data_5G28
#
_model_server_result.job_id            C64qN-RZlheFRGtPFZyP5A 
_model_server_result.datetime_utc      '2024-11-13 06:32:47' 
_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          5g28 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1268}' 
#
_entry.id    5G28 
#
_exptl.entry_id    5G28 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.436 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            RETINAL 
_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          109.85 
_cell.angle_gamma         90 
_cell.entry_id            5G28 
_cell.length_a            102.756 
_cell.length_b            49.402 
_cell.length_c            69.327 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5G28 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,K,L 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_struct_conn.conn_type_id                   covale 
_struct_conn.details                        ? 
_struct_conn.id                             covale1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            NZ 
_struct_conn.ptnr1_label_comp_id            LYS 
_struct_conn.ptnr1_label_seq_id             238 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             LYS 
_struct_conn.ptnr1_auth_seq_id              235 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            D 
_struct_conn.ptnr2_label_atom_id            C15 
_struct_conn.ptnr2_label_comp_id            RET 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             RET 
_struct_conn.ptnr2_auth_seq_id              1268 
_struct_conn.ptnr2_symmetry                 1_555 
_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                1.181 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C20 H28 O' 
_chem_comp.formula_weight    284.436 
_chem_comp.id                RET 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              RETINAL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C1 C2 RET sing 330 n n 
C1 C6 RET sing 331 n n 
C1 C16 RET sing 332 n n 
C1 C17 RET sing 333 n n 
C2 C3 RET sing 334 n n 
C2 H21 RET sing 335 n n 
C2 H22 RET sing 336 n n 
C3 C4 RET sing 337 n n 
C3 H31 RET sing 338 n n 
C3 H32 RET sing 339 n n 
C4 C5 RET sing 340 n n 
C4 H41 RET sing 341 n n 
C4 H42 RET sing 342 n n 
C5 C6 RET doub 343 n n 
C5 C18 RET sing 344 n n 
C6 C7 RET sing 345 n n 
C7 C8 RET doub 346 e n 
C7 H7 RET sing 347 n n 
C8 C9 RET sing 348 n n 
C8 H8 RET sing 349 n n 
C9 C10 RET doub 350 e n 
C9 C19 RET sing 351 n n 
C10 C11 RET sing 352 n n 
C10 H10 RET sing 353 n n 
C11 C12 RET doub 354 e n 
C11 H11 RET sing 355 n n 
C12 C13 RET sing 356 n n 
C12 H12 RET sing 357 n n 
C13 C14 RET doub 358 e n 
C13 C20 RET sing 359 n n 
C14 C15 RET sing 360 n n 
C14 H14 RET sing 361 n n 
C15 O1 RET doub 362 n n 
C15 H15 RET sing 363 n n 
C16 H161 RET sing 364 n n 
C16 H162 RET sing 365 n n 
C16 H163 RET sing 366 n n 
C17 H171 RET sing 367 n n 
C17 H172 RET sing 368 n n 
C17 H173 RET sing 369 n n 
C18 H181 RET sing 370 n n 
C18 H182 RET sing 371 n n 
C18 H183 RET sing 372 n n 
C19 H191 RET sing 373 n n 
C19 H192 RET sing 374 n n 
C19 H193 RET sing 375 n n 
C20 H201 RET sing 376 n n 
C20 H202 RET sing 377 n n 
C20 H203 RET sing 378 n n 
#
_atom_sites.entry_id                     5G28 
_atom_sites.fract_transf_matrix[1][1]    0.009732 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003513 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020242 
_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]    0.015336 
_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 CL A 1 1266 1266 CL CL . 
C 2 CL A 1 1267 1267 CL CL . 
D 3 RET A 1 1268 1268 RET RET . 
E 4 OLA A 1 1269 1269 OLA OLA . 
F 4 OLA A 1 1270 1270 OLA OLA . 
G 4 OLA A 1 1271 1271 OLA OLA . 
H 4 OLA A 1 1272 1272 OLA OLA . 
I 4 OLA A 1 1273 1273 OLA OLA . 
J 4 OLA A 1 1274 1274 OLA OLA . 
K 4 OLA A 1 1275 1275 OLA OLA . 
L 5 HOH A 1 2001 2001 HOH HOH . 
L 5 HOH A 2 2002 2002 HOH HOH . 
L 5 HOH A 3 2003 2003 HOH HOH . 
L 5 HOH A 4 2004 2004 HOH HOH . 
L 5 HOH A 5 2005 2005 HOH HOH . 
L 5 HOH A 6 2006 2006 HOH HOH . 
L 5 HOH A 7 2007 2007 HOH HOH . 
L 5 HOH A 8 2008 2008 HOH HOH . 
L 5 HOH A 9 2009 2009 HOH HOH . 
L 5 HOH A 10 2010 2010 HOH HOH . 
L 5 HOH A 11 2011 2011 HOH HOH . 
L 5 HOH A 12 2012 2012 HOH HOH . 
L 5 HOH A 13 2013 2013 HOH HOH . 
L 5 HOH A 14 2014 2014 HOH HOH . 
L 5 HOH A 15 2015 2015 HOH HOH . 
L 5 HOH A 16 2016 2016 HOH HOH . 
L 5 HOH A 17 2017 2017 HOH HOH . 
L 5 HOH A 18 2018 2018 HOH HOH . 
L 5 HOH A 19 2019 2019 HOH HOH . 
L 5 HOH A 20 2020 2020 HOH HOH . 
L 5 HOH A 21 2021 2021 HOH HOH . 
L 5 HOH A 22 2022 2022 HOH HOH . 
L 5 HOH A 23 2023 2023 HOH HOH . 
L 5 HOH A 24 2024 2024 HOH HOH . 
L 5 HOH A 25 2025 2025 HOH HOH . 
L 5 HOH A 26 2026 2026 HOH HOH . 
L 5 HOH A 27 2027 2027 HOH HOH . 
L 5 HOH A 28 2028 2028 HOH HOH . 
L 5 HOH A 29 2029 2029 HOH HOH . 
L 5 HOH A 30 2030 2030 HOH HOH . 
L 5 HOH A 31 2031 2031 HOH HOH . 
L 5 HOH A 32 2032 2032 HOH HOH . 
L 5 HOH A 33 2033 2033 HOH HOH . 
L 5 HOH A 34 2034 2034 HOH HOH . 
L 5 HOH A 35 2035 2035 HOH HOH . 
L 5 HOH A 36 2036 2036 HOH HOH . 
L 5 HOH A 37 2037 2037 HOH HOH . 
L 5 HOH A 38 2038 2038 HOH HOH . 
L 5 HOH A 39 2039 2039 HOH HOH . 
L 5 HOH A 40 2040 2040 HOH HOH . 
L 5 HOH A 41 2041 2041 HOH HOH . 
L 5 HOH A 42 2042 2042 HOH HOH . 
L 5 HOH A 43 2043 2043 HOH HOH . 
L 5 HOH A 44 2044 2044 HOH HOH . 
L 5 HOH A 45 2045 2045 HOH HOH . 
L 5 HOH A 46 2046 2046 HOH HOH . 
L 5 HOH A 47 2047 2047 HOH HOH . 
L 5 HOH A 48 2048 2048 HOH HOH . 
L 5 HOH A 49 2049 2049 HOH HOH . 
L 5 HOH A 50 2050 2050 HOH HOH . 
L 5 HOH A 51 2051 2051 HOH HOH . 
L 5 HOH A 52 2052 2052 HOH HOH . 
L 5 HOH A 53 2053 2053 HOH HOH . 
L 5 HOH A 54 2054 2054 HOH HOH . 
L 5 HOH A 55 2055 2055 HOH HOH . 
L 5 HOH A 56 2056 2056 HOH HOH . 
L 5 HOH A 57 2057 2057 HOH HOH . 
L 5 HOH A 58 2058 2058 HOH HOH . 
