data_6AGF # _model_server_result.job_id wUE5eKwfxzYD0_lcEgRZ-w _model_server_result.datetime_utc '2024-11-22 12:21:10' _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 6agf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1911}' # _entry.id 6AGF # _exptl.entry_id 6AGF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 717.996 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 5 F N N ? 5 G N N ? 5 H N N ? 5 I N N ? 5 J N N ? 5 K N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . 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 3 n C NAG 1 C 1 NAG A 1901 NAG 3 n C NAG 2 C 2 NAG A 1902 NAG 3 n C BMA 3 C 3 BMA A 1903 BMA 4 n D NAG 1 D 1 NAG A 1904 NAG 4 n D NAG 2 D 2 NAG A 1905 NAG 4 n E NAG 1 E 1 NAG A 1906 NAG 4 n E NAG 2 E 2 NAG A 1907 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 323 A CYS 280 1_555 A SG CYS 403 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf2 A SG CYS 412 A CYS 369 1_555 A SG CYS 418 A CYS 375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? disulf ? disulf3 A SG CYS 774 A CYS 731 1_555 A SG CYS 780 A CYS 737 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 1232 A CYS 1189 1_555 A SG CYS 1252 A CYS 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 A SG CYS 1596 A CYS 1553 1_555 A SG CYS 1611 A CYS 1568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? disulf ? disulf6 B SG CYS 21 B CYS 21 1_555 B SG CYS 43 B CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf7 B SG CYS 40 B CYS 40 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A ND2 ASN 405 A ASN 362 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale2 A ND2 ASN 1248 A ASN 1205 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 B ND2 ASN 110 B ASN 110 1_555 M C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 B ND2 ASN 114 B ASN 114 1_555 N C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _chem_comp.formula 'C39 H76 N O8 P' _chem_comp.formula_weight 717.996 _chem_comp.id 6OU _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate' _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 C48 C47 6OU sing 1 n n C48 C49 6OU sing 2 n n C47 C46 6OU sing 3 n n C41 C40 6OU doub 4 z n C41 C42 6OU sing 5 n n C40 C39 6OU sing 6 n n C27 C28 6OU sing 7 n n C27 O26 6OU sing 8 n n C28 N29 6OU sing 9 n n C01 C02 6OU sing 10 n n C42 C43 6OU sing 11 n n C02 C03 6OU sing 12 n n C45 C46 6OU sing 13 n n C45 C44 6OU sing 14 n n C39 C38 6OU sing 15 n n C33 C34 6OU sing 16 n n C33 C31 6OU sing 17 n n C44 C43 6OU sing 18 n n O26 P23 6OU sing 19 n n O24 P23 6OU doub 20 n n C35 C34 6OU sing 21 n n C35 C36 6OU sing 22 n n C38 C37 6OU sing 23 n n C36 C37 6OU sing 24 n n C31 O30 6OU sing 25 n n C31 O32 6OU doub 26 n n O22 P23 6OU sing 27 n n O22 C21 6OU sing 28 n n O30 C20 6OU sing 29 n n P23 O25 6OU sing 30 n n C03 C04 6OU sing 31 n n C04 C05 6OU sing 32 n n C19 C20 6OU sing 33 n n C19 O18 6OU sing 34 n n C21 C20 6OU sing 35 n n C15 C14 6OU sing 36 n n C15 C16 6OU sing 37 n n O18 C16 6OU sing 38 n n C14 C13 6OU sing 39 n n C05 C06 6OU sing 40 n n C16 O17 6OU doub 41 n n C06 C07 6OU sing 42 n n C11 C10 6OU sing 43 n n C11 C12 6OU sing 44 n n C13 C12 6OU sing 45 n n C10 C09 6OU sing 46 n n C07 C08 6OU sing 47 n n C09 C08 6OU sing 48 n n C01 H1 6OU sing 49 n n C01 H2 6OU sing 50 n n C01 H3 6OU sing 51 n n C02 H4 6OU sing 52 n n C02 H5 6OU sing 53 n n C03 H6 6OU sing 54 n n C03 H7 6OU sing 55 n n C04 H8 6OU sing 56 n n C04 H9 6OU sing 57 n n C05 H10 6OU sing 58 n n C05 H11 6OU sing 59 n n C06 H12 6OU sing 60 n n C06 H13 6OU sing 61 n n C07 H14 6OU sing 62 n n C07 H15 6OU sing 63 n n C08 H16 6OU sing 64 n n C08 H17 6OU sing 65 n n C09 H18 6OU sing 66 n n C09 H19 6OU sing 67 n n C10 H20 6OU sing 68 n n C10 H21 6OU sing 69 n n C11 H22 6OU sing 70 n n C11 H23 6OU sing 71 n n C12 H24 6OU sing 72 n n C12 H25 6OU sing 73 n n C13 H26 6OU sing 74 n n C13 H27 6OU sing 75 n n C14 H28 6OU sing 76 n n C14 H29 6OU sing 77 n n C15 H30 6OU sing 78 n n C15 H31 6OU sing 79 n n C19 H32 6OU sing 80 n n C19 H33 6OU sing 81 n n C20 H34 6OU sing 82 n n C21 H35 6OU sing 83 n n C21 H36 6OU sing 84 n n O25 H37 6OU sing 85 n n C27 H38 6OU sing 86 n n C27 H39 6OU sing 87 n n C28 H40 6OU sing 88 n n C28 H41 6OU sing 89 n n N29 H42 6OU sing 90 n n N29 H43 6OU sing 91 n n C33 H45 6OU sing 92 n n C33 H46 6OU sing 93 n n C34 H47 6OU sing 94 n n C34 H48 6OU sing 95 n n C35 H49 6OU sing 96 n n C35 H50 6OU sing 97 n n C36 H51 6OU sing 98 n n C36 H52 6OU sing 99 n n C37 H53 6OU sing 100 n n C37 H54 6OU sing 101 n n C38 H55 6OU sing 102 n n C38 H56 6OU sing 103 n n C39 H57 6OU sing 104 n n C39 H58 6OU sing 105 n n C40 H59 6OU sing 106 n n C41 H60 6OU sing 107 n n C42 H61 6OU sing 108 n n C42 H62 6OU sing 109 n n C43 H63 6OU sing 110 n n C43 H64 6OU sing 111 n n C44 H65 6OU sing 112 n n C44 H66 6OU sing 113 n n C45 H67 6OU sing 114 n n C45 H68 6OU sing 115 n n C46 H69 6OU sing 116 n n C46 H70 6OU sing 117 n n C47 H71 6OU sing 118 n n C47 H72 6OU sing 119 n n C48 H73 6OU sing 120 n n C48 H74 6OU sing 121 n n C49 H75 6OU sing 122 n n C49 H76 6OU sing 123 n n C49 H77 6OU sing 124 n n # _atom_sites.entry_id 6AGF _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 5 6OU A 1 1908 1 6OU LIG . G 5 6OU A 1 1909 2 6OU LIG . H 5 6OU A 1 1910 3 6OU LIG . I 5 6OU A 1 1911 4 6OU LIG . J 5 6OU A 1 1912 5 6OU LIG . K 5 6OU A 1 1913 6 6OU LIG . L 6 9Z9 A 1 1914 1 9Z9 GDN . M 7 NAG B 1 301 301 NAG NAG . N 7 NAG B 1 302 302 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 C11 6OU . . . I 5 126.814 147.221 125.081 1 31.78 ? C11 6OU 1911 A 1 HETATM 2 C C12 6OU . . . I 5 127.628 146.024 124.504 1 31.78 ? C12 6OU 1911 A 1 HETATM 3 C C13 6OU . . . I 5 128.289 145.239 125.671 1 31.78 ? C13 6OU 1911 A 1 HETATM 4 C C14 6OU . . . I 5 128.77 143.842 125.189 1 31.78 ? C14 6OU 1911 A 1 HETATM 5 C C15 6OU . . . I 5 129.452 143.09 126.374 1 31.78 ? C15 6OU 1911 A 1 HETATM 6 C C16 6OU . . . I 5 129.575 141.569 126.062 1 31.78 ? C16 6OU 1911 A 1 HETATM 7 O O17 6OU . . . I 5 130.337 141.185 125.255 1 31.78 ? O17 6OU 1911 A 1 HETATM 8 O O18 6OU . . . I 5 128.76 140.637 126.763 1 31.78 ? O18 6OU 1911 A 1 HETATM 9 C C19 6OU . . . I 5 129.238 139.307 126.724 1 31.78 ? C19 6OU 1911 A 1 HETATM 10 C C20 6OU . . . I 5 129.924 138.952 128.043 1 31.78 ? C20 6OU 1911 A 1 HETATM 11 C C21 6OU . . . I 5 130.815 137.713 127.832 1 31.78 ? C21 6OU 1911 A 1 HETATM 12 O O22 6OU . . . I 5 131.57 137.852 126.634 1 31.78 ? O22 6OU 1911 A 1 HETATM 13 P P23 6OU . . . I 5 133.049 138.645 126.684 1 31.78 ? P23 6OU 1911 A 1 HETATM 14 O O24 6OU . . . I 5 133.859 138.221 127.822 1 31.78 -1 O24 6OU 1911 A 1 HETATM 15 O O25 6OU . . . I 5 132.889 140.048 127.033 1 31.78 ? O25 6OU 1911 A 1 HETATM 16 O O26 6OU . . . I 5 133.845 138.471 125.221 1 31.78 ? O26 6OU 1911 A 1 HETATM 17 C C27 6OU . . . I 5 134.504 137.244 124.912 1 31.78 ? C27 6OU 1911 A 1 HETATM 18 C C28 6OU . . . I 5 135.935 137.31 125.458 1 31.78 ? C28 6OU 1911 A 1 HETATM 19 N N29 6OU . . . I 5 136.234 136.089 126.212 1 31.78 ? N29 6OU 1911 A 1 HETATM 20 O O30 6OU . . . I 5 128.974 138.682 129.039 1 31.78 ? O30 6OU 1911 A 1 HETATM 21 C C31 6OU . . . I 5 128.918 139.683 130.038 1 31.78 ? C31 6OU 1911 A 1 HETATM 22 O O32 6OU . . . I 5 129.676 139.642 130.946 1 31.78 ? O32 6OU 1911 A 1 HETATM 23 C C33 6OU . . . I 5 127.883 140.826 129.933 1 31.78 ? C33 6OU 1911 A 1 HETATM 24 C C34 6OU . . . I 5 128.634 142.176 129.93 1 31.78 ? C34 6OU 1911 A 1 HETATM 25 C C35 6OU . . . I 5 127.612 143.344 129.997 1 31.78 ? C35 6OU 1911 A 1 HETATM 26 C C36 6OU . . . I 5 126.63 143.247 128.791 1 31.78 ? C36 6OU 1911 A 1 HETATM 27 C C37 6OU . . . I 5 126 144.648 128.551 1 31.78 ? C37 6OU 1911 A 1 HETATM 28 C C38 6OU . . . I 5 124.977 144.938 129.675 1 31.78 ? C38 6OU 1911 A 1 HETATM 29 C C39 6OU . . . I 5 123.557 144.949 129.056 1 31.78 ? C39 6OU 1911 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #