data_7PEM # _model_server_result.job_id URUrJemh_BA0KGbw3HcXuw _model_server_result.datetime_utc '2024-12-27 03:27:00' _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":"I","auth_seq_id":1404}' # _entry.id 7PEM # _exptl.entry_id 7PEM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 764.022 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine _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 8 _struct_asym.id I _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 'C40 H78 N O10 P' _chem_comp.formula_weight 764.022 _chem_comp.id Q3G _chem_comp.mon_nstd_flag . _chem_comp.name O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _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 C10 Q3G . . . I 8 147.236 130.959 137.099 1 53 ? C10 Q3G 1404 A 1 HETATM 2 C C13 Q3G . . . I 8 144.668 130.125 139.814 1 53 ? C13 Q3G 1404 A 1 HETATM 3 C C15 Q3G . . . I 8 142.999 129.024 138.319 1 53 ? C15 Q3G 1404 A 1 HETATM 4 C C17 Q3G . . . I 8 143.975 126.768 137.909 1 53 ? C17 Q3G 1404 A 1 HETATM 5 C C21 Q3G . . . I 8 144.256 123.022 137.593 1 53 ? C21 Q3G 1404 A 1 HETATM 6 C C22 Q3G . . . I 8 144.706 122.411 136.268 1 53 ? C22 Q3G 1404 A 1 HETATM 7 C C09 Q3G . . . I 8 147.472 132.304 136.418 1 53 ? C09 Q3G 1404 A 1 HETATM 8 C C11 Q3G . . . I 8 146.432 131.168 138.38 1 53 ? C11 Q3G 1404 A 1 HETATM 9 C C12 Q3G . . . I 8 145.744 129.859 138.761 1 53 ? C12 Q3G 1404 A 1 HETATM 10 C C14 Q3G . . . I 8 143.594 129.041 139.726 1 53 ? C14 Q3G 1404 A 1 HETATM 11 C C16 Q3G . . . I 8 142.686 127.589 137.9 1 53 ? C16 Q3G 1404 A 1 HETATM 12 C C18 Q3G . . . I 8 143.645 125.281 137.798 1 53 ? C18 Q3G 1404 A 1 HETATM 13 C C23 Q3G . . . I 8 143.712 122.793 135.173 1 53 ? C23 Q3G 1404 A 1 HETATM 14 C C29 Q3G . . . I 8 142.319 119.901 131.824 1 53 ? C29 Q3G 1404 A 1 HETATM 15 C C30 Q3G . . . I 8 141.395 119.25 130.797 1 53 ? C30 Q3G 1404 A 1 HETATM 16 C C31 Q3G . . . I 8 142.23 118.607 129.693 1 53 ? C31 Q3G 1404 A 1 HETATM 17 C C36 Q3G . . . I 8 146.999 121.945 136.065 1 53 ? C36 Q3G 1404 A 1 HETATM 18 C C38 Q3G . . . I 8 148.457 122.397 136.107 1 53 ? C38 Q3G 1404 A 1 HETATM 19 C C39 Q3G . . . I 8 149.13 122.092 134.77 1 53 ? C39 Q3G 1404 A 1 HETATM 20 C C40 Q3G . . . I 8 148.553 122.989 133.677 1 53 ? C40 Q3G 1404 A 1 HETATM 21 C C41 Q3G . . . I 8 149.253 122.681 132.355 1 53 ? C41 Q3G 1404 A 1 HETATM 22 C C42 Q3G . . . I 8 148.727 123.612 131.266 1 53 ? C42 Q3G 1404 A 1 HETATM 23 C C43 Q3G . . . I 8 149.503 124.928 131.299 1 53 ? C43 Q3G 1404 A 1 HETATM 24 C C44 Q3G . . . I 8 150.792 124.787 130.492 1 53 ? C44 Q3G 1404 A 1 HETATM 25 C C45 Q3G . . . I 8 151.69 125.995 130.755 1 53 ? C45 Q3G 1404 A 1 HETATM 26 N N34 Q3G . . . I 8 140.527 120.26 130.221 1 53 ? N34 Q3G 1404 A 1 HETATM 27 O O19 Q3G . . . I 8 142.519 124.915 137.839 1 53 ? O19 Q3G 1404 A 1 HETATM 28 O O20 Q3G . . . I 8 144.679 124.353 137.64 1 53 ? O20 Q3G 1404 A 1 HETATM 29 O O24 Q3G . . . I 8 143.325 121.658 134.451 1 53 ? O24 Q3G 1404 A 1 HETATM 30 O O26 Q3G . . . I 8 140.776 121.929 134.723 1 53 ? O26 Q3G 1404 A 1 HETATM 31 O O27 Q3G . . . I 8 141.835 122.766 132.66 1 53 ? O27 Q3G 1404 A 1 HETATM 32 O O28 Q3G . . . I 8 141.589 120.218 132.974 1 53 ? O28 Q3G 1404 A 1 HETATM 33 O O32 Q3G . . . I 8 143.449 118.36 129.887 1 53 ? O32 Q3G 1404 A 1 HETATM 34 O O33 Q3G . . . I 8 141.7 118.324 128.587 1 53 ? O33 Q3G 1404 A 1 HETATM 35 O O35 Q3G . . . I 8 145.978 122.893 135.941 1 53 ? O35 Q3G 1404 A 1 HETATM 36 O O37 Q3G . . . I 8 146.735 120.793 136.137 1 53 ? O37 Q3G 1404 A 1 HETATM 37 P P25 Q3G . . . I 8 141.857 121.673 133.701 1 53 ? P25 Q3G 1404 A 1 HETATM 38 C C8 Q3G . . . I 8 147.853 132.074 134.96 1 53 ? C8 Q3G 1404 A 1 HETATM 39 C C7 Q3G . . . I 8 147.427 133.279 134.129 1 53 ? C7 Q3G 1404 A 1 HETATM 40 C C6 Q3G . . . I 8 148.535 134.327 134.148 1 53 ? C6 Q3G 1404 A 1 HETATM 41 C C5 Q3G . . . I 8 148.292 135.336 133.031 1 53 ? C5 Q3G 1404 A 1 HETATM 42 C C4 Q3G . . . I 8 149.481 136.285 132.931 1 53 ? C4 Q3G 1404 A 1 HETATM 43 C C3 Q3G . . . I 8 149.499 136.928 131.547 1 53 ? C3 Q3G 1404 A 1 HETATM 44 C C2 Q3G . . . I 8 150.688 137.879 131.44 1 53 ? C2 Q3G 1404 A 1 HETATM 45 C C46 Q3G . . . I 8 152.531 126.294 129.515 1 53 ? C46 Q3G 1404 A 1 HETATM 46 C C47 Q3G . . . I 8 151.613 126.477 128.307 1 53 ? C47 Q3G 1404 A 1 HETATM 47 C C48 Q3G . . . I 8 152.401 127.076 127.142 1 53 ? C48 Q3G 1404 A 1 HETATM 48 C C49 Q3G . . . I 8 152.661 128.557 127.411 1 53 ? C49 Q3G 1404 A 1 HETATM 49 C C50 Q3G . . . I 8 153.294 129.195 126.174 1 53 ? C50 Q3G 1404 A 1 HETATM 50 C C51 Q3G . . . I 8 153.495 130.69 126.415 1 53 ? C51 Q3G 1404 A 1 HETATM 51 C C1 Q3G . . . I 8 150.956 138.196 129.971 1 53 ? C1 Q3G 1404 A 1 HETATM 52 C C52 Q3G . . . I 8 153.931 131.361 125.115 1 53 ? C52 Q3G 1404 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 52 #