data_4AVK # _model_server_result.job_id Psk9pcJP32ihgbv-TULDbg _model_server_result.datetime_utc '2024-11-25 09:43:34' _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 4avk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 4AVK # _exptl.entry_id 4AVK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 295.288 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannopyranoside' _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 4AVK _cell.length_a 90.46 _cell.length_b 90.46 _cell.length_c 79.54 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AVK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,K 1 1 B,E,F,G,H,I,J,L 2 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 ? 2 C N N ? 2 E 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 3 A CYS 3 1_555 A SG CYS 44 A CYS 44 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 B SG CYS 3 B CYS 3 1_555 B SG CYS 44 B CYS 44 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.026 ? metalc ? metalc1 A NE2 HIS 45 A HIS 45 1_555 D NI NI . A NI 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc2 A OD1 ASP 47 A ASP 47 1_555 D NI NI . A NI 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc3 D NI NI . A NI 1159 1_555 K O HOH . A HOH 2034 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc4 D NI NI . A NI 1159 1_555 K O HOH . A HOH 2035 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc5 B NE2 HIS 45 B HIS 45 1_555 I NI NI . B NI 1162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc6 B OD1 ASP 47 B ASP 47 1_555 I NI NI . B NI 1162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc7 I NI NI . B NI 1162 1_555 L O HOH . B HOH 2042 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? # _chem_comp.formula 'C14 H17 N O6' _chem_comp.formula_weight 295.288 _chem_comp.id FVQ _chem_comp.mon_nstd_flag n _chem_comp.name '3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '3-pyridin-3-ylprop-2-yn-1-yl alpha-D-mannopyranoside;D-MANNOSE ALPHA1O-PROPYNYL PYRIDINE;3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannoside;3-(pyridin-3-yl)prop-2-yn-1-yl D-mannoside;3-(pyridin-3-yl)prop-2-yn-1-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 O6 C6 FVQ sing 83 n n C6 C5 FVQ sing 84 n n C5 O5 FVQ sing 85 n n C5 C4 FVQ sing 86 n n O5 C1 FVQ sing 87 n n C4 O4 FVQ sing 88 n n C4 C3 FVQ sing 89 n n C3 O3 FVQ sing 90 n n C3 C2 FVQ sing 91 n n C2 O2 FVQ sing 92 n n C2 C1 FVQ sing 93 n n C1 O1 FVQ sing 94 n n O1 C7 FVQ sing 95 n n C7 C8 FVQ sing 96 n n C8 C9 FVQ trip 97 n n C9 C10 FVQ sing 98 n n C10 C15 FVQ sing 99 n y C10 C11 FVQ doub 100 n y C15 C14 FVQ doub 101 n y C14 C13 FVQ sing 102 n y C13 N12 FVQ doub 103 n y C11 N12 FVQ sing 104 n y O6 HO6 FVQ sing 105 n n C6 H61 FVQ sing 106 n n C6 H62 FVQ sing 107 n n C5 H5 FVQ sing 108 n n C4 H4 FVQ sing 109 n n C1 H1 FVQ sing 110 n n O4 HO4 FVQ sing 111 n n C3 H3 FVQ sing 112 n n O3 HO3 FVQ sing 113 n n C2 H2 FVQ sing 114 n n O2 HO2 FVQ sing 115 n n C7 H71C FVQ sing 116 n n C7 H72C FVQ sing 117 n n C15 H15 FVQ sing 118 n n C11 H11 FVQ sing 119 n n C14 H14 FVQ sing 120 n n C13 H13 FVQ sing 121 n n # _atom_sites.entry_id 4AVK _atom_sites.fract_transf_matrix[1][1] 0.011055 _atom_sites.fract_transf_matrix[1][2] 0.006382 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012765 _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] 0.012572 _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 2 FVQ A 1 201 201 FVQ FVQ . D 3 NI A 1 1159 1159 NI NI . E 2 FVQ B 1 201 201 FVQ FVQ . F 4 SO4 B 1 1159 1159 SO4 SO4 . G 4 SO4 B 1 1160 1160 SO4 SO4 . H 4 SO4 B 1 1161 1161 SO4 SO4 . I 3 NI B 1 1162 1162 NI NI . J 4 SO4 B 1 1163 1163 SO4 SO4 . K 5 HOH A 1 2001 2001 HOH HOH . K 5 HOH A 2 2002 2002 HOH HOH . K 5 HOH A 3 2003 2003 HOH HOH . K 5 HOH A 4 2004 2004 HOH HOH . K 5 HOH A 5 2005 2005 HOH HOH . K 5 HOH A 6 2006 2006 HOH HOH . K 5 HOH A 7 2007 2007 HOH HOH . K 5 HOH A 8 2008 2008 HOH HOH . K 5 HOH A 9 2009 2009 HOH HOH . K 5 HOH A 10 2010 2010 HOH HOH . K 5 HOH A 11 2011 2011 HOH HOH . K 5 HOH A 12 2012 2012 HOH HOH . K 5 HOH A 13 2013 2013 HOH HOH . K 5 HOH A 14 2014 2014 HOH HOH . K 5 HOH A 15 2015 2015 HOH HOH . K 5 HOH A 16 2016 2016 HOH HOH . K 5 HOH A 17 2017 2017 HOH HOH . K 5 HOH A 18 2018 2018 HOH HOH . K 5 HOH A 19 2019 2019 HOH HOH . K 5 HOH A 20 2020 2020 HOH HOH . K 5 HOH A 21 2021 2021 HOH HOH . K 5 HOH A 22 2022 2022 HOH HOH . K 5 HOH A 23 2023 2023 HOH HOH . K 5 HOH A 24 2024 2024 HOH HOH . K 5 HOH A 25 2025 2025 HOH HOH . K 5 HOH A 26 2026 2026 HOH HOH . K 5 HOH A 27 2027 2027 HOH HOH . K 5 HOH A 28 2028 2028 HOH HOH . K 5 HOH A 29 2029 2029 HOH HOH . K 5 HOH A 30 2030 2030 HOH HOH . K 5 HOH A 31 2031 2031 HOH HOH . K 5 HOH A 32 2032 2032 HOH HOH . K 5 HOH A 33 2033 2033 HOH HOH . K 5 HOH A 34 2034 2034 HOH HOH . K 5 HOH A 35 2035 2035 HOH HOH . K 5 HOH A 36 2036 2036 HOH HOH . K 5 HOH A 37 2037 2037 HOH HOH . K 5 HOH A 38 2038 2038 HOH HOH . K 5 HOH A 39 2039 2039 HOH HOH . K 5 HOH A 40 2040 2040 HOH HOH . K 5 HOH A 41 2041 2041 HOH HOH . K 5 HOH A 42 2042 2042 HOH HOH . K 5 HOH A 43 2043 2043 HOH HOH . K 5 HOH A 44 2044 2044 HOH HOH . K 5 HOH A 45 2045 2045 HOH HOH . K 5 HOH A 46 2046 2046 HOH HOH . K 5 HOH A 47 2047 2047 HOH HOH . K 5 HOH A 48 2048 2048 HOH HOH . K 5 HOH A 49 2049 2049 HOH HOH . K 5 HOH A 50 2050 2050 HOH HOH . K 5 HOH A 51 2051 2051 HOH HOH . K 5 HOH A 52 2052 2052 HOH HOH . K 5 HOH A 53 2053 2053 HOH HOH . K 5 HOH A 54 2054 2054 HOH HOH . K 5 HOH A 55 2055 2055 HOH HOH . K 5 HOH A 56 2056 2056 HOH HOH . K 5 HOH