH A 73 373 93 HOH HOH . 
L 6 HOH A 74 374 124 HOH HOH . 
L 6 HOH A 75 375 127 HOH HOH . 
L 6 HOH A 76 376 130 HOH HOH . 
L 6 HOH A 77 377 103 HOH HOH . 
M 6 HOH B 1 301 150 HOH HOH . 
M 6 HOH B 2 302 74 HOH HOH . 
M 6 HOH B 3 303 112 HOH HOH . 
M 6 HOH B 4 304 145 HOH HOH . 
M 6 HOH B 5 305 91 HOH HOH . 
M 6 HOH B 6 306 111 HOH HOH . 
M 6 HOH B 7 307 63 HOH HOH . 
M 6 HOH B 8 308 28 HOH HOH . 
M 6 HOH B 9 309 60 HOH HOH . 
M 6 HOH B 10 310 35 HOH HOH . 
M 6 HOH B 11 311 138 HOH HOH . 
M 6 HOH B 12 312 68 HOH HOH . 
M 6 HOH B 13 313 122 HOH HOH . 
M 6 HOH B 14 314 7 HOH HOH . 
M 6 HOH B 15 315 26 HOH HOH . 
M 6 HOH B 16 316 38 HOH HOH . 
M 6 HOH B 17 317 4 HOH HOH . 
M 6 HOH B 18 318 1 HOH HOH . 
M 6 HOH B 19 319 45 HOH HOH . 
M 6 HOH B 20 320 42 HOH HOH . 
M 6 HOH B 21 321 155 HOH HOH . 
M 6 HOH B 22 322 66 HOH HOH . 
M 6 HOH B 23 323 156 HOH HOH . 
M 6 HOH B 24 324 32 HOH HOH . 
M 6 HOH B 25 325 85 HOH HOH . 
M 6 HOH B 26 326 84 HOH HOH . 
M 6 HOH B 27 327 54 HOH HOH . 
M 6 HOH B 28 328 121 HOH HOH . 
M 6 HOH B 29 329 23 HOH HOH . 
M 6 HOH B 30 330 97 HOH HOH . 
M 6 HOH B 31 331 128 HOH HOH . 
M 6 HOH B 32 332 11 HOH HOH . 
M 6 HOH B 33 333 59 HOH HOH . 
M 6 HOH B 34 334 36 HOH HOH . 
M 6 HOH B 35 335 46 HOH HOH . 
M 6 HOH B 36 336 15 HOH HOH . 
M 6 HOH B 37 337 120 HOH HOH . 
M 6 HOH B 38 338 81 HOH HOH . 
M 6 HOH B 39 339 20 HOH HOH . 
M 6 HOH B 40 340 25 HOH HOH . 
M 6 HOH B 41 341 19 HOH HOH . 
M 6 HOH B 42 342 34 HOH HOH . 
M 6 HOH B 43 343 75 HOH HOH . 
M 6 HOH B 44 344 21 HOH HOH . 
M 6 HOH B 45 345 17 HOH HOH . 
M 6 HOH B 46 346 44 HOH HOH . 
M 6 HOH B 47 347 5 HOH HOH . 
M 6 HOH B 48 348 137 HOH HOH . 
M 6 HOH B 49 349 104 HOH HOH . 
M 6 HOH B 50 350 149 HOH HOH . 
M 6 HOH B 51 351 27 HOH HOH . 
M 6 HOH B 52 352 102 HOH HOH . 
M 6 HOH B 53 353 30 HOH HOH . 
M 6 HOH B 54 354 115 HOH HOH . 
M 6 HOH B 55 355 76 HOH HOH . 
M 6 HOH B 56 356 47 HOH HOH . 
M 6 HOH B 57 357 70 HOH HOH . 
M 6 HOH B 58 358 139 HOH HOH . 
M 6 HOH B 59 359 8 HOH HOH . 
M 6 HOH B 60 360 129 HOH HOH . 
M 6 HOH B 61 361 64 HOH HOH . 
M 6 HOH B 62 362 89 HOH HOH . 
M 6 HOH B 63 363 144 HOH HOH . 
M 6 HOH B 64 364 109 HOH HOH . 
M 6 HOH B 65 365 86 HOH HOH . 
M 6 HOH B 66 366 79 HOH HOH . 
M 6 HOH B 67 367 61 HOH HOH . 
M 6 HOH B 68 368 135 HOH HOH . 
M 6 HOH B 69 369 140 HOH HOH . 
M 6 HOH B 70 370 143 HOH HOH . 
M 6 HOH B 71 371 147 HOH HOH . 
M 6 HOH B 72 372 153 HOH HOH . 
M 6 HOH B 73 373 132 HOH HOH . 
M 6 HOH B 74 374 119 HOH HOH . 
M 6 HOH B 75 375 16 HOH HOH . 
M 6 HOH B 76 376 67 HOH HOH . 
M 6 HOH B 77 377 71 HOH HOH . 
M 6 HOH B 78 378 142 HOH HOH . 
M 6 HOH B 79 379 100 HOH HOH . 
M 6 HOH B 80 380 159 HOH HOH . 
M 6 HOH B 81 381 101 HOH HOH . 
M 6 HOH B 82 382 105 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 . . . K 5 -16.848 -18.927 -11.885 1 58.93 ? C1 GOL 205 B 1 
HETATM 2 O O1 GOL . . . K 5 -15.466 -18.895 -12.138 1 59.71 ? O1 GOL 205 B 1 
HETATM 3 C C2 GOL . . . K 5 -17.244 -20.146 -11.074 1 58.62 ? C2 GOL 205 B 1 
HETATM 4 O O2 GOL . . . K 5 -17.485 -19.712 -9.764 1 64.02 ? O2 GOL 205 B 1 
HETATM 5 C C3 GOL . . . K 5 -18.53 -20.755 -11.623 1 53.45 ? C3 GOL 205 B 1 
HETATM 6 O O3 GOL . . . K 5 -19.26 -21.376 -10.566 1 50.19 ? O3 GOL 205 B 1 
HETATM 7 H H11 GOL . . . K 5 -17.136 -18.025 -11.345 1 70.73 ? H11 GOL 205 B 1 
HETATM 8 H H12 GOL . . . K 5 -17.387 -18.933 -12.832 1 70.73 ? H12 GOL 205 B 1 
HETATM 9 H HO1 GOL . . . K 5 -15.257 -18.133 -12.717 1 71.66 ? HO1 GOL 205 B 1 
HETATM 10 H H2 GOL . . . K 5 -16.443 -20.885 -11.099 1 70.36 ? H2 GOL 205 B 1 
HETATM 11 H HO2 GOL . . . K 5 -18.206 -19.048 -9.768 1 76.84 ? HO2 GOL 205 B 1 
HETATM 12 H H31 GOL . . . K 5 -19.139 -19.976 -12.082 1 64.15 ? H31 GOL 205 B 1 
HETATM 13 H H32 GOL . . . K 5 -18.29 -21.494 -12.388 1 64.15 ? H32 GOL 205 B 1 
HETATM 14 H HO3 GOL . . . K 5 -19.975 -21.929 -10.943 1 60.24 ? HO3 GOL 205 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           14 
#