data_6DNF
#
_model_server_result.job_id            JpKnHWbULyii4R4IUpj9Nw 
_model_server_result.datetime_utc      '2024-11-04 23:30:51' 
_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          6dnf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":501}' 
#
_entry.id    6DNF 
#
_exptl.entry_id    6DNF 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              734.981 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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,M,N,O 
_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    ? 
_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 E N N 
? 2 H N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O 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
metalc ? metalc1 A OE1 GLU 228 A GLU 228 1_555 G CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? 
metalc ? metalc2 A OE2 GLU 228 A GLU 228 1_555 G CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc3 G CA CA . A CA 403 1_555 B OE1 GLU 228 B GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? 
metalc ? metalc4 G CA CA . A CA 403 1_555 B OE2 GLU 228 B GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc5 G CA CA . A CA 403 1_555 C OE1 GLU 228 C GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? 
metalc ? metalc6 G CA CA . A CA 403 1_555 C OE2 GLU 228 C GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc7 G CA CA . A CA 403 1_555 D OE1 GLU 228 D GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? 
metalc ? metalc8 G CA CA . A CA 403 1_555 D OE2 GLU 228 D GLU 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
#
_chem_comp.formula           'C39 H75 O10 P' 
_chem_comp.formula_weight    734.981 
_chem_comp.id                DGG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL 
_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
C16 C15 DGG sing 83 n n 
C16 H161 DGG sing 84 n n 
C16 H162 DGG sing 85 n n 
C16 H163 DGG sing 86 n n 
C15 C14 DGG sing 87 n n 
C15 H151 DGG sing 88 n n 
C15 H152 DGG sing 89 n n 
C14 C13 DGG sing 90 n n 
C14 H141 DGG sing 91 n n 
C14 H142 DGG sing 92 n n 
C13 C12 DGG sing 93 n n 
C13 H131 DGG sing 94 n n 
C13 H132 DGG sing 95 n n 
C12 C11 DGG sing 96 n n 
C12 H121 DGG sing 97 n n 
C12 H122 DGG sing 98 n n 
C11 C10 DGG sing 99 n n 
C11 H111 DGG sing 100 n n 
C11 H112 DGG sing 101 n n 
C10 C9 DGG sing 102 n n 
C10 H101 DGG sing 103 n n 
C10 H102 DGG sing 104 n n 
C9 C8 DGG sing 105 n n 
C9 HC91 DGG sing 106 n n 
C9 HC92 DGG sing 107 n n 
C8 C7 DGG sing 108 n n 
C8 HC81 DGG sing 109 n n 
C8 HC82 DGG sing 110 n n 
C7 C6 DGG sing 111 n n 
C7 HC71 DGG sing 112 n n 
C7 HC72 DGG sing 113 n n 
C6 C5 DGG sing 114 n n 
C6 HC61 DGG sing 115 n n 
C6 HC62 DGG sing 116 n n 
C5 C4 DGG sing 117 n n 
C5 HC51 DGG sing 118 n n 
C5 HC52 DGG sing 119 n n 
C4 C3 DGG sing 120 n n 
C4 HC41 DGG sing 121 n n 
C4 HC42 DGG sing 122 n n 
C3 C2 DGG sing 123 n n 
C3 HC31 DGG sing 124 n n 
C3 HC32 DGG sing 125 n n 
C2 C1 DGG sing 126 n n 
C2 HC21 DGG sing 127 n n 
C2 HC22 DGG sing 128 n n 
C1 O1 DGG doub 129 n n 
C1 O17 DGG sing 130 n n 
O17 C17 DGG sing 131 n n 
C17 C19 DGG sing 132 n n 
C17 H171 DGG sing 133 n n 
C17 H172 DGG sing 134 n n 
C19 O19 DGG sing 135 n n 
C19 C18 DGG sing 136 n n 
C19 H191 DGG sing 137 n n 
O19 C21 DGG sing 138 n n 
C21 O21 DGG doub 139 n n 
C21 C22 DGG sing 140 n n 
C22 C23 DGG sing 141 n n 
C22 H221 DGG sing 142 n n 
C22 H222 DGG sing 143 n n 
C23 C24 DGG sing 144 n n 
C23 H231 DGG sing 145 n n 
C23 H232 DGG sing 146 n n 
C24 C25 DGG sing 147 n n 
C24 H241 DGG sing 148 n n 
C24 H242 DGG sing 149 n n 
C25 C26 DGG sing 150 n n 
C25 H251 DGG sing 151 n n 
C25 H252 DGG sing 152 n n 
C26 C27 DGG sing 153 n n 
C26 H261 DGG sing 154 n n 
C26 H262 DGG sing 155 n n 
C27 C28 DGG sing 156 n n 
C27 H271 DGG sing 157 n n 
C27 H272 DGG sing 158 n n 
C28 C29 DGG sing 159 n n 
C28 H281 DGG sing 160 n n 
C28 H282 DGG sing 161 n n 
C29 C30 DGG sing 162 n n 
C29 C39 DGG sing 163 n n 
C29 H291 DGG sing 164 n n 
C30 C39 DGG sing 165 n n 
C30 C31 DGG sing 166 n n 
C30 H301 DGG sing 167 n n 
C39 H391 DGG sing 168 n n 
C39 H392 DGG sing 169 n n 
C31 C32 DGG sing 170 n n 
C31 H311 DGG sing 171 n n 
C31 H312 DGG sing 172 n n 
C32 C33 DGG sing 173 n n 
C32 H321 DGG sing 174 n n 
C32 H322 DGG sing 175 n n 
C33 C34 DGG sing 176 n n 
C33 H331 DGG sing 177 n n 
C33 H332 DGG sing 178 n n 
C34 C35 DGG sing 179 n n 
C34 H341 DGG sing 180 n n 
C34 H342 DGG sing 181 n n 
C35 C36 DGG sing 182 n n 
C35 H351 DGG sing 183 n n 
C35 H352 DGG sing 184 n n 
C36 H361 DGG sing 185 n n 
C36 H362 DGG sing 186 n n 
C36 H363 DGG sing 187 n n 
C18 OP2 DGG sing 188 n n 
C18 H181 DGG sing 189 n n 
C18 H182 DGG sing 190 n n 
P OP1 DGG sing 191 n n 
P OP2 DGG sing 192 n n 
P OP3 DGG doub 193 n n 
P OP4 DGG sing 194 n n 
OP1 HOP1 DGG sing 195 n n 
OP4 C40 DGG sing 196 n n 
C40 C41 DGG sing 197 n n 
C40 H401 DGG sing 198 n n 
C40 H402 DGG sing 199 n n 
C41 O42 DGG sing 200 n n 
C41 C43 DGG sing 201 n n 
C41 H411 DGG sing 202 n n 
O42 H421 DGG sing 203 n n 
C43 O44 DGG sing 204 n n 
C43 H431 DGG sing 205 n n 
C43 H432 DGG sing 206 n n 
O44 H441 DGG sing 207 n n 
#
_atom_sites.entry_id                     6DNF 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
E 2 DGG A 1 401 500 DGG PGW . 
F 3 CA A 1 402 511 CA CA . 
G 3 CA A 1 403 512 CA CA . 
H 2 DGG A 1 404 501 DGG PGW . 
I 3 CA B 1 401 513 CA CA . 
J 2 DGG B 1 402 501 DGG PGW . 
K 2 DGG B 1 403 500 DGG PGW . 
L 2 DGG C 1 501 501 DGG PGW . 
M 2 DGG C 1 502 500 DGG PGW . 
N 2 DGG D 1 501 501 DGG PGW . 
O 2 DGG D 1 502 500 DGG PGW . 
#
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 C14 DGG . . . L 2 156.711 171.37 203.817 1 154.32 ? C14 DGG 501 C 1 
HETATM 2 C C13 DGG . . . L 2 157.563 170.856 204.95 1 154.32 ? C13 DGG 501 C 1 
HETATM 3 C C12 DGG . . . L 2 158.901 170.382 204.403 1 154.32 ? C12 DGG 501 C 1 
HETATM 4 C C11 DGG . . . L 2 159.869 170.063 205.535 1 154.32 ? C11 DGG 501 C 1 
HETATM 5 C C10 DGG . . . L 2 161.268 169.817 204.988 1 154.32 ? C10 DGG 501 C 1 
HETATM 6 C C9 DGG . . . L 2 162.296 169.715 206.106 1 154.32 ? C9 DGG 501 C 1 
HETATM 7 C C8 DGG . . . L 2 163.703 169.731 205.525 1 154.32 ? C8 DGG 501 C 1 
HETATM 8 C C7 DGG . . . L 2 164.76 169.694 206.62 1 154.32 ? C7 DGG 501 C 1 
HETATM 9 C C6 DGG . . . L 2 166.155 169.827 206.022 1 154.32 ? C6 DGG 501 C 1 
HETATM 10 H H131 DGG . . . L 2 157.054 170.029 205.45 1 154.32 ? H131 DGG 501 C 1 
HETATM 11 H H132 DGG . . . L 2 157.723 171.651 205.682 1 154.32 ? H132 DGG 501 C 1 
HETATM 12 H H121 DGG . . . L 2 159.33 171.158 203.766 1 154.32 ? H121 DGG 501 C 1 
HETATM 13 H H122 DGG . . . L 2 158.75 169.491 203.791 1 154.32 ? H122 DGG 501 C 1 
HETATM 14 H H111 DGG . . . L 2 159.525 169.176 206.071 1 154.32 ? H111 DGG 501 C 1 
HETATM 15 H H112 DGG . . . L 2 159.893 170.895 206.241 1 154.32 ? H112 DGG 501 C 1 
HETATM 16 H H101 DGG . . . L 2 161.543 170.634 204.318 1 154.32 ? H101 DGG 501 C 1 
HETATM 17 H H102 DGG . . . L 2 161.273 168.893 204.407 1 154.32 ? H102 DGG 501 C 1 
HETATM 18 H HC91 DGG . . . L 2 162.14 168.789 206.665 1 154.32 ? HC91 DGG 501 C 1 
HETATM 19 H HC92 DGG . . . L 2 162.174 170.552 206.796 1 154.32 ? HC92 DGG 501 C 1 
HETATM 20 H HC81 DGG . . . L 2 163.836 170.633 204.925 1 154.32 ? HC81 DGG 501 C 1 
HETATM 21 H HC82 DGG . . . L 2 163.834 168.87 204.867 1 154.32 ? HC82 DGG 501 C 1 
HETATM 22 H HC71 DGG . . . L 2 164.686 168.753 207.169 1 154.32 ? HC71 DGG 501 C 1 
HETATM 23 H HC72 DGG . . . L 2 164.586 170.51 207.325 1 154.32 ? HC72 DGG 501 C 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           23 
#