data_7TYS # _model_server_result.job_id qR19z03weyeoQrahpUBlFQ _model_server_result.datetime_utc '2024-10-25 20:32:21' _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 7tys # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":403}' # _entry.id 7TYS # _exptl.entry_id 7TYS _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 792.075 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine _entity.pdbx_number_of_molecules 6 _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 7TYS _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7TYS _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA _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 ? 7 K N N ? 7 L N N ? 7 O N N ? 7 R N N ? 7 T N N ? 7 BA N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 F NAG 1 F 1 NAG E 2010 NAG 3 n F NAG 2 F 2 NAG E 2011 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 110 A CYS 110 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 110 B CYS 110 1_555 B SG CYS 142 B CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 C SG CYS 110 C CYS 110 1_555 C SG CYS 142 C CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 D SG CYS 110 D CYS 110 1_555 D SG CYS 142 D CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 E SG CYS 6 E CYS 6 1_555 E SG CYS 26 E CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 E ND2 ASN 10 E ASN 10 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 A O THR 130 A THR 130 1_555 I K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc2 A O ILE 131 A ILE 131 1_555 I K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.196 ? metalc ? metalc3 A O PHE 133 A PHE 133 1_555 H K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc4 H K K . A K 402 1_555 B O PHE 133 B PHE 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc5 H K K . A K 402 1_555 C O PHE 133 C PHE 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc6 H K K . A K 402 1_555 D O PHE 133 D PHE 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc7 I K K . A K 403 1_555 B O THR 130 B THR 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc8 I K K . A K 403 1_555 B O ILE 131 B ILE 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.076 ? metalc ? metalc9 I K K . A K 403 1_555 C O THR 130 C THR 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc10 I K K . A K 403 1_555 C O ILE 131 C ILE 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc11 I K K . A K 403 1_555 D O THR 130 D THR 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc12 I K K . A K 403 1_555 D O ILE 131 D ILE 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.175 ? # _chem_comp.formula 'C42 H82 N O10 P' _chem_comp.formula_weight 792.075 _chem_comp.id P5S _chem_comp.mon_nstd_flag . _chem_comp.name O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'phosphatidyl serine' # _atom_sites.entry_id 7TYS _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 G 4 ATP A 1 401 401 ATP ATP . H 5 K A 1 402 500 K K . I 5 K A 1 403 503 K K . J 6 POV A 1 404 505 POV POV . K 7 P5S A 1 405 508 P5S P5S . L 7 P5S A 1 406 507 P5S P5S . M 4 ATP B 1 401 401 ATP ATP . N 6 POV B 1 402 505 POV POV . O 7 P5S B 1 403 506 P5S P5S . P 4 ATP C 1 401 401 ATP ATP . Q 6 POV C 1 402 505 POV POV . R 7 P5S C 1 403 506 P5S P5S . S 4 ATP D 1 401 401 ATP ATP . T 7 P5S D 1 402 505 P5S P5S . U 6 POV D 1 403 506 POV POV . V 8 65I E 1 1601 506 65I PTY . W 9 BJX E 1 1602 2001 BJX BJX . X 4 ATP E 1 1603 2002 ATP ATP . Y 8 65I E 1 1604 2003 65I PTY . Z 8 65I E 1 1605 2004 65I PTY . AA 8 65I E 1 1606 2005 65I PTY . BA 7 P5S E 1 1607 2006 P5S P5S . CA 6 POV E 1 1608 2007 POV POV . DA 8 65I E 1 1609 2008 65I PTY . EA 8 65I E 1 1610 2009 65I PTY . # 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 C P5S . . . R 7 135.512 168.026 155.931 1 65.79 ? C P5S 403 C 1 HETATM 2 N N P5S . . . R 7 133.443 166.56 155.901 1 67.19 ? N P5S 403 C 1 HETATM 3 O O P5S . . . R 7 135.158 169.188 155.651 1 61.4 ? O P5S 403 C 1 HETATM 4 C C1 P5S . . . R 7 138.43 168.707 162.357 1 61.08 ? C1 P5S 403 C 1 HETATM 5 C C2 P5S . . . R 7 137.418 167.653 162.747 1 61.99 ? C2 P5S 403 C 1 HETATM 6 C C3 P5S . . . R 7 136.436 167.261 161.657 1 63.99 ? C3 P5S 403 C 1 HETATM 7 C CA P5S . . . R 7 134.502 167.138 156.704 1 68.26 ? CA P5S 403 C 1 HETATM 8 C CB P5S . . . R 7 135.289 166.034 157.403 1 65.33 ? CB P5S 403 C 1 HETATM 9 O OG P5S . . . R 7 135.674 166.419 158.708 1 66.26 ? OG P5S 403 C 1 HETATM 10 P P12 P5S . . . R 7 136.059 165.338 159.869 1 71.72 ? P12 P5S 403 C 1 HETATM 11 O O13 P5S . . . R 7 134.895 165.016 160.747 1 66.17 ? O13 P5S 403 C 1 HETATM 12 O O15 P5S . . . R 7 136.894 164.25 159.261 1 59.28 ? O15 P5S 403 C 1 HETATM 13 O O16 P5S . . . R 7 137.001 166.316 160.786 1 67.7 ? O16 P5S 403 C 1 HETATM 14 C C17 P5S . . . R 7 140.776 168.442 162.211 1 67.47 ? C17 P5S 403 C 1 HETATM 15 O O18 P5S . . . R 7 141.705 168.677 161.477 1 61.9 ? O18 P5S 403 C 1 HETATM 16 O O19 P5S . . . R 7 139.573 168.102 161.762 1 65.71 ? O19 P5S 403 C 1 HETATM 17 C C20 P5S . . . R 7 140.84 168.479 163.711 1 66.04 ? C20 P5S 403 C 1 HETATM 18 C C21 P5S . . . R 7 141.715 167.389 164.298 1 61.13 ? C21 P5S 403 C 1 HETATM 19 C C22 P5S . . . R 7 142.166 167.709 165.716 1 64.24 ? C22 P5S 403 C 1 HETATM 20 C C23 P5S . . . R 7 141.698 166.666 166.721 1 64.49 ? C23 P5S 403 C 1 HETATM 21 C C24 P5S . . . R 7 142.717 166.388 167.817 1 63.72 ? C24 P5S 403 C 1 HETATM 22 C C25 P5S . . . R 7 142.12 166.514 169.21 1 63.17 ? C25 P5S 403 C 1 HETATM 23 C C26 P5S . . . R 7 142.734 167.632 170.04 1 62.47 ? C26 P5S 403 C 1 HETATM 24 C C27 P5S . . . R 7 143.006 167.205 171.474 1 61.61 ? C27 P5S 403 C 1 HETATM 25 C C28 P5S . . . R 7 142.004 167.703 172.504 1 61.98 ? C28 P5S 403 C 1 HETATM 26 C C29 P5S . . . R 7 140.699 166.918 172.476 1 62.53 ? C29 P5S 403 C 1 HETATM 27 C C30 P5S . . . R 7 140.483 166.064 173.716 1 62.66 ? C30 P5S 403 C 1 HETATM 28 C C31 P5S . . . R 7 139.045 165.595 173.895 1 65.98 ? C31 P5S 403 C 1 HETATM 29 C C32 P5S . . . R 7 138.928 164.423 174.86 1 63.89 ? C32 P5S 403 C 1 HETATM 30 C C33 P5S . . . R 7 137.578 164.319 175.559 1 64.45 ? C33 P5S 403 C 1 HETATM 31 C C34 P5S . . . R 7 137.518 163.165 176.552 1 61.34 ? C34 P5S 403 C 1 HETATM 32 C C35 P5S . . . R 7 136.125 162.909 177.11 1 61.18 ? C35 P5S 403 C 1 HETATM 33 C C36 P5S . . . R 7 136.058 161.66 177.977 1 62.2 ? C36 P5S 403 C 1 HETATM 34 O O37 P5S . . . R 7 136.747 168.102 163.932 1 64.76 ? O37 P5S 403 C 1 HETATM 35 C C38 P5S . . . R 7 137.225 167.717 165.111 1 63.94 ? C38 P5S 403 C 1 HETATM 36 C C39 P5S . . . R 7 136.36 168.184 166.249 1 61.64 ? C39 P5S 403 C 1 HETATM 37 C C40 P5S . . . R 7 135.31 167.154 166.629 1 61.48 ? C40 P5S 403 C 1 HETATM 38 C C41 P5S . . . R 7 134.166 167.73 167.452 1 67.01 ? C41 P5S 403 C 1 HETATM 39 C C42 P5S . . . R 7 132.842 167.066 167.094 1 67.57 ? C42 P5S 403 C 1 HETATM 40 C C43 P5S . . . R 7 131.805 167.075 168.208 1 65.56 ? C43 P5S 403 C 1 HETATM 41 C C44 P5S . . . R 7 130.488 166.438 167.778 1 66.41 ? C44 P5S 403 C 1 HETATM 42 C C45 P5S . . . R 7 130.652 165.189 166.92 1 62.63 ? C45 P5S 403 C 1 HETATM 43 C C46 P5S . . . R 7 130.149 163.923 167.603 1 65.83 ? C46 P5S 403 C 1 HETATM 44 O O47 P5S . . . R 7 138.23 167.066 165.239 1 63.73 ? O47 P5S 403 C 1 HETATM 45 C C48 P5S . . . R 7 130.811 163.648 168.947 1 66.8 ? C48 P5S 403 C 1 HETATM 46 C C49 P5S . . . R 7 131.612 162.352 168.97 1 62.3 ? C49 P5S 403 C 1 HETATM 47 C C50 P5S . . . R 7 132.483 162.207 170.21 1 63.64 ? C50 P5S 403 C 1 HETATM 48 C C51 P5S . . . R 7 133.619 163.221 170.265 1 64.13 ? C51 P5S 403 C 1 HETATM 49 C C52 P5S . . . R 7 134.228 163.367 171.654 1 66.62 ? C52 P5S 403 C 1 HETATM 50 C C53 P5S . . . R 7 134.84 162.077 172.185 1 63.57 ? C53 P5S 403 C 1 HETATM 51 C C54 P5S . . . R 7 134.733 161.936 173.697 1 62 ? C54 P5S 403 C 1 HETATM 52 C C55 P5S . . . R 7 133.707 160.893 174.124 1 64.14 ? C55 P5S 403 C 1 HETATM 53 C C56 P5S . . . R 7 133.291 161.025 175.582 1 65.26 ? C56 P5S 403 C 1 HETATM 54 O OXT P5S . . . R 7 136.609 167.497 155.651 1 66.05 ? OXT P5S 403 C 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 54 #