data_7VSG # _model_server_result.job_id 5sLKrDMzQzFmelUArsJNVw _model_server_result.datetime_utc '2024-11-04 23:19:55' _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 7vsg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1101}' # _entry.id 7VSG # _exptl.entry_id 7VSG _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 788.043 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-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 7VSG _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VSG _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 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 _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 D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 MAN 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 D 1 NAG D 1 NAG 3 n C NAG 2 D 2 NAG D 2 NAG 3 n C MAN 3 D 3 MAN D 3 MAN # 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 91 B CYS 91 1_555 B SG CYS 104 B CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 94 B CYS 94 1_555 B SG CYS 102 B CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 157 B CYS 157 1_555 B SG CYS 171 B CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A C THR 401 A THR 408 1_555 A N BFD 402 A BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C BFD 402 A BFD 409 1_555 A N LYS 403 A LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 B ND2 ASN 107 B ASN 107 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 B ND2 ASN 180 B ASN 180 1_555 C C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 B ND2 ASN 294 B ASN 294 1_555 F C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 C O4 NAG . D NAG 1 1_555 C C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 C O4 NAG . D NAG 2 1_555 C C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? # _chem_comp.formula 'C42 H78 N O10 P' _chem_comp.formula_weight 788.043 _chem_comp.id 17F _chem_comp.mon_nstd_flag . _chem_comp.name O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,2-Dioleoyl-sn-glycero-3-phospho-L-serine # _atom_sites.entry_id 7VSG _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 D 4 17F A 1 1101 1 17F 17F . E 5 NAG B 1 401 5 NAG NAG . F 5 NAG B 1 402 7 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 C1 17F . . . D 4 99.232 108.915 91.049 1 35.72 ? C1 17F 1101 A 1 HETATM 2 N N1 17F . . . D 4 100.842 110.687 91.584 1 35.72 ? N1 17F 1101 A 1 HETATM 3 O O1 17F . . . D 4 100.539 106.446 91.562 1 35.72 ? O1 17F 1101 A 1 HETATM 4 P P1 17F . . . D 4 100.137 107.169 92.817 1 35.72 ? P1 17F 1101 A 1 HETATM 5 C C2 17F . . . D 4 100.557 109.545 90.675 1 35.72 ? C2 17F 1101 A 1 HETATM 6 O O2 17F . . . D 4 101.172 107.547 93.84 1 35.72 ? O2 17F 1101 A 1 HETATM 7 C C3 17F . . . D 4 100.557 110.03 89.221 1 35.72 ? C3 17F 1101 A 1 HETATM 8 O O3 17F . . . D 4 99.29 108.478 92.428 1 35.72 ? O3 17F 1101 A 1 HETATM 9 C C4 17F . . . D 4 97.829 105.92 92.764 1 35.72 ? C4 17F 1101 A 1 HETATM 10 O O4 17F . . . D 4 101.559 110.659 88.83 1 35.72 ? O4 17F 1101 A 1 HETATM 11 C C5 17F . . . D 4 96.686 105.506 93.664 1 35.72 ? C5 17F 1101 A 1 HETATM 12 O O5 17F . . . D 4 99.549 109.771 88.534 1 35.72 ? O5 17F 1101 A 1 HETATM 13 C C6 17F . . . D 4 95.382 105.345 92.915 1 35.72 ? C6 17F 1101 A 1 HETATM 14 O O6 17F . . . D 4 99.011 106.274 93.53 1 35.72 ? O6 17F 1101 A 1 HETATM 15 C C7 17F . . . D 4 93.169 104.667 93.331 1 35.72 ? C7 17F 1101 A 1 HETATM 16 O O7 17F . . . D 4 94.425 104.679 93.766 1 35.72 ? O7 17F 1101 A 1 HETATM 17 C C8 17F . . . D 4 92.352 103.621 94.032 1 35.72 ? C8 17F 1101 A 1 HETATM 18 O O8 17F . . . D 4 92.76 105.413 92.48 1 35.72 ? O8 17F 1101 A 1 HETATM 19 C C9 17F . . . D 4 91.317 104.185 94.953 1 35.72 ? C9 17F 1101 A 1 HETATM 20 O O9 17F . . . D 4 96.979 104.273 94.377 1 35.72 ? O9 17F 1101 A 1 HETATM 21 C C10 17F . . . D 4 91.924 104.82 96.198 1 35.72 ? C10 17F 1101 A 1 HETATM 22 O O10 17F . . . D 4 96.784 105.293 96.342 1 35.72 ? O10 17F 1101 A 1 HETATM 23 C C11 17F . . . D 4 90.908 105.229 97.236 1 35.72 ? C11 17F 1101 A 1 HETATM 24 C C12 17F . . . D 4 89.96 104.121 97.627 1 35.72 ? C12 17F 1101 A 1 HETATM 25 C C17 17F . . . D 4 96.795 104.272 95.707 1 35.72 ? C17 17F 1101 A 1 HETATM 26 C C18 17F . . . D 4 96.532 102.916 96.3 1 35.72 ? C18 17F 1101 A 1 HETATM 27 C C19 17F . . . D 4 96.358 102.953 97.787 1 35.72 ? C19 17F 1101 A 1 HETATM 28 C C20 17F . . . D 4 95.44 101.858 98.305 1 35.72 ? C20 17F 1101 A 1 HETATM 29 C C1X 17F . . . D 4 90.64 102.887 98.207 1 35.72 ? C1X 17F 1101 A 1 HETATM 30 C C1Y 17F . . . D 4 95.906 100.45 98.028 1 35.72 ? C1Y 17F 1101 A 1 HETATM 31 C C1Z 17F . . . D 4 94.981 99.387 98.571 1 35.72 ? C1Z 17F 1101 A 1 HETATM 32 C C2X 17F . . . D 4 90.967 102.976 99.665 1 35.72 ? C2X 17F 1101 A 1 HETATM 33 C C21 17F . . . D 4 89.746 102.961 100.531 1 35.72 ? C21 17F 1101 A 1 HETATM 34 C C22 17F . . . D 4 89.412 102.003 101.358 1 35.72 ? C22 17F 1101 A 1 HETATM 35 C C23 17F . . . D 4 88.17 101.965 102.193 1 35.72 ? C23 17F 1101 A 1 HETATM 36 C C24 17F . . . D 4 88.11 103.059 103.212 1 35.72 ? C24 17F 1101 A 1 HETATM 37 C C25 17F . . . D 4 89.14 102.935 104.321 1 35.72 ? C25 17F 1101 A 1 HETATM 38 C C26 17F . . . D 4 89.196 104.123 105.249 1 35.72 ? C26 17F 1101 A 1 HETATM 39 C C27 17F . . . D 4 87.875 104.473 105.888 1 35.72 ? C27 17F 1101 A 1 HETATM 40 C C28 17F . . . D 4 87.923 105.69 106.778 1 35.72 ? C28 17F 1101 A 1 HETATM 41 C C29 17F . . . D 4 86.593 106.069 107.378 1 35.72 ? C29 17F 1101 A 1 HETATM 42 C C30 17F . . . D 4 86.647 107.303 108.246 1 35.72 ? C30 17F 1101 A 1 HETATM 43 C C31 17F . . . D 4 95.455 97.957 98.342 1 35.72 ? C31 17F 1101 A 1 HETATM 44 C C32 17F . . . D 4 95.552 97.559 96.903 1 35.72 ? C32 17F 1101 A 1 HETATM 45 C C33 17F . . . D 4 94.234 97.563 96.192 1 35.72 ? C33 17F 1101 A 1 HETATM 46 C C34 17F . . . D 4 93.688 96.528 95.609 1 35.72 ? C34 17F 1101 A 1 HETATM 47 C C35 17F . . . D 4 94.282 95.155 95.528 1 35.72 ? C35 17F 1101 A 1 HETATM 48 C C36 17F . . . D 4 94.435 94.656 94.125 1 35.72 ? C36 17F 1101 A 1 HETATM 49 C C37 17F . . . D 4 94.999 93.249 94.019 1 35.72 ? C37 17F 1101 A 1 HETATM 50 C C38 17F . . . D 4 96.391 93.096 94.582 1 35.72 ? C38 17F 1101 A 1 HETATM 51 C C39 17F . . . D 4 96.951 91.697 94.487 1 35.72 ? C39 17F 1101 A 1 HETATM 52 C C40 17F . . . D 4 96.162 90.66 95.248 1 35.72 ? C40 17F 1101 A 1 HETATM 53 C C41 17F . . . D 4 96.737 89.268 95.192 1 35.72 ? C41 17F 1101 A 1 HETATM 54 C C42 17F . . . D 4 96.822 88.7 93.796 1 35.72 ? C42 17F 1101 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 54 #