data_4B2K
#
_model_server_result.job_id            hpxfrbjSpYWTgsF0wc--ww 
_model_server_result.datetime_utc      '2024-11-24 17:20:43' 
_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          4b2k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1067}' 
#
_entry.id    4B2K 
#
_exptl.entry_id    4B2K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              376.364 
_entity.id                          6 
_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            4B2K 
_cell.length_a            142.301 
_cell.length_b            142.301 
_cell.length_c            142.301 
_cell.Z_PDB               96 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4B2K 
_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' 52_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
5 'crystal symmetry operation' 54_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 
6 'crystal symmetry operation' 59_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 
7 'crystal symmetry operation' 75_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
8 'crystal symmetry operation' 80_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 
9 'crystal symmetry operation' 82_555 -y,z,-x 0 -1 0 0 0 1 -1 0 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' 26_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
12 'crystal symmetry operation' 31_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             G 
_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
covale ? covale1 A C VAL 35 A VAL 35 1_555 A N 4IN 36 A 4IN 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? 
covale ? covale2 A C 4IN 36 A 4IN 36 1_555 A N ALA 37 A ALA 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? 
metalc ? metalc1 A OE2 GLU 14 A GLU 14 1_555 B MG MG . A MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
metalc ? metalc2 A OD2 ASP 41 A ASP 41 80_555 C MG MG . A MG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? 
metalc ? metalc3 B MG MG . A MG 101 1_555 H O HOH . A HOH 2025 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
metalc ? metalc4 B MG MG . A MG 101 1_555 H O HOH . A HOH 2026 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc5 B MG MG . A MG 101 1_555 H O HOH . A HOH 2032 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc6 B MG MG . A MG 101 1_555 H O HOH . A HOH 2083 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc7 C MG MG . A MG 102 1_555 H O HOH . A HOH 2090 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc8 C MG MG . A MG 102 1_555 H O HOH . A HOH 2091 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc9 C MG MG . A MG 102 1_555 H O HOH . A HOH 2092 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? 
metalc ? metalc10 C MG MG . A MG 102 1_555 H O HOH . A HOH 2093 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc11 D NA NA . A NA 103 1_555 E CL CL . A CL 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? 
metalc ? metalc12 D NA NA . A NA 103 1_555 E CL CL . A CL 104 59_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? 
metalc ? metalc13 D NA NA . A NA 103 1_555 E CL CL . A CL 104 80_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? 
metalc ? metalc14 D NA NA . A NA 103 1_555 H O HOH . A HOH 2094 80_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc15 D NA NA . A NA 103 1_555 H O HOH . A HOH 2094 59_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? 
metalc ? metalc16 D NA NA . A NA 103 1_555 H O HOH . A HOH 2094 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc17 D NA NA . A NA 103 1_555 H O HOH . A HOH 2095 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc18 D NA NA . A NA 103 1_555 H O HOH . A HOH 2095 59_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc19 D NA NA . A NA 103 1_555 H O HOH . A HOH 2095 80_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
#
_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 277 n n 
N1 C10 RBF doub 278 n n 
C2 O2 RBF doub 279 n n 
C2 N3 RBF sing 280 n n 
N3 C4 RBF sing 281 n n 
N3 HN3 RBF sing 282 n n 
C4 O4 RBF doub 283 n n 
C4 C4A RBF sing 284 n n 
C4A N5 RBF doub 285 n n 
C4A C10 RBF sing 286 n n 
N5 C5A RBF sing 287 n n 
C5A C6 RBF doub 288 n y 
C5A C9A RBF sing 289 n y 
C6 C7 RBF sing 290 n y 
C6 HC6 RBF sing 291 n n 
C7 C7M RBF sing 292 n n 
C7 C8 RBF doub 293 n y 
C7M HC71 RBF sing 294 n n 
C7M HC72 RBF sing 295 n n 
C7M HC73 RBF sing 296 n n 
C8 C8M RBF sing 297 n n 
C8 C9 RBF sing 298 n y 
C8M HC81 RBF sing 299 n n 
C8M HC82 RBF sing 300 n n 
C8M HC83 RBF sing 301 n n 
C9 C9A RBF doub 302 n y 
C9 HC9 RBF sing 303 n n 
C9A N10 RBF sing 304 n n 
N10 C10 RBF sing 305 n n 
N10 C1' RBF sing 306 n n 
C1' C2' RBF sing 307 n n 
C1' HC11 RBF sing 308 n n 
C1' HC12 RBF sing 309 n n 
C2' O2' RBF sing 310 n n 
C2' C3' RBF sing 311 n n 
C2' HC2' RBF sing 312 n n 
O2' HO2' RBF sing 313 n n 
C3' O3' RBF sing 314 n n 
C3' C4' RBF sing 315 n n 
C3' HC3' RBF sing 316 n n 
O3' HO3' RBF sing 317 n n 
C4' O4' RBF sing 318 n n 
C4' C5' RBF sing 319 n n 
C4' HC4' RBF sing 320 n n 
O4' HO4' RBF sing 321 n n 
C5' O5' RBF sing 322 n n 
C5' HC51 RBF sing 323 n n 
C5' HC52 RBF sing 324 n n 
O5' HO5' RBF sing 325 n n 
#
_atom_sites.entry_id                     4B2K 
_atom_sites.fract_transf_matrix[1][1]    0.007027 
_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]    0.007027 
_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]    0.007027 
_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 1 101 101 MG MG . 
C 2 MG A 1 102 102 MG MG . 
D 3 NA A 1 103 103 NA NA . 
E 4 CL A 1 104 104 CL CL . 
F 5 SO4 A 1 300 300 SO4 SO4 . 
G 6 RBF A 1 1067 1067 RBF RBF . 
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 . 
H 7 HOH A 82 2082 2082 HOH HOH . 
H 7 HOH A 83 2083 2083 HOH HOH . 
H 7 HOH A 84 2084 2084 HOH HOH . 
H 7 HOH A 85 2085 2085 HOH HOH . 
H 7 HOH A 86 2086 2086 HOH HOH . 
H 7 HOH A 87 2087 2087 HOH HOH . 
H 7 HOH A 88 2088 2088 HOH HOH . 
H 7 HOH A 89 2089 2089 HOH HOH . 
H 7 HOH A 90 2090 2090 HOH HOH . 
H 7 HOH A 91 2091 2091 HOH HOH . 
H 7 HOH A 92 2092 2092 HOH HOH . 
H 7 HOH A 93 2093 2093 HOH HOH . 
H 7 HOH A 94 2094 2094 HOH HOH . 
H 7 HOH A 95 2095 2095 HOH HOH . 
H 7 HOH A 96 2096 2096 HOH HOH . 
H 7 HOH A 97 2097 2097 HOH HOH . 
H 7 HOH A 98 2098 2098 HOH HOH . 
H 7 HOH A 99 2099 2099 HOH HOH . 
H 7 HOH A 100 2100 2100 HOH HOH . 
H 7 HOH A 101 2101 2101 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 . . . G 6 0.246 22.499 -2.686 1 49.16 ? N1 RBF 1067 A 1 
HETATM 2 C C2 RBF . . . G 6 -0.455 22.238 -3.836 1 41.34 ? C2 RBF 1067 A 1 
HETATM 3 O O2 RBF . . . G 6 -0.943 23.158 -4.566 1 53.91 ? O2 RBF 1067 A 1 
HETATM 4 N N3 RBF . . . G 6 -0.556 20.813 -4.14 1 37.81 ? N3 RBF 1067 A 1 
HETATM 5 C C4 RBF . . . G 6 -0.131 19.742 -3.376 1 40.95 ? C4 RBF 1067 A 1 
HETATM 6 O O4 RBF . . . G 6 -0.381 18.563 -3.803 1 41.57 ? O4 RBF 1067 A 1 
HETATM 7 C C4A RBF . . . G 6 0.607 20.008 -2.184 1 36.96 ? C4A RBF 1067 A 1 
HETATM 8 N N5 RBF . . . G 6 1.093 18.947 -1.438 1 42 ? N5 RBF 1067 A 1 
HETATM 9 C C5A RBF . . . G 6 1.811 19.346 -0.365 1 39.34 ? C5A RBF 1067 A 1 
HETATM 10 C C6 RBF . . . G 6 2.385 18.368 0.439 1 46.21 ? C6 RBF 1067 A 1 
HETATM 11 C C7 RBF . . . G 6 3.15 18.832 1.535 1 37.64 ? C7 RBF 1067 A 1 
HETATM 12 C C7M RBF . . . G 6 3.702 17.805 2.332 1 43.39 ? C7M RBF 1067 A 1 
HETATM 13 C C8 RBF . . . G 6 3.295 20.188 1.894 1 39.45 ? C8 RBF 1067 A 1 
HETATM 14 C C8M RBF . . . G 6 4.048 20.58 3.026 1 40.7 ? C8M RBF 1067 A 1 
HETATM 15 C C9 RBF . . . G 6 2.704 21.196 1.148 1 43.29 ? C9 RBF 1067 A 1 
HETATM 16 C C9A RBF . . . G 6 2.01 20.729 -0.009 1 39.4 ? C9A RBF 1067 A 1 
HETATM 17 N N10 RBF . . . G 6 1.469 21.708 -0.737 1 50.97 ? N10 RBF 1067 A 1 
HETATM 18 C C10 RBF . . . G 6 0.799 21.37 -1.829 1 41.51 ? C10 RBF 1067 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           18 
#