data_4D6T # _model_server_result.job_id a_NZ0dj-WwAFSYbN0mqCLw _model_server_result.datetime_utc '2024-11-24 02:31:44' _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 4d6t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"NA","auth_seq_id":505}' # _entry.id 4D6T # _exptl.entry_id 4D6T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 744.034 _entity.id 15 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine _entity.pdbx_number_of_molecules 4 _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 4D6T _cell.length_a 129.896 _cell.length_b 129.896 _cell.length_c 722.152 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D6T _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS decameric 10 software_defined_assembly 1 PQS decameric 10 software_defined_assembly 2 # 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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA 1 1 K,L,M,N,O,P,Q,R,S,T,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA 2 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 x,y,z _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 ? 15 Y N N ? 15 EA N N ? 15 NA N N ? 15 QA 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 H SG CYS 37 H CYS 24 1_555 H SG CYS 81 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf2 H SG CYS 53 H CYS 40 1_555 H SG CYS 67 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? disulf ? disulf3 O SG CYS 222 R CYS 144 1_555 O SG CYS 238 R CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 R SG CYS 37 U CYS 24 1_555 R SG CYS 81 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf5 R SG CYS 53 U CYS 40 1_555 R SG CYS 67 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 U FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 V FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc5 D NE2 HIS 65 D HIS 41 1_555 Z FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc6 D SD MET 184 D MET 160 1_555 Z FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc7 M NE2 HIS 83 P HIS 83 1_555 KA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc8 M NE2 HIS 97 P HIS 97 1_555 LA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc9 M NE2 HIS 182 P HIS 182 1_555 KA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc10 M NE2 HIS 196 P HIS 196 1_555 LA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc11 N NE2 HIS 65 Q HIS 41 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc12 N SD MET 184 Q MET 160 1_555 OA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc13 O SG CYS 236 R CYS 158 1_555 TA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? # _chem_comp.formula 'C41 H78 N O8 P' _chem_comp.formula_weight 744.034 _chem_comp.id PEE _chem_comp.mon_nstd_flag n _chem_comp.name 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DOPE # 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 N C5 PEE sing 718 n n C5 C4 PEE sing 719 n n C4 O4P PEE sing 720 n n O4P P PEE sing 721 n n O1P P PEE doub 722 n n C1 O3P PEE sing 723 n n C1 C2 PEE sing 724 n n O3P P PEE sing 725 n n P O2P PEE sing 726 n n C2 C3 PEE sing 727 n n C2 O2 PEE sing 728 n n C3 O3 PEE sing 729 n n O2 C10 PEE sing 730 n n C31 C30 PEE sing 731 n n C31 C32 PEE sing 732 n n C33 C32 PEE sing 733 n n C33 C34 PEE sing 734 n n C30 O3 PEE sing 735 n n C30 O5 PEE doub 736 n n C10 O4 PEE doub 737 n n C10 C11 PEE sing 738 n n C34 C35 PEE sing 739 n n C11 C12 PEE sing 740 n n C35 C36 PEE sing 741 n n C36 C37 PEE sing 742 n n C37 C38 PEE sing 743 n n C38 C39 PEE doub 744 z n C12 C13 PEE sing 745 n n C39 C40 PEE sing 746 n n C13 C14 PEE sing 747 n n C14 C15 PEE sing 748 n n C40 C41 PEE sing 749 n n C15 C16 PEE sing 750 n n C41 C42 PEE sing 751 n n C16 C17 PEE sing 752 n n C42 C43 PEE sing 753 n n C17 C18 PEE sing 754 n n C43 C44 PEE sing 755 n n C18 C19 PEE doub 756 z n C46 C47 PEE sing 757 n n C46 C45 PEE sing 758 n n C44 C45 PEE sing 759 n n C19 C20 PEE sing 760 n n C20 C21 PEE sing 761 n n C21 C22 PEE sing 762 n n C22 C23 PEE sing 763 n n C23 C24 PEE sing 764 n n C24 C25 PEE sing 765 n n C26 C25 PEE sing 766 n n C26 C27 PEE sing 767 n n C27 H7 PEE sing 768 n n C27 H8 PEE sing 769 n n C27 H82 PEE sing 770 n n C26 H5 PEE sing 771 n n C26 H6 PEE sing 772 n n C25 H12 PEE sing 773 n n C25 H4 PEE sing 774 n n C24 H10 PEE sing 775 n n C24 H11 PEE sing 776 n n C23 H83 PEE sing 777 n n C23 H9 PEE sing 778 n n C22 H2 PEE sing 779 n n C22 H3 PEE sing 780 n n C21 H14 PEE sing 781 n n C21 H1 PEE sing 782 n n C20 H16 PEE sing 783 n n C20 H13 PEE sing 784 n n C19 H18 PEE sing 785 n n C18 H20 PEE sing 786 n n C17 H22 PEE sing 787 n n C17 H19 PEE sing 788 n n C16 H21 PEE sing 789 n n C16 H28 PEE sing 790 n n C15 H23 PEE sing 791 n n C15 H24 PEE sing 792 n n C14 H25 PEE sing 793 n n C14 H26 PEE sing 794 n n C13 H17 PEE sing 795 n n C13 H27 PEE sing 796 n n C12 H15 PEE sing 797 n n C12 H29 PEE sing 798 n n C11 H30 PEE sing 799 n n C11 H31 PEE sing 800 n n C2 H32 PEE sing 801 n n C1 H33 PEE sing 802 n n C1 H34 PEE sing 803 n n O2P H35 PEE sing 804 n n C4 H36 PEE sing 805 n n C4 H37 PEE sing 806 n n C5 H38 PEE sing 807 n n C5 H39 PEE sing 808 n n N H40 PEE sing 809 n n N H41 PEE sing 810 n n C3 H43 PEE sing 811 n n C3 H44 PEE sing 812 n n C31 H45 PEE sing 813 n n C31 H46 PEE sing 814 n n C32 H47 PEE sing 815 n n C32 H48 PEE sing 816 n n C33 H49 PEE sing 817 n n C33 H50 PEE sing 818 n n C34 H51 PEE sing 819 n n C34 H52 PEE sing 820 n n C35 H53 PEE sing 821 n n C35 H54 PEE sing 822 n n C36 H55 PEE sing 823 n n C36 H56 PEE sing 824 n n C37 H57 PEE sing 825 n n C37 H58 PEE sing 826 n n C38 H59 PEE sing 827 n n C39 H60 PEE sing 828 n n C40 H81 PEE sing 829 n n C40 H61 PEE sing 830 n n C41 H80 PEE sing 831 n n C41 H62 PEE sing 832 n n C42 H63 PEE sing 833 n n C42 H64 PEE sing 834 n n C43 H65 PEE sing 835 n n C43 H66 PEE sing 836 n n C44 H67 PEE sing 837 n n C44 H68 PEE sing 838 n n C45 H69 PEE sing 839 n n C45 H70 PEE sing 840 n n C46 H71 PEE sing 841 n n C46 H72 PEE sing 842 n n C47 H73 PEE sing 843 n n C47 H74 PEE sing 844 n n C47 H75 PEE sing 845 n n # _atom_sites.entry_id 4D6T _atom_sites.fract_transf_matrix[1][1] 0.007698 _atom_sites.fract_transf_matrix[1][2] 0.004445 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008889 _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] 0.001385 _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 U 12 HEM C 1 501 501 HEM HEM . V 12 HEM C 1 502 502 HEM HEM . W 13 4X9 C 1 503 503 4X9 4X9 . X 14 PO4 C 1 504 504 PO4 PO4 . Y 15 PEE C 1 505 505 PEE PEE . Z 16 HEC D 1 501 501 HEC HEC . AA 14 PO4 D 1 502 502 PO4 PO4 . BA 14 PO4 D 1 503 503 PO4 PO4 . CA 14 PO4 D 1 504 504 PO4 PO4 . DA 17 CDL D 1 505 505 CDL CDL . EA 15 PEE D 1 506 506 PEE PEE . FA 14 PO4 E 1 501 501 PO4 PO4 . GA 14 PO4 F 1 501 501 PO4 PO4 . HA 17 CDL G 1 501 501 CDL CDL . IA 14 PO4 N 1 501 501 PO4 PO4 . JA 14 PO4 N 1 1001 1001 PO4 PO4 . KA 12 HEM P 1 501 501 HEM HEM . LA 12 HEM P 1 502 502 HEM HEM . MA 13 4X9 P 1 503 503 4X9 4X9 . NA 15 PEE P 1 505 505 PEE PEE . OA 16 HEC Q 1 501 501 HEC HEC . PA 17 CDL Q 1 505 505 CDL CDL . QA 15 PEE Q 1 506 506 PEE PEE . RA 14 PO4 Q 1 1001 1001 PO4 PO4 . SA 14 PO4 Q 1 1002 1002 PO4 PO4 . TA 18 FES R 1 501 501 FES FES . UA 19 GOL R 1 502 502 GOL GOL . VA 14 PO4 S 1 501 501 PO4 PO4 . WA 17 CDL T 1 501 501 CDL CDL . # 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 C26 PEE . . . NA 15 16.811 12.467 -3.907 1 100.47 ? C26 PEE 505 P 1 HETATM 2 C C25 PEE . . . NA 15 17.107 12.179 -5.376 1 110.13 ? C25 PEE 505 P 1 HETATM 3 C C24 PEE . . . NA 15 16.329 13.101 -6.322 1 118.76 ? C24 PEE 505 P 1 HETATM 4 C C23 PEE . . . NA 15 17.221 14.125 -7.038 1 128.1 ? C23 PEE 505 P 1 HETATM 5 C C22 PEE . . . NA 15 16.444 15.308 -7.647 1 126.72 ? C22 PEE 505 P 1 HETATM 6 C C21 PEE . . . NA 15 16.272 16.48 -6.668 1 116.05 ? C21 PEE 505 P 1 HETATM 7 C C20 PEE . . . NA 15 15.105 17.39 -7.054 1 107.91 ? C20 PEE 505 P 1 HETATM 8 C C19 PEE . . . NA 15 15.513 18.52 -7.991 1 107.37 ? C19 PEE 505 P 1 HETATM 9 C C18 PEE . . . NA 15 15.009 19.864 -7.451 1 114.79 ? C18 PEE 505 P 1 HETATM 10 C C17 PEE . . . NA 15 15.373 21.076 -8.319 1 119.26 ? C17 PEE 505 P 1 HETATM 11 C C16 PEE . . . NA 15 16.777 20.986 -8.939 1 119.96 ? C16 PEE 505 P 1 HETATM 12 C C15 PEE . . . NA 15 17.257 22.305 -9.552 1 118.43 ? C15 PEE 505 P 1 HETATM 13 C C14 PEE . . . NA 15 18.609 22.152 -10.257 1 113.23 ? C14 PEE 505 P 1 HETATM 14 C C13 PEE . . . NA 15 18.513 22.152 -11.784 1 117.37 ? C13 PEE 505 P 1 HETATM 15 C C12 PEE . . . NA 15 18.708 23.552 -12.366 1 123.59 ? C12 PEE 505 P 1 HETATM 16 C C11 PEE . . . NA 15 18.825 23.547 -13.893 1 123.35 ? C11 PEE 505 P 1 HETATM 17 C C10 PEE . . . NA 15 18.064 24.692 -14.544 1 125.6 ? C10 PEE 505 P 1 HETATM 18 O O4 PEE . . . NA 15 18.093 25.826 -14.068 1 102.04 ? O4 PEE 505 P 1 HETATM 19 O O2 PEE . . . NA 15 17.278 24.419 -15.762 1 141.93 ? O2 PEE 505 P 1 HETATM 20 C C2 PEE . . . NA 15 17.487 25.218 -16.942 1 123.99 ? C2 PEE 505 P 1 HETATM 21 C C1 PEE . . . NA 15 18.928 25.727 -17.013 1 116.68 ? C1 PEE 505 P 1 HETATM 22 O O3P PEE . . . NA 15 19.215 26.326 -18.268 1 108.22 ? O3P PEE 505 P 1 HETATM 23 P P PEE . . . NA 15 20.651 26.096 -18.956 1 116.68 ? P PEE 505 P 1 HETATM 24 O O2P PEE . . . NA 15 21.707 26.106 -17.869 1 126.21 ? O2P PEE 505 P 1 HETATM 25 O O1P PEE . . . NA 15 20.509 24.875 -19.835 1 105.15 ? O1P PEE 505 P 1 HETATM 26 O O4P PEE . . . NA 15 20.86 27.423 -19.865 1 122.46 ? O4P PEE 505 P 1 HETATM 27 C C4 PEE . . . NA 15 20.994 28.744 -19.32 1 142.57 ? C4 PEE 505 P 1 HETATM 28 C C5 PEE . . . NA 15 22.292 28.952 -18.513 1 156.5 ? C5 PEE 505 P 1 HETATM 29 N N PEE . . . NA 15 23.15 30.044 -19.067 1 155.41 ? N PEE 505 P 1 HETATM 30 C C3 PEE . . . NA 15 16.52 26.405 -17 1 123.66 ? C3 PEE 505 P 1 HETATM 31 O O3 PEE . . . NA 15 15.374 26.252 -16.16 1 117.83 ? O3 PEE 505 P 1 HETATM 32 C C30 PEE . . . NA 15 15.076 27.229 -15.108 1 118.88 ? C30 PEE 505 P 1 HETATM 33 O O5 PEE . . . NA 15 15.786 28.218 -14.943 1 117.54 ? O5 PEE 505 P 1 HETATM 34 C C31 PEE . . . NA 15 13.85 26.99 -14.251 1 115.67 ? C31 PEE 505 P 1 HETATM 35 C C32 PEE . . . NA 15 13.988 27.406 -12.783 1 114.35 ? C32 PEE 505 P 1 HETATM 36 C C33 PEE . . . NA 15 13.809 26.189 -11.871 1 119.4 ? C33 PEE 505 P 1 HETATM 37 C C34 PEE . . . NA 15 13.415 26.555 -10.443 1 124.48 ? C34 PEE 505 P 1 HETATM 38 C C35 PEE . . . NA 15 12.153 25.822 -9.993 1 133.08 ? C35 PEE 505 P 1 HETATM 39 C C36 PEE . . . NA 15 12.438 24.469 -9.337 1 136.23 ? C36 PEE 505 P 1 HETATM 40 C C37 PEE . . . NA 15 11.801 24.407 -7.947 1 135.13 ? C37 PEE 505 P 1 HETATM 41 C C38 PEE . . . NA 15 11.897 23.007 -7.348 1 133.95 ? C38 PEE 505 P 1 HETATM 42 C C39 PEE . . . NA 15 10.677 22.662 -6.485 1 137.41 ? C39 PEE 505 P 1 HETATM 43 C C40 PEE . . . NA 15 10.028 21.33 -6.874 1 142.33 ? C40 PEE 505 P 1 HETATM 44 C C41 PEE . . . NA 15 9.586 20.506 -5.667 1 145.76 ? C41 PEE 505 P 1 HETATM 45 C C42 PEE . . . NA 15 10.763 19.795 -4.994 1 154.42 ? C42 PEE 505 P 1 HETATM 46 C C43 PEE . . . NA 15 10.287 18.772 -3.962 1 156.57 ? C43 PEE 505 P 1 HETATM 47 C C44 PEE . . . NA 15 11.4 18.347 -3.001 1 148.3 ? C44 PEE 505 P 1 HETATM 48 C C45 PEE . . . NA 15 11.61 16.834 -3.008 1 139.36 ? C45 PEE 505 P 1 HETATM 49 C C46 PEE . . . NA 15 12.802 16.451 -2.139 1 124.45 ? C46 PEE 505 P 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 126 _model_server_stats.query_time_ms 454 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 49 #