L 5 HOH A 59 2059 2059 HOH HOH . 
L 5 HOH A 60 2060 2060 HOH HOH . 
L 5 HOH A 61 2061 2061 HOH HOH . 
L 5 HOH A 62 2062 2062 HOH HOH . 
L 5 HOH A 63 2063 2063 HOH HOH . 
L 5 HOH A 64 2064 2064 HOH HOH . 
L 5 HOH A 65 2065 2065 HOH HOH . 
L 5 HOH A 66 2066 2066 HOH HOH . 
L 5 HOH A 67 2067 2067 HOH HOH . 
L 5 HOH A 68 2068 2068 HOH HOH . 
L 5 HOH A 69 2069 2069 HOH HOH . 
L 5 HOH A 70 2070 2070 HOH HOH . 
L 5 HOH A 71 2071 2071 HOH HOH . 
L 5 HOH A 72 2072 2072 HOH HOH . 
L 5 HOH A 73 2073 2073 HOH HOH . 
L 5 HOH A 74 2074 2074 HOH HOH . 
L 5 HOH A 75 2075 2075 HOH HOH . 
L 5 HOH A 76 2076 2076 HOH HOH . 
L 5 HOH A 77 2077 2077 HOH HOH . 
L 5 HOH A 78 2078 2078 HOH HOH . 
L 5 HOH A 79 2079 2079 HOH HOH . 
L 5 HOH A 80 2080 2080 HOH HOH . 
L 5 HOH A 81 2081 2081 HOH HOH . 
L 5 HOH A 82 2082 2082 HOH HOH . 
L 5 HOH A 83 2083 2083 HOH HOH . 
L 5 HOH A 84 2084 2084 HOH HOH . 
L 5 HOH A 85 2085 2085 HOH HOH . 
L 5 HOH A 86 2086 2086 HOH HOH . 
L 5 HOH A 87 2087 2087 HOH HOH . 
L 5 HOH A 88 2088 2088 HOH HOH . 
L 5 HOH A 89 2089 2089 HOH HOH . 
L 5 HOH A 90 2090 2090 HOH HOH . 
L 5 HOH A 91 2091 2091 HOH HOH . 
L 5 HOH A 92 2092 2092 HOH HOH . 
L 5 HOH A 93 2093 2093 HOH HOH . 
L 5 HOH A 94 2094 2094 HOH HOH . 
L 5 HOH A 95 2095 2095 HOH HOH . 
L 5 HOH A 96 2096 2096 HOH HOH . 
L 5 HOH A 97 2097 2097 HOH HOH . 
L 5 HOH A 98 2098 2098 HOH HOH . 
L 5 HOH A 99 2099 2099 HOH HOH . 
L 5 HOH A 100 2100 2100 HOH HOH . 
L 5 HOH A 101 2101 2101 HOH HOH . 
L 5 HOH A 102 2102 2102 HOH HOH . 
L 5 HOH A 103 2103 2103 HOH HOH . 
L 5 HOH A 104 2104 2104 HOH HOH . 
L 5 HOH A 105 2105 2105 HOH HOH . 
L 5 HOH A 106 2106 2106 HOH HOH . 
L 5 HOH A 107 2107 2107 HOH HOH . 
L 5 HOH A 108 2108 2108 HOH HOH . 
L 5 HOH A 109 2109 2109 HOH HOH . 
L 5 HOH A 110 2110 2110 HOH HOH . 
L 5 HOH A 111 2111 2111 HOH HOH . 
L 5 HOH A 112 2112 2112 HOH HOH . 
L 5 HOH A 113 2113 2113 HOH HOH . 
L 5 HOH A 114 2114 2114 HOH HOH . 
L 5 HOH A 115 2115 2115 HOH HOH . 
L 5 HOH A 116 2116 2116 HOH HOH . 
L 5 HOH A 117 2117 2117 HOH HOH . 
L 5 HOH A 118 2118 2118 HOH HOH . 
L 5 HOH A 119 2119 2119 HOH HOH . 
