data_6YU6
#
_model_server_result.job_id            ocmmzsyBRMNI-OWa1FwnDg 
_model_server_result.datetime_utc      '2024-10-14 09:25:38' 
_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          6yu6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":508}' 
#
_entry.id    6YU6 
#
_exptl.entry_id    6YU6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.434 
_entity.id                          5 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'octyl 1-thio-beta-D-glucopyranoside' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.05 
_cell.angle_gamma         90 
_cell.entry_id            6YU6 
_cell.length_a            44.23 
_cell.length_b            215.56 
_cell.length_c            50.17 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YU6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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,G,H,I,J,Q 1 1 
B,K,L,M,N,O,P,R 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 I N N 
? 5 J N N 
? 5 O N N 
? 5 P 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
metalc ? metalc1 A O GLY 26 A GLY 24 1_555 C NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc2 A O ALA 28 A ALA 26 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc3 A O VAL 29 A VAL 27 1_555 C NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc4 A OD1 ASN 33 A ASN 31 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? 
metalc ? metalc5 A O THR 233 A THR 231 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc6 A OG1 THR 233 A THR 231 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc7 A OD1 ASP 265 A ASP 263 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? 
metalc ? metalc8 A O ALA 322 A ALA 320 1_555 C NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? 
metalc ? metalc9 A OG SER 325 A SER 323 1_555 C NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? 
metalc ? metalc10 A OG SER 326 A SER 324 1_555 C NA NA . A NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc11 D NA NA . A NA 502 1_555 E OXT LEU . A LEU 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc12 B O GLY 26 B GLY 24 1_555 L NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc13 B O ALA 28 B ALA 26 1_555 K NA NA . B NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc14 B O VAL 29 B VAL 27 1_555 L NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc15 B OD1 ASN 33 B ASN 31 1_555 K NA NA . B NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? 
metalc ? metalc16 B O THR 233 B THR 231 1_555 K NA NA . B NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? 
metalc ? metalc17 B OG1 THR 233 B THR 231 1_555 K NA NA . B NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc18 B OD1 ASP 265 B ASP 263 1_555 K NA NA . B NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? 
metalc ? metalc19 B O ALA 322 B ALA 320 1_555 L NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc20 B OG SER 325 B SER 323 1_555 L NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
metalc ? metalc21 B OG SER 326 B SER 324 1_555 L NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
metalc ? metalc22 K NA NA . B NA 501 1_555 M OXT LEU . B LEU 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
#
_chem_comp.formula           'C14 H28 O5 S' 
_chem_comp.formula_weight    308.434 
_chem_comp.id                SOG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'octyl 1-thio-beta-D-glucopyranoside' 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     '2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL;1-S-OCTYL-BETA-D-THIOGLUCOSIDE;octyl 1-thio-beta-D-glucoside;octyl 1-thio-D-glucoside;octyl 1-thio-glucoside' 
#
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 SOG sing 338 n n 
C1 S1 SOG sing 339 n n 
C1 O5 SOG sing 340 n n 
C1 H1 SOG sing 341 n n 
C2 C3 SOG sing 342 n n 
C2 O2 SOG sing 343 n n 
C2 H2 SOG sing 344 n n 
C3 C4 SOG sing 345 n n 
C3 O3 SOG sing 346 n n 
C3 H3 SOG sing 347 n n 
C4 C5 SOG sing 348 n n 
C4 O4 SOG sing 349 n n 
C4 H4 SOG sing 350 n n 
C5 C6 SOG sing 351 n n 
C5 O5 SOG sing 352 n n 
C5 H5 SOG sing 353 n n 
C6 O6 SOG sing 354 n n 
C6 H61 SOG sing 355 n n 
C6 H62 SOG sing 356 n n 
C1' C2' SOG sing 357 n n 
C1' S1 SOG sing 358 n n 
C1' "H1'1" SOG sing 359 n n 
C1' "H1'2" SOG sing 360 n n 
C2' C3' SOG sing 361 n n 
C2' "H2'1" SOG sing 362 n n 
C2' "H2'2" SOG sing 363 n n 
C3' C4' SOG sing 364 n n 
C3' "H3'1" SOG sing 365 n n 
C3' "H3'2" SOG sing 366 n n 
C4' C5' SOG sing 367 n n 
C4' "H4'1" SOG sing 368 n n 
C4' "H4'2" SOG sing 369 n n 
C5' C6' SOG sing 370 n n 
C5' "H5'1" SOG sing 371 n n 
C5' "H5'2" SOG sing 372 n n 
C6' C7' SOG sing 373 n n 
C6' "H6'1" SOG sing 374 n n 
C6' "H6'2" SOG sing 375 n n 
C7' C8' SOG sing 376 n n 
C7' "H7'1" SOG sing 377 n n 
C7' "H7'2" SOG sing 378 n n 
C8' "H8'1" SOG sing 379 n n 
C8' "H8'2" SOG sing 380 n n 
C8' "H8'3" SOG sing 381 n n 
O2 HO2 SOG sing 382 n n 
O3 HO3 SOG sing 383 n n 
O4 HO4 SOG sing 384 n n 
O6 HO6 SOG sing 385 n n 
#
_atom_sites.entry_id                     6YU6 
_atom_sites.fract_transf_matrix[1][1]    0.022609 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000019 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004639 
_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]    0.019932 
_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 NA A 1 501 1 NA NA . 
D 2 NA A 1 502 2 NA NA . 
E 3 LEU A 1 503 601 LEU LEU . 
F 4 LMT A 1 504 3 LMT LMT . 
G 4 LMT A 1 505 4 LMT LMT . 
H 4 LMT A 1 506 5 LMT LMT . 
I 5 SOG A 1 507 1452 SOG SOG . 
J 5 SOG A 1 508 1456 SOG SOG . 
K 2 NA B 1 501 3 NA NA . 
L 2 NA B 1 502 4 NA NA . 
M 3 LEU B 1 503 601 LEU LEU . 
N 4 LMT B 1 504 2 LMT LMT . 
O 5 SOG B 1 505 1454 SOG SOG . 
P 5 SOG B 1 506 1455 SOG SOG . 
Q 6 HOH A 1 601 5 HOH HOH . 
Q 6 HOH A 2 602 17 HOH HOH . 
Q 6 HOH A 3 603 29 HOH HOH . 
Q 6 HOH A 4 604 37 HOH HOH . 
Q 6 HOH A 5 605 4 HOH HOH . 
Q 6 HOH A 6 606 20 HOH HOH . 
Q 6 HOH A 7 607 18 HOH HOH . 
Q 6 HOH A 8 608 40 HOH HOH . 
Q 6 HOH A 9 609 36 HOH HOH . 
Q 6 HOH A 10 610 50 HOH HOH . 
Q 6 HOH A 11 611 3 HOH HOH . 
Q 6 HOH A 12 612 19 HOH HOH . 
Q 6 HOH A 13 613 39 HOH HOH . 
Q 6 HOH A 14 614 1 HOH HOH . 
Q 6 HOH A 15 615 11 HOH HOH . 
Q 6 HOH A 16 616 45 HOH HOH . 
Q 6 HOH A 17 617 34 HOH HOH . 
Q 6 HOH A 18 618 16 HOH HOH . 
Q 6 HOH A 19 619 38 HOH HOH . 
Q 6 HOH A 20 620 33 HOH HOH . 
Q 6 HOH A 21 621 14 HOH HOH . 
Q 6 HOH A 22 622 46 HOH HOH . 
Q 6 HOH A 23 623 41 HOH HOH . 
Q 6 HOH A 24 624 31 HOH HOH . 
Q 6 HOH A 25 625 42 HOH HOH . 
Q 6 HOH A 26 626 47 HOH HOH . 
Q 6 HOH A 27 627 26 HOH HOH . 
R 6 HOH B 1 601 49 HOH HOH . 
R 6 HOH B 2 602 24 HOH HOH . 
R 6 HOH B 3 603 8 HOH HOH . 
R 6 HOH B 4 604 10 HOH HOH . 
R 6 HOH B 5 605 51 HOH HOH . 
R 6 HOH B 6 606 22 HOH HOH . 
R 6 HOH B 7 607 9 HOH HOH . 
R 6 HOH B 8 608 25 HOH HOH . 
R 6 HOH B 9 609 2 HOH HOH . 
R 6 HOH B 10 610 21 HOH HOH . 
R 6 HOH B 11 611 12 HOH HOH . 
R 6 HOH B 12 612 6 HOH HOH . 
R 6 HOH B 13 613 43 HOH HOH . 
R 6 HOH B 14 614 7 HOH HOH . 
R 6 HOH B 15 615 35 HOH HOH . 
R 6 HOH B 16 616 44 HOH HOH . 
R 6 HOH B 17 617 15 HOH HOH . 
R 6 HOH B 18 618 48 HOH HOH . 
R 6 HOH B 19 619 28 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 SOG . . . J 5 21.256 37.92 -39.697 1 46.46 ? C1 SOG 508 A 1 
HETATM 2 C C2 SOG . . . J 5 20.897 39.22 -40.425 1 46.57 ? C2 SOG 508 A 1 
HETATM 3 C C3 SOG . . . J 5 21.14 39.07 -41.917 1 47.3 ? C3 SOG 508 A 1 
HETATM 4 C C4 SOG . . . J 5 22.576 38.641 -42.154 1 50.16 ? C4 SOG 508 A 1 
HETATM 5 C C5 SOG . . . J 5 22.846 37.344 -41.398 1 48.96 ? C5 SOG 508 A 1 
HETATM 6 C C6 SOG . . . J 5 24.278 36.879 -41.536 1 48.14 ? C6 SOG 508 A 1 
HETATM 7 C C1' SOG . . . J 5 21.021 36.337 -37.397 1 49.33 ? C1' SOG 508 A 1 
HETATM 8 C C2' SOG . . . J 5 21.235 36.328 -35.889 1 45.01 ? C2' SOG 508 A 1 
HETATM 9 C C3' SOG . . . J 5 20.138 35.599 -35.119 1 60.18 ? C3' SOG 508 A 1 
HETATM 10 C C4' SOG . . . J 5 20.361 35.526 -33.61 1 57.07 ? C4' SOG 508 A 1 
HETATM 11 C C5' SOG . . . J 5 19.128 35.091 -32.827 1 46.77 ? C5' SOG 508 A 1 
HETATM 12 C C6' SOG . . . J 5 19.342 34.976 -31.324 1 55.02 ? C6' SOG 508 A 1 
HETATM 13 C C7' SOG . . . J 5 18.062 34.726 -30.539 1 41.66 ? C7' SOG 508 A 1 
HETATM 14 C C8' SOG . . . J 5 18.301 34.458 -29.069 1 37.75 ? C8' SOG 508 A 1 
HETATM 15 S S1 SOG . . . J 5 21.002 38.074 -37.91 1 73.62 ? S1 SOG 508 A 1 
HETATM 16 O O2 SOG . . . J 5 19.54 39.571 -40.193 1 53.13 ? O2 SOG 508 A 1 
HETATM 17 O O3 SOG . . . J 5 20.865 40.291 -42.592 1 48.3 ? O3 SOG 508 A 1 
HETATM 18 O O4 SOG . . . J 5 22.807 38.435 -43.541 1 62.2 ? O4 SOG 508 A 1 
HETATM 19 O O5 SOG . . . J 5 22.594 37.536 -39.994 1 52.98 ? O5 SOG 508 A 1 
HETATM 20 O O6 SOG . . . J 5 24.468 35.585 -40.977 1 45.96 ? O6 SOG 508 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           20 
#