data_2YCX
#
_model_server_result.job_id            vF5s125obyAWeFbarLMpLA 
_model_server_result.datetime_utc      '2024-11-22 22:20:05' 
_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          2ycx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1361}' 
#
_entry.id    2YCX 
#
_exptl.entry_id    2YCX 
_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    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          118.33 
_cell.angle_gamma         90 
_cell.entry_id            2YCX 
_cell.length_a            150.029 
_cell.length_b            56.434 
_cell.length_c            111.41 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YCX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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 1 1 
B,D,E,F,G 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
? 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 84 A CYS 114 1_555 A SG CYS 169 A CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf2 A SG CYS 162 A CYS 192 1_555 A SG CYS 168 A CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf3 B SG CYS 84 B CYS 114 1_555 B SG CYS 169 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 B SG CYS 162 B CYS 192 1_555 B SG CYS 168 B CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
#
_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 331 n n 
C1 S1 SOG sing 332 n n 
C1 O5 SOG sing 333 n n 
C1 H1 SOG sing 334 n n 
C2 C3 SOG sing 335 n n 
C2 O2 SOG sing 336 n n 
C2 H2 SOG sing 337 n n 
C3 C4 SOG sing 338 n n 
C3 O3 SOG sing 339 n n 
C3 H3 SOG sing 340 n n 
C4 C5 SOG sing 341 n n 
C4 O4 SOG sing 342 n n 
C4 H4 SOG sing 343 n n 
C5 C6 SOG sing 344 n n 
C5 O5 SOG sing 345 n n 
C5 H5 SOG sing 346 n n 
C6 O6 SOG sing 347 n n 
C6 H61 SOG sing 348 n n 
C6 H62 SOG sing 349 n n 
C1' C2' SOG sing 350 n n 
C1' S1 SOG sing 351 n n 
C1' "H1'1" SOG sing 352 n n 
C1' "H1'2" SOG sing 353 n n 
C2' C3' SOG sing 354 n n 
C2' "H2'1" SOG sing 355 n n 
C2' "H2'2" SOG sing 356 n n 
C3' C4' SOG sing 357 n n 
C3' "H3'1" SOG sing 358 n n 
C3' "H3'2" SOG sing 359 n n 
C4' C5' SOG sing 360 n n 
C4' "H4'1" SOG sing 361 n n 
C4' "H4'2" SOG sing 362 n n 
C5' C6' SOG sing 363 n n 
C5' "H5'1" SOG sing 364 n n 
C5' "H5'2" SOG sing 365 n n 
C6' C7' SOG sing 366 n n 
C6' "H6'1" SOG sing 367 n n 
C6' "H6'2" SOG sing 368 n n 
C7' C8' SOG sing 369 n n 
C7' "H7'1" SOG sing 370 n n 
C7' "H7'2" SOG sing 371 n n 
C8' "H8'1" SOG sing 372 n n 
C8' "H8'2" SOG sing 373 n n 
C8' "H8'3" SOG sing 374 n n 
O2 HO2 SOG sing 375 n n 
O3 HO3 SOG sing 376 n n 
O4 HO4 SOG sing 377 n n 
O6 HO6 SOG sing 378 n n 
#
_atom_sites.entry_id                     2YCX 
_atom_sites.fract_transf_matrix[1][1]    0.006665 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003593 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01772 
_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]    0.010197 
_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 P32 A 1 1355 1355 P32 P32 . 
D 2 P32 B 1 1359 1359 P32 P32 . 
E 3 SOG B 1 1360 1360 SOG SOG . 
F 3 SOG B 1 1361 1361 SOG SOG . 
G 3 SOG B 1 1362 1362 SOG SOG . 
#
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 . . . F 3 35.214 16.537 -16.206 1 121.29 ? C1 SOG 1361 B 1 
HETATM 2 C C2 SOG . . . F 3 35.224 16.332 -17.751 1 121.29 ? C2 SOG 1361 B 1 
HETATM 3 C C3 SOG . . . F 3 34.117 17.092 -18.535 1 121.57 ? C3 SOG 1361 B 1 
HETATM 4 C C4 SOG . . . F 3 32.878 17.538 -17.713 1 121.6 ? C4 SOG 1361 B 1 
HETATM 5 C C5 SOG . . . F 3 33.189 17.707 -16.202 1 121.31 ? C5 SOG 1361 B 1 
HETATM 6 C C6 SOG . . . F 3 32.002 18.136 -15.29 1 120.94 ? C6 SOG 1361 B 1 
HETATM 7 C C1' SOG . . . F 3 35.634 14.028 -14.606 1 120.45 ? C1' SOG 1361 B 1 
HETATM 8 C C2' SOG . . . F 3 36.603 13.101 -13.829 1 119.41 ? C2' SOG 1361 B 1 
HETATM 9 C C3' SOG . . . F 3 37.098 11.89 -14.656 1 118.43 ? C3' SOG 1361 B 1 
HETATM 10 C C4' SOG . . . F 3 38.614 11.948 -14.954 1 117.25 ? C4' SOG 1361 B 1 
HETATM 11 C C5' SOG . . . F 3 39.154 10.646 -15.585 1 115.98 ? C5' SOG 1361 B 1 
HETATM 12 C C6' SOG . . . F 3 40.312 10.922 -16.563 1 115.02 ? C6' SOG 1361 B 1 
HETATM 13 C C7' SOG . . . F 3 40.683 9.688 -17.402 1 114.27 ? C7' SOG 1361 B 1 
HETATM 14 C C8' SOG . . . F 3 41.443 10.074 -18.682 1 113.13 ? C8' SOG 1361 B 1 
HETATM 15 S S1 SOG . . . F 3 36.484 15.49 -15.343 1 121.43 ? S1 SOG 1361 B 1 
HETATM 16 O O2 SOG . . . F 3 36.499 16.719 -18.278 1 120.87 ? O2 SOG 1361 B 1 
HETATM 17 O O3 SOG . . . F 3 33.678 16.264 -19.624 1 121.81 ? O3 SOG 1361 B 1 
HETATM 18 O O4 SOG . . . F 3 32.346 18.753 -18.276 1 121.31 ? O4 SOG 1361 B 1 
HETATM 19 O O5 SOG . . . F 3 33.832 16.477 -15.718 1 121.49 ? O5 SOG 1361 B 1 
HETATM 20 O O6 SOG . . . F 3 30.737 17.673 -15.814 1 120.39 ? O6 SOG 1361 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#