data_1F8Q
#
_model_server_result.job_id            jEA8kBfbWc2SpJuGgSDOUQ 
_model_server_result.datetime_utc      '2024-12-19 11:59:10' 
_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          1f8q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":367}' 
#
_entry.id    1F8Q 
#
_exptl.entry_id    1F8Q 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              100.116 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            PENTANEDIAL 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            1F8Q 
_cell.length_a            131.51 
_cell.length_b            131.51 
_cell.length_c            39.81 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1F8Q 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D N N 
? 3 E N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 2 3 2 MAN NAG C1 O1 . O4 HO4 . sing 
3 ? 2 4 3 XYS MAN C1 O1 . O2 HO2 . 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 B 301 NAG 
2 n B NAG 2 B 2 NAG B 302 NAG 
2 n B MAN 3 B 3 MAN B 303 MAN 
2 n B XYS 4 B 4 XYS B 304 XYS 
#
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 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? 
covale ? covale3 B O4 NAG . B NAG 2 1_555 B C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? 
covale ? covale4 B O2 MAN . B MAN 3 1_555 B C1 XYS . B XYS 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? 
#
_chem_comp.formula           'C5 H8 O2' 
_chem_comp.formula_weight    100.116 
_chem_comp.id                PTD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              PENTANEDIAL 
_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 PTD sing 323 n n 
C1 O1 PTD doub 324 n n 
C1 HC1 PTD sing 325 n n 
C2 C3 PTD sing 326 n n 
C2 HC21 PTD sing 327 n n 
C2 HC22 PTD sing 328 n n 
C3 C4 PTD sing 329 n n 
C3 HC31 PTD sing 330 n n 
C3 HC32 PTD sing 331 n n 
C4 C5 PTD sing 332 n n 
C4 HC41 PTD sing 333 n n 
C4 HC42 PTD sing 334 n n 
C5 O5 PTD doub 335 n n 
C5 HC5 PTD sing 336 n n 
#
_atom_sites.entry_id                     1F8Q 
_atom_sites.fract_transf_matrix[1][1]    0.007604 
_atom_sites.fract_transf_matrix[1][2]    0.00439 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00878 
_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]    0.025119 
_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 PTD A 1 307 307 PTD PTD . 
D 3 PTD A 1 367 367 PTD PTD . 
E 3 PTD A 1 401 401 PTD PTD . 
F 4 CCN A 1 305 305 CCN CCN . 
G 4 CCN A 1 306 306 CCN CCN . 
H 5 HOH A 1 308 308 HOH HOH . 
H 5 HOH A 2 309 309 HOH HOH . 
H 5 HOH A 3 310 310 HOH HOH . 
H 5 HOH A 4 311 311 HOH HOH . 
H 5 HOH A 5 312 312 HOH HOH . 
H 5 HOH A 6 313 313 HOH HOH . 
H 5 HOH A 7 314 314 HOH HOH . 
H 5 HOH A 8 315 315 HOH HOH . 
H 5 HOH A 9 316 316 HOH HOH . 
H 5 HOH A 10 317 317 HOH HOH . 
H 5 HOH A 11 318 318 HOH HOH . 
H 5 HOH A 12 319 319 HOH HOH . 
H 5 HOH A 13 320 320 HOH HOH . 
H 5 HOH A 14 321 321 HOH HOH . 
H 5 HOH A 15 322 322 HOH HOH . 
H 5 HOH A 16 323 323 HOH HOH . 
H 5 HOH A 17 324 324 HOH HOH . 
H 5 HOH A 18 325 325 HOH HOH . 
H 5 HOH A 19 326 326 HOH HOH . 
H 5 HOH A 20 327 327 HOH HOH . 
H 5 HOH A 21 328 328 HOH HOH . 
H 5 HOH A 22 329 329 HOH HOH . 
H 5 HOH A 23 330 330 HOH HOH . 
H 5 HOH A 24 331 331 HOH HOH . 
H 5 HOH A 25 332 332 HOH HOH . 
H 5 HOH A 26 333 333 HOH HOH . 
H 5 HOH A 27 334 334 HOH HOH . 
H 5 HOH A 28 335 335 HOH HOH . 
H 5 HOH A 29 336 336 HOH HOH . 
H 5 HOH A 30 337 337 HOH HOH . 
H 5 HOH A 31 338 338 HOH HOH . 
H 5 HOH A 32 339 339 HOH HOH . 
H 5 HOH A 33 340 340 HOH HOH . 
H 5 HOH A 34 341 341 HOH HOH . 
H 5 HOH A 35 342 342 HOH HOH . 
H 5 HOH A 36 343 343 HOH HOH . 
H 5 HOH A 37 344 344 HOH HOH . 
H 5 HOH A 38 345 345 HOH HOH . 
H 5 HOH A 39 346 346 HOH HOH . 
H 5 HOH A 40 347 347 HOH HOH . 
H 5 HOH A 41 348 348 HOH HOH . 
H 5 HOH A 42 349 349 HOH HOH . 
H 5 HOH A 43 350 350 HOH HOH . 
H 5 HOH A 44 351 351 HOH HOH . 
H 5 HOH A 45 352 352 HOH HOH . 
H 5 HOH A 46 353 353 HOH HOH . 
H 5 HOH A 47 354 354 HOH HOH . 
H 5 HOH A 48 355 355 HOH HOH . 
H 5 HOH A 49 356 356 HOH HOH . 
H 5 HOH A 50 357 357 HOH HOH . 
H 5 HOH A 51 358 358 HOH HOH . 
H 5 HOH A 52 359 359 HOH HOH . 
H 5 HOH A 53 360 360 HOH HOH . 
H 5 HOH A 54 361 361 HOH HOH . 
H 5 HOH A 55 362 362 HOH HOH . 
H 5 HOH A 56 363 363 HOH HOH . 
H 5 HOH A 57 364 364 HOH HOH . 
H 5 HOH A 58 365 365 HOH HOH . 
H 5 HOH A 59 366 366 HOH HOH . 
H 5 HOH A 60 369 369 HOH HOH . 
H 5 HOH A 61 370 370 HOH HOH . 
H 5 HOH A 62 371 371 HOH HOH . 
H 5 HOH A 63 372 372 HOH HOH . 
H 5 HOH A 64 373 373 HOH HOH . 
H 5 HOH A 65 374 374 HOH HOH . 
H 5 HOH A 66 375 375 HOH HOH . 
H 5 HOH A 67 376 376 HOH HOH . 
H 5 HOH A 68 377 377 HOH HOH . 
H 5 HOH A 69 378 378 HOH HOH . 
H 5 HOH A 70 379 379 HOH HOH . 
H 5 HOH A 71 380 380 HOH HOH . 
H 5 HOH A 72 381 381 HOH HOH . 
H 5 HOH A 73 382 382 HOH HOH . 
H 5 HOH A 74 383 383 HOH HOH . 
H 5 HOH A 75 384 384 HOH HOH . 
H 5 HOH A 76 385 385 HOH HOH . 
H 5 HOH A 77 386 386 HOH HOH . 
H 5 HOH A 78 387 387 HOH HOH . 
H 5 HOH A 79 388 388 HOH HOH . 
H 5 HOH A 80 389 389 HOH HOH . 
H 5 HOH A 81 390 390 HOH HOH . 
H 5 HOH A 82 391 391 HOH HOH . 
H 5 HOH A 83 392 392 HOH HOH . 
H 5 HOH A 84 393 393 HOH HOH . 
H 5 HOH A 85 394 394 HOH HOH . 
H 5 HOH A 86 395 395 HOH HOH . 
H 5 HOH A 87 396 396 HOH HOH . 
H 5 HOH A 88 397 397 HOH HOH . 
H 5 HOH A 89 398 398 HOH HOH . 
H 5 HOH A 90 399 399 HOH HOH . 
H 5 HOH A 91 400 400 HOH HOH . 
H 5 HOH A 92 402 402 HOH HOH . 
H 5 HOH A 93 403 403 HOH HOH . 
H 5 HOH A 94 404 404 HOH HOH . 
H 5 HOH A 95 406 406 HOH HOH . 
H 5 HOH A 96 407 407 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 PTD . . . D 3 62.006 118.403 9.571 1 62.03 ? C1 PTD 367 A 1 
HETATM 2 C C2 PTD . . . D 3 61.715 118.123 8.089 1 61.51 ? C2 PTD 367 A 1 
HETATM 3 C C3 PTD . . . D 3 60.208 118.056 7.757 1 61.35 ? C3 PTD 367 A 1 
HETATM 4 C C4 PTD . . . D 3 59.964 117.595 6.296 1 66.21 ? C4 PTD 367 A 1 
HETATM 5 C C5 PTD . . . D 3 58.471 117.34 5.97 1 68.11 ? C5 PTD 367 A 1 
HETATM 6 O O1 PTD . . . D 3 61.112 118.363 10.435 1 62.13 ? O1 PTD 367 A 1 
HETATM 7 O O5 PTD . . . D 3 58.096 116.974 4.832 1 67.87 ? O5 PTD 367 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           7 
#