data_2YDV
#
_model_server_result.job_id            40Y8bzuN4-XW_OWntLI0_A 
_model_server_result.datetime_utc      '2024-11-24 10:34:30' 
_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          2ydv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    2YDV 
#
_exptl.entry_id    2YDV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.434 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'octyl 1-thio-beta-D-glucopyranoside' 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          93.31 
_cell.angle_gamma         90 
_cell.entry_id            2YDV 
_cell.length_a            76.936 
_cell.length_b            99.551 
_cell.length_c            79.655 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YDV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_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,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 
? 3 F N N 
? 3 G 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 71 A CYS 71 1_555 A SG CYS 159 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 A SG CYS 74 A CYS 74 1_555 A SG CYS 146 A CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf3 A SG CYS 77 A CYS 77 1_555 A SG CYS 166 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf4 A SG CYS 259 A CYS 259 1_555 A SG CYS 262 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
#
_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 330 n n 
C1 S1 SOG sing 331 n n 
C1 O5 SOG sing 332 n n 
C1 H1 SOG sing 333 n n 
C2 C3 SOG sing 334 n n 
C2 O2 SOG sing 335 n n 
C2 H2 SOG sing 336 n n 
C3 C4 SOG sing 337 n n 
C3 O3 SOG sing 338 n n 
C3 H3 SOG sing 339 n n 
C4 C5 SOG sing 340 n n 
C4 O4 SOG sing 341 n n 
C4 H4 SOG sing 342 n n 
C5 C6 SOG sing 343 n n 
C5 O5 SOG sing 344 n n 
C5 H5 SOG sing 345 n n 
C6 O6 SOG sing 346 n n 
C6 H61 SOG sing 347 n n 
C6 H62 SOG sing 348 n n 
C1' C2' SOG sing 349 n n 
C1' S1 SOG sing 350 n n 
C1' "H1'1" SOG sing 351 n n 
C1' "H1'2" SOG sing 352 n n 
C2' C3' SOG sing 353 n n 
C2' "H2'1" SOG sing 354 n n 
C2' "H2'2" SOG sing 355 n n 
C3' C4' SOG sing 356 n n 
C3' "H3'1" SOG sing 357 n n 
C3' "H3'2" SOG sing 358 n n 
C4' C5' SOG sing 359 n n 
C4' "H4'1" SOG sing 360 n n 
C4' "H4'2" SOG sing 361 n n 
C5' C6' SOG sing 362 n n 
C5' "H5'1" SOG sing 363 n n 
C5' "H5'2" SOG sing 364 n n 
C6' C7' SOG sing 365 n n 
C6' "H6'1" SOG sing 366 n n 
C6' "H6'2" SOG sing 367 n n 
C7' C8' SOG sing 368 n n 
C7' "H7'1" SOG sing 369 n n 
C7' "H7'2" SOG sing 370 n n 
C8' "H8'1" SOG sing 371 n n 
C8' "H8'2" SOG sing 372 n n 
C8' "H8'3" SOG sing 373 n n 
O2 HO2 SOG sing 374 n n 
O3 HO3 SOG sing 375 n n 
O4 HO4 SOG sing 376 n n 
O6 HO6 SOG sing 377 n n 
#
_atom_sites.entry_id                     2YDV 
_atom_sites.fract_transf_matrix[1][1]    0.012998 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000752 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010045 
_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]    0.012575 
_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
B 2 NEC A 1 400 400 NEC NEC . 
C 3 SOG A 1 501 501 SOG SOG . 
D 3 SOG A 1 502 502 SOG SOG . 
E 3 SOG A 1 503 503 SOG SOG . 
F 3 SOG A 1 504 504 SOG SOG . 
G 3 SOG A 1 505 505 SOG SOG . 
H 4 HOH A 1 2001 2001 HOH HOH . 
H 4 HOH A 2 2002 2002 HOH HOH . 
H 4 HOH A 3 2003 2003 HOH HOH . 
H 4 HOH A 4 2004 2004 HOH HOH . 
H 4 HOH A 5 2005 2005 HOH HOH . 
H 4 HOH A 6 2006 2006 HOH HOH . 
H 4 HOH A 7 2007 2007 HOH HOH . 
H 4 HOH A 8 2008 2008 HOH HOH . 
H 4 HOH A 9 2009 2009 HOH HOH . 
H 4 HOH A 10 2010 2010 HOH HOH . 
H 4 HOH A 11 2011 2011 HOH HOH . 
H 4 HOH A 12 2012 2012 HOH HOH . 
H 4 HOH A 13 2013 2013 HOH HOH . 
H 4 HOH A 14 2014 2014 HOH HOH . 
H 4 HOH A 15 2015 2015 HOH HOH . 
H 4 HOH A 16 2016 2016 HOH HOH . 
H 4 HOH A 17 2017 2017 HOH HOH . 
H 4 HOH A 18 2018 2018 HOH HOH . 
H 4 HOH A 19 2019 2019 HOH HOH . 
H 4 HOH A 20 2020 2020 HOH HOH . 
H 4 HOH A 21 2021 2021 HOH HOH . 
H 4 HOH A 22 2022 2022 HOH HOH . 
H 4 HOH A 23 2023 2023 HOH HOH . 
H 4 HOH A 24 2024 2024 HOH HOH . 
H 4 HOH A 25 2025 2025 HOH HOH . 
H 4 HOH A 26 2026 2026 HOH HOH . 
H 4 HOH A 27 2027 2027 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 . . . D 3 46.158 0.087 -5.7 1 97.45 ? C1 SOG 502 A 1 
HETATM 2 C C2 SOG . . . D 3 44.749 -0.183 -6.226 1 95.7 ? C2 SOG 502 A 1 
HETATM 3 C C3 SOG . . . D 3 44.748 -1.017 -7.511 1 94.3 ? C3 SOG 502 A 1 
HETATM 4 C C4 SOG . . . D 3 45.905 -0.734 -8.469 1 95.16 ? C4 SOG 502 A 1 
HETATM 5 C C5 SOG . . . D 3 47.226 -0.424 -7.769 1 98.08 ? C5 SOG 502 A 1 
HETATM 6 C C6 SOG . . . D 3 48.295 0.105 -8.733 1 98.16 ? C6 SOG 502 A 1 
HETATM 7 C C1' SOG . . . D 3 47.337 2.427 -5.019 1 93.79 ? C1' SOG 502 A 1 
HETATM 8 C C2' SOG . . . D 3 47.609 3.54 -4.024 1 91.25 ? C2' SOG 502 A 1 
HETATM 9 C C3' SOG . . . D 3 48.996 4.118 -4.282 1 91.99 ? C3' SOG 502 A 1 
HETATM 10 C C4' SOG . . . D 3 48.994 5.629 -4.093 1 93.44 ? C4' SOG 502 A 1 
HETATM 11 C C5' SOG . . . D 3 50.378 6.165 -3.726 1 93.19 ? C5' SOG 502 A 1 
HETATM 12 C C6' SOG . . . D 3 50.256 7.291 -2.702 1 91.76 ? C6' SOG 502 A 1 
HETATM 13 C C7' SOG . . . D 3 51.216 8.442 -2.964 1 89.3 ? C7' SOG 502 A 1 
HETATM 14 C C8' SOG . . . D 3 50.752 9.659 -2.195 1 88.46 ? C8' SOG 502 A 1 
HETATM 15 S S1 SOG . . . D 3 46.109 1.309 -4.419 1 99.04 ? S1 SOG 502 A 1 
HETATM 16 O O2 SOG . . . D 3 43.978 -0.859 -5.218 1 94.31 ? O2 SOG 502 A 1 
HETATM 17 O O3 SOG . . . D 3 43.534 -0.752 -8.223 1 92.85 ? O3 SOG 502 A 1 
HETATM 18 O O4 SOG . . . D 3 46.087 -1.877 -9.315 1 97.24 ? O4 SOG 502 A 1 
HETATM 19 O O5 SOG . . . D 3 46.982 0.558 -6.768 1 97.5 ? O5 SOG 502 A 1 
HETATM 20 O O6 SOG . . . D 3 49.235 -0.924 -9.069 1 96.9 ? O6 SOG 502 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           232 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#