data_2AT9
#
_model_server_result.job_id            DNmwBEMK4u0oRowyC28BkA 
_model_server_result.datetime_utc      '2024-12-26 15:53:21' 
_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          2at9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":262}' 
#
_entry.id    2AT9 
#
_exptl.entry_id    2AT9 
_exptl.method      'ELECTRON CRYSTALLOGRAPHY' 
#
_entity.details                     ? 
_entity.formula_weight              901.222 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            3-[[3-METHYLPHOSPHONO-GLYCEROLYL]PHOSPHONYL]-[1,2-DI[2,6,10,14-TETRAMETHYL-HEXADECAN-16-YL]GLYCEROL 
_entity.pdbx_number_of_molecules    8 
_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         120 
_cell.entry_id            2AT9 
_cell.length_a            62.45 
_cell.length_b            62.45 
_cell.length_c            100 
_cell.Z_PDB               3 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2AT9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        143 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 3' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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 
? 3 H N N 
? 3 I N N 
? 3 J N 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             216 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             LYS 
_struct_conn.ptnr1_auth_seq_id              216 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            B 
_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              249 
_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        A 
_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                1.343 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C47 H98 O11 P2' 
_chem_comp.formula_weight    901.222 
_chem_comp.id                2DP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              3-[[3-METHYLPHOSPHONO-GLYCEROLYL]PHOSPHONYL]-[1,2-DI[2,6,10,14-TETRAMETHYL-HEXADECAN-16-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
C1 C2 2DP sing 1 n n 
C1 O1 2DP sing 2 n n 
C1 H11 2DP sing 3 n n 
C1 H12 2DP sing 4 n n 
C2 C3 2DP sing 5 n n 
C2 O2 2DP sing 6 n n 
C2 H2 2DP sing 7 n n 
C3 O3 2DP sing 8 n n 
C3 H31 2DP sing 9 n n 
C3 H32 2DP sing 10 n n 
C4 C5 2DP sing 11 n n 
C4 O6 2DP sing 12 n n 
C4 H41 2DP sing 13 n n 
C4 H42 2DP sing 14 n n 
C5 C6 2DP sing 15 n n 
C5 O7 2DP sing 16 n n 
C5 H5 2DP sing 17 n n 
C6 O8 2DP sing 18 n n 
C6 H61 2DP sing 19 n n 
C6 H62 2DP sing 20 n n 
C11 C12 2DP sing 21 n n 
C11 O1 2DP sing 22 n n 
C11 H111 2DP sing 23 n n 
C11 H112 2DP sing 24 n n 
C12 C13 2DP sing 25 n n 
C12 H121 2DP sing 26 n n 
C12 H122 2DP sing 27 n n 
C13 C14 2DP sing 28 n n 
C13 C15 2DP sing 29 n n 
C13 H13 2DP sing 30 n n 
C14 H141 2DP sing 31 n n 
C14 H142 2DP sing 32 n n 
C14 H143 2DP sing 33 n n 
C15 C16 2DP sing 34 n n 
C15 H151 2DP sing 35 n n 
C15 H152 2DP sing 36 n n 
C16 C17 2DP sing 37 n n 
C16 H161 2DP sing 38 n n 
C16 H162 2DP sing 39 n n 
C17 C18 2DP sing 40 n n 
C17 H171 2DP sing 41 n n 
C17 H172 2DP sing 42 n n 
C18 C19 2DP sing 43 n n 
C18 C20 2DP sing 44 n n 
C18 H18 2DP sing 45 n n 
C19 H191 2DP sing 46 n n 
C19 H192 2DP sing 47 n n 
C19 H193 2DP sing 48 n n 
C20 C21 2DP sing 49 n n 
C20 H201 2DP sing 50 n n 
C20 H202 2DP sing 51 n n 
C21 C22 2DP sing 52 n n 
C21 H211 2DP sing 53 n n 
C21 H212 2DP sing 54 n n 
C22 C23 2DP sing 55 n n 
C22 H221 2DP sing 56 n n 
C22 H222 2DP sing 57 n n 
C23 C24 2DP sing 58 n n 
C23 C25 2DP sing 59 n n 
C23 H23 2DP sing 60 n n 
C24 H241 2DP sing 61 n n 
C24 H242 2DP sing 62 n n 
C24 H243 2DP sing 63 n n 
C25 C26 2DP sing 64 n n 
C25 H251 2DP sing 65 n n 
C25 H252 2DP sing 66 n n 
C26 C27 2DP sing 67 n n 
C26 H261 2DP sing 68 n n 
C26 H262 2DP sing 69 n n 
C27 C28 2DP sing 70 n n 
C27 H271 2DP sing 71 n n 
C27 H272 2DP sing 72 n n 
C28 C29 2DP sing 73 n n 
C28 C30 2DP sing 74 n n 
C28 H28 2DP sing 75 n n 
C29 H291 2DP sing 76 n n 
C29 H292 2DP sing 77 n n 
C29 H293 2DP sing 78 n n 
C30 H301 2DP sing 79 n n 
C30 H302 2DP sing 80 n n 
C30 H303 2DP sing 81 n n 
C41 C42 2DP sing 82 n n 
C41 O2 2DP sing 83 n n 
C41 H411 2DP sing 84 n n 
C41 H412 2DP sing 85 n n 
C42 C43 2DP sing 86 n n 
C42 H421 2DP sing 87 n n 
C42 H422 2DP sing 88 n n 
C43 C44 2DP sing 89 n n 
C43 C45 2DP sing 90 n n 
C43 H43 2DP sing 91 n n 
C44 H441 2DP sing 92 n n 
C44 H442 2DP sing 93 n n 
C44 H443 2DP sing 94 n n 
C45 C46 2DP sing 95 n n 
C45 H451 2DP sing 96 n n 
C45 H452 2DP sing 97 n n 
C46 C47 2DP sing 98 n n 
C46 H461 2DP sing 99 n n 
C46 H462 2DP sing 100 n n 
C47 C48 2DP sing 101 n n 
C47 H471 2DP sing 102 n n 
C47 H472 2DP sing 103 n n 
C48 C49 2DP sing 104 n n 
C48 C50 2DP sing 105 n n 
C48 H48 2DP sing 106 n n 
C49 H491 2DP sing 107 n n 
C49 H492 2DP sing 108 n n 
C49 H493 2DP sing 109 n n 
C50 C51 2DP sing 110 n n 
C50 H501 2DP sing 111 n n 
C50 H502 2DP sing 112 n n 
C51 C52 2DP sing 113 n n 
C51 H511 2DP sing 114 n n 
C51 H512 2DP sing 115 n n 
C52 C53 2DP sing 116 n n 
C52 H521 2DP sing 117 n n 
C52 H522 2DP sing 118 n n 
C53 C54 2DP sing 119 n n 
C53 C55 2DP sing 120 n n 
C53 H53 2DP sing 121 n n 
C54 H541 2DP sing 122 n n 
C54 H542 2DP sing 123 n n 
C54 H543 2DP sing 124 n n 
C55 C56 2DP sing 125 n n 
C55 H551 2DP sing 126 n n 
C55 H552 2DP sing 127 n n 
C56 C57 2DP sing 128 n n 
C56 H561 2DP sing 129 n n 
C56 H562 2DP sing 130 n n 
C57 C58 2DP sing 131 n n 
C57 H571 2DP sing 132 n n 
C57 H572 2DP sing 133 n n 
C58 C59 2DP sing 134 n n 
C58 C60 2DP sing 135 n n 
C58 H58 2DP sing 136 n n 
C59 H591 2DP sing 137 n n 
C59 H592 2DP sing 138 n n 
C59 H593 2DP sing 139 n n 
C60 H601 2DP sing 140 n n 
C60 H602 2DP sing 141 n n 
C60 H603 2DP sing 142 n n 
O3 P1 2DP sing 143 n n 
O4 P1 2DP doub 144 n n 
O5 P1 2DP sing 145 n n 
O5 HO5 2DP sing 146 n n 
O6 P1 2DP sing 147 n n 
O7 HO7 2DP sing 148 n n 
O8 P2 2DP sing 149 n n 
O9 P2 2DP doub 150 n n 
O10 P2 2DP sing 151 n n 
O10 HOA 2DP sing 152 n n 
O11 P2 2DP sing 153 n n 
O11 CM 2DP sing 154 n n 
CM HM1 2DP sing 155 n n 
CM HM2 2DP sing 156 n n 
CM HM3 2DP sing 157 n n 
#
_atom_sites.entry_id                     2AT9 
_atom_sites.fract_transf_matrix[1][1]    0.016013 
_atom_sites.fract_transf_matrix[1][2]    0.009245 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01849 
_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]    0.01 
_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 RET A 1 249 216 RET RET A 
C 3 2DP A 1 261 261 2DP 2DP . 
D 3 2DP A 1 262 262 2DP 2DP . 
E 3 2DP A 1 263 263 2DP 2DP . 
F 3 2DP A 1 264 264 2DP 2DP . 
G 3 2DP A 1 265 265 2DP 2DP . 
H 3 2DP A 1 267 267 2DP 2DP . 
I 3 2DP A 1 268 268 2DP 2DP . 
J 3 2DP A 1 269 269 2DP 2DP . 
K 4 HOH A 1 270 1 HOH HOH . 
K 4 HOH A 2 271 2 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 2DP . . . D 3 31.407 12.833 -17.613 1 23.52 ? C1 2DP 262 A 1 
HETATM 2 C C2 2DP . . . D 3 32.515 11.846 -18.019 1 23.03 ? C2 2DP 262 A 1 
HETATM 3 C C3 2DP . . . D 3 33.024 12.088 -19.466 1 22.83 ? C3 2DP 262 A 1 
HETATM 4 C C4 2DP . . . D 3 30.565 8.93 -21.861 1 23.52 ? C4 2DP 262 A 1 
HETATM 5 C C5 2DP . . . D 3 29.797 10.355 -21.95 1 26.11 ? C5 2DP 262 A 1 
HETATM 6 C C6 2DP . . . D 3 28.58 10.226 -22.922 1 28.11 ? C6 2DP 262 A 1 
HETATM 7 C C11 2DP . . . D 3 31.331 13.537 -15.248 1 24.73 ? C11 2DP 262 A 1 
HETATM 8 C C12 2DP . . . D 3 31.699 14.782 -14.389 1 26.07 ? C12 2DP 262 A 1 
HETATM 9 C C13 2DP . . . D 3 31.548 14.633 -12.838 1 25.29 ? C13 2DP 262 A 1 
HETATM 10 C C14 2DP . . . D 3 32.967 14.482 -12.277 1 25.34 ? C14 2DP 262 A 1 
HETATM 11 C C15 2DP . . . D 3 30.878 15.887 -12.203 1 22.65 ? C15 2DP 262 A 1 
HETATM 12 C C16 2DP . . . D 3 30.973 16.032 -10.674 1 23.24 ? C16 2DP 262 A 1 
HETATM 13 C C17 2DP . . . D 3 30.323 14.932 -9.802 1 25.33 ? C17 2DP 262 A 1 
HETATM 14 C C18 2DP . . . D 3 30.953 14.574 -8.42 1 28.05 ? C18 2DP 262 A 1 
HETATM 15 C C19 2DP . . . D 3 32.472 14.355 -8.333 1 30.2 ? C19 2DP 262 A 1 
HETATM 16 C C20 2DP . . . D 3 30.072 14.426 -7.123 1 28.37 ? C20 2DP 262 A 1 
HETATM 17 C C21 2DP . . . D 3 30.713 14.483 -5.701 1 25.32 ? C21 2DP 262 A 1 
HETATM 18 C C22 2DP . . . D 3 29.845 14.912 -4.488 1 22.89 ? C22 2DP 262 A 1 
HETATM 19 C C23 2DP . . . D 3 29.314 16.368 -4.315 1 22.15 ? C23 2DP 262 A 1 
HETATM 20 C C24 2DP . . . D 3 28.435 16.954 -5.397 1 21.05 ? C24 2DP 262 A 1 
HETATM 21 C C25 2DP . . . D 3 29.666 17.238 -3.056 1 21.11 ? C25 2DP 262 A 1 
HETATM 22 C C26 2DP . . . D 3 28.809 16.987 -1.79 1 21.01 ? C26 2DP 262 A 1 
HETATM 23 C C27 2DP . . . D 3 27.84 18.136 -1.632 1 21.96 ? C27 2DP 262 A 1 
HETATM 24 C C28 2DP . . . D 3 26.503 17.996 -2.331 1 20.53 ? C28 2DP 262 A 1 
HETATM 25 C C29 2DP . . . D 3 26.208 19.131 -3.284 1 20.28 ? C29 2DP 262 A 1 
HETATM 26 C C30 2DP . . . D 3 25.353 17.844 -1.349 1 21.21 ? C30 2DP 262 A 1 
HETATM 27 C C41 2DP . . . D 3 32.597 9.66 -16.749 1 19.26 ? C41 2DP 262 A 1 
HETATM 28 C C42 2DP . . . D 3 31.753 10.056 -15.486 1 19.62 ? C42 2DP 262 A 1 
HETATM 29 C C43 2DP . . . D 3 32.307 9.981 -13.993 1 17.6 ? C43 2DP 262 A 1 
