data_8AGC # _model_server_result.job_id 234HGyF3FbFrJCwnWYi8cQ _model_server_result.datetime_utc '2024-11-14 23:30:01' _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 8agc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1001}' # _entry.id 8AGC # _exptl.entry_id 8AGC _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 452.459 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate' _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 8AGC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AGC _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 nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,P,Q,R,S,T,U,V,W,X _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 # _struct_asym.details ? _struct_asym.entity_id 13 _struct_asym.id N _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 10 oligosaccharide 11 oligosaccharide 12 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 10 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 10 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 10 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 10 5 4 MAN MAN C1 O1 . O2 HO2 . sing 5 ? 10 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 10 7 3 MAN BMA C1 O1 . O6 HO6 . sing 7 ? 11 2 1 NAG NAG C1 O1 . O4 HO4 . sing 8 ? 12 2 1 NAG NDG C1 O1 . O4 HO4 . sing 9 ? 12 3 2 BMA NAG C1 O1 . O4 HO4 . sing 10 ? 12 4 3 MAN BMA C1 O1 . O3 HO3 . sing 11 ? 12 5 4 MAN MAN C1 O1 . O2 HO2 . sing 12 ? 12 6 5 MAN MAN C1 O1 . O2 HO2 . sing 13 ? 12 7 6 GLC MAN C1 O1 . O3 HO3 . sing 14 ? 12 8 7 GLC GLC C1 O1 . O3 HO3 . sing 15 ? 12 9 8 GLC GLC C1 O1 . O2 HO2 . sing 16 ? 12 10 3 MAN BMA C1 O1 . O6 HO6 . sing 17 ? 12 11 10 MAN MAN C1 O1 . O3 HO3 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 10 n J NAG 1 I 1 NAG A 1002 NAG 10 n J NAG 2 I 2 NAG A 1009 NAG 10 n J BMA 3 I 3 BMA A 1010 BMA 10 n J MAN 4 I 4 MAN A 1011 MAN 10 n J MAN 5 I 5 MAN A 1006 MAN 10 n J MAN 6 I 6 MAN A 1007 MAN 10 n J MAN 7 I 7 MAN A 1008 MAN 11 n K NAG 1 J 1 NAG I 1 NAG 11 n K NAG 2 J 2 NAG I 2 NAG 11 n L NAG 1 K 1 NAG J 1 NAG 11 n L NAG 2 K 2 NAG J 2 NAG 12 n M NDG 1 L 1 NDG K 1 NDG 12 n M NAG 2 L 2 NAG K 2 NAG 12 n M BMA 3 L 3 BMA K 3 BMA 12 n M MAN 4 L 4 MAN K 4 MAN 12 n M MAN 5 L 5 MAN K 5 MAN 12 n M MAN 6 L 6 MAN K 6 MAN 12 n M GLC 7 L 7 GLC K 7 GLC 12 n M GLC 8 L 8 GLC K 8 GLC 12 n M GLC 9 L 9 GLC K 9 GLC 12 n M MAN 10 L 10 MAN K 10 MAN 12 n M MAN 11 L 11 MAN K 11 MAN # 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 ND2 ASN 539 A ASN 539 1_555 J C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 N O1B ELU . A ELU 1001 1_555 M C1 NDG . L NDG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale3 E ND2 ASN 336 E ASN 336 1_555 K C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 E ND2 ASN 400 E ASN 400 1_555 L C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale5 G ND2 ASN 60 G ASN 60 1_555 V C1 NAG . G NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale6 G ND2 ASN 332 G ASN 332 1_555 U C1 NAG . G NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 I N TYR 1 P TYR 2 1_555 X C25 323 . P 323 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale8 I C ALA 2 P ALA 3 1_555 I N DAB 3 P DAB 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 I C DAB 3 P DAB 4 1_555 I N ALA 4 P ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 