data_2VX9 # _model_server_result.job_id u7Y4d8mewt_lrm5BTwQnyQ _model_server_result.datetime_utc '2024-11-24 15:29:00' _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 2vx9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1064}' # _entry.id 2VX9 # _exptl.entry_id 2VX9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.364 _entity.id 2 _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 2VX9 _cell.length_a 142.94 _cell.length_b 142.94 _cell.length_c 142.94 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VX9 _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 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 1,2,3,4,5,6,7,8,9,10,11,12 # 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' 34_555 -y+1/2,z,-x+1/2 0 -1 0 0 0 1 -1 0 0 71.47 0 71.47 3 'crystal symmetry operation' 55_555 -z+1/2,-x+1/2,y 0 0 -1 -1 0 0 0 1 0 71.47 71.47 0 4 'crystal symmetry operation' 11_465 y-1/2,-z+1,-x+1/2 0 1 0 0 0 -1 -1 0 0 -71.47 142.94 71.47 5 'crystal symmetry operation' 8_556 -z+1/2,x+1/2,-y+1 0 0 -1 1 0 0 0 -1 0 71.47 71.47 142.94 6 'crystal symmetry operation' 77_455 z-1/2,x+1/2,y 0 0 1 1 0 0 0 1 0 -71.47 71.47 0 7 'crystal symmetry operation' 52_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 142.94 142.94 8 'crystal symmetry operation' 26_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 142.94 0 9 'crystal symmetry operation' 84_565 -y+1/2,-z+1,x+1/2 0 -1 0 0 0 -1 1 0 0 71.47 142.94 71.47 10 'crystal symmetry operation' 30_456 z-1/2,-x+1/2,-y+1 0 0 1 -1 0 0 0 -1 0 -71.47 71.47 142.94 11 'crystal symmetry operation' 57_455 y-1/2,z,x+1/2 0 1 0 0 0 1 1 0 0 -71.47 0 71.47 12 'crystal symmetry operation' 75_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 142.94 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 C NA NA . A NA 1065 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc2 A OD2 ASP 41 A ASP 41 8_556 I NA NA . A NA 1071 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc3 B O2' RBF . A RBF 1064 1_555 D NA NA . A NA 1066 55_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.997 ? metalc ? metalc4 B O3' RBF . A RBF 1064 1_555 D NA NA . A NA 1066 55_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc5 B O2' RBF . A RBF 1064 34_555 D NA NA . A NA 1066 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.997 ? metalc ? metalc6 B O3' RBF . A RBF 1064 34_555 D NA NA . A NA 1066 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc7 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2020 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc8 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2025 43_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc9 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2027 43_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc10 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2033 43_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc11 C NA NA . A NA 1065 1_555 J O HOH . A HOH 2056 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc12 E NA NA . A NA 1067 1_555 F CL CL . A CL 1068 11_465 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc13 E NA NA . A NA 1067 1_555 F CL CL . A CL 1068 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc14 E NA NA . A NA 1067 1_555 F CL CL . A CL 1068 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc15 E NA NA . A NA 1067 1_555 G CL CL . A CL 1069 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc16 E NA NA . A NA 1067 1_555 G CL CL . A CL 1069 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc17 E NA NA . A NA 1067 1_555 G CL CL . A CL 1069 11_465 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc18 E NA NA . A NA 1067 1_555 J O HOH . A HOH 2065 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc19 E NA NA . A NA 1067 1_555 J O HOH . A HOH 2065 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc20 E NA NA . A NA 1067 1_555 J O HOH . A HOH 2065 11_465 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc21 I NA NA . A NA 1071 1_555 J O HOH . A HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? # _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 2VX9 _atom_sites.fract_transf_matrix[1][1] 0.006996 _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] 0.006996 _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] 0.006996 _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 RBF A 1 1064 1064 RBF RBF . C 3 NA A 1 1065 1065 NA NA . D 3 NA A 1 1066 1066 NA NA . E 3 NA A 1 1067 1067 NA NA . F 4 CL A 1 1068 1068 CL CL . G 4 CL A 1 1069 1069 CL CL . H 4 CL A 1 1070 1070 CL CL . I 3 NA A 1 1071 1071 NA NA . J 5 HOH A 1 2001 2001 HOH HOH . J 5 HOH A 2 2002 2002 HOH HOH . J 5 HOH A 3 2003 2003 HOH HOH . J 5 HOH A 4 2004 2004 HOH HOH . J 5 HOH A 5 2005 2005 HOH HOH . J 5 HOH A 6 2006 2006 HOH HOH . J 5 HOH A 7 2007 2007 HOH HOH . J 5 HOH A 8 2008 2008 HOH HOH . J 5 HOH A 9 2009 2009 HOH HOH . J 5 HOH A 10 2010 2010 HOH HOH . J 5 HOH A 11 2011 2011 HOH HOH . J 5 HOH A 12 2012 2012 HOH HOH . J 5 HOH A 13 2013 2013 HOH HOH . J 5 HOH A 14 2014 2014 HOH HOH . J 5 HOH A 15 2015 2015 HOH HOH . J 5 HOH A 16 2016 2016 HOH HOH . J 5 HOH A 17 2017 2017 HOH HOH . J 5 HOH A 18 2018 2018 HOH HOH . J 5 HOH A 19 2019 2019 HOH HOH . J 5 HOH A 20 2020 2020 HOH HOH . J 5 HOH A 21 2021 2021 HOH HOH . J 5 HOH A 22 2022 2022 HOH HOH . J 5 HOH A 23 2023 2023 HOH HOH . J 5 HOH A 24 2024 2024 HOH HOH . J 5 HOH A 25 2025 2025 HOH HOH . J 5 HOH A 26 2026 2026 HOH HOH . J 5 HOH A 27 2027 2027 HOH HOH . J 5 HOH A 28 2028 2028 HOH HOH . J 5 HOH A 29 2029 2029 HOH HOH . J 5 HOH A 30 2030 2030 HOH HOH . J 5 HOH A 31 2031 2031 HOH HOH . J 5 HOH A 32 2032 2032 HOH HOH . J 5 HOH A 33 2033 2033 HOH HOH . J 5 HOH A 34 2034 2034 HOH HOH . J 5 HOH A 35 2035 2035 HOH HOH . J 5 HOH A 36 2036 2036 HOH HOH . J 5 HOH A 37 2037 2037 HOH HOH . J 5 HOH A 38 2038 2038 HOH HOH . J 5 HOH A 39 2039 2039 HOH HOH . J 5 HOH A 40 2040 2040 HOH HOH . J 5 HOH A 41 2041 2041 HOH HOH . J 5 HOH A 42 2042 2042 HOH HOH . J 5 HOH A 43 2043 2043 HOH HOH . J 5 HOH A 44 2044 2044 HOH HOH . J 5 HOH A 45 2045 2045 HOH HOH . J 5 HOH A 46 2046 2046 HOH HOH . J 5 HOH A 47 2047 2047 HOH HOH . J 5 HOH A 48 2048 2048 HOH HOH . J 5 HOH A 49 2049 2049 HOH HOH . J 5 HOH A 50 2050 2050 HOH HOH . J 5 HOH A 51 2051 2051 HOH HOH . J 5 HOH A 52 2052 2052 HOH HOH . J 5 HOH A 53 2053 2053 HOH HOH . J 5 HOH A 54 2054 2054 HOH HOH . J 5 HOH A 55 2055 2055 HOH HOH . J 5 HOH A 56 2056 2056 HOH HOH . J 5 HOH A 57 2057 2057 HOH HOH . J 5 HOH A 58 2058 2058 HOH HOH . J 5 HOH A 59 2059 2059 HOH HOH . J 5 HOH A 60 2060 2060 HOH HOH . J 5 HOH A 61 2061 2061 HOH HOH . J 5 HOH A 62 2062 2062 HOH HOH . J 5 HOH A 63 2063 2063 HOH HOH . J 5 HOH A 64 2064 2064 HOH HOH . J 5 HOH A 65 2065 2065 HOH HOH . J 5 HOH A 66 2066 2066 HOH HOH . J 5 HOH A 67 2067 2067 HOH HOH . J 5 HOH A 68 2068 2068 HOH HOH . J 5 HOH A 69 2069 2069 HOH HOH . J 5 HOH A 70 2070 2070 HOH HOH . J 5 HOH A 71 2071 2071 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 . . . B 2 22.959 74.426 71.319 1 27.26 ? N1 RBF 1064 A 1 HETATM 2 C C2 RBF . . . B 2 22.531 75.516 71.986 1 26.66 ? C2 RBF 1064 A 1 HETATM 3 O O2 RBF . . . B 2 23.411 76.287 72.487 1 29.49 ? O2 RBF 1064 A 1 HETATM 4 N N3 RBF . . . B 2 21.218 75.792 72.117 1 25.27 ? N3 RBF 1064 A 1 HETATM 5 C C4 RBF . . . B 2 20.233 75.032 71.649 1 24.97 ? C4 RBF 1064 A 1 HETATM 6 O O4 RBF . . . B 2 19.016 75.342 71.807 1 25.79 ? O4 RBF 1064 A 1 HETATM 7 C C4A RBF . . . B 2 20.613 73.816 70.895 1 25.46 ? C4A RBF 1064 A 1 HETATM 8 N N5 RBF . . . B 2 19.69 72.998 70.362 1 27.44 ? N5 RBF 1064 A 1 HETATM 9 C C5A RBF . . . B 2 20.107 71.895 69.692 1 25.53 ? C5A RBF 1064 A 1 HETATM 10 C C6 RBF . . . B 2 19.15 71.047 69.165 1 26.98 ? C6 RBF 1064 A 1 HETATM 11 C C7 RBF . . . B 2 19.549 69.914 68.452 1 24.58 ? C7 RBF 1064 A 1 HETATM 12 C C7M RBF . . . B 2 18.476 69.022 67.866 1 26.27 ? C7M RBF 1064 A 1 HETATM 13 C C8 RBF . . . B 2 20.993 69.603 68.29 1 24.91 ? C8 RBF 1064 A 1 HETATM 14 C C8M RBF . . . B 2 21.409 68.362 67.535 1 26.61 ? C8M RBF 1064 A 1 HETATM 15 C C9 RBF . . . B 2 21.963 70.439 68.836 1 26.68 ? C9 RBF 1064 A 1 HETATM 16 C C9A RBF . . . B 2 21.548 71.577 69.535 1 26.2 ? C9A RBF 1064 A 1 HETATM 17 N N10 RBF . . . B 2 22.518 72.447 70.086 1 29.16 ? N10 RBF 1064 A 1 HETATM 18 C C10 RBF . . . B 2 22.061 73.564 70.765 1 25.84 ? C10 RBF 1064 A 1 HETATM 19 C C1' RBF . . . B 2 23.975 72.21 69.972 1 30.8 ? C1' RBF 1064 A 1 HETATM 20 C C2' RBF . . . B 2 24.665 73.147 68.976 1 34.73 ? C2' RBF 1064 A 1 HETATM 21 O O2' RBF . . . B 2 24.368 72.677 67.654 1 32.25 ? O2' RBF 1064 A 1 HETATM 22 C C3' RBF . . . B 2 26.19 73.192 69.166 1 38.24 ? C3' RBF 1064 A 1 HETATM 23 O O3' RBF . . . B 2 26.694 71.854 69.304 1 41.72 ? O3' RBF 1064 A 1 HETATM 24 C C4' RBF . . . B 2 26.644 74.004 70.385 1 40.8 ? C4' RBF 1064 A 1 HETATM 25 O O4' RBF . . . B 2 26.173 73.391 71.588 1 43.5 ? O4' RBF 1064 A 1 HETATM 26 C C5' RBF . . . B 2 26.194 75.47 70.304 1 42.13 ? C5' RBF 1064 A 1 HETATM 27 O O5' RBF . . . B 2 26.667 75.98 69.052 1 45.04 ? O5' RBF 1064 A 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #