data_4YPT
#
_model_server_result.job_id            v5wWYkbplc0f-D9g3ltfpA 
_model_server_result.datetime_utc      '2024-11-22 14:33:51' 
_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          4ypt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":2004}' 
#
_entry.id    4YPT 
#
_exptl.entry_id    4YPT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    5 
_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            4YPT 
_cell.length_a            155.576 
_cell.length_b            155.576 
_cell.length_c            155.576 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YPT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        199 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 21 3' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
PISA trimeric 3 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H 1 1 
A,B,C,D,E,F,G,H 2 1,2,3 
#
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' 8_555 -z,x+1/2,-y+1/2 0 0 -1 1 0 0 0 -1 0 0 77.788 77.788 
3 'crystal symmetry operation' 11_455 y-1/2,-z+1/2,-x 0 1 0 0 0 -1 -1 0 0 -77.788 77.788 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D N N 
? 3 E N N 
? 3 F N N 
? 3 G N 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 ASN 191 A ASN 1715 1_555 A N OCS 192 A OCS 1716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale2 A C OCS 192 A OCS 1716 1_555 A N TYR 193 A TYR 1717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
metalc ? metalc1 A SG CYS 270 A CYS 1794 1_555 B ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc2 A SG CYS 272 A CYS 1796 1_555 B ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc3 A SG CYS 304 A CYS 1828 1_555 B ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc4 A SG CYS 306 A CYS 1830 1_555 B ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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 O1 GOL sing 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     4YPT 
_atom_sites.fract_transf_matrix[1][1]    0.006428 
_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]    0.006428 
_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]    0.006428 
_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 ZN A 1 2001 1 ZN ZN . 
C 3 GOL A 1 2002 1 GOL GOL . 
D 3 GOL A 1 2003 2 GOL GOL . 
E 3 GOL A 1 2004 3 GOL GOL . 
F 3 GOL A 1 2005 4 GOL GOL . 
G 3 GOL A 1 2006 5 GOL GOL . 
H 4 HOH A 1 2101 61 HOH HOH . 
H 4 HOH A 2 2102 72 HOH HOH . 
H 4 HOH A 3 2103 34 HOH HOH . 
H 4 HOH A 4 2104 7 HOH HOH . 
H 4 HOH A 5 2105 30 HOH HOH . 
H 4 HOH A 6 2106 17 HOH HOH . 
H 4 HOH A 7 2107 42 HOH HOH . 
H 4 HOH A 8 2108 25 HOH HOH . 
H 4 HOH A 9 2109 40 HOH HOH . 
H 4 HOH A 10 2110 6 HOH HOH . 
H 4 HOH A 11 2111 20 HOH HOH . 
H 4 HOH A 12 2112 67 HOH HOH . 
H 4 HOH A 13 2113 8 HOH HOH . 
H 4 HOH A 14 2114 14 HOH HOH . 
H 4 HOH A 15 2115 9 HOH HOH . 
H 4 HOH A 16 2116 87 HOH HOH . 
H 4 HOH A 17 2117 38 HOH HOH . 
H 4 HOH A 18 2118 53 HOH HOH . 
H 4 HOH A 19 2119 23 HOH HOH . 
H 4 HOH A 20 2120 1 HOH HOH . 
H 4 HOH A 21 2121 27 HOH HOH . 
H 4 HOH A 22 2122 22 HOH HOH . 
H 4 HOH A 23 2123 11 HOH HOH . 
H 4 HOH A 24 2124 13 HOH HOH . 
H 4 HOH A 25 2125 64 HOH HOH . 
H 4 HOH A 26 2126 2 HOH HOH . 
H 4 HOH A 27 2127 74 HOH HOH . 
H 4 HOH A 28 2128 16 HOH HOH . 
H 4 HOH A 29 2129 84 HOH HOH . 
H 4 HOH A 30 2130 73 HOH HOH . 
H 4 HOH A 31 2131 21 HOH HOH . 
H 4 HOH A 32 2132 68 HOH HOH . 
H 4 HOH A 33 2133 4 HOH HOH . 
H 4 HOH A 34 2134 28 HOH HOH . 
H 4 HOH A 35 2135 83 HOH HOH . 
H 4 HOH A 36 2136 39 HOH HOH . 
H 4 HOH A 37 2137 99 HOH HOH . 
H 4 HOH A 38 2138 5 HOH HOH . 
H 4 HOH A 39 2139 36 HOH HOH . 
H 4 HOH A 40 2140 62 HOH HOH . 
H 4 HOH A 41 2141 60 HOH HOH . 
H 4 HOH A 42 2142 31 HOH HOH . 
H 4 HOH A 43 2143 79 HOH HOH . 
H 4 HOH A 44 2144 94 HOH HOH . 
H 4 HOH A 45 2145 54 HOH HOH . 
H 4 HOH A 46 2146 55 HOH HOH . 
H 4 HOH A 47 2147 19 HOH HOH . 
H 4 HOH A 48 2148 24 HOH HOH . 
H 4 HOH A 49 2149 47 HOH HOH . 
H 4 HOH A 50 2150 58 HOH HOH . 
H 4 HOH A 51 2151 102 HOH HOH . 
H 4 HOH A 52 2152 32 HOH HOH . 
H 4 HOH A 53 2153 71 HOH HOH . 
H 4 HOH A 54 2154 33 HOH HOH . 
H 4 HOH A 55 2155 91 HOH HOH . 
H 4 HOH A 56 2156 100 HOH HOH . 
H 4 HOH A 57 2157 92 HOH HOH . 
H 4 HOH A 58 2158 85 HOH HOH . 
H 4 HOH A 59 2159 98 HOH HOH . 
H 4 HOH A 60 2160 57 HOH HOH . 
H 4 HOH A 61 2161 88 HOH HOH . 
H 4 HOH A 62 2162 103 HOH HOH . 
H 4 HOH A 63 2163 41 HOH HOH . 
H 4 HOH A 64 2164 96 HOH HOH . 
H 4 HOH A 65 2165 44 HOH HOH . 
H 4 HOH A 66 2166 81 HOH HOH . 
H 4 HOH A 67 2167 101 HOH HOH . 
H 4 HOH A 68 2168 93 HOH HOH . 
H 4 HOH A 69 2169 69 HOH HOH . 
H 4 HOH A 70 2170 66 HOH HOH . 
H 4 HOH A 71 2171 80 HOH HOH . 
H 4 HOH A 72 2172 43 HOH HOH . 
H 4 HOH A 73 2173 90 HOH HOH . 
H 4 HOH A 74 2174 70 HOH HOH . 
H 4 HOH A 75 2175 45 HOH HOH . 
H 4 HOH A 76 2176 63 HOH HOH . 
H 4 HOH A 77 2177 82 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 GOL . . . E 3 -15.325 11.23 38.527 1 71.53 ? C1 GOL 2004 A 1 
HETATM 2 O O1 GOL . . . E 3 -15.523 11.901 39.752 1 69.87 ? O1 GOL 2004 A 1 
HETATM 3 C C2 GOL . . . E 3 -15.608 12.204 37.393 1 72.17 ? C2 GOL 2004 A 1 
HETATM 4 O O2 GOL . . . E 3 -16.993 12.479 37.357 1 73.72 ? O2 GOL 2004 A 1 
HETATM 5 C C3 GOL . . . E 3 -14.855 13.495 37.667 1 75.12 ? C3 GOL 2004 A 1 
HETATM 6 O O3 GOL . . . E 3 -13.488 13.311 37.385 1 83.44 ? O3 GOL 2004 A 1 
#
_model_server_stats.io_time_ms              322 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           6 
#