A 57 2057 2057 HOH HOH . K 5 HOH A 58 2058 2058 HOH HOH . K 5 HOH A 59 2059 2059 HOH HOH . K 5 HOH A 60 2060 2060 HOH HOH . K 5 HOH A 61 2061 2061 HOH HOH . K 5 HOH A 62 2062 2062 HOH HOH . K 5 HOH A 63 2063 2063 HOH HOH . K 5 HOH A 64 2064 2064 HOH HOH . K 5 HOH A 65 2065 2065 HOH HOH . K 5 HOH A 66 2066 2066 HOH HOH . K 5 HOH A 67 2067 2067 HOH HOH . K 5 HOH A 68 2068 2068 HOH HOH . K 5 HOH A 69 2069 2069 HOH HOH . K 5 HOH A 70 2070 2070 HOH HOH . K 5 HOH A 71 2071 2071 HOH HOH . K 5 HOH A 72 2072 2072 HOH HOH . K 5 HOH A 73 2073 2073 HOH HOH . K 5 HOH A 74 2074 2074 HOH HOH . K 5 HOH A 75 2075 2075 HOH HOH . K 5 HOH A 76 2076 2076 HOH HOH . K 5 HOH A 77 2077 2077 HOH HOH . K 5 HOH A 78 2078 2078 HOH HOH . K 5 HOH A 79 2079 2079 HOH HOH . K 5 HOH A 80 2080 2080 HOH HOH . K 5 HOH A 81 2081 2081 HOH HOH . K 5 HOH A 82 2082 2082 HOH HOH . K 5 HOH A 83 2083 2083 HOH HOH . K 5 HOH A 84 2084 2084 HOH HOH . K 5 HOH A 85 2085 2085 HOH HOH . K 5 HOH A 86 2086 2086 HOH HOH . K 5 HOH A 87 2087 2087 HOH HOH . K 5 HOH A 88 2088 2088 HOH HOH . K 5 HOH A 89 2089 2089 HOH HOH . K 5 HOH A 90 2090 2090 HOH HOH . K 5 HOH A 91 2091 2091 HOH HOH . L 5 HOH B 1 2001 2001 HOH HOH . L 5 HOH B 2 2002 2002 HOH HOH . L 5 HOH B 3 2003 2003 HOH HOH . L 5 HOH B 4 2004 2004 HOH HOH . L 5 HOH B 5 2005 2005 HOH HOH . L 5 HOH B 6 2006 2006 HOH HOH . L 5 HOH B 7 2007 2007 HOH HOH . L 5 HOH B 8 2008 2008 HOH HOH . L 5 HOH B 9 2009 2009 HOH HOH . L 5 HOH B 10 2010 2010 HOH HOH . L 5 HOH B 11 2011 2011 HOH HOH . L 5 HOH B 12 2012 2012 HOH HOH . L 5 HOH B 13 2013 2013 HOH HOH . L 5 HOH B 14 2014 2014 HOH HOH . L 5 HOH B 15 2015 2015 HOH HOH . L 5 HOH B 16 2016 2016 HOH HOH . L 5 HOH B 17 2017 2017 HOH HOH . L 5 HOH B 18 2018 2018 HOH HOH . L 5 HOH B 19 2019 2019 HOH HOH . L 5 HOH B 20 2020 2020 HOH HOH . L 5 HOH B 21 2021 2021 HOH HOH . L 5 HOH B 22 2022 2022 HOH HOH . L 5 HOH B 23 2023 2023 HOH HOH . L 5 HOH B 24 2024 2024 HOH HOH . L 5 HOH B 25 2025 2025 HOH HOH . L 5 HOH B 26 2026 2026 HOH HOH . L 5 HOH B 27 2027 2027 HOH HOH . L 5 HOH B 28 2028 2028 HOH HOH . L 5 HOH B 29 2029 2029 HOH HOH . L 5 HOH B 30 2030 2030 HOH HOH . L 5 HOH B 31 2031 2031 HOH HOH . L 5 HOH B 32 2032 2032 HOH HOH . L 5 HOH B 33 2033 2033 HOH HOH . L 5 HOH B 34 2034 2034 HOH HOH . L 5 HOH B 35 2035 2035 HOH HOH . L 5 HOH B 36 2036 2036 HOH HOH . L 5 HOH B 37 2037 2037 HOH HOH . L 5 HOH B 38 2038 2038 HOH HOH . L 5 HOH B 39 2039 2039 HOH HOH . L 5 HOH B 40 2040 2040 HOH HOH . L 5 HOH B 41 2041 2041 HOH HOH . L 5 HOH B 42 2042 2042 HOH HOH . L 5 HOH B 43 2043 2043 HOH HOH . L 5 HOH B 44 2044 2044 HOH HOH . L 5 HOH B 45 2045 2045 HOH HOH . L 5 HOH B 46 2046 2046 HOH HOH . L 5 HOH B 47 2047 2047 HOH HOH . L 5 HOH B 48 2048 2048 HOH HOH . L 5 HOH B 49 2049 2049 HOH HOH . L 5 HOH B 50 2050 2050 HOH HOH . L 5 HOH B 51 2051 2051 HOH HOH . L 5 HOH B 52 2052 2052 HOH HOH . L 5 HOH B 53 2053 2053 HOH HOH . L 5 HOH B 54 2054 2054 HOH HOH . L 5 HOH B 55 2055 2055 HOH HOH . L 5 HOH B 56 2056 2056 HOH HOH . L 5 HOH B 57 2057 2057 HOH HOH . L 5 HOH B 58 2058 2058 HOH HOH . L 5 HOH B 59 2059 2059 HOH HOH . L 5 HOH B 60 2060 2060 HOH HOH . L 5 HOH B 61 2061 2061 HOH HOH . L 5 HOH B 62 2062 2062 HOH HOH . L 5 HOH B 63 2063 2063 HOH HOH . L 5 HOH B 64 2064 2064 HOH HOH . L 5 HOH B 65 2065 2065 HOH HOH . L 5 HOH B 66 2066 2066 HOH HOH . L 5 HOH B 67 2067 2067 HOH HOH . L 5 HOH B 68 2068 2068 HOH HOH . L 5 HOH B 69 2069 2069 HOH HOH . L 5 HOH B 70 2070 2070 HOH HOH . L 5 HOH B 71 2071 2071 HOH HOH . L 5 HOH B 72 2072 2072 HOH HOH . L 5 HOH B 73 2073 2073 HOH HOH . L 5 HOH B 74 2074 2074 HOH HOH . L 5 HOH B 75 2075 2075 HOH HOH . L 5 HOH B 76 2076 2076 HOH HOH . L 5 HOH B 77 2077 2077 HOH HOH . L 5 HOH B 78 2078 2078 HOH HOH . L 5 HOH B 79 2079 2079 HOH HOH . L 5 HOH B 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 O6 FVQ . . . E 2 -13.337 -41.057 -8.617 1 26.22 ? O6 FVQ 201 B 1 HETATM 2 C C6 FVQ . . . E 2 -14.554 -41.026 -7.866 1 22.81 ? C6 FVQ 201 B 1 HETATM 3 C C5 FVQ . . . E 2 -14.66 -41.875 -6.686 1 25.87 ? C5 FVQ 201 B 1 HETATM 4 O O5 FVQ . . . E 2 -13.945 -43.171 -6.932 1 24.74 ? O5 FVQ 201 B 1 HETATM 5 C C4 FVQ . . . E 2 -14.142 -41.208 -5.47 1 20.87 ? C4 FVQ 201 B 1 HETATM 6 O O4 FVQ . . . E 2 -14.845 -39.967 -5.209 1 23.39 ? O4 FVQ 201 B 1 HETATM 7 C C3 FVQ . . . E 2 -14.18 -42.056 -4.305 1 22.83 ? C3 FVQ 201 B 1 HETATM 8 O O3 FVQ . . . E 2 -13.646 -41.378 -3.183 1 20.67 ? O3 FVQ 201 B 1 HETATM 9 C C2 FVQ . . . E 2 -13.442 -43.338 -4.553 1 23.66 ? C2 FVQ 201 B 1 HETATM 10 O O2 FVQ . . . E 2 -12.059 -43.141 -4.716 1 24.79 ? O2 FVQ 201 B 1 HETATM 11 C C1 FVQ . . . E 2 -13.956 -44.007 -5.784 1 26.16 ? C1 FVQ 201 B 1 HETATM 12 O O1 FVQ . . . E 2 -15.23 -44.295 -5.477 1 31.72 ? O1 FVQ 201 B 1 HETATM 13 C C7 FVQ . . . E 2 -15.852 -45.476 -6.051 1 35.69 ? C7 FVQ 201 B 1 HETATM 14 C C8 FVQ . . . E 2 -17.282 -45.396 -6.396 1 40.3 ? C8 FVQ 201 B 1 HETATM 15 C C9 FVQ . . . E 2 -18.444 -45.269 -6.743 1 54.99 ? C9 FVQ 201 B 1 HETATM 16 C C10 FVQ . . . E 2 -19.868 -45.093 -7.269 1 54.44 ? C10 FVQ 201 B 1 HETATM 17 C C15 FVQ . . . E 2 -20.168 -44.256 -8.403 1 60.23 ? C15 FVQ 201 B 1 HETATM 18 C C14 FVQ . . . E 2 -21.52 -44.121 -8.824 1 64.82 ? C14 FVQ 201 B 1 HETATM 19 C C13 FVQ . . . E 2 -22.509 -44.812 -8.118 1 65.99 ? C13 FVQ 201 B 1 HETATM 20 N N12 FVQ . . . E 2 -22.184 -45.6 -7.043 1 61.87 ? N12 FVQ 201 B 1 HETATM 21 C C11 FVQ . . . E 2 -20.899 -45.738 -6.624 1 64.66 ? C11 FVQ 201 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 21 #