data_2CCB # _model_server_result.job_id LQckHq6e6PiuYfI2V2p2CQ _model_server_result.datetime_utc '2024-11-24 09:11:13' _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 2ccb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1067}' # _entry.id 2CCB # _exptl.entry_id 2CCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.364 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RIBOFLAVIN _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 2CCB _cell.length_a 142.04 _cell.length_b 142.04 _cell.length_c 142.04 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2CCB _symmetry.cell_setting ? _symmetry.Int_Tables_number 210 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'F 41 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10,11,12 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 4 'crystal symmetry operation' 26_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 5 'crystal symmetry operation' 31_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 6 'crystal symmetry operation' 36_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 7 'crystal symmetry operation' 52_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 54_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 9 'crystal symmetry operation' 59_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 10 'crystal symmetry operation' 75_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 11 'crystal symmetry operation' 80_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 12 'crystal symmetry operation' 82_555 -y,z,-x 0 -1 0 0 0 1 -1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 14 A GLU 14 1_555 E MG MG . A MG 1066 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc2 A OD2 ASP 41 A ASP 41 80_555 B MG MG . A MG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc3 B MG MG . A MG 102 1_555 H O HOH . A HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc4 B MG MG . A MG 102 1_555 H O HOH . A HOH 2047 75_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc5 B MG MG . A MG 102 1_555 H O HOH . A HOH 2049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc6 B MG MG . A MG 102 1_555 H O HOH . A HOH 2070 80_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc7 C NA NA . A NA 104 1_555 H O HOH . A HOH 2072 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc8 C NA NA . A NA 104 1_555 H O HOH . A HOH 2072 80_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc9 C NA NA . A NA 104 1_555 H O HOH . A HOH 2072 59_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc10 E MG MG . A MG 1066 1_555 H O HOH . A HOH 2016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc11 E MG MG . A MG 1066 1_555 H O HOH . A HOH 2023 24_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc12 E MG MG . A MG 1066 1_555 H O HOH . A HOH 2024 24_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc13 E MG MG . A MG 1066 1_555 H O HOH . A HOH 2032 24_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc14 E MG MG . A MG 1066 1_555 H O HOH . A HOH 2062 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? # _chem_comp.formula 'C17 H20 N4 O6' _chem_comp.formula_weight 376.364 _chem_comp.id RBF _chem_comp.mon_nstd_flag . _chem_comp.name RIBOFLAVIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVINE;VITAMIN B2' # 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 N1 C2 RBF sing 226 n n N1 C10 RBF doub 227 n n C2 O2 RBF doub 228 n n C2 N3 RBF sing 229 n n N3 C4 RBF sing 230 n n N3 HN3 RBF sing 231 n n C4 O4 RBF doub 232 n n C4 C4A RBF sing 233 n n C4A N5 RBF doub 234 n n C4A C10 RBF sing 235 n n N5 C5A RBF sing 236 n n C5A C6 RBF doub 237 n y C5A C9A RBF sing 238 n y C6 C7 RBF sing 239 n y C6 HC6 RBF sing 240 n n C7 C7M RBF sing 241 n n C7 C8 RBF doub 242 n y C7M HC71 RBF sing 243 n n C7M HC72 RBF sing 244 n n C7M HC73 RBF sing 245 n n C8 C8M RBF sing 246 n n C8 C9 RBF sing 247 n y C8M HC81 RBF sing 248 n n C8M HC82 RBF sing 249 n n C8M HC83 RBF sing 250 n n C9 C9A RBF doub 251 n y C9 HC9 RBF sing 252 n n C9A N10 RBF sing 253 n n N10 C10 RBF sing 254 n n N10 C1' RBF sing 255 n n C1' C2' RBF sing 256 n n C1' HC11 RBF sing 257 n n C1' HC12 RBF sing 258 n n C2' O2' RBF sing 259 n n C2' C3' RBF sing 260 n n C2' HC2' RBF sing 261 n n O2' HO2' RBF sing 262 n n C3' O3' RBF sing 263 n n C3' C4' RBF sing 264 n n C3' HC3' RBF sing 265 n n O3' HO3' RBF sing 266 n n C4' O4' RBF sing 267 n n C4' C5' RBF sing 268 n n C4' HC4' RBF sing 269 n n O4' HO4' RBF sing 270 n n C5' O5' RBF sing 271 n n C5' HC51 RBF sing 272 n n C5' HC52 RBF sing 273 n n O5' HO5' RBF sing 274 n n # _atom_sites.entry_id 2CCB _atom_sites.fract_transf_matrix[1][1] 0.00704 _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] 0.00704 _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] 0.00704 _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 MG A 1 102 102 MG MG . C 3 NA A 1 104 104 NA NA . D 4 CL A 1 105 105 CL CL . E 2 MG A 1 1066 1066 MG MG . F 5 RBF A 1 1067 1067 RBF RBF . G 6 SO4 A 1 1068 1068 SO4 SO4 . H 7 HOH A 1 2001 2001 HOH HOH . H 7 HOH A 2 2002 2002 HOH HOH . H 7 HOH A 3 2003 2003 HOH HOH . H 7 HOH A 4 2004 2004 HOH HOH . H 7 HOH A 5 2005 2005 HOH HOH . H 7 HOH A 6 2006 2006 HOH HOH . H 7 HOH A 7 2007 2007 HOH HOH . H 7 HOH A 8 2008 2008 HOH HOH . H 7 HOH A 9 2009 2009 HOH HOH . H 7 HOH A 10 2010 2010 HOH HOH . H 7 HOH A 11 2011 2011 HOH HOH . H 7 HOH A 12 2012 2012 HOH HOH . H 7 HOH A 13 2013 2013 HOH HOH . H 7 HOH A 14 2014 2014 HOH HOH . H 7 HOH A 15 2015 2015 HOH HOH . H 7 HOH A 16 2016 2016 HOH HOH . H 7 HOH A 17 2017 2017 HOH HOH . H 7 HOH A 18 2018 2018 HOH HOH . H 7 HOH A 19 2019 2019 HOH HOH . H 7 HOH A 20 2020 2020 HOH HOH . H 7 HOH A 21 2021 2021 HOH HOH . H 7 HOH A 22 2022 2022 HOH HOH . H 7 HOH A 23 2023 2023 HOH HOH . H 7 HOH A 24 2024 2024 HOH HOH . H 7 HOH A 25 2025 2025 HOH HOH . H 7 HOH A 26 2026 2026 HOH HOH . H 7 HOH A 27 2027 2027 HOH HOH . H 7 HOH A 28 2028 2028 HOH HOH . H 7 HOH A 29 2029 2029 HOH HOH . H 7 HOH A 30 2030 2030 HOH HOH . H 7 HOH A 31 2031 2031 HOH HOH . H 7 HOH A 32 2032 2032 HOH HOH . H 7 HOH A 33 2033 2033 HOH HOH . H 7 HOH A 34 2034 2034 HOH HOH . H 7 HOH A 35 2035 2035 HOH HOH . H 7 HOH A 36 2036 2036 HOH HOH . H 7 HOH A 37 2037 2037 HOH HOH . H 7 HOH A 38 2038 2038 HOH HOH . H 7 HOH A 39 2039 2039 HOH HOH . H 7 HOH A 40 2040 2040 HOH HOH . H 7 HOH A 41 2041 2041 HOH HOH . H 7 HOH A 42 2042 2042 HOH HOH . H 7 HOH A 43 2043 2043 HOH HOH . H 7 HOH A 44 2044 2044 HOH HOH . H 7 HOH A 45 2045 2045 HOH HOH . H 7 HOH A 46 2046 2046 HOH HOH . H 7 HOH A 47 2047 2047 HOH HOH . H 7 HOH A 48 2048 2048 HOH HOH . H 7 HOH A 49 2049 2049 HOH HOH . H 7 HOH A 50 2050 2050 HOH HOH . H 7 HOH A 51 2051 2051 HOH HOH . H 7 HOH A 52 2052 2052 HOH HOH . H 7 HOH A 53 2053 2053 HOH HOH . H 7 HOH A 54 2054 2054 HOH HOH . H 7 HOH A 55 2055 2055 HOH HOH . H 7 HOH A 56 2056 2056 HOH HOH . H 7 HOH A 57 2057 2057 HOH HOH . H 7 HOH A 58 2058 2058 HOH HOH . H 7 HOH A 59 2059 2059 HOH HOH . H 7 HOH A 60 2060 2060 HOH HOH . H 7 HOH A 61 2061 2061 HOH HOH . H 7 HOH A 62 2062 2062 HOH HOH . H 7 HOH A 63 2063 2063 HOH HOH . H 7 HOH A 64 2064 2064 HOH HOH . H 7 HOH A 65 2065 2065 HOH HOH . H 7 HOH A 66 2066 2066 HOH HOH . H 7 HOH A 67 2067 2067 HOH HOH . H 7 HOH A 68 2068 2068 HOH HOH . H 7 HOH A 69 2069 2069 HOH HOH . H 7 HOH A 70 2070 2070 HOH HOH . H 7 HOH A 71 2071 2071 HOH HOH . H 7 HOH A 72 2072 2072 HOH HOH . H 7 HOH A 73 2073 2073 HOH HOH . H 7 HOH A 74 2074 2074 HOH HOH . H 7 HOH A 75 2075 2075 HOH HOH . H 7 HOH A 76 2076 2076 HOH HOH . H 7 HOH A 77 2077 2077 HOH HOH . H 7 HOH A 78 2078 2078 HOH HOH . H 7 HOH A 79 2079 2079 HOH HOH . H 7 HOH A 80 2080 2080 HOH HOH . H 7 HOH A 81 2081 2081 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 N N1 RBF . . . F 5 0.229 22.714 -2.893 1 22.75 ? N1 RBF 1067 A 1 HETATM 2 C C2 RBF . . . F 5 -0.465 22.331 -3.992 1 20.38 ? C2 RBF 1067 A 1 HETATM 3 O O2 RBF . . . F 5 -0.923 23.247 -4.708 1 24.66 ? O2 RBF 1067 A 1 HETATM 4 N N3 RBF . . . F 5 -0.639 21.043 -4.326 1 20.86 ? N3 RBF 1067 A 1 HETATM 5 C C4 RBF . . . F 5 -0.195 20.031 -3.595 1 19.11 ? C4 RBF 1067 A 1 HETATM 6 O O4 RBF . . . F 5 -0.358 18.84 -3.92 1 23.57 ? O4 RBF 1067 A 1 HETATM 7 C C4A RBF . . . F 5 0.567 20.357 -2.369 1 21.51 ? C4A RBF 1067 A 1 HETATM 8 N N5 RBF . . . F 5 1.061 19.389 -1.581 1 22.79 ? N5 RBF 1067 A 1 HETATM 9 C C5A RBF . . . F 5 1.756 19.72 -0.453 1 21.19 ? C5A RBF 1067 A 1 HETATM 10 C C6 RBF . . . F 5 2.252 18.71 0.355 1 21.56 ? C6 RBF 1067 A 1 HETATM 11 C C7 RBF . . . F 5 2.977 19.021 1.514 1 19.21 ? C7 RBF 1067 A 1 HETATM 12 C C7M RBF . . . F 5 3.533 17.889 2.372 1 19.67 ? C7M RBF 1067 A 1 HETATM 13 C C8 RBF . . . F 5 3.192 20.443 1.874 1 18.8 ? C8 RBF 1067 A 1 HETATM 14 C C8M RBF . . . F 5 3.966 20.782 3.135 1 19.76 ? C8M RBF 1067 A 1 HETATM 15 C C9 RBF . . . F 5 2.687 21.475 1.081 1 18.43 ? C9 RBF 1067 A 1 HETATM 16 C C9A RBF . . . F 5 1.969 21.145 -0.088 1 19.31 ? C9A RBF 1067 A 1 HETATM 17 N N10 RBF . . . F 5 1.457 22.172 -0.922 1 22.27 ? N10 RBF 1067 A 1 HETATM 18 C C10 RBF . . . F 5 0.739 21.785 -2.065 1 21.05 ? C10 RBF 1067 A 1 HETATM 19 C C1' RBF . . . F 5 1.596 23.6 -0.593 1 22.05 ? C1' RBF 1067 A 1 HETATM 20 C C2' RBF . . . F 5 2.57 24.38 -1.447 1 25.16 ? C2' RBF 1067 A 1 HETATM 21 O O2' RBF . . . F 5 3.858 24.147 -0.886 1 22.94 ? O2' RBF 1067 A 1 HETATM 22 C C3' RBF . . . F 5 2.177 25.863 -1.506 1 30.01 ? C3' RBF 1067 A 1 HETATM 23 O O3' RBF . . . F 5 2.08 26.382 -0.179 1 32.03 ? O3' RBF 1067 A 1 HETATM 24 C C4' RBF . . . F 5 0.851 25.991 -2.317 1 32.5 ? C4' RBF 1067 A 1 HETATM 25 O O4' RBF . . . F 5 1.143 25.771 -3.698 1 37.44 ? O4' RBF 1067 A 1 HETATM 26 C C5' RBF . . . F 5 0.08 27.301 -2.183 1 38.09 ? C5' RBF 1067 A 1 HETATM 27 O O5' RBF . . . F 5 -1.066 27.325 -3.063 1 40.92 ? O5' RBF 1067 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #