data_3NFM
#
_model_server_result.job_id            DYL3z0COm4vSp9WjDEzJkg 
_model_server_result.datetime_utc      '2024-10-19 15:25:58' 
_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          3nfm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":249}' 
#
_entry.id    3NFM 
#
_exptl.entry_id    3NFM 
_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    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         120 
_cell.entry_id            3NFM 
_cell.length_a            129.85 
_cell.length_b            129.85 
_cell.length_c            40.42 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NFM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
_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                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   NAG 
_pdbx_entity_branch_link.comp_id_2                   NAG 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O4 
_pdbx_entity_branch_link.leaving_atom_id_2           HO4 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n B NAG 1 B 1 NAG C 1 NAG 
2 n B NAG 2 B 2 NAG C 2 NAG 
#
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
covale ? covale1 A ND2 ASN 227 A ASN 227 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? 
covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
#
_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 140 n n 
C1 C2 GOL sing 141 n n 
C1 H11 GOL sing 142 n n 
C1 H12 GOL sing 143 n n 
O1 HO1 GOL sing 144 n n 
C2 O2 GOL sing 145 n n 
C2 C3 GOL sing 146 n n 
C2 H2 GOL sing 147 n n 
O2 HO2 GOL sing 148 n n 
C3 O3 GOL sing 149 n n 
C3 H31 GOL sing 150 n n 
C3 H32 GOL sing 151 n n 
O3 HO3 GOL sing 152 n n 
#
_atom_sites.entry_id                     3NFM 
_atom_sites.fract_transf_matrix[1][1]    0.007701 
_atom_sites.fract_transf_matrix[1][2]    0.004446 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008893 
_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]    0.02474 
_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 3 FRU A 1 693 693 FRU FRU . 
D 4 GOL A 1 249 1 GOL GOL . 
E 5 HOH A 1 250 1 HOH HOH . 
E 5 HOH A 2 251 2 HOH HOH . 
E 5 HOH A 3 252 3 HOH HOH . 
E 5 HOH A 4 253 4 HOH HOH . 
E 5 HOH A 5 254 5 HOH HOH . 
E 5 HOH A 6 255 6 HOH HOH . 
E 5 HOH A 7 256 7 HOH HOH . 
E 5 HOH A 8 257 8 HOH HOH . 
E 5 HOH A 9 258 9 HOH HOH . 
E 5 HOH A 10 259 10 HOH HOH . 
E 5 HOH A 11 260 11 HOH HOH . 
E 5 HOH A 12 261 12 HOH HOH . 
E 5 HOH A 13 262 13 HOH HOH . 
E 5 HOH A 14 263 14 HOH HOH . 
E 5 HOH A 15 264 15 HOH HOH . 
E 5 HOH A 16 265 16 HOH HOH . 
E 5 HOH A 17 266 17 HOH HOH . 
E 5 HOH A 18 267 18 HOH HOH . 
E 5 HOH A 19 268 19 HOH HOH . 
E 5 HOH A 20 269 20 HOH HOH . 
E 5 HOH A 21 270 21 HOH HOH . 
E 5 HOH A 22 271 22 HOH HOH . 
E 5 HOH A 23 272 23 HOH HOH . 
E 5 HOH A 24 273 24 HOH HOH . 
E 5 HOH A 25 274 25 HOH HOH . 
E 5 HOH A 26 275 26 HOH HOH . 
E 5 HOH A 27 276 27 HOH HOH . 
E 5 HOH A 28 277 28 HOH HOH . 
E 5 HOH A 29 278 29 HOH HOH . 
E 5 HOH A 30 279 30 HOH HOH . 
E 5 HOH A 31 280 31 HOH HOH . 
E 5 HOH A 32 281 32 HOH HOH . 
E 5 HOH A 33 282 33 HOH HOH . 
E 5 HOH A 34 283 34 HOH HOH . 
E 5 HOH A 35 284 35 HOH HOH . 
E 5 HOH A 36 285 37 HOH HOH . 
E 5 HOH A 37 286 38 HOH HOH . 
E 5 HOH A 38 287 39 HOH HOH . 
E 5 HOH A 39 288 40 HOH HOH . 
E 5 HOH A 40 289 41 HOH HOH . 
E 5 HOH A 41 290 42 HOH HOH . 
E 5 HOH A 42 291 43 HOH HOH . 
E 5 HOH A 43 292 44 HOH HOH . 
E 5 HOH A 44 293 45 HOH HOH . 
E 5 HOH A 45 294 46 HOH HOH . 
E 5 HOH A 46 295 47 HOH HOH . 
E 5 HOH A 47 296 48 HOH HOH . 
E 5 HOH A 48 297 49 HOH HOH . 
E 5 HOH A 49 298 50 HOH HOH . 
E 5 HOH A 50 299 51 HOH HOH . 
E 5 HOH A 51 300 52 HOH HOH . 
E 5 HOH A 52 301 53 HOH HOH . 
E 5 HOH A 53 302 54 HOH HOH . 
E 5 HOH A 54 303 55 HOH HOH . 
E 5 HOH A 55 304 56 HOH HOH . 
E 5 HOH A 56 305 57 HOH HOH . 
E 5 HOH A 57 306 58 HOH HOH . 
E 5 HOH A 58 307 59 HOH HOH . 
E 5 HOH A 59 308 60 HOH HOH . 
E 5 HOH A 60 309 61 HOH HOH . 
E 5 HOH A 61 310 62 HOH HOH . 
E 5 HOH A 62 311 63 HOH HOH . 
E 5 HOH A 63 312 64 HOH HOH . 
E 5 HOH A 64 313 65 HOH HOH . 
E 5 HOH A 65 314 66 HOH HOH . 
E 5 HOH A 66 315 67 HOH HOH . 
E 5 HOH A 67 316 68 HOH HOH . 
E 5 HOH A 68 317 72 HOH HOH . 
E 5 HOH A 69 318 77 HOH HOH . 
E 5 HOH A 70 319 84 HOH HOH . 
E 5 HOH A 71 320 85 HOH HOH . 
E 5 HOH A 72 321 86 HOH HOH . 
E 5 HOH A 73 322 87 HOH HOH . 
E 5 HOH A 74 323 88 HOH HOH . 
E 5 HOH A 75 324 89 HOH HOH . 
E 5 HOH A 76 325 90 HOH HOH . 
E 5 HOH A 77 326 91 HOH HOH . 
E 5 HOH A 78 327 92 HOH HOH . 
E 5 HOH A 79 328 93 HOH HOH . 
E 5 HOH A 80 329 94 HOH HOH . 
E 5 HOH A 81 330 95 HOH HOH . 
E 5 HOH A 82 331 96 HOH HOH . 
E 5 HOH A 83 332 97 HOH HOH . 
E 5 HOH A 84 333 98 HOH HOH . 
E 5 HOH A 85 334 99 HOH HOH . 
E 5 HOH A 86 335 100 HOH HOH . 
E 5 HOH A 87 336 101 HOH HOH . 
E 5 HOH A 88 337 102 HOH HOH . 
E 5 HOH A 89 338 103 HOH HOH . 
E 5 HOH A 90 339 104 HOH HOH . 
E 5 HOH A 91 340 105 HOH HOH . 
E 5 HOH A 92 341 106 HOH HOH . 
E 5 HOH A 93 342 107 HOH HOH . 
E 5 HOH A 94 343 108 HOH HOH . 
E 5 HOH A 95 344 109 HOH HOH . 
E 5 HOH A 96 345 110 HOH HOH . 
E 5 HOH A 97 346 112 HOH HOH . 
E 5 HOH A 98 347 113 HOH HOH . 
E 5 HOH A 99 348 114 HOH HOH . 
E 5 HOH A 100 349 115 HOH HOH . 
E 5 HOH A 101 350 116 HOH HOH . 
E 5 HOH A 102 351 117 HOH HOH . 
E 5 HOH A 103 352 118 HOH HOH . 
E 5 HOH A 104 353 119 HOH HOH . 
E 5 HOH A 105 354 120 HOH HOH . 
E 5 HOH A 106 355 121 HOH HOH . 
E 5 HOH A 107 356 122 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 13.618 14.323 -10.074 1 35.28 ? C1 GOL 249 A 1 
HETATM 2 O O1 GOL . . . D 4 13.515 15.661 -10.506 1 35.74 ? O1 GOL 249 A 1 
HETATM 3 C C2 GOL . . . D 4 12.249 13.658 -10.148 1 30.99 ? C2 GOL 249 A 1 
HETATM 4 O O2 GOL . . . D 4 11.302 14.586 -10.629 1 37.25 ? O2 GOL 249 A 1 
HETATM 5 C C3 GOL . . . D 4 11.837 13.188 -8.758 1 32.26 ? C3 GOL 249 A 1 
HETATM 6 O O3 GOL . . . D 4 12.985 12.81 -8.031 1 28.95 ? O3 GOL 249 A 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#