data_4X1H # _model_server_result.job_id yw1Ck-saIAJg739uZUwkhw _model_server_result.datetime_utc '2024-11-23 02:34:46' _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 4x1h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":407}' # _entry.id 4X1H # _exptl.entry_id 4X1H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'nonyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 2 _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 4X1H _cell.length_a 242.136 _cell.length_b 242.136 _cell.length_c 109.721 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X1H _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _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,H,I,J _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 # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 BMA BMA C1 O1 . O2 HO2 . sing 4 ? 4 2 1 NAG NAG C1 O1 . O3 HO3 . 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 B 1 NAG A 401 NAG 3 n C NAG 2 B 2 NAG A 402 NAG 3 n C BMA 3 B 3 BMA A 403 BMA 3 n C BMA 4 B 4 BMA A 404 BMA 4 n D NAG 1 D 1 NAG A 405 NAG 4 n D NAG 2 D 2 NAG A 406 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 110 A CYS 110 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 2 A ASN 2 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 15 A ASN 15 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 A SG CYS 322 A CYS 322 1_555 G C1 PLM . A PLM 1322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? covale ? covale4 A SG CYS 323 A CYS 323 1_555 H C1 PLM . A PLM 1323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? covale ? covale5 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 C O4 NAG . B NAG 2 1_555 C C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale7 C O2 BMA . B BMA 3 1_555 C C1 BMA . B BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale8 D O3 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _chem_comp.formula 'C15 H30 O6' _chem_comp.formula_weight 306.395 _chem_comp.id BNG _chem_comp.mon_nstd_flag n _chem_comp.name 'nonyl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'Beta-NONYLGLUCOSIDE;nonyl beta-D-glucoside;nonyl D-glucoside;nonyl 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 BNG sing 94 n n C1 O1 BNG sing 95 n n C1 O5 BNG sing 96 n n C1 H1 BNG sing 97 n n C2 C3 BNG sing 98 n n C2 O2 BNG sing 99 n n C2 H2 BNG sing 100 n n C3 C4 BNG sing 101 n n C3 O3 BNG sing 102 n n C3 H3 BNG sing 103 n n C4 C5 BNG sing 104 n n C4 O4 BNG sing 105 n n C4 H4 BNG sing 106 n n C5 C6 BNG sing 107 n n C5 O5 BNG sing 108 n n C5 H5 BNG sing 109 n n C6 O6 BNG sing 110 n n C6 H61 BNG sing 111 n n C6 H62 BNG sing 112 n n C1' C2' BNG sing 113 n n C1' O1 BNG sing 114 n n C1' "H1'1" BNG sing 115 n n C1' "H1'2" BNG sing 116 n n C2' C3' BNG sing 117 n n C2' "H2'1" BNG sing 118 n n C2' "H2'2" BNG sing 119 n n C3' C4' BNG sing 120 n n C3' "H3'1" BNG sing 121 n n C3' "H3'2" BNG sing 122 n n C4' C5' BNG sing 123 n n C4' "H4'1" BNG sing 124 n n C4' "H4'2" BNG sing 125 n n C5' C6' BNG sing 126 n n C5' "H5'1" BNG sing 127 n n C5' "H5'2" BNG sing 128 n n C6' C7' BNG sing 129 n n C6' "H6'1" BNG sing 130 n n C6' "H6'2" BNG sing 131 n n C7' C8' BNG sing 132 n n C7' "H7'1" BNG sing 133 n n C7' "H7'2" BNG sing 134 n n C8' C9' BNG sing 135 n n C8' "H8'1" BNG sing 136 n n C8' "H8'2" BNG sing 137 n n C9' "H9'1" BNG sing 138 n n C9' "H9'2" BNG sing 139 n n C9' "H9'3" BNG sing 140 n n O2 HO2 BNG sing 141 n n O3 HO3 BNG sing 142 n n O4 HO4 BNG sing 143 n n O6 HO6 BNG sing 144 n n # _pdbx_chem_comp_identifier.comp_id BNG _pdbx_chem_comp_identifier.identifier b-nonylglucoside _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 4X1H _atom_sites.fract_transf_matrix[1][1] 0.00413 _atom_sites.fract_transf_matrix[1][2] 0.002384 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004769 _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] 0.009114 _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 5 BNG A 1 407 407 BNG BNG . F 5 BNG A 1 410 410 BNG BNG . G 6 PLM A 1 1322 1322 PLM PLM . H 6 PLM A 1 1323 1323 PLM PLM . I 7 HOH A 1 501 501 HOH HOH . I 7 HOH A 2 502 502 HOH HOH . I 7 HOH A 3 503 503 HOH HOH . I 7 HOH A 4 504 504 HOH HOH . I 7 HOH A 5 505 505 HOH HOH . I 7 HOH A 6 506 506 HOH HOH . I 7 HOH A 7 507 507 HOH HOH . I 7 HOH A 8 508 508 HOH HOH . I 7 HOH A 9 509 509 HOH HOH . I 7 HOH A 10 510 510 HOH HOH . I 7 HOH A 11 511 511 HOH HOH . I 7 HOH A 12 512 512 HOH HOH . I 7 HOH A 13 513 513 HOH HOH . I 7 HOH A 14 514 514 HOH HOH . I 7 HOH A 15 515 515 HOH HOH . I 7 HOH A 16 516 516 HOH HOH . I 7 HOH A 17 517 517 HOH HOH . I 7 HOH A 18 518 518 HOH HOH . I 7 HOH A 19 519 519 HOH HOH . I 7 HOH A 20 520 520 HOH HOH . I 7 HOH A 21 521 521 HOH HOH . I 7 HOH A 22 522 522 HOH HOH . I 7 HOH A 23 523 523 HOH HOH . I 7 HOH A 24 524 524 HOH HOH . I 7 HOH A 25 525 525 HOH HOH . I 7 HOH A 26 526 526 HOH HOH . I 7 HOH A 27 527 527 HOH HOH . I 7 HOH A 28 528 528 HOH HOH . I 7 HOH A 29 529 529 HOH HOH . I 7 HOH A 30 530 530 HOH HOH . I 7 HOH A 31 531 531 HOH HOH . I 7 HOH A 32 532 532 HOH HOH . I 7 HOH A 33 533 533 HOH HOH . I 7 HOH A 34 534 534 HOH HOH . I 7 HOH A 35 535 535 HOH HOH . I 7 HOH A 36 536 536 HOH HOH . I 7 HOH A 37 537 537 HOH HOH . I 7 HOH A 38 538 538 HOH HOH . I 7 HOH A 39 539 539 HOH HOH . I 7 HOH A 40 540 540 HOH HOH . I 7 HOH A 41 541 541 HOH HOH . I 7 HOH A 42 542 542 HOH HOH . I 7 HOH A 43 543 543 HOH HOH . I 7 HOH A 44 544 544 HOH HOH . I 7 HOH A 45 545 545 HOH HOH . I 7 HOH A 46 546 546 HOH HOH . I 7 HOH A 47 547 547 HOH HOH . I 7 HOH A 48 548 548 HOH HOH . I 7 HOH A 49 549 549 HOH HOH . I 7 HOH A 50 550 550 HOH HOH . I 7 HOH A 51 551 551 HOH HOH . I 7 HOH A 52 552 552 HOH HOH . I 7 HOH A 53 553 553 HOH HOH . I 7 HOH A 54 554 554 HOH HOH . I 7 HOH A 55 555 555 HOH HOH . I 7 HOH A 56 556 556 HOH HOH . I 7 HOH A 57 557 557 HOH HOH . I 7 HOH A 58 558 558 HOH HOH . I 7 HOH A 59 559 559 HOH HOH . I 7 HOH A 60 560 560 HOH HOH . I 7 HOH A 61 561 561 HOH HOH . I 7 HOH A 62 562 562 HOH HOH . I 7 HOH A 63 563 563 HOH HOH . J 7 HOH C 1 501 501 HOH HOH . J 7 HOH C 2 502 502 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 BNG . . . E 5 13.177 -45.507 -36.092 1 101.92 ? C1 BNG 407 A 1 HETATM 2 C C2 BNG . . . E 5 13.279 -44.29 -35.178 1 98.53 ? C2 BNG 407 A 1 HETATM 3 C C3 BNG . . . E 5 13.471 -43.021 -35.994 1 96.48 ? C3 BNG 407 A 1 HETATM 4 C C4 BNG . . . E 5 14.676 -43.182 -36.909 1 105.55 ? C4 BNG 407 A 1 HETATM 5 C C5 BNG . . . E 5 14.521 -44.424 -37.782 1 104.58 ? C5 BNG 407 A 1 HETATM 6 C C6 BNG . . . E 5 15.764 -44.638 -38.641 1 108.34 ? C6 BNG 407 A 1 HETATM 7 C C1' BNG . . . E 5 11.927 -47.466 -35.592 1 86.17 ? C1' BNG 407 A 1 HETATM 8 C C2' BNG . . . E 5 11.671 -48.411 -34.425 1 80.76 ? C2' BNG 407 A 1 HETATM 9 C C3' BNG . . . E 5 10.328 -48.147 -33.755 1 75.22 ? C3' BNG 407 A 1 HETATM 10 C C4' BNG . . . E 5 9.217 -48.933 -34.441 1 80.4 ? C4' BNG 407 A 1 HETATM 11 C C5' BNG . . . E 5 8.133 -49.334 -33.445 1 85.59 ? C5' BNG 407 A 1 HETATM 12 C C6' BNG . . . E 5 7.213 -48.166 -33.114 1 83.07 ? C6' BNG 407 A 1 HETATM 13 C C7' BNG . . . E 5 6.184 -47.957 -34.218 1 78.23 ? C7' BNG 407 A 1 HETATM 14 C C8' BNG . . . E 5 5.515 -46.596 -34.079 1 75.85 ? C8' BNG 407 A 1 HETATM 15 C C9' BNG . . . E 5 6.544 -45.49 -34.162 1 77.65 ? C9' BNG 407 A 1 HETATM 16 O O1 BNG . . . E 5 13.079 -46.682 -35.286 1 97.68 ? O1 BNG 407 A 1 HETATM 17 O O2 BNG . . . E 5 12.09 -44.19 -34.382 1 92.48 ? O2 BNG 407 A 1 HETATM 18 O O3 BNG . . . E 5 13.673 -41.908 -35.115 1 77.17 ? O3 BNG 407 A 1 HETATM 19 O O4 BNG . . . E 5 14.808 -42.019 -37.735 1 106.54 ? O4 BNG 407 A 1 HETATM 20 O O5 BNG . . . E 5 14.294 -45.595 -36.987 1 105.02 ? O5 BNG 407 A 1 HETATM 21 O O6 BNG . . . E 5 16.869 -45.009 -37.807 1 109.71 ? O6 BNG 407 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #