data_3GSB
#
_model_server_result.job_id            jbAZqLSFN16mzTQkU9h4_A 
_model_server_result.datetime_utc      '2024-11-28 21:29:37' 
_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          3gsb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":600}' 
#
_entry.id    3GSB 
#
_exptl.entry_id    3GSB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              248.173 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" 
_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         90 
_cell.entry_id            3GSB 
_cell.length_a            68.6 
_cell.length_b            108.6 
_cell.length_c            123.5 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3GSB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_chem_comp.formula           'C8 H13 N2 O5 P' 
_chem_comp.formula_weight    248.173 
_chem_comp.id                PMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "PYRIDOXAMINE-5'-PHOSPHATE" 
#
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 PMP doub 277 n y 
N1 C6 PMP sing 278 n y 
C2 C2A PMP sing 279 n n 
C2 C3 PMP sing 280 n y 
C2A H2A1 PMP sing 281 n n 
C2A H2A2 PMP sing 282 n n 
C2A H2A3 PMP sing 283 n n 
C3 O3 PMP sing 284 n n 
C3 C4 PMP doub 285 n y 
O3 HO3 PMP sing 286 n n 
C4 C4A PMP sing 287 n n 
C4 C5 PMP sing 288 n y 
C4A N4A PMP sing 289 n n 
C4A H4A1 PMP sing 290 n n 
C4A H4A2 PMP sing 291 n n 
N4A HNA1 PMP sing 292 n n 
N4A HNA2 PMP sing 293 n n 
C5 C6 PMP doub 294 n y 
C5 C5A PMP sing 295 n n 
C6 H6 PMP sing 296 n n 
C5A O4P PMP sing 297 n n 
C5A H5A1 PMP sing 298 n n 
C5A H5A2 PMP sing 299 n n 
O4P P PMP sing 300 n n 
P O1P PMP doub 301 n n 
P O2P PMP sing 302 n n 
P O3P PMP sing 303 n n 
O2P HOP2 PMP sing 304 n n 
O3P HOP3 PMP sing 305 n n 
#
_atom_sites.entry_id                     3GSB 
_atom_sites.fract_transf_matrix[1][1]    0.014577 
_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]    0.009208 
_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]    0.008097 
_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 PMP A 1 600 600 PMP PMP . 
D 3 GAB A 1 500 500 GAB GAB . 
E 2 PMP B 1 601 600 PMP PMP . 
F 4 HOH A 1 2002 2002 HOH HOH . 
F 4 HOH A 2 2003 2003 HOH HOH . 
F 4 HOH A 3 2005 2005 HOH HOH . 
F 4 HOH A 4 2007 2007 HOH HOH . 
F 4 HOH A 5 2008 2008 HOH HOH . 
F 4 HOH A 6 2009 2009 HOH HOH . 
F 4 HOH A 7 2011 2011 HOH HOH . 
F 4 HOH A 8 2012 2012 HOH HOH . 
F 4 HOH A 9 2013 2013 HOH HOH . 
F 4 HOH A 10 2015 2015 HOH HOH . 
F 4 HOH A 11 2017 2017 HOH HOH . 
F 4 HOH A 12 2018 2018 HOH HOH . 
F 4 HOH A 13 2021 2021 HOH HOH . 
F 4 HOH A 14 2022 2022 HOH HOH . 
F 4 HOH A 15 2031 2031 HOH HOH . 
F 4 HOH A 16 2032 2032 HOH HOH . 
F 4 HOH A 17 2035 2035 HOH HOH . 
F 4 HOH A 18 2036 2036 HOH HOH . 
F 4 HOH A 19 2037 2037 HOH HOH . 
F 4 HOH A 20 2038 2038 HOH HOH . 
F 4 HOH A 21 2040 2040 HOH HOH . 
F 4 HOH A 22 2043 2043 HOH HOH . 
F 4 HOH A 23 2044 2044 HOH HOH . 
F 4 HOH A 24 2059 2059 HOH HOH . 
F 4 HOH A 25 2073 2073 HOH HOH . 
F 4 HOH A 26 2078 2078 HOH HOH . 
F 4 HOH A 27 2082 2082 HOH HOH . 
F 4 HOH A 28 2085 2085 HOH HOH . 
F 4 HOH A 29 2087 2087 HOH HOH . 
F 4 HOH A 30 2089 2089 HOH HOH . 
F 4 HOH A 31 2090 2090 HOH HOH . 
F 4 HOH A 32 2092 2092 HOH HOH . 
F 4 HOH A 33 2093 2093 HOH HOH . 
F 4 HOH A 34 2110 2110 HOH HOH . 
F 4 HOH A 35 2111 2111 HOH HOH . 
F 4 HOH A 36 2119 2119 HOH HOH . 
F 4 HOH A 37 2120 2120 HOH HOH . 
F 4 HOH A 38 2122 2122 HOH HOH . 
F 4 HOH A 39 2126 2126 HOH HOH . 
F 4 HOH A 40 2127 2127 HOH HOH . 
F 4 HOH A 41 2136 2136 HOH HOH . 
F 4 HOH A 42 2137 2137 HOH HOH . 
F 4 HOH A 43 2140 2140 HOH HOH . 
F 4 HOH A 44 2147 2147 HOH HOH . 
F 4 HOH A 45 2149 2149 HOH HOH . 
F 4 HOH A 46 2157 2157 HOH HOH . 
F 4 HOH A 47 2159 2159 HOH HOH . 
F 4 HOH A 48 2160 2160 HOH HOH . 
F 4 HOH A 49 2161 2161 HOH HOH . 
F 4 HOH A 50 2162 2162 HOH HOH . 
F 4 HOH A 51 2164 2164 HOH HOH . 
F 4 HOH A 52 2166 2166 HOH HOH . 
F 4 HOH A 53 2170 2170 HOH HOH . 
F 4 HOH A 54 2171 2171 HOH HOH . 
F 4 HOH A 55 2188 2188 HOH HOH . 
F 4 HOH A 56 2189 2189 HOH HOH . 
F 4 HOH A 57 2192 2192 HOH HOH . 
F 4 HOH A 58 2205 2205 HOH HOH . 
F 4 HOH A 59 2206 2206 HOH HOH . 
F 4 HOH A 60 2208 2208 HOH HOH . 
F 4 HOH A 61 2209 2209 HOH HOH . 
F 4 HOH A 62 2211 2211 HOH HOH . 
F 4 HOH A 63 2216 2216 HOH HOH . 
F 4 HOH A 64 2217 2217 HOH HOH . 
F 4 HOH A 65 2220 2220 HOH HOH . 
F 4 HOH A 66 2240 2240 HOH HOH . 
F 4 HOH A 67 2246 2246 HOH HOH . 
F 4 HOH A 68 2247 2247 HOH HOH . 
F 4 HOH A 69 2248 2248 HOH HOH . 
F 4 HOH A 70 2255 2255 HOH HOH . 
F 4 HOH A 71 2258 2258 HOH HOH . 
F 4 HOH A 72 2284 2284 HOH HOH . 
F 4 HOH A 73 2296 2296 HOH HOH . 
F 4 HOH A 74 2300 2300 HOH HOH . 
F 4 HOH A 75 2320 2320 HOH HOH . 
F 4 HOH A 76 2327 2327 HOH HOH . 
F 4 HOH A 77 2338 2338 HOH HOH . 
F 4 HOH A 78 2339 2339 HOH HOH . 
F 4 HOH A 79 2341 2341 HOH HOH . 
F 4 HOH A 80 2342 2342 HOH HOH . 
F 4 HOH A 81 2343 2343 HOH HOH . 
G 4 HOH B 1 2001 2001 HOH HOH . 
G 4 HOH B 2 2006 2006 HOH HOH . 
G 4 HOH B 3 2010 2010 HOH HOH . 
G 4 HOH B 4 2014 2014 HOH HOH . 
G 4 HOH B 5 2016 2016 HOH HOH . 
G 4 HOH B 6 2019 2019 HOH HOH . 
G 4 HOH B 7 2020 2020 HOH HOH . 
G 4 HOH B 8 2024 2024 HOH HOH . 
G 4 HOH B 9 2028 2028 HOH HOH . 
G 4 HOH B 10 2029 2029 HOH HOH . 
G 4 HOH B 11 2033 2033 HOH HOH . 
G 4 HOH B 12 2048 2048 HOH HOH . 
G 4 HOH B 13 2049 2049 HOH HOH . 
G 4 HOH B 14 2050 2050 HOH HOH . 
G 4 HOH B 15 2052 2052 HOH HOH . 
G 4 HOH B 16 2057 2057 HOH HOH . 
G 4 HOH B 17 2064 2064 HOH HOH . 
G 4 HOH B 18 2071 2071 HOH HOH . 
G 4 HOH B 19 2079 2079 HOH HOH . 
G 4 HOH B 20 2081 2081 HOH HOH . 
G 4 HOH B 21 2083 2083 HOH HOH . 
G 4 HOH B 22 2084 2084 HOH HOH . 
G 4 HOH B 23 2091 2091 HOH HOH . 
G 4 HOH B 24 2095 2095 HOH HOH . 
G 4 HOH B 25 2098 2098 HOH HOH . 
G 4 HOH B 26 2100 2100 HOH HOH . 
G 4 HOH B 27 2101 2101 HOH HOH . 
G 4 HOH B 28 2102 2102 HOH HOH . 
G 4 HOH B 29 2104 2104 HOH HOH . 
G 4 HOH B 30 2105 2105 HOH HOH . 
G 4 HOH B 31 2108 2108 HOH HOH . 
G 4 HOH B 32 2109 2109 HOH HOH . 
G 4 HOH B 33 2112 2112 HOH HOH . 
G 4 HOH B 34 2113 2113 HOH HOH . 
