data_2JDZ # _model_server_result.job_id t_ByVEths1hFc_i1YPN8OA _model_server_result.datetime_utc '2024-10-13 02:23:34' _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 2jdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":249}' # _entry.id 2JDZ # _exptl.entry_id 2JDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 408.629 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside' _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 90 _cell.entry_id 2JDZ _cell.length_a 89.222 _cell.length_b 89.222 _cell.length_c 106.069 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2JDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details 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 1,2,3,4 # 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' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 10_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 4 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A OE2 GLU 10 A GLU 10 1_555 B MN MN . A MN 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc2 A OD2 ASP 12 A ASP 12 1_555 B MN MN . A MN 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc3 A OD1 ASP 12 A ASP 12 1_555 C CA CA . A CA 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc4 A OD2 ASP 12 A ASP 12 1_555 C CA CA . A CA 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc5 A O TYR 14 A TYR 14 1_555 C CA CA . A CA 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc6 A OD1 ASN 16 A ASN 16 1_555 C CA CA . A CA 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc7 A OD1 ASP 21 A ASP 21 1_555 B MN MN . A MN 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc8 A OD2 ASP 21 A ASP 21 1_555 C CA CA . A CA 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc9 A NE2 HIS 26 A HIS 26 1_555 B MN MN . A MN 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc10 A NE2 HIS 53 A HIS 53 1_555 H MN MN . A MN 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc11 A OE1 GLU 89 A GLU 89 1_555 E CD CD . A CD 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc12 A OE2 GLU 89 A GLU 89 6_555 E CD CD . A CD 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc13 A OE1 GLU 89 A GLU 89 6_555 E CD CD . A CD 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc14 A OG SER 127 A SER 127 1_555 F MN MN . A MN 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc15 A NE2 HIS 129 A HIS 129 15_555 F MN MN . A MN 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc16 A ND1 HIS 182 A HIS 182 1_555 D MN MN . A MN 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc17 A OE1 GLU 185 A GLU 185 1_555 E CD CD . A CD 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc18 A OE1 GLU 185 A GLU 185 6_555 E CD CD . A CD 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc19 A OD1 ASP 207 A ASP 207 1_555 G MN MN . A MN 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc20 B MN MN . A MN 240 1_555 J O HOH . A HOH 2068 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc21 B MN MN . A MN 240 1_555 J O HOH . A HOH 2069 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? metalc ? metalc22 C CA CA . A CA 241 1_555 J O HOH . A HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc23 C CA CA . A CA 241 1_555 J O HOH . A HOH 2057 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc24 D MN MN . A MN 244 1_555 J O HOH . A HOH 2070 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc25 D MN MN . A MN 244 1_555 J O HOH . A HOH 2072 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc26 F MN MN . A MN 246 1_555 J O HOH . A HOH 2073 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc27 F MN MN . A MN 246 1_555 J O HOH . A HOH 2075 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? metalc ? metalc28 G MN MN . A MN 247 1_555 J O HOH . A HOH 2076 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc29 H MN MN . A MN 248 1_555 J O HOH . A HOH 2078 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc30 H MN MN . A MN 248 1_555 J O HOH . A HOH 2079 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? # _chem_comp.formula 'C14 H15 Br Cl N O6' _chem_comp.formula_weight 408.629 _chem_comp.id XMM _chem_comp.mon_nstd_flag n _chem_comp.name '5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL;(5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE;5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside;5-bromo-4-chloro-1H-indol-3-yl D-mannoside;5-bromo-4-chloro-1H-indol-3-yl mannoside' # 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 O2 C2 XMM sing 363 n n O2 HO2 XMM sing 364 n n C2 C3 XMM sing 365 n n C2 C1 XMM sing 366 n n C2 H2 XMM sing 367 n n C3 O3 XMM sing 368 n n C3 C4 XMM sing 369 n n C3 H3 XMM sing 370 n n O3 HO3 XMM sing 371 n n C4 O4 XMM sing 372 n n C4 C5 XMM sing 373 n n C4 H4 XMM sing 374 n n O4 HO4 XMM sing 375 n n C5 O5 XMM sing 376 n n C5 C6 XMM sing 377 n n C5 H5 XMM sing 378 n n O5 C1 XMM sing 379 n n C6 O6 XMM sing 380 n n C6 H61 XMM sing 381 n n C6 H62 XMM sing 382 n n O6 HO6 XMM sing 383 n n C1 O1 XMM sing 384 n n C1 H1 XMM sing 385 n n O1 C7 XMM sing 386 n n C7 C8 XMM sing 387 n y C7 C11 XMM doub 388 n y C8 C9 XMM doub 389 n y C8 C10 XMM sing 390 n y C9 N1 XMM sing 391 n y C9 C12 XMM sing 392 n y N1 C11 XMM sing 393 n y N1 HN1 XMM sing 394 n n C11 H11 XMM sing 395 n n C10 CL XMM sing 396 n n C10 C13 XMM doub 397 n y C13 BR XMM sing 398 n n C13 C14 XMM sing 399 n y C14 C12 XMM doub 400 n y C14 H14 XMM sing 401 n n C12 H12 XMM sing 402 n n # _atom_sites.entry_id 2JDZ _atom_sites.fract_transf_matrix[1][1] 0.011208 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011208 _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] 0.009428 _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 B 2 MN A 1 240 240 MN MN . C 3 CA A 1 241 241 CA CA . D 2 MN A 1 244 244 MN MN . E 4 CD A 1 245 245 CD CD . F 2 MN A 1 246 246 MN MN . G 2 MN A 1 247 247 MN MN . H 2 MN A 1 248 248 MN MN . I 5 XMM A 1 249 249 XMM XMM . J 6 HOH A 1 2001 2001 HOH HOH . J 6 HOH A 2 2002 2002 HOH HOH . J 6 HOH A 3 2003 2003 HOH HOH . J 6 HOH A 4 2004 2004 HOH HOH . J 6 HOH A 5 2005 2005 HOH HOH . J 6 HOH A 6 2006 2006 HOH HOH . J 6 HOH A 7 2007 2007 HOH HOH . J 6 HOH A 8 2008 2008 HOH HOH . J 6 HOH A 9 2009 2009 HOH HOH . J 6 HOH A 10 2010 2010 HOH HOH . J 6 HOH A 11 2011 2011 HOH HOH . J 6 HOH A 12 2012 2012 HOH HOH . J 6 HOH A 13 2013 2013 HOH HOH . J 6 HOH A 14 2014 2014 HOH HOH . J 6 HOH A 15 2015 2015 HOH HOH . J 6 HOH A 16 2016 2016 HOH HOH . J 6 HOH A 17 2017 2017 HOH HOH . J 6 HOH A 18 2018 2018 HOH HOH . J 6 HOH A 19 2019 2019 HOH HOH . J 6 HOH A 20 2020 2020 HOH HOH . J 6 HOH A 21 2021 2021 HOH HOH . J 6 HOH A 22 2022 2022 HOH HOH . J 6 HOH A 23 2023 2023 HOH HOH . J 6 HOH A 24 2024 2024 HOH HOH . J 6 HOH A 25 2025 2025 HOH HOH . J 6 HOH A 26 2026 2026 HOH HOH . J 6 HOH A 27 2027 2027 HOH HOH . J 6 HOH A 28 2028 2028 HOH HOH . J 6 HOH A 29 2029 2029 HOH HOH . J 6 HOH A 30 2030 2030 HOH HOH . J 6 HOH A 31 