data_2YIO
#
_model_server_result.job_id            ldx8Uot3bsHL4hT3dSEevA 
_model_server_result.datetime_utc      '2024-10-20 08:25:32' 
_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          2yio 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1141}' 
#
_entry.id    2YIO 
#
_exptl.entry_id    2YIO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              196.221 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-thio-beta-D-galactopyranose 
_entity.pdbx_number_of_molecules    2 
_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         90 
_cell.entry_id            2YIO 
_cell.length_a            74.73 
_cell.length_b            81.99 
_cell.length_c            130.96 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YIO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_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,K,R 1 1,2 
B,L,M,N,O,P,Q,S 2 1,3 
#
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' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 81.99 130.96 
3 'crystal symmetry operation' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 74.73 0 65.48 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 K N N 
? 5 Q 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 9 A CYS 9 1_555 A SG CYS 78 A CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
disulf ? disulf2 A SG CYS 34 A CYS 34 1_555 A SG CYS 56 A CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
disulf ? disulf3 A SG CYS 38 A CYS 38 1_555 A SG CYS 44 A CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
disulf ? disulf4 A SG CYS 82 A CYS 82 1_555 A SG CYS 86 A CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 107 A CYS 107 1_555 A SG CYS 127 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
disulf ? disulf6 A SG CYS 111 A CYS 111 1_555 A SG CYS 117 A CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf7 B SG CYS 9 B CYS 9 1_555 B SG CYS 78 B CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
disulf ? disulf8 B SG CYS 34 B CYS 34 1_555 B SG CYS 56 B CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
disulf ? disulf9 B SG CYS 38 B CYS 38 1_555 B SG CYS 44 B CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf10 B SG CYS 82 B CYS 82 1_555 B SG CYS 86 B CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
disulf ? disulf11 B SG CYS 107 B CYS 107 1_555 B SG CYS 127 B CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
disulf ? disulf12 B SG CYS 111 B CYS 111 1_555 B SG CYS 117 B CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
#
_chem_comp.formula           'C6 H12 O5 S' 
_chem_comp.formula_weight    196.221 
_chem_comp.id                YIO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-thio-beta-D-galactopyranose 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     (2R,3R,4S,5R,6S)-2-(HYDROXYMETHYL)-6-SULFANYL-OXANE-3,4,5-TRIOL;1-thio-beta-D-galactose;1-thio-D-galactose;1-thio-galactose 
#
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 YIO sing 393 n n 
C1 O5 YIO sing 394 n n 
C1 S1 YIO sing 395 n n 
C2 C3 YIO sing 396 n n 
C2 O2 YIO sing 397 n n 
C3 C4 YIO sing 398 n n 
C3 O3 YIO sing 399 n n 
C4 C5 YIO sing 400 n n 
C4 O4 YIO sing 401 n n 
C5 C6 YIO sing 402 n n 
C5 O5 YIO sing 403 n n 
C6 O6 YIO sing 404 n n 
C1 H1 YIO sing 405 n n 
C2 H2 YIO sing 406 n n 
C3 H3 YIO sing 407 n n 
O2 HO2 YIO sing 408 n n 
C4 H4 YIO sing 409 n n 
O3 HO3 YIO sing 410 n n 
C5 H5 YIO sing 411 n n 
O4 HO4 YIO sing 412 n n 
C6 H61 YIO sing 413 n n 
C6 H62 YIO sing 414 n n 
S1 HS1 YIO sing 415 n n 
O6 HO6 YIO sing 416 n n 
#
_pdbx_chem_comp_identifier.comp_id            YIO 
_pdbx_chem_comp_identifier.identifier         b-D-Galp1SH 
_pdbx_chem_comp_identifier.type               'IUPAC CARBOHYDRATE SYMBOL' 
_pdbx_chem_comp_identifier.program            PDB-CARE 
_pdbx_chem_comp_identifier.program_version    1 
#
_atom_sites.entry_id                     2YIO 
_atom_sites.fract_transf_matrix[1][1]    0.013382 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012197 
_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]    0.007636 
_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 CL A 1 1133 1133 CL CL . 
D 2 CL A 1 1134 1134 CL CL . 
E 2 CL A 1 1135 1135 CL CL . 
F 2 CL A 1 1136 1136 CL CL . 
G 2 CL A 1 1137 1137 CL CL . 
H 3 SO4 A 1 1138 1138 SO4 SO4 . 
I 3 SO4 A 1 1139 1139 SO4 SO4 . 
J 4 GOL A 1 1140 1140 GOL GOL . 
K 5 YIO A 1 1141 1141 YIO YIO . 
L 2 CL B 1 1133 1133 CL CL . 
M 2 CL B 1 1134 1134 CL CL . 
N 2 CL B 1 1135 1135 CL CL . 
O 2 CL B 1 1136 1136 CL CL . 
P 4 GOL B 1 1137 1137 GOL GOL . 
Q 5 YIO B 1 1138 1138 YIO YIO . 
R 6 HOH A 1 2001 2001 HOH HOH . 
R 6 HOH A 2 2002 2002 HOH HOH . 
R 6 HOH A 3 2003 2003 HOH HOH . 
R 6 HOH A 4 2004 2004 HOH HOH . 
R 6 HOH A 5 2005 2005 HOH HOH . 
R 6 HOH A 6 2006 2006 HOH HOH . 
R 6 HOH A 7 2007 2007 HOH HOH . 
R 6 HOH A 8 2008 2008 HOH HOH . 
R 6 HOH A 9 2009 2009 HOH HOH . 
R 6 HOH A 10 2010 2010 HOH HOH . 
R 6 HOH A 11 2011 2011 HOH HOH . 
R 6 HOH A 12 2012 2012 HOH HOH . 
R 6 HOH A 13 2013 2013 HOH HOH . 
R 6 HOH A 14 2014 2014 HOH HOH . 
R 6 HOH A 15 2015 2015 HOH HOH . 
R 6 HOH A 16 2016 2016 HOH HOH . 
R 6 HOH A 17 2017 2017 HOH HOH . 
R 6 HOH A 18 2018 2018 HOH HOH . 
R 6 HOH A 19 2019 2019 HOH HOH . 
R 6 HOH A 20 2020 2020 HOH HOH . 
R 6 HOH A 21 2021 2021 HOH HOH . 
R 6 HOH A 22 2022 2022 HOH HOH . 
R 6 HOH A 23 2023 2023 HOH HOH . 
R 6 HOH A 24 2024 2024 HOH HOH . 
R 6 HOH A 25 2025 2025 HOH HOH . 
R 6 HOH A 26 2026 2026 HOH HOH . 
R 6 HOH A 27 2027 2027 HOH HOH . 
R 6 HOH A 28 2028 2028 HOH HOH . 
R 6 HOH A 29 2029 2029 HOH HOH . 
R 6 HOH A 30 2030 2030 HOH HOH . 
R 6 HOH A 31 2031 2031 HOH HOH . 
R 6 HOH A 32 2032 2032 HOH HOH . 
R 6 HOH A 33 2033 2033 HOH HOH . 
R 6 HOH A 34 2034 2034 HOH HOH . 
R 6 HOH A 35 2035 2035 HOH HOH . 
R 6 HOH A 36 2036 2036 HOH HOH . 
R 6 HOH A 37 2037 2037 HOH HOH . 
R 6 HOH A 38 2038 2038 HOH HOH . 
R 6 HOH A 39 2039 2039 HOH HOH . 
R 6 HOH A 40 2040 2040 HOH HOH . 
R 6 HOH A 41 2041 2041 HOH HOH . 
R 6 HOH A 42 2042 2042 HOH HOH . 
R 6 HOH A 43 2043 2043 HOH HOH . 
R 6 HOH A 44 2044 2044 HOH HOH . 
R 6 HOH A 45 2045 2045 HOH HOH . 
R 6 HOH A 46 2046 2046 HOH HOH . 
R 6 HOH A 47 2047 2047 HOH HOH . 
R 6 HOH A 48 2048 2048 HOH HOH . 
R 6 HOH A 49 2049 2049 HOH HOH . 
R 6 HOH A 50 2050 2050 HOH HOH . 
R 6 HOH A 51 2051 2051 HOH HOH . 
R 6 HOH A 52 2052 2052 HOH HOH . 
R 6 HOH A 53 2053 2053 HOH HOH . 
R 6 HOH A 54 2054 2054 HOH HOH . 
S 6 HOH B 1 2001 2001 HOH HOH . 
S 6 HOH B 2 2002 2002 HOH HOH . 
S 6 HOH B 3 2003 2003 HOH HOH . 
S 6 HOH B 4 2004 2004 HOH HOH . 
S 6 HOH B 5 2005 2005 HOH HOH . 
S 6 HOH B 6 2006 2006 HOH HOH . 
S 6 HOH B 7 2007 2007 HOH HOH . 
S 6 HOH B 8 2008 2008 HOH HOH . 
S 6 HOH B 9 2009 2009 HOH HOH . 
S 6 HOH B 10 2010 2010 HOH HOH . 
S 6 HOH B 11 2011 2011 HOH HOH . 
S 6 HOH B 12 2012 2012 HOH HOH . 
S 6 HOH B 13 2013 2013 HOH HOH . 
S 6 HOH B 14 2014 2014 HOH HOH . 
S 6 HOH B 15 2015 2015 HOH HOH . 
S 6 HOH B 16 2016 2016 HOH HOH . 
S 6 HOH B 17 2017 2017 HOH HOH . 
S 6 HOH B 18 2018 2018 HOH HOH . 
S 6 HOH B 19 2019 2019 HOH HOH . 
S 6 HOH B 20 2020 2020 HOH HOH . 
S 6 HOH B 21 2021 2021 HOH HOH . 
S 6 HOH B 22 2022 2022 HOH HOH . 
S 6 HOH B 23 2023 2023 HOH HOH . 
S 6 HOH B 24 2024 2024 HOH HOH . 
S 6 HOH B 25 2025 2025 HOH HOH . 
S 6 HOH B 26 2026 2026 HOH HOH . 
S 6 HOH B 27 2027 2027 HOH HOH . 
S 6 HOH B 28 2028 2028 HOH HOH . 
S 6 HOH B 29 2029 2029 HOH HOH . 
S 6 HOH B 30 2030 2030 HOH HOH . 
S 6 HOH B 31 2031 2031 HOH HOH . 
S 6 HOH B 32 2032 2032 HOH HOH . 
S 6 HOH B 33 2033 2033 HOH HOH . 
S 6 HOH B 34 2034 2034 HOH HOH . 
S 6 HOH B 35 2035 2035 HOH HOH . 
S 6 HOH B 36 2036 2036 HOH HOH . 
S 6 HOH B 37 2037 2037 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 YIO . . . K 5 43.379 9.778 53.595 0.7 56.7 ? C1 YIO 1141 A 1 
HETATM 2 C C2 YIO . . . K 5 43.31 11.279 54.065 0.7 52.63 ? C2 YIO 1141 A 1 
HETATM 3 C C3 YIO . . . K 5 43.906 12.155 52.929 0.7 47.04 ? C3 YIO 1141 A 1 
HETATM 4 C C4 YIO . . . K 5 45.372 11.87 52.771 0.7 46.99 ? C4 YIO 1141 A 1 
HETATM 5 C C5 YIO . . . K 5 45.455 10.328 52.561 0.7 47.2 ? C5 YIO 1141 A 1 
HETATM 6 C C6 YIO . . . K 5 46.862 9.934 52.208 0.7 46.45 ? C6 YIO 1141 A 1 
HETATM 7 O O2 YIO . . . K 5 41.984 11.7 54.417 0.7 54.1 ? O2 YIO 1141 A 1 
HETATM 8 O O3 YIO . . . K 5 43.794 13.549 53.098 0.7 49.41 ? O3 YIO 1141 A 1 
HETATM 9 O O4 YIO . . . K 5 46.112 12.338 53.906 0.7 41.68 ? O4 YIO 1141 A 1 
HETATM 10 O O5 YIO . . . K 5 44.843 9.619 53.679 0.7 50.29 ? O5 YIO 1141 A 1 
HETATM 11 O O6 YIO . . . K 5 47.405 11.017 51.441 0.7 47.2 ? O6 YIO 1141 A 1 
HETATM 12 S S1 YIO . . . K 5 42.505 8.282 54.326 0.7 68.23 ? S1 YIO 1141 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           256 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           12 
#