G 4 HOH B 35 2114 2114 HOH HOH . 
G 4 HOH B 36 2115 2115 HOH HOH . 
G 4 HOH B 37 2116 2116 HOH HOH . 
G 4 HOH B 38 2117 2117 HOH HOH . 
G 4 HOH B 39 2118 2118 HOH HOH . 
G 4 HOH B 40 2121 2121 HOH HOH . 
G 4 HOH B 41 2123 2123 HOH HOH . 
G 4 HOH B 42 2124 2124 HOH HOH . 
G 4 HOH B 43 2125 2125 HOH HOH . 
G 4 HOH B 44 2128 2128 HOH HOH . 
G 4 HOH B 45 2130 2130 HOH HOH . 
G 4 HOH B 46 2134 2134 HOH HOH . 
G 4 HOH B 47 2141 2141 HOH HOH . 
G 4 HOH B 48 2156 2156 HOH HOH . 
G 4 HOH B 49 2158 2158 HOH HOH . 
G 4 HOH B 50 2163 2163 HOH HOH . 
G 4 HOH B 51 2165 2165 HOH HOH . 
G 4 HOH B 52 2167 2167 HOH HOH . 
G 4 HOH B 53 2168 2168 HOH HOH . 
G 4 HOH B 54 2174 2174 HOH HOH . 
G 4 HOH B 55 2176 2176 HOH HOH . 
G 4 HOH B 56 2177 2177 HOH HOH . 
G 4 HOH B 57 2180 2180 HOH HOH . 
G 4 HOH B 58 2193 2193 HOH HOH . 
G 4 HOH B 59 2198 2198 HOH HOH . 
G 4 HOH B 60 2204 2204 HOH HOH . 
G 4 HOH B 61 2212 2212 HOH HOH . 
G 4 HOH B 62 2213 2213 HOH HOH . 
G 4 HOH B 63 2218 2218 HOH HOH . 
G 4 HOH B 64 2219 2219 HOH HOH . 
G 4 HOH B 65 2221 2221 HOH HOH . 
G 4 HOH B 66 2223 2223 HOH HOH . 
G 4 HOH B 67 2249 2249 HOH HOH . 
G 4 HOH B 68 2251 2251 HOH HOH . 
G 4 HOH B 69 2263 2263 HOH HOH . 
G 4 HOH B 70 2269 2269 HOH HOH . 
G 4 HOH B 71 2285 2285 HOH HOH . 
G 4 HOH B 72 2297 2297 HOH HOH . 
G 4 HOH B 73 2321 2321 HOH HOH . 
G 4 HOH B 74 2336 2336 HOH HOH . 
G 4 HOH B 75 2337 2337 HOH HOH . 
G 4 HOH B 76 2340 2340 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 PMP . . . C 2 4.454 16.62 -34.442 1 22.5 ? N1 PMP 600 A 1 
HETATM 2 C C2 PMP . . . C 2 4.476 17.598 -35.447 1 27.25 ? C2 PMP 600 A 1 
HETATM 3 C C2A PMP . . . C 2 3.816 17.311 -36.834 1 9.79 ? C2A PMP 600 A 1 
HETATM 4 C C3 PMP . . . C 2 5.125 18.815 -35.222 1 18.51 ? C3 PMP 600 A 1 
HETATM 5 O O3 PMP . . . C 2 4.896 19.821 -36.068 1 9.95 ? O3 PMP 600 A 1 
HETATM 6 C C4 PMP . . . C 2 5.857 19.01 -34.047 1 34.56 ? C4 PMP 600 A 1 
HETATM 7 C C4A PMP . . . C 2 6.569 20.327 -33.829 1 41.75 ? C4A PMP 600 A 1 
HETATM 8 N N4A PMP . . . C 2 6.47 21.487 -34.696 1 45.99 ? N4A PMP 600 A 1 
HETATM 9 C C5 PMP . . . C 2 5.887 17.956 -33.105 1 25.94 ? C5 PMP 600 A 1 
HETATM 10 C C6 PMP . . . C 2 5.163 16.809 -33.286 1 20.77 ? C6 PMP 600 A 1 
HETATM 11 C C5A PMP . . . C 2 6.773 18.044 -31.905 1 31.78 ? C5A PMP 600 A 1 
HETATM 12 O O4P PMP . . . C 2 5.962 18.096 -30.716 1 45.63 ? O4P PMP 600 A 1 
HETATM 13 P P PMP . . . C 2 6.288 19.136 -29.553 1 32.54 ? P PMP 600 A 1 
HETATM 14 O O1P PMP . . . C 2 4.967 19.522 -29.011 1 27.24 ? O1P PMP 600 A 1 
HETATM 15 O O2P PMP . . . C 2 7.09 18.298 -28.441 1 35.51 ? O2P PMP 600 A 1 
HETATM 16 O O3P PMP . . . C 2 7.293 20.089 -30.084 1 47.7 ? O3P PMP 600 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           259 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           16 
#