2031 2031 HOH HOH . J 6 HOH A 32 2032 2032 HOH HOH . J 6 HOH A 33 2033 2033 HOH HOH . J 6 HOH A 34 2034 2034 HOH HOH . J 6 HOH A 35 2035 2035 HOH HOH . J 6 HOH A 36 2036 2036 HOH HOH . J 6 HOH A 37 2037 2037 HOH HOH . J 6 HOH A 38 2038 2038 HOH HOH . J 6 HOH A 39 2039 2039 HOH HOH . J 6 HOH A 40 2040 2040 HOH HOH . J 6 HOH A 41 2041 2041 HOH HOH . J 6 HOH A 42 2042 2042 HOH HOH . J 6 HOH A 43 2043 2043 HOH HOH . J 6 HOH A 44 2044 2044 HOH HOH . J 6 HOH A 45 2045 2045 HOH HOH . J 6 HOH A 46 2046 2046 HOH HOH . J 6 HOH A 47 2047 2047 HOH HOH . J 6 HOH A 48 2048 2048 HOH HOH . J 6 HOH A 49 2049 2049 HOH HOH . J 6 HOH A 50 2050 2050 HOH HOH . J 6 HOH A 51 2051 2051 HOH HOH . J 6 HOH A 52 2052 2052 HOH HOH . J 6 HOH A 53 2053 2053 HOH HOH . J 6 HOH A 54 2054 2054 HOH HOH . J 6 HOH A 55 2055 2055 HOH HOH . J 6 HOH A 56 2056 2056 HOH HOH . J 6 HOH A 57 2057 2057 HOH HOH . J 6 HOH A 58 2058 2058 HOH HOH . J 6 HOH A 59 2059 2059 HOH HOH . J 6 HOH A 60 2060 2060 HOH HOH . J 6 HOH A 61 2061 2061 HOH HOH . J 6 HOH A 62 2062 2062 HOH HOH . J 6 HOH A 63 2063 2063 HOH HOH . J 6 HOH A 64 2064 2064 HOH HOH . J 6 HOH A 65 2065 2065 HOH HOH . J 6 HOH A 66 2066 2066 HOH HOH . J 6 HOH A 67 2067 2067 HOH HOH . J 6 HOH A 68 2068 2068 HOH HOH . J 6 HOH A 69 2069 2069 HOH HOH . J 6 HOH A 70 2070 2070 HOH HOH . J 6 HOH A 71 2071 2071 HOH HOH . J 6 HOH A 72 2072 2072 HOH HOH . J 6 HOH A 73 2073 2073 HOH HOH . J 6 HOH A 74 2074 2074 HOH HOH . J 6 HOH A 75 2075 2075 HOH HOH . J 6 HOH A 76 2076 2076 HOH HOH . J 6 HOH A 77 2077 2077 HOH HOH . J 6 HOH A 78 2078 2078 HOH HOH . J 6 HOH A 79 2079 2079 HOH HOH . J 6 HOH A 80 2080 2080 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 O O2 XMM . . . I 5 35.282 1.577 22.11 1 30.97 ? O2 XMM 249 A 1 HETATM 2 C C2 XMM . . . I 5 34.903 1.312 23.466 1 33.52 ? C2 XMM 249 A 1 HETATM 3 C C3 XMM . . . I 5 33.386 1.23 23.624 1 33.03 ? C3 XMM 249 A 1 HETATM 4 O O3 XMM . . . I 5 32.77 2.429 23.131 1 31.57 ? O3 XMM 249 A 1 HETATM 5 C C4 XMM . . . I 5 32.795 0.012 22.887 1 32.23 ? C4 XMM 249 A 1 HETATM 6 O O4 XMM . . . I 5 31.494 -0.203 23.426 1 31.39 ? O4 XMM 249 A 1 HETATM 7 C C5 XMM . . . I 5 33.67 -1.255 23.148 1 34.94 ? C5 XMM 249 A 1 HETATM 8 O O5 XMM . . . I 5 35.093 -0.975 22.972 1 33.92 ? O5 XMM 249 A 1 HETATM 9 C C6 XMM . . . I 5 33.39 -2.479 22.244 1 34.44 ? C6 XMM 249 A 1 HETATM 10 O O6 XMM . . . I 5 33.518 -2.142 20.826 1 33.62 ? O6 XMM 249 A 1 HETATM 11 C C1 XMM . . . I 5 35.59 0.009 23.886 1 38.07 ? C1 XMM 249 A 1 HETATM 12 O O1 XMM . . . I 5 35.391 -0.22 25.312 1 46.51 ? O1 XMM 249 A 1 HETATM 13 C C7 XMM . . . I 5 36.05 -1.312 25.765 1 49.27 ? C7 XMM 249 A 1 HETATM 14 C C8 XMM . . . I 5 37.37 -1.35 26.167 1 49.85 ? C8 XMM 249 A 1 HETATM 15 C C9 XMM . . . I 5 37.603 -2.659 26.566 1 50.68 ? C9 XMM 249 A 1 HETATM 16 N N1 XMM . . . I 5 36.462 -3.328 26.412 1 51.23 ? N1 XMM 249 A 1 HETATM 17 C C11 XMM . . . I 5 35.514 -2.512 25.927 1 50.44 ? C11 XMM 249 A 1 HETATM 18 C C10 XMM . . . I 5 38.391 -0.424 26.222 1 50.36 ? C10 XMM 249 A 1 HETATM 19 CL CL XMM . . . I 5 38.184 1.225 25.743 1 51.62 ? CL XMM 249 A 1 HETATM 20 C C13 XMM . . . I 5 39.641 -0.818 26.694 1 50.54 ? C13 XMM 249 A 1 HETATM 21 BR BR XMM . . . I 5 40.987 0.493 26.729 1 52.96 ? BR XMM 249 A 1 HETATM 22 C C14 XMM . . . I 5 39.897 -2.124 27.101 1 49.84 ? C14 XMM 249 A 1 HETATM 23 C C12 XMM . . . I 5 38.86 -3.051 27.033 1 50.34 ? C12 XMM 249 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #