data_9GE3
#
_model_server_result.job_id            qqYw2pCo5gjhzCAOatoS1Q 
_model_server_result.datetime_utc      '2025-04-01 16:32:34' 
_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          9ge3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    9GE3 
#
_exptl.entry_id    9GE3 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              572.623 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R)-2-oxidanyl-3-[oxidanyl-[(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate' 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            9GE3 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9GE3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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 
_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                      6 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 C SG CYS 158 F CYS 158 1_555 C SG CYS 228 F CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 E SG CYS 375 R CYS 94 1_555 E SG CYS 449 R CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
covale ? covale1 E ND2 ASN 452 R ASN 171 1_555 G C1 NAG . R NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
#
_chem_comp.formula           'C25 H49 O12 P' 
_chem_comp.formula_weight    572.623 
_chem_comp.id                A1IKT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R)-2-oxidanyl-3-[oxidanyl-[(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "[(2R)-2-hydroxy-3-[hydroxy-[(2R,3R,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]-oxyphosphoryl]oxypropyl] hexadecanoate;1-hexadecanoyl-sn-glycero-3-phospho-(1'-myo-inositol)" 
#
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
O34 C31 A1IKT sing 1 n n 
O35 C30 A1IKT sing 2 n n 
C30 C31 A1IKT sing 3 n n 
C30 C29 A1IKT sing 4 n n 
C31 C32 A1IKT sing 5 n n 
O33 C32 A1IKT sing 6 n n 
C32 C27 A1IKT sing 7 n n 
O36 C29 A1IKT sing 8 n n 
C29 C28 A1IKT sing 9 n n 
C28 C27 A1IKT sing 10 n n 
C28 O37 A1IKT sing 11 n n 
C27 O26 A1IKT sing 12 n n 
O26 P23 A1IKT sing 13 n n 
O22 P23 A1IKT sing 14 n n 
O22 C21 A1IKT sing 15 n n 
P23 O24 A1IKT doub 16 n n 
P23 O25 A1IKT sing 17 n n 
O38 C20 A1IKT sing 18 n n 
C21 C20 A1IKT sing 19 n n 
C20 C19 A1IKT sing 20 n n 
C19 O18 A1IKT sing 21 n n 
O18 C16 A1IKT sing 22 n n 
C16 O17 A1IKT doub 23 n n 
C16 C15 A1IKT sing 24 n n 
C15 C14 A1IKT sing 25 n n 
C14 C13 A1IKT sing 26 n n 
C13 C12 A1IKT sing 27 n n 
C12 C11 A1IKT sing 28 n n 
C11 C10 A1IKT sing 29 n n 
C10 C09 A1IKT sing 30 n n 
C09 C08 A1IKT sing 31 n n 
C08 C07 A1IKT sing 32 n n 
C07 C06 A1IKT sing 33 n n 
