data_4D6T # _model_server_result.job_id FFBeHr2kr_ovOXjY0tt7oA _model_server_result.datetime_utc '2024-11-05 13:34:42' _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":"EA","auth_seq_id":506}' # _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 C13 PEE . . . EA 15 43.636 -9.176 25.124 1 108.83 ? C13 PEE 506 D 1 HETATM 2 C C12 PEE . . . EA 15 42.766 -10.09 26.007 1 122.03 ? C12 PEE 506 D 1 HETATM 3 C C11 PEE . . . EA 15 41.446 -10.554 25.356 1 126.61 ? C11 PEE 506 D 1 HETATM 4 C C10 PEE . . . EA 15 40.504 -11.267 26.329 1 129.01 ? C10 PEE 506 D 1 HETATM 5 O O4 PEE . . . EA 15 40.949 -12.03 27.168 1 140.01 ? O4 PEE 506 D 1 HETATM 6 O O2 PEE . . . EA 15 39.049 -11.092 26.285 1 123.94 ? O2 PEE 506 D 1 HETATM 7 C C2 PEE . . . EA 15 38.374 -11.116 27.555 1 124.47 ? C2 PEE 506 D 1 HETATM 8 C C1 PEE . . . EA 15 37.141 -12.031 27.489 1 127.86 ? C1 PEE 506 D 1 HETATM 9 O O3P PEE . . . EA 15 36.824 -12.776 28.689 1 125.01 ? O3P PEE 506 D 1 HETATM 10 P P PEE . . . EA 15 35.4 -13.586 28.797 1 121.5 ? P PEE 506 D 1 HETATM 11 O O2P PEE . . . EA 15 34.378 -12.727 29.526 1 107.6 ? O2P PEE 506 D 1 HETATM 12 O O1P PEE . . . EA 15 35.098 -14.19 27.434 1 121.59 ? O1P PEE 506 D 1 HETATM 13 O O4P PEE . . . EA 15 35.605 -14.857 29.756 1 132.81 ? O4P PEE 506 D 1 HETATM 14 C C4 PEE . . . EA 15 34.494 -15.416 30.477 1 156.65 ? C4 PEE 506 D 1 HETATM 15 C C5 PEE . . . EA 15 33.408 -15.965 29.546 1 169.8 ? C5 PEE 506 D 1 HETATM 16 N N PEE . . . EA 15 32.208 -15.081 29.496 1 176.77 ? N PEE 506 D 1 HETATM 17 C C3 PEE . . . EA 15 37.949 -9.688 27.841 1 123.97 ? C3 PEE 506 D 1 HETATM 18 O O3 PEE . . . EA 15 39.083 -8.818 27.906 1 141.3 ? O3 PEE 506 D 1 HETATM 19 C C30 PEE . . . EA 15 39.054 -7.468 27.312 1 164.64 ? C30 PEE 506 D 1 HETATM 20 O O5 PEE . . . EA 15 38.277 -6.642 27.781 1 173.19 ? O5 PEE 506 D 1 HETATM 21 C C31 PEE . . . EA 15 39.963 -7.083 26.144 1 159.26 ? C31 PEE 506 D 1 HETATM 22 C C32 PEE . . . EA 15 40.381 -5.603 26.183 1 147.61 ? C32 PEE 506 D 1 HETATM 23 C C33 PEE . . . EA 15 41.156 -5.145 24.938 1 135.3 ? C33 PEE 506 D 1 HETATM 24 C C34 PEE . . . EA 15 41.413 -3.627 24.945 1 130.43 ? C34 PEE 506 D 1 HETATM 25 C C35 PEE . . . EA 15 41.594 -3.003 23.554 1 118.51 ? C35 PEE 506 D 1 HETATM 26 C C36 PEE . . . EA 15 41.936 -1.511 23.606 1 108.79 ? C36 PEE 506 D 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #