data_2VT4
#
_model_server_result.job_id            SCXzp0077cAnhj8H0Af3Tg 
_model_server_result.datetime_utc      '2024-11-25 16:02:45' 
_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          2vt4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":405}' 
#
_entry.id    2VT4 
#
_exptl.entry_id    2VT4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.434 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'octyl 1-thio-beta-D-glucopyranoside' 
_entity.pdbx_number_of_molecules    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         67.6 
_cell.angle_beta          73.3 
_cell.angle_gamma         85.8 
_cell.entry_id            2VT4 
_cell.length_a            55.5 
_cell.length_b            86.8 
_cell.length_c            95.5 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VT4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 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
PQS dimeric 2 software_defined_assembly 1 
PQS dimeric 2 software_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
? monomeric 1 author_defined_assembly 5 
? monomeric 1 author_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,I,J,K,L,M,N,O,AA,BA 1 1 
C,D,P,Q,R,S,T,U,V,W,X,Y,Z,CA,DA 2 1 
A,E,F,G,H,I,J,AA 3 1 
B,K,L,M,N,O,BA 4 1 
C,P,Q,R,S,T,U,CA 5 1 
D,V,W,X,Y,Z,DA 6 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
? 4 G N N 
? 4 H N N 
? 4 I N N 
? 4 M N N 
? 4 N N N 
? 4 O N N 
? 4 R N N 
? 4 S N N 
? 4 T N N 
? 4 X N N 
? 4 Y N N 
? 4 Z 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf2 A SG CYS 162 A CYS 192 1_555 A SG CYS 168 A CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
disulf ? disulf3 B SG CYS 84 B CYS 114 1_555 B SG CYS 169 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf4 B SG CYS 162 B CYS 192 1_555 B SG CYS 168 B CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
disulf ? disulf5 C SG CYS 84 C CYS 114 1_555 C SG CYS 169 C CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf6 C SG CYS 162 C CYS 192 1_555 C SG CYS 168 C CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
disulf ? disulf7 D SG CYS 84 D CYS 114 1_555 D SG CYS 169 D CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf8 D SG CYS 162 D CYS 192 1_555 D SG CYS 168 D CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc1 A O CYS 162 A CYS 192 1_555 F NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? 
metalc ? metalc2 A O ASP 165 A ASP 195 1_555 F NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc3 A O CYS 168 A CYS 198 1_555 F NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc4 F NA NA . A NA 401 1_555 AA O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc5 F NA NA . A NA 401 1_555 AA O HOH . A HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? 
metalc ? metalc6 B O ASP 165 B ASP 195 1_555 L NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc7 B O CYS 168 B CYS 198 1_555 L NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? 
metalc ? metalc8 C O ASP 165 C ASP 195 1_555 Q NA NA . C NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? 
metalc ? metalc9 C O CYS 168 C CYS 198 1_555 Q NA NA . C NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc10 Q NA NA . C NA 401 1_555 CA O HOH . C HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? 
metalc ? metalc11 D O CYS 162 D CYS 192 1_555 W NA NA . D NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc12 D O ASP 165 D ASP 195 1_555 W NA NA . D NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc13 D O CYS 168 D CYS 198 1_555 W NA NA . D NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc14 W NA NA . D NA 401 1_555 DA O HOH . D HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? 
#
_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 364 n n 
C1 S1 SOG sing 365 n n 
C1 O5 SOG sing 366 n n 
C1 H1 SOG sing 367 n n 
C2 C3 SOG sing 368 n n 
C2 O2 SOG sing 369 n n 
C2 H2 SOG sing 370 n n 
C3 C4 SOG sing 371 n n 
C3 O3 SOG sing 372 n n 
C3 H3 SOG sing 373 n n 
C4 C5 SOG sing 374 n n 
C4 O4 SOG sing 375 n n 
C4 H4 SOG sing 376 n n 
C5 C6 SOG sing 377 n n 
C5 O5 SOG sing 378 n n 
C5 H5 SOG sing 379 n n 
C6 O6 SOG sing 380 n n 
C6 H61 SOG sing 381 n n 
C6 H62 SOG sing 382 n n 
C1' C2' SOG sing 383 n n 
C1' S1 SOG sing 384 n n 
C1' "H1'1" SOG sing 385 n n 
C1' "H1'2" SOG sing 386 n n 
C2' C3' SOG sing 387 n n 
C2' "H2'1" SOG sing 388 n n 
C2' "H2'2" SOG sing 389 n n 
C3' C4' SOG sing 390 n n 
C3' "H3'1" SOG sing 391 n n 
C3' "H3'2" SOG sing 392 n n 
C4' C5' SOG sing 393 n n 
C4' "H4'1" SOG sing 394 n n 
C4' "H4'2" SOG sing 395 n n 
C5' C6' SOG sing 396 n n 
C5' "H5'1" SOG sing 397 n n 
C5' "H5'2" SOG sing 398 n n 
C6' C7' SOG sing 399 n n 
C6' "H6'1" SOG sing 400 n n 
C6' "H6'2" SOG sing 401 n n 
C7' C8' SOG sing 402 n n 
C7' "H7'1" SOG sing 403 n n 
C7' "H7'2" SOG sing 404 n n 
C8' "H8'1" SOG sing 405 n n 
C8' "H8'2" SOG sing 406 n n 
C8' "H8'3" SOG sing 407 n n 
O2 HO2 SOG sing 408 n n 
O3 HO3 SOG sing 409 n n 
O4 HO4 SOG sing 410 n n 
O6 HO6 SOG sing 411 n n 
#
_atom_sites.entry_id                     2VT4 
_atom_sites.fract_transf_matrix[1][1]    0.018018 
_atom_sites.fract_transf_matrix[1][2]    -0.001323 
_atom_sites.fract_transf_matrix[1][3]    -0.005298 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011552 
_atom_sites.fract_transf_matrix[2][3]    -0.0047 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.011803 
_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
E 2 P32 A 1 400 400 P32 P32 . 
F 3 NA A 1 401 401 NA NA . 
G 4 SOG A 1 402 402 SOG SOG . 
H 4 SOG A 1 403 403 SOG SOG . 
I 4 SOG A 1 405 405 SOG SOG . 
J 5 D10 A 1 406 406 D10 D10 . 
K 2 P32 B 1 400 400 P32 P32 . 
L 3 NA B 1 401 401 NA NA . 
M 4 SOG B 1 402 402 SOG SOG . 
N 4 SOG B 1 404 404 SOG SOG . 
O 4 SOG B 1 405 405 SOG SOG . 
P 2 P32 C 1 400 400 P32 P32 . 
Q 3 NA C 1 401 401 NA NA . 
R 4 SOG C 1 402 402 SOG SOG . 
S 4 SOG C 1 404 404 SOG SOG . 
T 4 SOG C 1 405 405 SOG SOG . 
U 5 D10 C 1 406 406 D10 D10 . 
V 2 P32 D 1 400 400 P32 P32 . 
W 3 NA D 1 401 401 NA NA . 
X 4 SOG D 1 402 402 SOG SOG . 
Y 4 SOG D 1 403 403 SOG SOG . 
Z 4 SOG D 1 405 405 SOG SOG . 
AA 6 HOH A 1 2001 2001 HOH HOH . 
AA 6 HOH A 2 2002 2002 HOH HOH . 
AA 6 HOH A 3 2003 2003 HOH HOH . 
AA 6 HOH A 4 2004 2004 HOH HOH . 
AA 6 HOH A 5 2005 2005 HOH HOH . 
AA 6 HOH A 6 2006 2006 HOH HOH . 
AA 6 HOH A 7 2007 2007 HOH HOH . 
AA 6 HOH A 8 2008 2008 HOH HOH . 
AA 6 HOH A 9 2009 2009 HOH HOH . 
BA 6 HOH B 1 2001 2001 HOH HOH . 
BA 6 HOH B 2 2002 2002 HOH HOH . 
BA 6 HOH B 3 2003 2003 HOH HOH . 
BA 6 HOH B 4 2004 2004 HOH HOH . 
BA 6 HOH B 5 2005 2005 HOH HOH . 
BA 6 HOH B 6 2006 2006 HOH HOH . 
BA 6 HOH B 7 2007 2007 HOH HOH . 
CA 6 HOH C 1 2001 2001 HOH HOH . 
CA 6 HOH C 2 2002 2002 HOH HOH . 
CA 6 HOH C 3 2003 2003 HOH HOH . 
CA 6 HOH C 4 2004 2004 HOH HOH . 
CA 6 HOH C 5 2005 2005 HOH HOH . 
CA 6 HOH C 6 2006 2006 HOH HOH . 
CA 6 HOH C 7 2007 2007 HOH HOH . 
DA 6 HOH D 1 2001 2001 HOH HOH . 
DA 6 HOH D 2 2002 2002 HOH HOH . 
DA 6 HOH D 3 2003 2003 HOH HOH . 
DA 6 HOH D 4 2004 2004 HOH HOH . 
DA 6 HOH D 5 2005 2005 HOH HOH . 
DA 6 HOH D 6 2006 2006 HOH HOH . 
DA 6 HOH D 7 2007 2007 HOH HOH . 
DA 6 HOH D 8 2008 2008 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 . . . Z 4 56.506 33.87 -55.005 1 133.68 ? C1 SOG 405 D 1 
HETATM 2 C C2 SOG . . . Z 4 56.198 33.465 -56.434 1 126.55 ? C2 SOG 405 D 1 
HETATM 3 C C3 SOG . . . Z 4 56.91 34.429 -57.342 1 119.95 ? C3 SOG 405 D 1 
HETATM 4 C C4 SOG . . . Z 4 56.418 35.831 -57.031 1 127.8 ? C4 SOG 405 D 1 
HETATM 5 C C5 SOG . . . Z 4 56.722 36.164 -55.566 1 124.55 ? C5 SOG 405 D 1 
HETATM 6 C C6 SOG . . . Z 4 56.245 37.587 -55.265 1 117.22 ? C6 SOG 405 D 1 
HETATM 7 C C1' SOG . . . Z 4 56.029 33.332 -52.319 1 107.07 ? C1' SOG 405 D 1 
HETATM 8 C C2' SOG . . . Z 4 55.575 32.342 -51.274 1 82.24 ? C2' SOG 405 D 1 
HETATM 9 C C3' SOG . . . Z 4 55.835 32.839 -49.869 1 60.87 ? C3' SOG 405 D 1 
HETATM 10 C C4' SOG . . . Z 4 55.37 31.713 -48.955 1 58.3 ? C4' SOG 405 D 1 
HETATM 11 C C5' SOG . . . Z 4 55.554 32.026 -47.489 1 52.67 ? C5' SOG 405 D 1 
HETATM 12 C C6' SOG . . . Z 4 55.163 30.819 -46.663 1 44.49 ? C6' SOG 405 D 1 
HETATM 13 C C7' SOG . . . Z 4 55.477 31.127 -45.215 1 41.38 ? C7' SOG 405 D 1 
HETATM 14 C C8' SOG . . . Z 4 55.173 29.923 -44.359 1 54.38 ? C8' SOG 405 D 1 
HETATM 15 S S1 SOG . . . Z 4 55.657 32.641 -53.958 1 131.63 ? S1 SOG 405 D 1 
HETATM 16 O O2 SOG . . . Z 4 56.67 32.147 -56.729 1 115.3 ? O2 SOG 405 D 1 
HETATM 17 O O3 SOG . . . Z 4 56.571 34.084 -58.677 1 117.68 ? O3 SOG 405 D 1 
HETATM 18 O O4 SOG . . . Z 4 57.086 36.766 -57.877 1 123.06 ? O4 SOG 405 D 1 
HETATM 19 O O5 SOG . . . Z 4 56.046 35.21 -54.719 1 129.74 ? O5 SOG 405 D 1 
HETATM 20 O O6 SOG . . . Z 4 56.536 37.922 -53.905 1 98.17 ? O6 SOG 405 D 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           253 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#