C06 C05 A1IKT sing 34 n n 
C02 C03 A1IKT sing 35 n n 
C02 C01 A1IKT sing 36 n n 
C05 C04 A1IKT sing 37 n n 
C03 C04 A1IKT sing 38 n n 
C10 H1 A1IKT sing 39 n n 
C10 H2 A1IKT sing 40 n n 
C15 H3 A1IKT sing 41 n n 
C15 H4 A1IKT sing 42 n n 
C19 H5 A1IKT sing 43 n n 
C19 H6 A1IKT sing 44 n n 
C28 H7 A1IKT sing 45 n n 
C27 H8 A1IKT sing 46 n n 
C01 H9 A1IKT sing 47 n n 
C01 H10 A1IKT sing 48 n n 
C01 H11 A1IKT sing 49 n n 
C02 H12 A1IKT sing 50 n n 
C02 H13 A1IKT sing 51 n n 
C03 H14 A1IKT sing 52 n n 
C03 H15 A1IKT sing 53 n n 
C04 H16 A1IKT sing 54 n n 
C04 H17 A1IKT sing 55 n n 
C05 H18 A1IKT sing 56 n n 
C05 H19 A1IKT sing 57 n n 
C06 H20 A1IKT sing 58 n n 
C06 H21 A1IKT sing 59 n n 
C07 H22 A1IKT sing 60 n n 
C07 H23 A1IKT sing 61 n n 
C08 H24 A1IKT sing 62 n n 
C08 H25 A1IKT sing 63 n n 
C09 H26 A1IKT sing 64 n n 
C09 H27 A1IKT sing 65 n n 
C11 H28 A1IKT sing 66 n n 
C11 H29 A1IKT sing 67 n n 
C12 H30 A1IKT sing 68 n n 
C12 H31 A1IKT sing 69 n n 
C13 H32 A1IKT sing 70 n n 
C13 H33 A1IKT sing 71 n n 
C14 H34 A1IKT sing 72 n n 
C14 H35 A1IKT sing 73 n n 
C20 H36 A1IKT sing 74 n n 
C21 H37 A1IKT sing 75 n n 
C21 H38 A1IKT sing 76 n n 
C29 H39 A1IKT sing 77 n n 
C30 H40 A1IKT sing 78 n n 
C31 H41 A1IKT sing 79 n n 
C32 H42 A1IKT sing 80 n n 
O25 H43 A1IKT sing 81 n n 
O33 H44 A1IKT sing 82 n n 
O34 H45 A1IKT sing 83 n n 
O35 H46 A1IKT sing 84 n n 
O36 H47 A1IKT sing 85 n n 
O37 H48 A1IKT sing 86 n n 
O38 H49 A1IKT sing 87 n n 
#
_atom_sites.entry_id                     9GE3 
_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
F 6 A1IKT R 1 401 401 A1IKT LPI . 
G 7 NAG R 1 402 302 NAG NAG . 
H 8 HOH R 1 501 8 HOH HOH . 
H 8 HOH R 2 502 1 HOH HOH . 
H 8 HOH R 3 503 7 HOH HOH . 
H 8 HOH R 4 504 4 HOH HOH . 
H 8 HOH R 5 505 9 HOH HOH . 
H 8 HOH R 6 506 5 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 C10 A1IKT . . . F 6 145.816 128.467 118.246 1 31.19 ? C10 A1IKT 401 R 1 
HETATM 2 C C15 A1IKT . . . F 6 147.051 128.27 113.54 1 17.55 ? C15 A1IKT 401 R 1 
HETATM 3 C C19 A1IKT . . . F 6 149.197 129.122 110.657 1 27.46 ? C19 A1IKT 401 R 1 
HETATM 4 C C28 A1IKT . . . F 6 151.231 127.374 105.535 1 31.71 ? C28 A1IKT 401 R 1 
HETATM 5 C C27 A1IKT . . . F 6 149.829 126.792 105.645 1 31.91 ? C27 A1IKT 401 R 1 
HETATM 6 C C01 A1IKT . . . F 6 141.559 125.916 124.515 1 26.59 ? C01 A1IKT 401 R 1 
HETATM 7 C C02 A1IKT . . . F 6 141.644 127.29 123.89 1 28.19 ? C02 A1IKT 401 R 1 
HETATM 8 C C03 A1IKT . . . F 6 142.816 128.111 124.4 1 30.99 ? C03 A1IKT 401 R 1 
HETATM 9 C C04 A1IKT . . . F 6 144.111 127.325 124.528 1 34.17 ? C04 A1IKT 401 R 1 
HETATM 10 C C05 A1IKT . . . F 6 145.35 128.129 124.172 1 26.09 ? C05 A1IKT 401 R 1 
HETATM 11 C C06 A1IKT . . . F 6 145.491 128.349 122.674 1 29.37 ? C06 A1IKT 401 R 1 
HETATM 12 C C07 A1IKT . . . F 6 145.778 127.07 121.902 1 33.75 ? C07 A1IKT 401 R 1 
HETATM 13 C C08 A1IKT . . . F 6 145.513 127.163 120.407 1 39.82 ? C08 A1IKT 401 R 1 
HETATM 14 C C09 A1IKT . . . F 6 146.199 128.329 119.712 1 35.85 ? C09 A1IKT 401 R 1 
HETATM 15 C C11 A1IKT . . . F 6 146.357 127.362 117.352 1 26.16 ? C11 A1IKT 401 R 1 
HETATM 16 C C12 A1IKT . . . F 6 145.615 127.222 116.032 1 22.16 ? C12 A1IKT 401 R 1 
HETATM 17 C C13 A1IKT . . . F 6 146.319 126.346 115.008 1 20.01 ? C13 A1IKT 401 R 1 
HETATM 18 C C14 A1IKT . . . F 6 147.485 127.032 114.313 1 21.27 ? C14 A1IKT 401 R 1 
HETATM 19 C C16 A1IKT . . . F 6 148.169 128.928 112.785 1 18.63 ? C16 A1IKT 401 R 1 
HETATM 20 C C20 A1IKT . . . F 6 148.579 129.503 109.333 1 26.67 ? C20 A1IKT 401 R 1 
HETATM 21 C C21 A1IKT . . . F 6 147.891 128.346 108.649 1 27.61 ? C21 A1IKT 401 R 1 
HETATM 22 C C29 A1IKT . . . F 6 151.268 128.446 104.454 1 32.84 ? C29 A1IKT 401 R 1 
HETATM 23 C C30 A1IKT . . . F 6 150.808 127.88 103.118 1 36.84 ? C30 A1IKT 401 R 1 
HETATM 24 C C31 A1IKT . . . F 6 149.411 127.285 103.237 1 31.4 ? C31 A1IKT 401 R 1 
HETATM 25 C C32 A1IKT . . . F 6 149.374 126.21 104.314 1 28.64 ? C32 A1IKT 401 R 1 
HETATM 26 O O17 A1IKT . . . F 6 148.964 129.693 113.261 1 24.72 ? O17 A1IKT 401 R 1 
HETATM 27 O O18 A1IKT . . . F 6 148.171 128.556 111.504 1 21.28 ? O18 A1IKT 401 R 1 
HETATM 28 O O22 A1IKT . . . F 6 148.844 127.664 107.807 1 31.29 ? O22 A1IKT 401 R 1 
HETATM 29 O O24 A1IKT . . . F 6 147.972 125.349 108.307 1 23.68 ? O24 A1IKT 401 R 1 
HETATM 30 O O25 A1IKT . . . F 6 150.291 126.088 109.094 1 26.08 ? O25 A1IKT 401 R 1 
HETATM 31 O O26 A1IKT . . . F 6 149.835 125.742 106.637 1 31.2 ? O26 A1IKT 401 R 1 
HETATM 32 O O33 A1IKT . . . F 6 150.208 125.118 103.943 1 35.29 ? O33 A1IKT 401 R 1 
HETATM 33 O O34 A1IKT . . . F 6 149.002 126.742 101.988 1 43.61 ? O34 A1IKT 401 R 1 
HETATM 34 O O35 A1IKT . . . F 6 150.818 128.903 102.13 1 48.13 ? O35 A1IKT 401 R 1 
HETATM 35 O O36 A1IKT . . . F 6 152.583 128.975 104.335 1 34.14 ? O36 A1IKT 401 R 1 
HETATM 36 O O37 A1IKT . . . F 6 151.634 127.928 106.782 1 38.97 ? O37 A1IKT 401 R 1 
HETATM 37 O O38 A1IKT . . . F 6 149.582 130.045 108.471 1 26.36 ? O38 A1IKT 401 R 1 
HETATM 38 P P23 A1IKT . . . F 6 149.207 126.138 108.09 1 25 ? P23 A1IKT 401 R 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           260 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           38 
#