data_3VI0
#
_model_server_result.job_id            r2HgOWmBe6RFmSrbzmn33A 
_model_server_result.datetime_utc      '2024-11-28 05:11:27' 
_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          3vi0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":302}' 
#
_entry.id    3VI0 
#
_exptl.entry_id    3VI0 
_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    1 
_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         120 
_cell.entry_id            3VI0 
_cell.length_a            102.3 
_cell.length_b            102.3 
_cell.length_c            112.3 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VI0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        177 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 6 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.3 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.15 88.594399 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 2 2 1 MAN GLC C1 O1 . O2 HO2 . sing 
2 ? 2 3 2 SGA MAN C1 O1 . O6 HO6 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n B GLC 1 B 1 GLC ? 400 GLC 
2 n B MAN 2 B 2 MAN ? 410 MAN 
2 n B SGA 3 B 3 SGA ? 420 SGA 
#
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
covale ? covale1 A NZ LYS 229 A LYS 216 1_555 C C15 RET . A RET 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? 
covale ? covale2 E O3 L2P . A L2P 303 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
covale ? covale4 B O6 MAN . B MAN 2 1_555 B C1 SGA . B SGA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? 
#
_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 514 n n 
C1 S1 SOG sing 515 n n 
C1 O5 SOG sing 516 n n 
C1 H1 SOG sing 517 n n 
C2 C3 SOG sing 518 n n 
C2 O2 SOG sing 519 n n 
C2 H2 SOG sing 520 n n 
C3 C4 SOG sing 521 n n 
C3 O3 SOG sing 522 n n 
C3 H3 SOG sing 523 n n 
C4 C5 SOG sing 524 n n 
C4 O4 SOG sing 525 n n 
C4 H4 SOG sing 526 n n 
C5 C6 SOG sing 527 n n 
C5 O5 SOG sing 528 n n 
C5 H5 SOG sing 529 n n 
C6 O6 SOG sing 530 n n 
C6 H61 SOG sing 531 n n 
C6 H62 SOG sing 532 n n 
C1' C2' SOG sing 533 n n 
C1' S1 SOG sing 534 n n 
C1' "H1'1" SOG sing 535 n n 
C1' "H1'2" SOG sing 536 n n 
C2' C3' SOG sing 537 n n 
C2' "H2'1" SOG sing 538 n n 
C2' "H2'2" SOG sing 539 n n 
C3' C4' SOG sing 540 n n 
C3' "H3'1" SOG sing 541 n n 
C3' "H3'2" SOG sing 542 n n 
C4' C5' SOG sing 543 n n 
C4' "H4'1" SOG sing 544 n n 
C4' "H4'2" SOG sing 545 n n 
C5' C6' SOG sing 546 n n 
C5' "H5'1" SOG sing 547 n n 
C5' "H5'2" SOG sing 548 n n 
C6' C7' SOG sing 549 n n 
C6' "H6'1" SOG sing 550 n n 
C6' "H6'2" SOG sing 551 n n 
C7' C8' SOG sing 552 n n 
C7' "H7'1" SOG sing 553 n n 
C7' "H7'2" SOG sing 554 n n 
C8' "H8'1" SOG sing 555 n n 
C8' "H8'2" SOG sing 556 n n 
C8' "H8'3" SOG sing 557 n n 
O2 HO2 SOG sing 558 n n 
O3 HO3 SOG sing 559 n n 
O4 HO4 SOG sing 560 n n 
O6 HO6 SOG sing 561 n n 
#
_atom_sites.entry_id                     3VI0 
_atom_sites.fract_transf_matrix[1][1]    0.009775 
_atom_sites.fract_transf_matrix[1][2]    0.005644 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011287 
_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]    0.008905 
_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 3 RET A 1 301 250 RET RET . 
D 4 SOG A 1 302 430 SOG SOG . 
E 5 L2P A 1 303 270 L2P L2P . 
F 6 HOH A 1 401 600 HOH HOH . 
F 6 HOH A 2 402 601 HOH HOH . 
F 6 HOH A 3 403 604 HOH HOH . 
F 6 HOH A 4 404 605 HOH HOH . 
F 6 HOH A 5 405 606 HOH HOH . 
F 6 HOH A 6 406 607 HOH HOH . 
F 6 HOH A 7 407 608 HOH HOH . 
F 6 HOH A 8 408 609 HOH HOH . 
F 6 HOH A 9 409 610 HOH HOH . 
F 6 HOH A 10 410 611 HOH HOH . 
F 6 HOH A 11 411 612 HOH HOH . 
F 6 HOH A 12 412 613 HOH HOH . 
F 6 HOH A 13 413 614 HOH HOH . 
F 6 HOH A 14 414 617 HOH HOH . 
F 6 HOH A 15 415 618 HOH HOH . 
F 6 HOH A 16 416 619 HOH HOH . 
F 6 HOH A 17 417 621 HOH HOH . 
F 6 HOH A 18 418 622 HOH HOH . 
F 6 HOH A 19 419 623 HOH HOH . 
F 6 HOH A 20 420 624 HOH HOH . 
F 6 HOH A 21 421 625 HOH HOH . 
F 6 HOH A 22 422 626 HOH HOH . 
F 6 HOH A 23 423 629 HOH HOH . 
F 6 HOH A 24 424 630 HOH HOH . 
F 6 HOH A 25 425 633 HOH HOH . 
F 6 HOH A 26 426 636 HOH HOH . 
F 6 HOH A 27 427 701 HOH HOH . 
F 6 HOH A 28 428 703 HOH HOH . 
F 6 HOH A 29 429 704 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 4 35.021 38.828 39.293 1 44.05 ? C1 SOG 302 A 1 
HETATM 2 C C2 SOG . . . D 4 34.227 38.308 40.513 1 44.31 ? C2 SOG 302 A 1 
HETATM 3 C C3 SOG . . . D 4 34.303 39.312 41.662 1 44.8 ? C3 SOG 302 A 1 
HETATM 4 C C4 SOG . . . D 4 35.812 39.441 42.047 1 45.43 ? C4 SOG 302 A 1 
HETATM 5 C C5 SOG . . . D 4 36.6 40.007 40.781 1 45.87 ? C5 SOG 302 A 1 
HETATM 6 C C6 SOG . . . D 4 38.053 40.185 41.021 1 46.93 ? C6 SOG 302 A 1 
HETATM 7 C C1' SOG . . . D 4 35.934 38.414 36.631 1 42.05 ? C1' SOG 302 A 1 
HETATM 8 C C2' SOG . . . D 4 36.03 37.535 35.439 1 41.08 ? C2' SOG 302 A 1 
HETATM 9 C C3' SOG . . . D 4 36.781 38.405 34.493 1 41.09 ? C3' SOG 302 A 1 
HETATM 10 C C4' SOG . . . D 4 36.109 38.472 33.192 1 41.24 ? C4' SOG 302 A 1 
HETATM 11 C C5' SOG . . . D 4 36.859 39.394 32.305 1 41.08 ? C5' SOG 302 A 1 
HETATM 12 C C6' SOG . . . D 4 36.221 39.498 30.982 1 41.7 ? C6' SOG 302 A 1 
HETATM 13 C C7' SOG . . . D 4 37.028 40.447 30.141 1 42.29 ? C7' SOG 302 A 1 
HETATM 14 C C8' SOG . . . D 4 36.396 40.582 28.766 1 43.02 ? C8' SOG 302 A 1 
HETATM 15 S S1 SOG . . . D 4 35.024 37.669 37.949 1 43.28 ? S1 SOG 302 A 1 
HETATM 16 O O2 SOG . . . D 4 32.863 38.158 40.103 1 43.54 ? O2 SOG 302 A 1 
HETATM 17 O O3 SOG . . . D 4 33.554 38.782 42.785 1 44.97 ? O3 SOG 302 A 1 
HETATM 18 O O4 SOG . . . D 4 35.972 40.368 43.121 1 46.8 ? O4 SOG 302 A 1 
HETATM 19 O O5 SOG . . . D 4 36.436 39.037 39.626 1 44.72 ? O5 SOG 302 A 1 
HETATM 20 O O6 SOG . . . D 4 38.523 41.179 40.051 1 48.69 ? O6 SOG 302 A 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#