data_6AGF # _model_server_result.job_id kI565FGGK929RpeJ-rESfw _model_server_result.datetime_utc '2024-11-02 20:28:11' _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":"H","auth_seq_id":1910}' # _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 ? # _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 C01 6OU . . . H 5 137.215 118.341 125.557 1 29.58 ? C01 6OU 1910 A 1 HETATM 2 C C02 6OU . . . H 5 136.591 119.699 125.926 1 29.58 ? C02 6OU 1910 A 1 HETATM 3 C C03 6OU . . . H 5 137.667 120.668 126.438 1 29.58 ? C03 6OU 1910 A 1 HETATM 4 C C04 6OU . . . H 5 138.723 120.87 125.329 1 29.58 ? C04 6OU 1910 A 1 HETATM 5 C C05 6OU . . . H 5 138.665 122.312 124.783 1 29.58 ? C05 6OU 1910 A 1 HETATM 6 C C06 6OU . . . H 5 139.776 123.178 125.457 1 29.58 ? C06 6OU 1910 A 1 HETATM 7 C C07 6OU . . . H 5 139.783 124.577 124.777 1 29.58 ? C07 6OU 1910 A 1 HETATM 8 C C08 6OU . . . H 5 138.921 125.555 125.616 1 29.58 ? C08 6OU 1910 A 1 HETATM 9 C C09 6OU . . . H 5 139.826 126.342 126.6 1 29.58 ? C09 6OU 1910 A 1 HETATM 10 C C10 6OU . . . H 5 138.945 127.431 127.256 1 29.58 ? C10 6OU 1910 A 1 HETATM 11 C C11 6OU . . . H 5 139.783 128.285 128.239 1 29.58 ? C11 6OU 1910 A 1 HETATM 12 C C12 6OU . . . H 5 139.683 127.727 129.684 1 29.58 ? C12 6OU 1910 A 1 HETATM 13 C C13 6OU . . . H 5 138.188 127.595 130.072 1 29.58 ? C13 6OU 1910 A 1 HETATM 14 C C14 6OU . . . H 5 137.608 129.011 130.334 1 29.58 ? C14 6OU 1910 A 1 HETATM 15 C C15 6OU . . . H 5 136.241 129.154 129.601 1 29.58 ? C15 6OU 1910 A 1 HETATM 16 C C16 6OU . . . H 5 135.299 130.076 130.418 1 29.58 ? C16 6OU 1910 A 1 HETATM 17 O O17 6OU . . . H 5 134.423 129.6 131.043 1 29.58 ? O17 6OU 1910 A 1 HETATM 18 O O18 6OU . . . H 5 135.493 131.488 130.423 1 29.58 ? O18 6OU 1910 A 1 HETATM 19 C C19 6OU . . . H 5 135.798 132.044 129.157 1 29.58 ? C19 6OU 1910 A 1 HETATM 20 C C20 6OU . . . H 5 135.666 133.568 129.175 1 29.58 ? C20 6OU 1910 A 1 HETATM 21 C C21 6OU . . . H 5 134.241 133.984 128.784 1 29.58 ? C21 6OU 1910 A 1 HETATM 22 O O22 6OU . . . H 5 133.305 133.158 129.464 1 29.58 ? O22 6OU 1910 A 1 HETATM 23 P P23 6OU . . . H 5 132.946 133.51 131.062 1 29.58 ? P23 6OU 1910 A 1 HETATM 24 O O24 6OU . . . H 5 134.023 133.102 131.966 1 29.58 -1 O24 6OU 1910 A 1 HETATM 25 O O25 6OU . . . H 5 132.929 134.956 131.272 1 29.58 ? O25 6OU 1910 A 1 HETATM 26 O O26 6OU . . . H 5 131.491 132.811 131.485 1 29.58 ? O26 6OU 1910 A 1 HETATM 27 C C27 6OU . . . H 5 131.469 131.429 131.838 1 29.58 ? C27 6OU 1910 A 1 HETATM 28 C C28 6OU . . . H 5 130.013 131.001 132.079 1 29.58 ? C28 6OU 1910 A 1 HETATM 29 N N29 6OU . . . H 5 129.924 129.538 132.09 1 29.58 ? N29 6OU 1910 A 1 HETATM 30 O O30 6OU . . . H 5 136.529 134.101 128.218 1 29.58 ? O30 6OU 1910 A 1 HETATM 31 C C31 6OU . . . H 5 137.662 134.746 128.754 1 29.58 ? C31 6OU 1910 A 1 HETATM 32 O O32 6OU . . . H 5 138.71 134.215 128.685 1 29.58 ? O32 6OU 1910 A 1 HETATM 33 C C33 6OU . . . H 5 137.512 136.122 129.43 1 29.58 ? C33 6OU 1910 A 1 HETATM 34 C C34 6OU . . . H 5 138.576 137.081 128.869 1 29.58 ? C34 6OU 1910 A 1 HETATM 35 C C35 6OU . . . H 5 139.784 137.102 129.841 1 29.58 ? C35 6OU 1910 A 1 HETATM 36 C C36 6OU . . . H 5 140.299 138.56 129.997 1 29.58 ? C36 6OU 1910 A 1 HETATM 37 C C37 6OU . . . H 5 140.507 139.241 128.619 1 29.58 ? C37 6OU 1910 A 1 HETATM 38 C C38 6OU . . . H 5 141.805 140.066 128.726 1 29.58 ? C38 6OU 1910 A 1 HETATM 39 C C39 6OU . . . H 5 142.657 139.816 127.456 1 29.58 ? C39 6OU 1910 A 1 HETATM 40 C C40 6OU . . . H 5 141.952 140.468 126.23 1 29.58 ? C40 6OU 1910 A 1 HETATM 41 C C41 6OU . . . H 5 142.666 140.85 125.16 1 29.58 ? C41 6OU 1910 A 1 HETATM 42 C C42 6OU . . . H 5 144.186 140.678 125.121 1 29.58 ? C42 6OU 1910 A 1 HETATM 43 C C43 6OU . . . H 5 144.696 140.734 123.656 1 29.58 ? C43 6OU 1910 A 1 HETATM 44 C C44 6OU . . . H 5 146.24 140.842 123.682 1 29.58 ? C44 6OU 1910 A 1 HETATM 45 C C45 6OU . . . H 5 146.767 140.861 122.225 1 29.58 ? C45 6OU 1910 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 45 #