data_7W9P # _model_server_result.job_id NdZUByck1DrjkE2K718DWQ _model_server_result.datetime_utc '2024-11-05 09:20:29' _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 7w9p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":2003}' # _entry.id 7W9P # _exptl.entry_id 7W9P _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 3 _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 7W9P _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W9P _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,FA,GA,HA,IA,JA,KA,LA,MA,NA _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 I N N ? 7 W N N ? 7 IA N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 D 1 NAG D 2007 NAG 4 n D NAG 2 D 2 NAG D 2008 NAG 4 n E NAG 1 E 1 NAG D 2009 NAG 4 n E NAG 2 E 2 NAG F 2004 NAG 4 n F NAG 1 F 1 NAG E 304 NAG 4 n F NAG 2 F 2 NAG E 305 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 318 A CYS 275 1_555 A SG CYS 367 A CYS 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 358 A CYS 315 1_555 A SG CYS 373 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 938 A CYS 895 1_555 C SG CYS 55 C CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? disulf ? disulf4 A SG CYS 940 A CYS 897 1_555 A SG CYS 946 A CYS 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 978 A CYS 935 1_555 A SG CYS 987 A CYS 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 A SG CYS 1393 A CYS 1350 1_555 A SG CYS 1413 A CYS 1370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 1758 A CYS 1715 1_555 A SG CYS 1773 A CYS 1730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 21 B CYS 21 1_555 B SG CYS 43 B CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf9 B SG CYS 40 B CYS 40 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 C SG CYS 50 C CYS 50 1_555 C SG CYS 127 C CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf11 C SG CYS 72 C CYS 72 1_555 C SG CYS 75 C CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 326 A ASN 283 1_555 H C1 NAG . A NAG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.578 ? covale ? covale2 A ND2 ASN 1395 A ASN 1352 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? covale ? covale3 A ND2 ASN 1409 A ASN 1366 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.519 ? covale ? covale4 A ND2 ASN 1418 A ASN 1375 1_555 N C1 NAG . A NAG 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.53 ? covale ? covale5 B ND2 ASN 93 B ASN 93 1_555 KA C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale6 B ND2 ASN 110 B ASN 110 1_555 LA C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.516 ? covale ? covale7 B ND2 ASN 114 B ASN 114 1_555 MA C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.508 ? covale ? covale8 B ND2 ASN 135 B ASN 135 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.545 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.517 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? # _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 7W9P _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 5 9SL A 1 2001 1901 9SL STX . H 6 NAG A 1 2002 2006 NAG NAG . I 7 P5S A 1 2003 2012 P5S P5S . J 8 Y01 A 1 2004 2015 Y01 Y01 . K 8 Y01 A 1 2005 2016 Y01 Y01 . L 8 Y01 A 1 2006 2017 Y01 Y01 . M 8 Y01 A 1 2007 2020 Y01 Y01 . N 6 NAG A 1 2008 2021 NAG NAG . O 8 Y01 A 1 2009 2022 Y01 Y01 . P 9 LPE A 1 2010 2010 LPE LPE . Q 10 1PW A 1 2011 2011 1PW 1PW . R 9 LPE A 1 2012 2012 LPE LPE . S 11 PCW A 1 2013 2013 PCW PCW . T 9 LPE A 1 2014 2014 LPE LPE . U 9 LPE A 1 2015 2015 LPE LPE . V 11 PCW A 1 2016 2016 PCW PCW . W 7 P5S A 1 2017 2017 P5S LPE . X 11 PCW A 1 2018 2018 PCW PCW . Y 9 LPE A 1 2019 2019 LPE LPE . Z 9 LPE A 1 2020 2020 LPE LPE . AA 9 LPE A 1 2021 2021 LPE LPE . BA 9 LPE A 1 2022 2022 LPE LPE . CA 9 LPE A 1 2023 2023 LPE LPE . DA 9 LPE A 1 2024 2024 LPE LPE . EA 9 LPE A 1 2025 2031 LPE LPE . FA 9 LPE A 1 2026 2032 LPE LPE . GA 11 PCW A 1 2027 2035 PCW PCW . HA 11 PCW A 1 2028 2036 PCW PCW . IA 7 P5S A 1 2029 2039 P5S P5S . JA 8 Y01 A 1 2030 2040 Y01 Y01 . KA 6 NAG B 1 301 301 NAG NAG . LA 6 NAG B 1 302 302 NAG NAG . MA 6 NAG B 1 303 303 NAG NAG . NA 9 LPE B 1 304 306 LPE LPE . # 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 . . . I 7 111.099 88.342 107.829 1 20 ? C P5S 2003 A 1 HETATM 2 N N P5S . . . I 7 109.905 90.132 109.023 1 20 ? N P5S 2003 A 1 HETATM 3 O O P5S . . . I 7 111.978 87.899 107.116 1 20 ? O P5S 2003 A 1 HETATM 4 C C1 P5S . . . I 7 116.683 89.589 108.664 1 20 ? C1 P5S 2003 A 1 HETATM 5 C C2 P5S . . . I 7 116.538 88.462 109.667 1 20 ? C2 P5S 2003 A 1 HETATM 6 C C3 P5S . . . I 7 115.649 88.955 110.795 1 20 ? C3 P5S 2003 A 1 HETATM 7 C CA P5S . . . I 7 111.216 89.702 108.486 1 20 ? CA P5S 2003 A 1 HETATM 8 C CB P5S . . . I 7 112.284 89.731 109.592 1 20 ? CB P5S 2003 A 1 HETATM 9 O OG P5S . . . I 7 113.208 88.655 109.54 1 20 ? OG P5S 2003 A 1 HETATM 10 P P12 P5S . . . I 7 113.419 87.578 110.716 1 20 ? P12 P5S 2003 A 1 HETATM 11 O O13 P5S . . . I 7 112.372 87.629 111.737 1 20 1 O13 P5S 2003 A 1 HETATM 12 O O15 P5S . . . I 7 113.422 86.102 110.086 1 20 ? O15 P5S 2003 A 1 HETATM 13 O O16 P5S . . . I 7 114.856 87.898 111.323 1 20 ? O16 P5S 2003 A 1 HETATM 14 O O19 P5S . . . I 7 117.596 90.579 109.111 1 20 ? O19 P5S 2003 A 1 HETATM 15 O O37 P5S . . . I 7 117.809 88.101 110.191 1 20 ? O37 P5S 2003 A 1 HETATM 16 C C38 P5S . . . I 7 118.487 87.15 109.358 1 20 ? C38 P5S 2003 A 1 HETATM 17 C C39 P5S . . . I 7 119.979 87.17 109.282 1 20 ? C39 P5S 2003 A 1 HETATM 18 C C40 P5S . . . I 7 120.488 85.929 109.978 1 20 ? C40 P5S 2003 A 1 HETATM 19 C C41 P5S . . . I 7 121.214 86.314 111.242 1 20 ? C41 P5S 2003 A 1 HETATM 20 C C42 P5S . . . I 7 122.223 85.241 111.552 1 20 ? C42 P5S 2003 A 1 HETATM 21 C C43 P5S . . . I 7 122.347 85.13 113.051 1 20 ? C43 P5S 2003 A 1 HETATM 22 C C44 P5S . . . I 7 121.571 83.947 113.585 1 20 ? C44 P5S 2003 A 1 HETATM 23 C C45 P5S . . . I 7 121.415 84.108 115.082 1 20 ? C45 P5S 2003 A 1 HETATM 24 C C46 P5S . . . I 7 120.157 83.403 115.546 1 20 ? C46 P5S 2003 A 1 HETATM 25 O O47 P5S . . . I 7 117.845 86.332 108.727 1 20 ? O47 P5S 2003 A 1 HETATM 26 C C48 P5S . . . I 7 119.669 83.93 116.88 1 20 ? C48 P5S 2003 A 1 HETATM 27 C C49 P5S . . . I 7 120.542 83.409 118.001 1 20 ? C49 P5S 2003 A 1 HETATM 28 C C50 P5S . . . I 7 119.734 82.588 118.984 1 20 ? C50 P5S 2003 A 1 HETATM 29 C C51 P5S . . . I 7 120.04 82.982 120.412 1 20 ? C51 P5S 2003 A 1 HETATM 30 C C52 P5S . . . I 7 119.714 81.809 121.305 1 20 ? C52 P5S 2003 A 1 HETATM 31 C C53 P5S . . . I 7 119.267 82.288 122.676 1 20 ? C53 P5S 2003 A 1 HETATM 32 C C54 P5S . . . I 7 120.044 81.6 123.786 1 20 ? C54 P5S 2003 A 1 HETATM 33 C C55 P5S . . . I 7 119.272 80.447 124.414 1 20 ? C55 P5S 2003 A 1 HETATM 34 C C56 P5S . . . I 7 117.881 80.849 124.848 1 20 ? C56 P5S 2003 A 1 HETATM 35 O OXT P5S . . . I 7 110.036 87.578 107.934 1 20 ? OXT P5S 2003 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 35 #