data_9GCX # _model_server_result.job_id GkXxenW4zxnlNs0_oo6-3Q _model_server_result.datetime_utc '2025-01-22 20:01:13' _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 9gcx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":202}' # _entry.id 9GCX # _exptl.entry_id 9GCX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 661.89 _entity.id 11 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description '(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE' _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 120 _cell.entry_id 9GCX _cell.length_a 210.082 _cell.length_b 210.082 _cell.length_c 344.844 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9GCX _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 22-meric _pdbx_struct_assembly.oligomeric_count 22 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression 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 1 1 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 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 10_445 -y-1,-x-1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -105.041 -181.936349 57.474 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 11 L N N ? 11 P N N ? 11 S N N ? 11 T N N ? 11 Y N N ? 11 BA N N # 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 E SG CYS 222 E CYS 144 1_555 E SG CYS 238 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf2 H SG CYS 55 H CYS 24 1_555 H SG CYS 99 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 H SG CYS 71 H CYS 40 1_555 H SG CYS 85 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? covale ? covale1 D SG CYS 121 D CYS 37 1_555 V CAB HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.759 ? covale ? covale2 D SG CYS 124 D CYS 40 1_555 V CAC HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.8 ? metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 N FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 O FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 N FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 O FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc5 D NE2 HIS 125 D HIS 41 1_555 V FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc6 D SD MET 244 D MET 160 1_555 V FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc7 E SG CYS 217 E CYS 139 1_555 X FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc8 E ND1 HIS 219 E HIS 141 1_555 X FE2 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc9 E SG CYS 236 E CYS 158 1_555 X FE1 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc10 E ND1 HIS 239 E HIS 161 1_555 X FE2 FES . E FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C35 H68 N O8 P' _chem_comp.formula_weight 661.89 _chem_comp.id LOP _chem_comp.mon_nstd_flag . _chem_comp.name '(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C1 LOP sing 752 n n N1 HN11 LOP sing 753 n n N1 HN12 LOP sing 754 n n C1 C2 LOP sing 755 n n C1 H11 LOP sing 756 n n C1 H12 LOP sing 757 n n C2 O1 LOP sing 758 n n C2 H21 LOP sing 759 n n C2 H22 LOP sing 760 n n O1 P1 LOP sing 761 n n P1 O2 LOP sing 762 n n P1 O3 LOP sing 763 n n P1 O4 LOP doub 764 n n O2 C3 LOP sing 765 n n O3 HO3 LOP sing 766 n n C3 C4 LOP sing 767 n n C3 H31 LOP sing 768 n n C3 H32 LOP sing 769 n n C4 C5 LOP sing 770 n n C4 O5 LOP sing 771 n n C4 H4 LOP sing 772 n n C5 O6 LOP sing 773 n n C5 H51 LOP sing 774 n n C5 H52 LOP sing 775 n n O5 C6 LOP sing 776 n n O6 C24 LOP sing 777 n n C6 O7 LOP doub 778 n n C6 C7 LOP sing 779 n n C7 C8 LOP sing 780 n n C7 H71 LOP sing 781 n n C7 H72 LOP sing 782 n n C8 C9 LOP sing 783 n n C8 H81 LOP sing 784 n n C8 H82 LOP sing 785 n n C9 C10 LOP sing 786 n n C9 H91 LOP sing 787 n n C9 H92 LOP sing 788 n n C10 C11 LOP sing 789 n n C10 H101 LOP sing 790 n n C10 H102 LOP sing 791 n n C11 C12 LOP sing 792 n n C11 H111 LOP sing 793 n n C11 H112 LOP sing 794 n n C12 C13 LOP sing 795 n n C12 H121 LOP sing 796 n n C12 H122 LOP sing 797 n n C13 C14 LOP sing 798 n n C13 H131 LOP sing 799 n n C13 H132 LOP sing 800 n n C14 C15 LOP doub 801 z n C14 H14 LOP sing 802 n n C15 C16 LOP sing 803 n n C15 H15 LOP sing 804 n n C16 C17 LOP sing 805 n n C16 H161 LOP sing 806 n n C16 H162 LOP sing 807 n n C17 C18 LOP sing 808 n n C17 H171 LOP sing 809 n n C17 H172 LOP sing 810 n n C18 C19 LOP sing 811 n n C18 H181 LOP sing 812 n n C18 H182 LOP sing 813 n n C19 C20 LOP sing 814 n n C19 H191 LOP sing 815 n n C19 H192 LOP sing 816 n n C20 C21 LOP sing 817 n n C20 H201 LOP sing 818 n n C20 H202 LOP sing 819 n n C21 C22 LOP sing 820 n n C21 H211 LOP sing 821 n n C21 H212 LOP sing 822 n n C22 C23 LOP sing 823 n n C22 H221 LOP sing 824 n n C22 H222 LOP sing 825 n n C23 H231 LOP sing 826 n n C23 H232 LOP sing 827 n n C23 H233 LOP sing 828 n n C24 O8 LOP doub 829 n n C24 C25 LOP sing 830 n n C25 C26 LOP sing 831 n n C25 H251 LOP sing 832 n n C25 H252 LOP sing 833 n n C26 C27 LOP sing 834 n n C26 H261 LOP sing 835 n n C26 H262 LOP sing 836 n n C27 C28 LOP sing 837 n n C27 H271 LOP sing 838 n n C27 H272 LOP sing 839 n n C28 C29 LOP sing 840 n n C28 H281 LOP sing 841 n n C28 H282 LOP sing 842 n n C29 C30 LOP sing 843 n n C29 H291 LOP sing 844 n n C29 H292 LOP sing 845 n n C30 C31 LOP sing 846 n n C30 H301 LOP sing 847 n n C30 H302 LOP sing 848 n n C31 C32 LOP sing 849 n n C31 H311 LOP sing 850 n n C31 H312 LOP sing 851 n n C32 C33 LOP sing 852 n n C32 H321 LOP sing 853 n n C32 H322 LOP sing 854 n n C33 C34 LOP sing 855 n n C33 H331 LOP sing 856 n n C33 H332 LOP sing 857 n n C34 C35 LOP sing 858 n n C34 H341 LOP sing 859 n n C34 H342 LOP sing 860 n n C35 H351 LOP sing 861 n n C35 H352 LOP sing 862 n n C35 H353 LOP sing 863 n n # _atom_sites.entry_id 9GCX _atom_sites.fract_transf_matrix[1][1] 0.00476 _atom_sites.fract_transf_matrix[1][2] 0.002748 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005496 _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] 0.0029 _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 L 11 LOP A 1 501 501 LOP LOP . M 12 CDL A 1 502 502 CDL CDL . N 13 HEM C 1 501 501 HEM HEM . O 13 HEM C 1 502 502 HEM HEM . P 11 LOP C 1 503 503 LOP LOP . Q 12 CDL C 1 504 504 CDL CDL . R 14 A1IKG C 1 505 509 A1IKG SG1 . S 11 LOP C 1 506 512 LOP LOP . T 11 LOP C 1 507 513 LOP LOP . U 15 LMT C 1 508 515 LMT LMT . V 16 HEC D 1 501 501 HEC HEC . W 12 CDL D 1 502 502 CDL CDL . X 17 FES E 1 201 201 FES FES . Y 11 LOP E 1 202 201 LOP LOP . Z 18 PSC E 1 203 202 PSC PSC . AA 19 SO4 F 1 201 3 SO4 SO4 . BA 11 LOP G 1 101 514 LOP LOP . CA 19 SO4 G 1 102 1 SO4 SO4 . DA 19 SO4 G 1 103 2 SO4 SO4 . EA 20 HOH A 1 601 301 HOH HOH . EA 20 HOH A 2 602 521 HOH HOH . EA 20 HOH A 3 603 518 HOH HOH . FA 20 HOH B 1 501 522 HOH HOH . GA 20 HOH C 1 601 16 HOH HOH . GA 20 HOH C 2 602 254 HOH HOH . GA 20 HOH C 3 603 523 HOH HOH . GA 20 HOH C 4 604 516 HOH HOH . HA 20 HOH E 1 301 514 HOH HOH . IA 20 HOH F 1 301 519 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 N N1 LOP . . . Y 11 -43.344 -66.916 11.231 1 111.46 ? N1 LOP 202 E 1 HETATM 2 C C1 LOP . . . Y 11 -42.596 -65.75 11.656 1 106.32 ? C1 LOP 202 E 1 HETATM 3 C C2 LOP . . . Y 11 -41.263 -66.103 12.316 1 115.91 ? C2 LOP 202 E 1 HETATM 4 O O1 LOP . . . Y 11 -41.359 -67.096 13.397 1 119.45 ? O1 LOP 202 E 1 HETATM 5 P P1 LOP . . . Y 11 -40.692 -66.792 14.834 1 111.67 ? P1 LOP 202 E 1 HETATM 6 O O2 LOP . . . Y 11 -41.839 -66.1 15.728 1 113.39 ? O2 LOP 202 E 1 HETATM 7 O O3 LOP . . . Y 11 -39.644 -65.736 14.617 1 121.07 ? O3 LOP 202 E 1 HETATM 8 O O4 LOP . . . Y 11 -40.339 -68.121 15.452 1 106.62 ? O4 LOP 202 E 1 HETATM 9 C C3 LOP . . . Y 11 -42.915 -66.957 16.22 1 125.32 ? C3 LOP 202 E 1 HETATM 10 C C4 LOP . . . Y 11 -44.005 -66.357 17.084 1 123.17 ? C4 LOP 202 E 1 HETATM 11 C C5 LOP . . . Y 11 -44.032 -66.921 18.479 1 117.84 ? C5 LOP 202 E 1 HETATM 12 O O5 LOP . . . Y 11 -43.942 -64.982 17.527 1 129.82 ? O5 LOP 202 E 1 HETATM 13 O O6 LOP . . . Y 11 -44.906 -66.09 19.273 1 115.47 ? O6 LOP 202 E 1 HETATM 14 C C6 LOP . . . Y 11 -44.382 -64.031 16.706 1 140.19 ? C6 LOP 202 E 1 HETATM 15 O O7 LOP . . . Y 11 -44.405 -64.13 15.515 1 175.67 ? O7 LOP 202 E 1 HETATM 16 C C7 LOP . . . Y 11 -44.986 -62.919 17.484 1 118.81 ? C7 LOP 202 E 1 HETATM 17 C C8 LOP . . . Y 11 -46.282 -63.262 18.066 1 93.77 ? C8 LOP 202 E 1 HETATM 18 C C9 LOP . . . Y 11 -46.503 -62.437 19.311 1 100.47 ? C9 LOP 202 E 1 HETATM 19 C C10 LOP . . . Y 11 -47.929 -62.457 19.775 1 111.75 ? C10 LOP 202 E 1 HETATM 20 C C11 LOP . . . Y 11 -48.388 -61.254 20.551 1 104.52 ? C11 LOP 202 E 1 HETATM 21 C C12 LOP . . . Y 11 -49.859 -60.917 20.322 1 101.74 ? C12 LOP 202 E 1 HETATM 22 C C13 LOP . . . Y 11 -50.82 -61.694 21.15 1 95.23 ? C13 LOP 202 E 1 HETATM 23 C C14 LOP . . . Y 11 -51.838 -62.439 20.364 1 94.96 ? C14 LOP 202 E 1 HETATM 24 C C15 LOP . . . Y 11 -53.064 -62.607 20.777 1 104.81 ? C15 LOP 202 E 1 HETATM 25 C C16 LOP . . . Y 11 -54.121 -63.431 20.109 1 111.7 ? C16 LOP 202 E 1 HETATM 26 C C17 LOP . . . Y 11 -53.721 -64.863 19.879 1 111.62 ? C17 LOP 202 E 1 HETATM 27 C C18 LOP . . . Y 11 -54.74 -65.686 19.097 1 107.19 ? C18 LOP 202 E 1 HETATM 28 C C19 LOP . . . Y 11 -54.824 -67.169 19.482 1 104.59 ? C19 LOP 202 E 1 HETATM 29 C C20 LOP . . . Y 11 -54.877 -68.141 18.297 1 100.97 ? C20 LOP 202 E 1 HETATM 30 C C21 LOP . . . Y 11 -55.737 -69.368 18.486 1 98.37 ? C21 LOP 202 E 1 HETATM 31 C C22 LOP . . . Y 11 -56.493 -69.89 17.267 1 112.71 ? C22 LOP 202 E 1 HETATM 32 C C23 LOP . . . Y 11 -57.661 -70.816 17.56 1 114.45 ? C23 LOP 202 E 1 HETATM 33 C C24 LOP . . . Y 11 -45.847 -66.772 19.919 1 133.47 ? C24 LOP 202 E 1 HETATM 34 O O8 LOP . . . Y 11 -45.982 -67.963 19.795 1 164.9 ? O8 LOP 202 E 1 HETATM 35 C C25 LOP . . . Y 11 -46.701 -65.915 20.821 1 131.9 ? C25 LOP 202 E 1 HETATM 36 C C26 LOP . . . Y 11 -48.155 -66.301 20.791 1 114.99 ? C26 LOP 202 E 1 HETATM 37 C C27 LOP . . . Y 11 -48.896 -65.998 22.073 1 106.42 ? C27 LOP 202 E 1 HETATM 38 C C28 LOP . . . Y 11 -50.333 -66.44 22.049 1 109.55 ? C28 LOP 202 E 1 HETATM 39 C C29 LOP . . . Y 11 -50.758 -67.203 23.284 1 117.08 ? C29 LOP 202 E 1 HETATM 40 C C30 LOP . . . Y 11 -52.236 -67.135 23.608 1 123.6 ? C30 LOP 202 E 1 HETATM 41 C C31 LOP . . . Y 11 -53.025 -68.3 23.09 1 141.51 ? C31 LOP 202 E 1 HETATM 42 C C32 LOP . . . Y 11 -52.683 -69.603 23.764 1 174.18 ? C32 LOP 202 E 1 HETATM 43 C C33 LOP . . . Y 11 -52.477 -70.811 22.853 1 211.6 ? C33 LOP 202 E 1 HETATM 44 C C34 LOP . . . Y 11 -52.523 -72.106 23.639 1 262.07 ? C34 LOP 202 E 1 HETATM 45 C C35 LOP . . . Y 11 -53.174 -73.322 23.014 1 245.24 ? C35 LOP 202 E 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 45 #