HETATM 30 C C44 2DP . . . D 3 33.648 10.772 -13.819 1 18.26 ? C44 2DP 262 A 1 
HETATM 31 C C45 2DP . . . D 3 31.217 10.522 -12.974 1 16.45 ? C45 2DP 262 A 1 
HETATM 32 C C46 2DP . . . D 3 31.589 11 -11.52 1 15.78 ? C46 2DP 262 A 1 
HETATM 33 C C47 2DP . . . D 3 31.992 9.945 -10.411 1 14.96 ? C47 2DP 262 A 1 
HETATM 34 C C48 2DP . . . D 3 31.542 10.094 -8.899 1 15.45 ? C48 2DP 262 A 1 
HETATM 35 C C49 2DP . . . D 3 30.318 11.015 -8.717 1 16.3 ? C49 2DP 262 A 1 
HETATM 36 C C50 2DP . . . D 3 32.703 10.625 -8.071 1 16.76 ? C50 2DP 262 A 1 
HETATM 37 C C51 2DP . . . D 3 32.997 9.766 -6.837 1 18.01 ? C51 2DP 262 A 1 
HETATM 38 C C52 2DP . . . D 3 32.703 10.415 -5.485 1 18.52 ? C52 2DP 262 A 1 
HETATM 39 C C53 2DP . . . D 3 32.916 9.539 -4.182 1 21.33 ? C53 2DP 262 A 1 
HETATM 40 C C54 2DP . . . D 3 34.252 9.827 -3.399 1 22.35 ? C54 2DP 262 A 1 
HETATM 41 C C55 2DP . . . D 3 31.583 9.683 -3.312 1 20.93 ? C55 2DP 262 A 1 
HETATM 42 C C56 2DP . . . D 3 31.594 9.303 -1.814 1 22.79 ? C56 2DP 262 A 1 
HETATM 43 C C57 2DP . . . D 3 30.726 8.073 -1.394 1 21.28 ? C57 2DP 262 A 1 
HETATM 44 C C58 2DP . . . D 3 29.543 8.355 -0.433 1 18.3 ? C58 2DP 262 A 1 
HETATM 45 C C59 2DP . . . D 3 28.444 7.297 -0.527 1 17.81 ? C59 2DP 262 A 1 
HETATM 46 C C60 2DP . . . D 3 29.99 8.52 1.041 1 15.86 ? C60 2DP 262 A 1 
HETATM 47 O O1 2DP . . . D 3 31.909 13.731 -16.577 1 24.63 ? O1 2DP 262 A 1 
HETATM 48 O O2 2DP . . . D 3 32.054 10.464 -17.846 1 21 ? O2 2DP 262 A 1 
HETATM 49 O O3 2DP . . . D 3 32.387 11.16 -20.406 1 23.98 ? O3 2DP 262 A 1 
HETATM 50 O O4 2DP . . . D 3 33.994 9.211 -19.714 1 23.28 ? O4 2DP 262 A 1 
HETATM 51 O O5 2DP . . . D 3 33.688 9.806 -22.177 1 22.56 ? O5 2DP 262 A 1 
HETATM 52 O O6 2DP . . . D 3 31.659 8.772 -20.871 1 22.57 ? O6 2DP 262 A 1 
HETATM 53 O O7 2DP . . . D 3 30.606 11.464 -22.481 1 25.42 ? O7 2DP 262 A 1 
HETATM 54 O O8 2DP . . . D 3 27.302 10.082 -22.219 1 30.05 ? O8 2DP 262 A 1 
HETATM 55 O O9 2DP . . . D 3 24.716 9.821 -22.447 1 29.27 ? O9 2DP 262 A 1 
HETATM 56 O O10 2DP . . . D 3 26.173 9.307 -24.462 1 31.72 ? O10 2DP 262 A 1 
HETATM 57 O O11 2DP . . . D 3 26.153 7.738 -22.503 1 27.67 ? O11 2DP 262 A 1 
HETATM 58 P P1 2DP . . . D 3 33.045 9.686 -20.804 1 22.16 ? P1 2DP 262 A 1 
HETATM 59 P P2 2DP . . . D 3 26.052 9.207 -22.919 1 28.81 ? P2 2DP 262 A 1 
HETATM 60 C CM 2DP . . . D 3 27.028 7.225 -21.392 1 23.68 ? CM 2DP 262 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           449 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           60 
#