data_7PEM # _model_server_result.job_id D9IwqX1e3j4qyY2eUvObpA _model_server_result.datetime_utc '2024-12-27 03:21:50' _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 7pem # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1401}' # _entry.id 7PEM # _exptl.entry_id 7PEM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 967.108 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate' _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 7PEM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PEM _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,I,J _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 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 BMA BMA 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 3 n C NAG 1 B 1 NAG C 501 NAG 3 n C NAG 2 B 2 NAG C 502 NAG 3 n D NAG 1 D 1 NAG C 505 NAG 3 n D NAG 2 D 2 NAG C 506 NAG 4 n E NAG 1 E 1 NAG C 507 NAG 4 n E NAG 2 E 2 NAG C 508 NAG 4 n E BMA 3 E 3 BMA C 509 BMA 4 n E BMA 4 E 4 BMA C 510 BMA # 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 B SG CYS 80 C CYS 80 1_555 B SG CYS 123 C CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 B SG CYS 176 C CYS 176 1_555 B SG CYS 190 C CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A C SER 559 A SER 559 1_555 A N PHD 560 A PHD 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C PHD 560 A PHD 560 1_555 A N LYS 561 A LYS 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B ND2 ASN 199 C ASN 199 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale4 B ND2 ASN 216 C ASN 216 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale5 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 E O3 BMA . E BMA 3 1_555 E C1 BMA . E BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? metalc ? metalc1 A OD2 PHD 560 A PHD 560 1_555 G MG MG . A MG 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc2 A OP2 PHD 560 A PHD 560 1_555 G MG MG . A MG 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc3 A O THR 562 A THR 562 1_555 G MG MG . A MG 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc4 A O ASP 954 A ASP 954 1_555 G MG MG . A MG 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc5 G MG MG . A MG 1402 1_555 J O HOH . A HOH 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc6 G MG MG . A MG 1402 1_555 J O HOH . A HOH 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? # _chem_comp.formula 'C47 H84 O16 P2' _chem_comp.formula_weight 967.108 _chem_comp.id 2Y5 _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Phosphatidylinositol-4-phosphate;PI4P # _atom_sites.entry_id 7PEM _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 2Y5 A 1 1401 1301 2Y5 2Y5 . G 6 MG A 1 1402 1501 MG MG . H 7 ATP A 1 1403 1503 ATP ATP . I 8 Q3G A 1 1404 2031 Q3G Q3G . J 9 HOH A 1 1501 1602 HOH HOH . J 9 HOH A 2 1502 1601 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 C1 2Y5 . . . F 5 118.678 139.757 135.808 1 46.29 ? C1 2Y5 1401 A 1 HETATM 2 O O1 2Y5 . . . F 5 119.781 138.935 135.514 1 46.29 ? O1 2Y5 1401 A 1 HETATM 3 P P1 2Y5 . . . F 5 119.598 137.791 134.341 1 46.29 ? P1 2Y5 1401 A 1 HETATM 4 C C2 2Y5 . . . F 5 118.877 141.146 135.164 1 46.29 ? C2 2Y5 1401 A 1 HETATM 5 O O2 2Y5 . . . F 5 119.432 140.972 133.884 1 46.29 ? O2 2Y5 1401 A 1 HETATM 6 C C3 2Y5 . . . F 5 119.794 142.081 135.966 1 46.29 ? C3 2Y5 1401 A 1 HETATM 7 O O3 2Y5 . . . F 5 119.707 143.377 135.428 1 46.29 ? O3 2Y5 1401 A 1 HETATM 8 C C4 2Y5 . . . F 5 119.396 142.131 137.446 1 46.29 ? C4 2Y5 1401 A 1 HETATM 9 O O4 2Y5 . . . F 5 120.223 143.012 138.174 1 46.29 ? O4 2Y5 1401 A 1 HETATM 10 P P4 2Y5 . . . F 5 121.857 143.095 137.942 1 46.29 ? P4 2Y5 1401 A 1 HETATM 11 C C5 2Y5 . . . F 5 119.43 140.727 138.065 1 46.29 ? C5 2Y5 1401 A 1 HETATM 12 O O5 2Y5 . . . F 5 119.052 140.81 139.416 1 46.29 ? O5 2Y5 1401 A 1 HETATM 13 C C6 2Y5 . . . F 5 118.466 139.783 137.333 1 46.29 ? C6 2Y5 1401 A 1 HETATM 14 O O6 2Y5 . . . F 5 117.147 140.193 137.598 1 46.29 ? O6 2Y5 1401 A 1 HETATM 15 C C7 2Y5 . . . F 5 118.686 135.33 134.218 1 46.29 ? C7 2Y5 1401 A 1 HETATM 16 C C8 2Y5 . . . F 5 117.54 135.401 133.209 1 46.29 ? C8 2Y5 1401 A 1 HETATM 17 C C9 2Y5 . . . F 5 117.367 134.038 132.543 1 46.29 ? C9 2Y5 1401 A 1 HETATM 18 C C10 2Y5 . . . F 5 115.808 136.969 133.42 1 46.29 ? C10 2Y5 1401 A 1 HETATM 19 C C11 2Y5 . . . F 5 117.797 134.137 130.243 1 46.29 ? C11 2Y5 1401 A 1 HETATM 20 O O11 2Y5 . . . F 5 120.956 137.312 133.888 1 46.29 ? O11 2Y5 1401 A 1 HETATM 21 C C12 2Y5 . . . F 5 115.567 137.206 131.931 1 46.29 ? C12 2Y5 1401 A 1 HETATM 22 O O12 2Y5 . . . F 5 118.858 138.387 133.169 1 46.29 ? O12 2Y5 1401 A 1 HETATM 23 C C13 2Y5 . . . F 5 114.119 136.863 131.588 1 46.29 ? C13 2Y5 1401 A 1 HETATM 24 O O13 2Y5 . . . F 5 118.746 136.519 134.953 1 46.29 ? O13 2Y5 1401 A 1 HETATM 25 C C14 2Y5 . . . F 5 113.931 136.911 130.074 1 46.29 ? C14 2Y5 1401 A 1 HETATM 26 C C15 2Y5 . . . F 5 112.46 136.67 129.74 1 46.29 ? C15 2Y5 1401 A 1 HETATM 27 C C16 2Y5 . . . F 5 112.124 135.914 128.717 1 46.29 ? C16 2Y5 1401 A 1 HETATM 28 O O16 2Y5 . . . F 5 116.355 135.758 133.861 1 46.29 ? O16 2Y5 1401 A 1 HETATM 29 C C17 2Y5 . . . F 5 113.199 135.266 127.847 1 46.29 ? C17 2Y5 1401 A 1 HETATM 30 O O17 2Y5 . . . F 5 115.531 137.813 134.205 1 46.29 ? O17 2Y5 1401 A 1 HETATM 31 C C18 2Y5 . . . F 5 113.168 135.899 126.458 1 46.29 ? C18 2Y5 1401 A 1 HETATM 32 O O18 2Y5 . . . F 5 118.313 133.905 131.522 1 46.29 ? O18 2Y5 1401 A 1 HETATM 33 C C19 2Y5 . . . F 5 113.377 135.16 125.389 1 46.29 ? C19 2Y5 1401 A 1 HETATM 34 O O19 2Y5 . . . F 5 117.896 135.209 129.75 1 46.29 ? O19 2Y5 1401 A 1 HETATM 35 C C20 2Y5 . . . F 5 113.343 135.805 124.005 1 46.29 ? C20 2Y5 1401 A 1 HETATM 36 C C21 2Y5 . . . F 5 112.391 136.998 124.028 1 46.29 ? C21 2Y5 1401 A 1 HETATM 37 C C22 2Y5 . . . F 5 111.533 137.188 123.048 1 46.29 ? C22 2Y5 1401 A 1 HETATM 38 C C23 2Y5 . . . F 5 111.476 136.219 121.869 1 46.29 ? C23 2Y5 1401 A 1 HETATM 39 C C24 2Y5 . . . F 5 111.371 137.013 120.569 1 46.29 ? C24 2Y5 1401 A 1 HETATM 40 C C25 2Y5 . . . F 5 111.42 136.399 119.404 1 46.29 ? C25 2Y5 1401 A 1 HETATM 41 C C26 2Y5 . . . F 5 111.581 134.882 119.335 1 46.29 ? C26 2Y5 1401 A 1 HETATM 42 C C27 2Y5 . . . F 5 111.202 134.398 117.937 1 46.29 ? C27 2Y5 1401 A 1 HETATM 43 C C28 2Y5 . . . F 5 111.205 132.872 117.903 1 46.29 ? C28 2Y5 1401 A 1 HETATM 44 C C29 2Y5 . . . F 5 110.691 132.394 116.547 1 46.29 ? C29 2Y5 1401 A 1 HETATM 45 C C30 2Y5 . . . F 5 110.416 130.893 116.605 1 46.29 ? C30 2Y5 1401 A 1 HETATM 46 C C31 2Y5 . . . F 5 117.107 133.007 129.485 1 46.29 ? C31 2Y5 1401 A 1 HETATM 47 C C32 2Y5 . . . F 5 117.394 133.149 127.992 1 46.29 ? C32 2Y5 1401 A 1 HETATM 48 C C33 2Y5 . . . F 5 116.401 132.294 127.211 1 46.29 ? C33 2Y5 1401 A 1 HETATM 49 C C34 2Y5 . . . F 5 116.213 132.87 125.809 1 46.29 ? C34 2Y5 1401 A 1 HETATM 50 C C35 2Y5 . . . F 5 115.958 131.743 124.807 1 46.29 ? C35 2Y5 1401 A 1 HETATM 51 C C36 2Y5 . . . F 5 115.072 130.666 125.43 1 46.29 ? C36 2Y5 1401 A 1 HETATM 52 C C37 2Y5 . . . F 5 115.272 129.347 124.686 1 46.29 ? C37 2Y5 1401 A 1 HETATM 53 C C38 2Y5 . . . F 5 116.702 128.858 124.9 1 46.29 ? C38 2Y5 1401 A 1 HETATM 54 C C39 2Y5 . . . F 5 116.826 127.419 124.404 1 46.29 ? C39 2Y5 1401 A 1 HETATM 55 C C40 2Y5 . . . F 5 118.194 127.217 123.757 1 46.29 ? C40 2Y5 1401 A 1 HETATM 56 C C41 2Y5 . . . F 5 118.253 125.828 123.125 1 46.29 ? C41 2Y5 1401 A 1 HETATM 57 O O41 2Y5 . . . F 5 122.163 144.031 136.797 1 46.29 ? O41 2Y5 1401 A 1 HETATM 58 C C42 2Y5 . . . F 5 118.814 125.938 121.71 1 46.29 ? C42 2Y5 1401 A 1 HETATM 59 O O42 2Y5 . . . F 5 122.497 143.642 139.196 1 46.29 ? O42 2Y5 1401 A 1 HETATM 60 C C43 2Y5 . . . F 5 119.006 124.541 121.124 1 46.29 ? C43 2Y5 1401 A 1 HETATM 61 O O43 2Y5 . . . F 5 122.439 141.731 137.652 1 46.29 ? O43 2Y5 1401 A 1 HETATM 62 C C44 2Y5 . . . F 5 119.024 124.625 119.6 1 46.29 ? C44 2Y5 1401 A 1 HETATM 63 C C45 2Y5 . . . F 5 119.93 123.53 119.041 1 46.29 ? C45 2Y5 1401 A 1 HETATM 64 C C46 2Y5 . . . F 5 119.919 123.585 117.515 1 46.29 ? C46 2Y5 1401 A 1 HETATM 65 C C47 2Y5 . . . F 5 121.117 122.812 116.968 1 46.29 ? C47 2Y5 1401 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 65 #