J O4 NAG . I NAG 1 1_555 J C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale11 J O4 NAG . I NAG 2 1_555 J C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale12 J O3 BMA . I BMA 3 1_555 J C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 J O6 BMA . I BMA 3 1_555 J C1 MAN . I MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 J O2 MAN . I MAN 4 1_555 J C1 MAN . I MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale15 J O2 MAN . I MAN 5 1_555 J C1 MAN . I MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale16 K O4 NAG . J NAG 1 1_555 K C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale17 L O4 NAG . K NAG 1 1_555 L C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale18 M O4 NDG . L NDG 1 1_555 M C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 M O4 NAG . L NAG 2 1_555 M C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale20 M O3 BMA . L BMA 3 1_555 M C1 MAN . L MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale21 M O6 BMA . L BMA 3 1_555 M C1 MAN . L MAN 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale22 M O2 MAN . L MAN 4 1_555 M C1 MAN . L MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale23 M O2 MAN . L MAN 5 1_555 M C1 MAN . L MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale24 M O3 MAN . L MAN 6 1_555 M C1 GLC . L GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale25 M O3 GLC . L GLC 7 1_555 M C1 GLC . L GLC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale26 M O2 GLC . L GLC 8 1_555 M C1 GLC . L GLC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale27 M O3 MAN . L MAN 10 1_555 M C1 MAN . L MAN 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A OD2 ASP 166 A ASP 166 1_555 Q MN MN . A MN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 N O2B ELU . A ELU 1001 1_555 Q MN MN . A MN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? # _chem_comp.formula 'C20 H38 O7 P2' _chem_comp.formula_weight 452.459 _chem_comp.id ELU _chem_comp.mon_nstd_flag . _chem_comp.name 'phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate' _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 C9 C11 ELU sing 311 n n C9 C8 ELU sing 312 n n C14 C13 ELU sing 313 n n C10 C8 ELU sing 314 n n C11 C12 ELU sing 315 n n C8 C7 ELU doub 316 e n C20 C18 ELU sing 317 n n C7 C6 ELU sing 318 n n C13 C12 ELU doub 319 e n C13 C15 ELU sing 320 n n C16 C15 ELU sing 321 n n C16 C17 ELU sing 322 n n C6 C5 ELU sing 323 n n C18 C17 ELU doub 324 n n C18 C19 ELU sing 325 n n C5 C3 ELU sing 326 n n C2 C3 ELU sing 327 n n C2 C1 ELU sing 328 n n C3 C4 ELU sing 329 n n C1 O1 ELU sing 330 n n O1 PA ELU sing 331 n n O2B PB ELU doub 332 n n PA O2A ELU doub 333 n n PA O3A ELU sing 334 n n PA O1A ELU sing 335 n n O3A PB ELU sing 336 n n PB O3B ELU sing 337 n n PB O1B ELU sing 338 n n O1A H1 ELU sing 339 n n O1B H2 ELU sing 340 n n O3B H3 ELU sing 341 n n C1 H4 ELU sing 342 n n C1 H5 ELU sing 343 n n C2 H6 ELU sing 344 n n C2 H7 ELU sing 345 n n C3 H8 ELU sing 346 n n C4 H9 ELU sing 347 n n C4 H10 ELU sing 348 n n C4 H11 ELU sing 349 n n C5 H12 ELU sing 350 n n C5 H13 ELU sing 351 n n C6 H14 ELU sing 352 n n C6 H15 ELU sing 353 n n C7 H16 ELU sing 354 n n C10 H17 ELU sing 355 n n C10 H18 ELU sing 356 n n C10 H19 ELU sing 357 n n C9 H20 ELU sing 358 n n C9 H21 ELU sing 359 n n C11 H22 ELU sing 360 n n C11 H23 ELU sing 361 n n C12 H24 ELU sing 362 n n C14 H25 ELU sing 363 n n C14 H26 ELU sing 364 n n C14 H27 ELU sing 365 n n C15 H28 ELU sing 366 n n C15 H29 ELU sing 367 n n C16 H30 ELU sing 368 n n C16 H31 ELU sing 369 n n C17 H32 ELU sing 370 n n C20 H33 ELU sing 371 n n C20 H34 ELU sing 372 n n C20 H35 ELU sing 373 n n C19 H36 ELU sing 374 n n C19 H37 ELU sing 375 n n C19 H38 ELU sing 376 n n # _atom_sites.entry_id 8AGC _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 N 13 ELU A 1 1001 1001 ELU ELU . O 14 CPL A 1 1002 1003 CPL CPL . P 15 PTY A 1 1003 1004 PTY PTY . Q 16 MN A 1 1004 1005 MN MN . R 14 CPL C 1 101 101 CPL CPL . S 14 CPL E 1 501 501 CPL CPL . T 14 CPL F 1 301 301 CPL CPL . U 17 NAG G 1 501 501 NAG NAG . V 17 NAG G 1 502 502 NAG NAG . W 15 PTY H 1 901 901 PTY PTY . X 18 323 P 1 101 1 323 323 . # 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 O O2A ELU . . . N 13 156.383 153.853 155.614 1 57.34 ? O2A ELU 1001 A 1 HETATM 2 P PA ELU . . . N 13 157.835 154.11 155.925 1 57.34 ? PA ELU 1001 A 1 HETATM 3 O O1A ELU . . . N 13 158 155.502 156.48 1 57.34 ? O1A ELU 1001 A 1 HETATM 4 O O3A ELU . . . N 13 158.744 153.971 154.556 1 57.34 ? O3A ELU 1001 A 1 HETATM 5 P PB ELU . . . N 13 158.63 152.723 153.492 1 57.34 ? PB ELU 1001 A 1 HETATM 6 O O2B ELU . . . N 13 160.001 152.415 152.944 1 57.34 ? O2B ELU 1001 A 1 HETATM 7 O O1B ELU . . . N 13 157.703 153.092 152.357 1 57.34 ? O1B ELU 1001 A 1 HETATM 8 O O3B ELU . . . N 13 158.092 151.517 154.214 1 57.34 ? O3B ELU 1001 A 1 HETATM 9 O O1 ELU . . . N 13 158.346 153.026 157.051 1 57.34 ? O1 ELU 1001 A 1 HETATM 10 C C1 ELU . . . N 13 157.408 152.486 157.945 1 57.34 ? C1 ELU 1001 A 1 HETATM 11 C C2 ELU . . . N 13 158.062 152.377 159.315 1 57.34 ? C2 ELU 1001 A 1 HETATM 12 C C3 ELU . . . N 13 157.575 151.135 160.055 1 57.34 ? C3 ELU 1001 A 1 HETATM 13 C C4 ELU . . . N 13 156.08 151.243 160.306 1 57.34 ? C4 ELU 1001 A 1 HETATM 14 C C5 ELU . . . N 13 158.335 151.051 161.374 1 57.34 ? C5 ELU 1001 A 1 HETATM 15 C C6 ELU . . . N 13 157.635 150.139 162.378 1 57.34 ? C6 ELU 1001 A 1 HETATM 16 C C7 ELU . . . N 13 158.612 149.884 163.526 1 57.34 ? C7 ELU 1001 A 1 HETATM 17 C C8 ELU . . . N 13 158.284 149.21 164.61 1 57.34 ? C8 ELU 1001 A 1 HETATM 18 C C10 ELU . . . N 13 159.332 148.998 165.697 1 57.34 ? C10 ELU 1001 A 1 HETATM 19 C C9 ELU . . . N 13 156.875 148.663 164.816 1 57.34 ? C9 ELU 1001 A 1 HETATM 20 C C11 ELU . . . N 13 156.14 149.667 165.701 1 57.34 ? C11 ELU 1001 A 1 HETATM 21 C C12 ELU . . . N 13 154.664 149.295 165.806 1 57.34 ? C12 ELU 1001 A 1 HETATM 22 C C13 ELU . . . N 13 154.2 148.47 166.727 1 57.34 ? C13 ELU 1001 A 1 HETATM 23 C C14 ELU . . . N 13 152.707 148.175 166.731 1 57.34 ? C14 ELU 1001 A 1 HETATM 24 C C15 ELU . . . N 13 155.084 147.833 167.803 1 57.34 ? C15 ELU 1001 A 1 HETATM 25 C C16 ELU . . . N 13 155.127 148.75 169.021 1 57.34 ? C16 ELU 1001 A 1 HETATM 26 C C17 ELU . . . N 13 155.168 147.992 170.351 1 57.34 ? C17 ELU 1001 A 1 HETATM 27 C C18 ELU . . . N 13 154.156 147.349 170.9 1 57.34 ? C18 ELU 1001 A 1 HETATM 28 C C20 ELU . . . N 13 152.775 147.276 170.264 1 57.34 ? C20 ELU 1001 A 1 HETATM 29 C C19 ELU . . . N 13 154.362 146.657 172.238 1 57.34 ? C19 ELU 1001 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 29 #