data_2CC8
#
_model_server_result.job_id            RvWLB6oNup79jsU15_Gshw 
_model_server_result.datetime_utc      '2024-11-24 08:53:55' 
_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          2cc8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1067}' 
#
_entry.id    2CC8 
#
_exptl.entry_id    2CC8 
_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            2CC8 
_cell.length_a            142.35 
_cell.length_b            142.35 
_cell.length_c            142.35 
_cell.Z_PDB               96 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2CC8 
_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 
_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' 80_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 
5 'crystal symmetry operation' 59_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 
6 'crystal symmetry operation' 82_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' 75_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
9 'crystal symmetry operation' 54_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 
10 'crystal symmetry operation' 36_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 
11 'crystal symmetry operation' 31_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 
12 'crystal symmetry operation' 26_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc2 A OD2 ASP 41 A ASP 41 80_555 B MG MG . A MG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc3 B MG MG . A MG 102 1_555 H O HOH . A HOH 2043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? 
metalc ? metalc4 B MG MG . A MG 102 1_555 H O HOH . A HOH 2044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? 
metalc ? metalc5 B MG MG . A MG 102 1_555 H O HOH . A HOH 2045 75_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? 
metalc ? metalc6 B MG MG . A MG 102 1_555 H O HOH . A HOH 2071 80_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? 
metalc ? metalc7 C NA NA . A NA 103 1_555 D CL CL . A CL 104 80_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? 
metalc ? metalc8 C NA NA . A NA 103 1_555 D CL CL . A CL 104 59_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? 
metalc ? metalc9 C NA NA . A NA 103 1_555 D CL CL . A CL 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? 
metalc ? metalc10 C NA NA . A NA 103 1_555 H O HOH . A HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? 
metalc ? metalc11 C NA NA . A NA 103 1_555 H O HOH . A HOH 2003 59_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? 
metalc ? metalc12 C NA NA . A NA 103 1_555 H O HOH . A HOH 2003 80_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? 
metalc ? metalc13 C NA NA . A NA 103 1_555 H O HOH . A HOH 2074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc14 C NA NA . A NA 103 1_555 H O HOH . A HOH 2074 80_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc15 C NA NA . A NA 103 1_555 H O HOH . A HOH 2074 59_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc16 E MG MG . A MG 1066 1_555 H O HOH . A HOH 2020 24_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc17 E MG MG . A MG 1066 1_555 H O HOH . A HOH 2022 24_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc18 E MG MG . A MG 1066 1_555 H O HOH . A HOH 2028 24_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc19 E MG MG . A MG 1066 1_555 H O HOH . A HOH 2061 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
#
_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                     2CC8 
_atom_sites.fract_transf_matrix[1][1]    0.007025 
_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]    0.007025 
_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]    0.007025 
_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 1 103 103 NA NA . 
D 4 CL A 1 104 104 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 . 
#
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 0.187 22.686 -2.886 1 25.88 ? N1 RBF 1067 A 1 
HETATM 2 C C2 RBF . . . F 5 -0.506 22.318 -3.978 1 26.05 ? C2 RBF 1067 A 1 
HETATM 3 O O2 RBF . . . F 5 -0.969 23.227 -4.682 1 27.25 ? O2 RBF 1067 A 1 
HETATM 4 N N3 RBF . . . F 5 -0.688 21.035 -4.342 1 25.02 ? N3 RBF 1067 A 1 
HETATM 5 C C4 RBF . . . F 5 -0.25 20.026 -3.61 1 23.63 ? C4 RBF 1067 A 1 
HETATM 6 O O4 RBF . . . F 5 -0.436 18.854 -3.956 1 27.16 ? O4 RBF 1067 A 1 
HETATM 7 C C4A RBF . . . F 5 0.497 20.323 -2.368 1 25.91 ? C4A RBF 1067 A 1 
HETATM 8 N N5 RBF . . . F 5 1.005 19.349 -1.578 1 27.27 ? N5 RBF 1067 A 1 
HETATM 9 C C5A RBF . . . F 5 1.7 19.678 -0.462 1 24.84 ? C5A RBF 1067 A 1 
HETATM 10 C C6 RBF . . . F 5 2.186 18.671 0.333 1 23.83 ? C6 RBF 1067 A 1 
HETATM 11 C C7 RBF . . . F 5 2.922 18.959 1.483 1 23.24 ? C7 RBF 1067 A 1 
HETATM 12 C C7M RBF . . . F 5 3.439 17.805 2.306 1 23.17 ? C7M RBF 1067 A 1 
HETATM 13 C C8 RBF . . . F 5 3.159 20.367 1.871 1 21.03 ? C8 RBF 1067 A 1 
HETATM 14 C C8M RBF . . . F 5 3.94 20.696 3.125 1 23.77 ? C8M RBF 1067 A 1 
HETATM 15 C C9 RBF . . . F 5 2.655 21.398 1.089 1 21.52 ? C9 RBF 1067 A 1 
HETATM 16 C C9A RBF . . . F 5 1.924 21.086 -0.081 1 24.18 ? C9A RBF 1067 A 1 
HETATM 17 N N10 RBF . . . F 5 1.435 22.102 -0.929 1 28.09 ? N10 RBF 1067 A 1 
HETATM 18 C C10 RBF . . . F 5 0.712 21.738 -2.063 1 27.41 ? C10 RBF 1067 A 1 
HETATM 19 C C1' RBF . . . F 5 1.567 23.545 -0.601 1 28.72 ? C1' RBF 1067 A 1 
HETATM 20 C C2' RBF . . . F 5 2.554 24.378 -1.403 1 31.42 ? C2' RBF 1067 A 1 
HETATM 21 O O2' RBF . . . F 5 3.813 24.11 -0.812 1 28.02 ? O2' RBF 1067 A 1 
HETATM 22 C C3' RBF . . . F 5 2.157 25.868 -1.363 1 36.43 ? C3' RBF 1067 A 1 
HETATM 23 O O3' RBF . . . F 5 2.175 26.354 -0.017 1 37.87 ? O3' RBF 1067 A 1 
HETATM 24 C C4' RBF . . . F 5 0.773 26.069 -2.048 1 40.33 ? C4' RBF 1067 A 1 
HETATM 25 O O4' RBF . . . F 5 0.869 25.622 -3.393 1 44.58 ? O4' RBF 1067 A 1 
HETATM 26 C C5' RBF . . . F 5 0.251 27.503 -2.11 1 46.76 ? C5' RBF 1067 A 1 
HETATM 27 O O5' RBF . . . F 5 -1.053 27.509 -2.735 1 51.43 ? O5' RBF 1067 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#