L 5 HOH A 120 2120 2120 HOH HOH . 
L 5 HOH A 121 2121 2121 HOH HOH . 
L 5 HOH A 122 2122 2122 HOH HOH . 
L 5 HOH A 123 2123 2123 HOH HOH . 
L 5 HOH A 124 2124 2124 HOH HOH . 
L 5 HOH A 125 2125 2125 HOH HOH . 
L 5 HOH A 126 2126 2126 HOH HOH . 
L 5 HOH A 127 2127 2127 HOH HOH . 
L 5 HOH A 128 2128 2128 HOH HOH . 
L 5 HOH A 129 2129 2129 HOH HOH . 
L 5 HOH A 130 2130 2130 HOH HOH . 
L 5 HOH A 131 2131 2131 HOH HOH . 
L 5 HOH A 132 2132 2132 HOH HOH . 
L 5 HOH A 133 2133 2133 HOH HOH . 
L 5 HOH A 134 2134 2134 HOH HOH . 
L 5 HOH A 135 2135 2135 HOH HOH . 
L 5 HOH A 136 2136 2136 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 C C1 RET . . . D 3 -20.399 -16.592 5.214 1 15.2 ? C1 RET 1268 A 1 
HETATM 2 C C2 RET . . . D 3 -21.259 -15.797 6.171 1 15.62 ? C2 RET 1268 A 1 
HETATM 3 C C3 RET . . . D 3 -22.722 -15.936 5.987 1 14.29 ? C3 RET 1268 A 1 
HETATM 4 C C4 RET . . . D 3 -23.098 -15.496 4.575 1 15.3 ? C4 RET 1268 A 1 
HETATM 5 C C5 RET . . . D 3 -22.222 -16.158 3.558 1 16.37 ? C5 RET 1268 A 1 
HETATM 6 C C6 RET . . . D 3 -21.061 -16.789 3.804 1 14.29 ? C6 RET 1268 A 1 
HETATM 7 C C7 RET . . . D 3 -20.446 -17.552 2.727 1 15.04 ? C7 RET 1268 A 1 
HETATM 8 C C8 RET . . . D 3 -19.429 -18.338 2.753 1 13.47 ? C8 RET 1268 A 1 
HETATM 9 C C9 RET . . . D 3 -18.902 -19.16 1.668 1 15.18 ? C9 RET 1268 A 1 
HETATM 10 C C10 RET . . . D 3 -17.813 -19.928 1.874 1 15.07 ? C10 RET 1268 A 1 
HETATM 11 C C11 RET . . . D 3 -17.168 -20.801 0.944 1 15.2 ? C11 RET 1268 A 1 
HETATM 12 C C12 RET . . . D 3 -16.177 -21.575 1.281 1 15.25 ? C12 RET 1268 A 1 
HETATM 13 C C13 RET . . . D 3 -15.569 -22.562 0.419 1 18.23 ? C13 RET 1268 A 1 
HETATM 14 C C14 RET . . . D 3 -14.564 -23.299 0.949 1 20.08 ? C14 RET 1268 A 1 
HETATM 15 C C15 RET . . . D 3 -13.924 -24.245 0.146 1 38.6 ? C15 RET 1268 A 1 
HETATM 16 C C16 RET . . . D 3 -20.482 -18.019 5.758 1 15.4 ? C16 RET 1268 A 1 
HETATM 17 C C17 RET . . . D 3 -18.944 -16.182 5.142 1 15.59 ? C17 RET 1268 A 1 
HETATM 18 C C18 RET . . . D 3 -22.811 -16.067 2.165 1 16.96 ? C18 RET 1268 A 1 
HETATM 19 C C19 RET . . . D 3 -19.639 -19.105 0.325 1 12.38 ? C19 RET 1268 A 1 
HETATM 20 C C20 RET . . . D 3 -16.011 -22.698 -1.006 1 16.99 ? C20 RET 1268 A 1 
#
_model_server_stats.io_time_ms              58 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           346 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           20 
#