data_5NX2 # _model_server_result.job_id JTsi_L6wdwbVEUwNKpQrnQ _model_server_result.datetime_utc '2025-01-18 13:00:29' _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 5nx2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":605}' # _entry.id 5NX2 # _exptl.entry_id 5NX2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.434 _entity.id 5 _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 90 _cell.angle_gamma 120 _cell.entry_id 5NX2 _cell.length_a 94.435 _cell.length_b 94.435 _cell.length_c 163.905 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NX2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 5 E N N ? 5 F N N ? 5 G N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 3 n C NAG 1 C 1 NAG A 601 NAG 3 n C NAG 2 C 2 NAG A 602 NAG # 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 27 A CYS 46 1_555 A SG CYS 52 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 43 A CYS 62 1_555 A SG CYS 85 A CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 66 A CYS 85 1_555 A SG CYS 107 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 A SG CYS 207 A CYS 226 1_555 A SG CYS 277 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 44 A ASN 63 1_555 D C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale2 A ND2 ASN 63 A ASN 82 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 B C67 9DK 1 B 9DK 1 1_555 B N 9DQ 2 B 9DQ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale4 B C 9DQ 2 B 9DQ 2 1_555 B N GLY 3 B GLY 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale5 B C THR 4 B THR 4 1_555 B N 9DT 5 B 9DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale6 B C 9DT 5 B 9DT 5 1_555 B N THR 6 B THR 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale7 B C ASP 8 B ASP 8 1_555 B N 9DW 9 B 9DW 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale8 B C 9DW 9 B 9DW 9 1_555 B N90 9DZ 10 B 9DZ 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? # _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 473 n n C1 S1 SOG sing 474 n n C1 O5 SOG sing 475 n n C1 H1 SOG sing 476 n n C2 C3 SOG sing 477 n n C2 O2 SOG sing 478 n n C2 H2 SOG sing 479 n n C3 C4 SOG sing 480 n n C3 O3 SOG sing 481 n n C3 H3 SOG sing 482 n n C4 C5 SOG sing 483 n n C4 O4 SOG sing 484 n n C4 H4 SOG sing 485 n n C5 C6 SOG sing 486 n n C5 O5 SOG sing 487 n n C5 H5 SOG sing 488 n n C6 O6 SOG sing 489 n n C6 H61 SOG sing 490 n n C6 H62 SOG sing 491 n n C1' C2' SOG sing 492 n n C1' S1 SOG sing 493 n n C1' "H1'1" SOG sing 494 n n C1' "H1'2" SOG sing 495 n n C2' C3' SOG sing 496 n n C2' "H2'1" SOG sing 497 n n C2' "H2'2" SOG sing 498 n n C3' C4' SOG sing 499 n n C3' "H3'1" SOG sing 500 n n C3' "H3'2" SOG sing 501 n n C4' C5' SOG sing 502 n n C4' "H4'1" SOG sing 503 n n C4' "H4'2" SOG sing 504 n n C5' C6' SOG sing 505 n n C5' "H5'1" SOG sing 506 n n C5' "H5'2" SOG sing 507 n n C6' C7' SOG sing 508 n n C6' "H6'1" SOG sing 509 n n C6' "H6'2" SOG sing 510 n n C7' C8' SOG sing 511 n n C7' "H7'1" SOG sing 512 n n C7' "H7'2" SOG sing 513 n n C8' "H8'1" SOG sing 514 n n C8' "H8'2" SOG sing 515 n n C8' "H8'3" SOG sing 516 n n O2 HO2 SOG sing 517 n n O3 HO3 SOG sing 518 n n O4 HO4 SOG sing 519 n n O6 HO6 SOG sing 520 n n # _atom_sites.entry_id 5NX2 _atom_sites.fract_transf_matrix[1][1] 0.010589 _atom_sites.fract_transf_matrix[1][2] 0.006114 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012227 _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] 0.006101 _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 D 4 NAG A 1 603 903 NAG NAG . E 5 SOG A 1 604 1 SOG SOG . F 5 SOG A 1 605 2 SOG SOG . G 5 SOG A 1 606 3 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 5 -9.047 42.489 11.519 1 198.38 ? C1 SOG 605 A 1 HETATM 2 C C2 SOG . . . F 5 -10.454 42.821 11.885 1 194.38 ? C2 SOG 605 A 1 HETATM 3 C C3 SOG . . . F 5 -11.428 42.187 10.985 1 211.91 ? C3 SOG 605 A 1 HETATM 4 C C4 SOG . . . F 5 -11.141 42.402 9.55 1 206.33 ? C4 SOG 605 A 1 HETATM 5 C C5 SOG . . . F 5 -9.716 42.072 9.2 1 203.29 ? C5 SOG 605 A 1 HETATM 6 C C6 SOG . . . F 5 -9.443 42.479 7.795 1 196.59 ? C6 SOG 605 A 1 HETATM 7 C C1' SOG . . . F 5 -6.362 43.458 11.737 1 191.2 ? C1' SOG 605 A 1 HETATM 8 C C2' SOG . . . F 5 -5.151 43.584 12.651 1 192.83 ? C2' SOG 605 A 1 HETATM 9 C C3' SOG . . . F 5 -3.893 44.195 12.072 1 179.16 ? C3' SOG 605 A 1 HETATM 10 C C4' SOG . . . F 5 -2.621 44.104 12.899 1 142.65 ? C4' SOG 605 A 1 HETATM 11 C C5' SOG . . . F 5 -1.551 45.089 12.622 1 126.47 ? C5' SOG 605 A 1 HETATM 12 C C6' SOG . . . F 5 -0.231 44.893 13.303 1 135.52 ? C6' SOG 605 A 1 HETATM 13 C C7' SOG . . . F 5 0.802 45.969 13.138 1 152.15 ? C7' SOG 605 A 1 HETATM 14 C C8' SOG . . . F 5 2.095 45.829 13.916 1 157.42 ? C8' SOG 605 A 1 HETATM 15 S S1 SOG . . . F 5 -7.958 43.429 12.494 1 192.51 ? S1 SOG 605 A 1 HETATM 16 O O2 SOG . . . F 5 -10.676 42.452 13.241 1 160.3 ? O2 SOG 605 A 1 HETATM 17 O O3 SOG . . . F 5 -12.752 42.655 11.292 1 229.35 ? O3 SOG 605 A 1 HETATM 18 O O4 SOG . . . F 5 -12.003 41.64 8.736 1 205.38 ? O4 SOG 605 A 1 HETATM 19 O O5 SOG . . . F 5 -8.766 42.719 10.079 1 204.55 ? O5 SOG 605 A 1 HETATM 20 O O6 SOG . . . F 5 -9.623 41.528 6.8 1 190.11 ? O6 SOG 605 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #