data_7V6Y # _model_server_result.job_id dO3rbsOCeiZ9SsrltP7TAw _model_server_result.datetime_utc '2025-08-02 23:07:36' _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 7v6y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1203}' # _entry.id 7V6Y # _exptl.entry_id 7V6Y _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 481.474 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid' _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 7V6Y _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7V6Y _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 2 n B NAG 1 B 1 NAG B 1402 NAG 2 n B NAG 2 B 2 NAG B 1403 NAG # 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 A SG CYS 191 A CYS 189 1_555 A SG CYS 214 A CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 222 A CYS 220 1_555 A SG CYS 315 A CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 284 A CYS 282 1_555 A SG CYS 292 A CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 129 A ASN 127 1_555 F C1 NAG . A NAG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 A ND2 ASN 402 A ASN 400 1_555 H C1 NAG . A NAG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? # _chem_comp.formula 'C20 H36 N O10 P' _chem_comp.formula_weight 481.474 _chem_comp.id 5VI _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid' _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 O31 C29 5VI doub 1 n n N32 C28 5VI sing 2 n n O22 C21 5VI sing 3 n n O22 P23 5VI sing 4 n n C21 C20 5VI sing 5 n n O26 C27 5VI sing 6 n n O26 P23 5VI sing 7 n n C29 C28 5VI sing 8 n n C29 O30 5VI sing 9 n n C28 C27 5VI sing 10 n n O33 C20 5VI sing 11 n n O33 C34 5VI sing 12 n n P23 O25 5VI doub 13 n n P23 O24 5VI sing 14 n n C20 C19 5VI sing 15 n n C34 C36 5VI sing 16 n n C34 O35 5VI doub 17 n n C36 C37 5VI sing 18 n n C19 O18 5VI sing 19 n n C37 C38 5VI sing 20 n n O18 C16 5VI sing 21 n n C38 C39 5VI sing 22 n n C16 O17 5VI doub 23 n n C16 C15 5VI sing 24 n n C15 C14 5VI sing 25 n n C39 C40 5VI sing 26 n n C14 C13 5VI sing 27 n n C40 C41 5VI sing 28 n n C41 C42 5VI sing 29 n n C42 C43 5VI sing 30 n n C43 C44 5VI doub 31 n n C13 H1 5VI sing 32 n n C13 H2 5VI sing 33 n n C13 H3 5VI sing 34 n n C14 H4 5VI sing 35 n n C14 H5 5VI sing 36 n n C15 H6 5VI sing 37 n n C15 H7 5VI sing 38 n n C19 H8 5VI sing 39 n n C19 H9 5VI sing 40 n n C20 H10 5VI sing 41 n n C21 H11 5VI sing 42 n n C21 H12 5VI sing 43 n n O24 H13 5VI sing 44 n n C27 H14 5VI sing 45 n n C27 H15 5VI sing 46 n n C28 H16 5VI sing 47 n n O30 H17 5VI sing 48 n n N32 H18 5VI sing 49 n n N32 H19 5VI sing 50 n n C36 H21 5VI sing 51 n n C36 H22 5VI sing 52 n n C37 H23 5VI sing 53 n n C37 H24 5VI sing 54 n n C38 H25 5VI sing 55 n n C38 H26 5VI sing 56 n n C39 H27 5VI sing 57 n n C39 H28 5VI sing 58 n n C40 H29 5VI sing 59 n n C40 H30 5VI sing 60 n n C41 H31 5VI sing 61 n n C41 H32 5VI sing 62 n n C42 H33 5VI sing 63 n n C42 H34 5VI sing 64 n n C43 H35 5VI sing 65 n n C44 H36 5VI sing 66 n n C44 H37 5VI sing 67 n n # _atom_sites.entry_id 7V6Y _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 C 3 CLR A 1 1201 1201 CLR CLR . D 3 CLR A 1 1202 1202 CLR CLR . E 4 5VI A 1 1203 1203 5VI POP . F 5 NAG A 1 1204 1204 NAG NAG . G 5 NAG A 1 1205 1405 NAG NAG . H 5 NAG A 1 1206 1406 NAG NAG . # 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 C13 5VI . . . E 4 104.421 117.361 133.062 1 20 ? C13 5VI 1203 A 1 HETATM 2 C C14 5VI . . . E 4 105.568 116.407 132.752 1 20 ? C14 5VI 1203 A 1 HETATM 3 C C15 5VI . . . E 4 106.204 116.72 131.403 1 20 ? C15 5VI 1203 A 1 HETATM 4 C C16 5VI . . . E 4 107.213 115.661 130.967 1 20 ? C16 5VI 1203 A 1 HETATM 5 O O17 5VI . . . E 4 108.332 115.693 131.353 1 20 ? O17 5VI 1203 A 1 HETATM 6 O O18 5VI . . . E 4 106.792 114.647 130.107 1 20 ? O18 5VI 1203 A 1 HETATM 7 C C19 5VI . . . E 4 106.972 114.938 128.756 1 20 ? C19 5VI 1203 A 1 HETATM 8 C C20 5VI . . . E 4 105.826 114.302 127.983 1 20 ? C20 5VI 1203 A 1 HETATM 9 C C21 5VI . . . E 4 105.366 115.121 126.789 1 20 ? C21 5VI 1203 A 1 HETATM 10 O O22 5VI . . . E 4 103.971 115.164 126.764 1 20 ? O22 5VI 1203 A 1 HETATM 11 P P23 5VI . . . E 4 103.148 116.184 127.752 1 20 ? P23 5VI 1203 A 1 HETATM 12 O O24 5VI . . . E 4 102.303 115.362 128.679 1 20 ? O24 5VI 1203 A 1 HETATM 13 O O25 5VI . . . E 4 104.094 117.035 128.554 1 20 ? O25 5VI 1203 A 1 HETATM 14 O O26 5VI . . . E 4 102.171 117.172 126.877 1 20 ? O26 5VI 1203 A 1 HETATM 15 C C27 5VI . . . E 4 100.977 117.593 127.464 1 20 ? C27 5VI 1203 A 1 HETATM 16 C C28 5VI . . . E 4 100.855 119.092 127.239 1 20 ? C28 5VI 1203 A 1 HETATM 17 C C29 5VI . . . E 4 102.208 119.713 126.919 1 20 ? C29 5VI 1203 A 1 HETATM 18 O O30 5VI . . . E 4 103.088 119.796 127.81 1 20 ? O30 5VI 1203 A 1 HETATM 19 O O31 5VI . . . E 4 102.449 120.14 125.763 1 20 ? O31 5VI 1203 A 1 HETATM 20 N N32 5VI . . . E 4 99.91 119.365 126.177 1 20 ? N32 5VI 1203 A 1 HETATM 21 O O33 5VI . . . E 4 106.247 113.057 127.538 1 20 ? O33 5VI 1203 A 1 HETATM 22 C C34 5VI . . . E 4 105.647 112.07 128.31 1 20 ? C34 5VI 1203 A 1 HETATM 23 O O35 5VI . . . E 4 104.627 112.313 128.856 1 20 ? O35 5VI 1203 A 1 HETATM 24 C C36 5VI . . . E 4 106.293 110.711 128.513 1 20 ? C36 5VI 1203 A 1 HETATM 25 C C37 5VI . . . E 4 106.109 110.31 129.967 1 20 ? C37 5VI 1203 A 1 HETATM 26 C C38 5VI . . . E 4 106.888 111.223 130.906 1 20 ? C38 5VI 1203 A 1 HETATM 27 C C39 5VI . . . E 4 106.009 111.78 132.012 1 20 ? C39 5VI 1203 A 1 HETATM 28 C C40 5VI . . . E 4 106.702 111.684 133.357 1 20 ? C40 5VI 1203 A 1 HETATM 29 C C41 5VI . . . E 4 105.814 112.234 134.454 1 20 ? C41 5VI 1203 A 1 HETATM 30 C C42 5VI . . . E 4 106.471 112.022 135.8 1 20 ? C42 5VI 1203 A 1 HETATM 31 C C43 5VI . . . E 4 106.415 113.287 136.631 1 20 ? C43 5VI 1203 A 1 HETATM 32 C C44 5VI . . . E 4 107.39 113.519 137.473 1 20 ? C44 5VI 1203 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 32 #