data_8FD7 # _model_server_result.job_id z8zDZS4q5g-3dJWoLDVUNQ _model_server_result.datetime_utc '2024-11-04 22:36:50' _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 8fd7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":1702}' # _entry.id 8FD7 # _exptl.entry_id 8FD7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 579.746 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl dodecanoate' _entity.pdbx_number_of_molecules 1 _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 8FD7 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FD7 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 10 _struct_asym.id Q _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 F 1 NAG F 2 NAG 4 n D NAG 2 F 2 NAG F 1 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 305 D CYS 305 1_555 A SG CYS 1046 D CYS 1046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 356 D CYS 356 1_555 A SG CYS 1061 D CYS 1061 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 406 D CYS 406 1_555 A SG CYS 1073 D CYS 1073 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 669 D CYS 669 1_555 A SG CYS 699 D CYS 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 906 D CYS 906 1_555 A SG CYS 976 D CYS 976 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 A SG CYS 998 D CYS 998 1_555 A SG CYS 1028 D CYS 1028 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 1001 D CYS 1001 1_555 A SG CYS 1026 D CYS 1026 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 316 K CYS 316 1_555 B SG CYS 332 K CYS 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 1058 K CYS 1058 1_555 B SG CYS 1069 K CYS 1069 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 B SG CYS 1431 K CYS 1431 1_555 B SG CYS 1447 K CYS 1447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 94 D ASN 94 1_555 G C1 NAG . D NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 470 D ASN 470 1_555 H C1 NAG . D NAG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 D O4 NAG . F NAG 1 1_555 D C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A OG SER 263 D SER 263 1_555 N CA CA . D CA 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc2 A OG SER 265 D SER 265 1_555 N CA CA . D CA 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc3 A OG1 THR 333 D THR 333 1_555 N CA CA . D CA 1210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc4 A O TRP 448 D TRP 448 1_555 O NA NA . D NA 1211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc5 B OE1 GLU 363 K GLU 363 1_555 V CA CA . K CA 1707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc6 B OE2 GLU 363 K GLU 363 1_555 V CA CA . K CA 1707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.185 ? metalc ? metalc7 B OE2 GLU 1115 K GLU 1115 1_555 V CA CA . K CA 1707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.048 ? # _chem_comp.formula 'C29 H58 N O8 P' _chem_comp.formula_weight 579.746 _chem_comp.id YSW _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl dodecanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N25 C24 YSW sing 623 n n C24 C23 YSW sing 624 n n C23 O22 YSW sing 625 n n O22 P19 YSW sing 626 n n O18 P19 YSW sing 627 n n O18 C17 YSW sing 628 n n P19 O20 YSW doub 629 n n P19 O21 YSW sing 630 n n C17 C16 YSW sing 631 n n O28 C27 YSW doub 632 n n C16 C15 YSW sing 633 n n C16 O26 YSW sing 634 n n C15 O14 YSW sing 635 n n O26 C27 YSW sing 636 n n C27 C29 YSW sing 637 n n O13 C12 YSW doub 638 n n O14 C12 YSW sing 639 n n C12 C11 YSW sing 640 n n C29 C30 YSW sing 641 n n C11 C10 YSW sing 642 n n C30 C31 YSW sing 643 n n C10 C09 YSW sing 644 n n C31 C32 YSW sing 645 n n C09 C08 YSW sing 646 n n C08 C07 YSW sing 647 n n C32 C33 YSW sing 648 n n C33 C34 YSW sing 649 n n C07 C06 YSW sing 650 n n C06 C05 YSW sing 651 n n C34 C35 YSW sing 652 n n C05 C04 YSW sing 653 n n C35 C36 YSW sing 654 n n C04 C03 YSW sing 655 n n C36 C37 YSW sing 656 n n C03 C02 YSW sing 657 n n C37 C38 YSW sing 658 n n C02 C01 YSW sing 659 n n C38 C39 YSW sing 660 n n C01 H1 YSW sing 661 n n C01 H2 YSW sing 662 n n C01 H3 YSW sing 663 n n C02 H4 YSW sing 664 n n C02 H5 YSW sing 665 n n C03 H6 YSW sing 666 n n C03 H7 YSW sing 667 n n C04 H8 YSW sing 668 n n C04 H9 YSW sing 669 n n C05 H10 YSW sing 670 n n C05 H11 YSW sing 671 n n C06 H12 YSW sing 672 n n C06 H13 YSW sing 673 n n C07 H14 YSW sing 674 n n C07 H15 YSW sing 675 n n C08 H16 YSW sing 676 n n C08 H17 YSW sing 677 n n C09 H18 YSW sing 678 n n C09 H19 YSW sing 679 n n C10 H20 YSW sing 680 n n C10 H21 YSW sing 681 n n C11 H22 YSW sing 682 n n C11 H23 YSW sing 683 n n C15 H24 YSW sing 684 n n C15 H25 YSW sing 685 n n C16 H26 YSW sing 686 n n C17 H27 YSW sing 687 n n C17 H28 YSW sing 688 n n C23 H29 YSW sing 689 n n C23 H30 YSW sing 690 n n C24 H31 YSW sing 691 n n C24 H32 YSW sing 692 n n C29 H33 YSW sing 693 n n C29 H34 YSW sing 694 n n C30 H35 YSW sing 695 n n C30 H36 YSW sing 696 n n C31 H37 YSW sing 697 n n C31 H38 YSW sing 698 n n C32 H39 YSW sing 699 n n C32 H40 YSW sing 700 n n C33 H41 YSW sing 701 n n C33 H42 YSW sing 702 n n C34 H43 YSW sing 703 n n C34 H44 YSW sing 704 n n C35 H45 YSW sing 705 n n C35 H46 YSW sing 706 n n C36 H47 YSW sing 707 n n C36 H48 YSW sing 708 n n C37 H49 YSW sing 709 n n C37 H50 YSW sing 710 n n C38 H51 YSW sing 711 n n C38 H52 YSW sing 712 n n C39 H53 YSW sing 713 n n C39 H54 YSW sing 714 n n C39 H55 YSW sing 715 n n N25 H56 YSW sing 716 n n N25 H57 YSW sing 717 n n O21 H59 YSW sing 718 n n # _atom_sites.entry_id 8FD7 _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 E 5 NAG D 1 1201 1103 NAG NAG . F 6 GBN D 1 1202 1116 GBN GBN . G 5 NAG D 1 1203 1117 NAG NAG . H 5 NAG D 1 1204 1118 NAG NAG . I 5 NAG D 1 1205 1119 NAG NAG . J 5 NAG D 1 1206 1120 NAG NAG . K 5 NAG D 1 1207 3 NAG NAG . L 5 NAG D 1 1208 4 NAG NAG . M 5 NAG D 1 1209 5 NAG NAG . N 7 CA D 1 1210 1 CA CA . O 8 NA D 1 1211 1 NA NA . P 9 WO9 K 1 1701 1710 WO9 WO9 . Q 10 YSW K 1 1702 1711 YSW WNZ . R 11 CLR K 1 1703 1712 CLR CLR . S 11 CLR K 1 1704 1713 CLR CLR . T 11 CLR K 1 1705 1714 CLR CLR . U 7 CA K 1 1706 3 CA CA . V 7 CA K 1 1707 4 CA CA . W 12 HOH K 1 1801 1 HOH HOH . W 12 HOH K 2 1802 3 HOH HOH . W 12 HOH K 3 1803 2 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 C C01 YSW . . . Q 10 158.204 195.041 189.344 1 0.5 ? C01 YSW 1702 K 1 HETATM 2 C C02 YSW . . . Q 10 159.269 195.43 188.44 1 0.5 ? C02 YSW 1702 K 1 HETATM 3 C C03 YSW . . . Q 10 158.588 196.301 187.445 1 0.5 ? C03 YSW 1702 K 1 HETATM 4 C C04 YSW . . . Q 10 158.698 195.864 186.052 1 0.5 ? C04 YSW 1702 K 1 HETATM 5 C C05 YSW . . . Q 10 159.321 196.844 185.195 1 0.5 ? C05 YSW 1702 K 1 HETATM 6 C C06 YSW . . . Q 10 158.675 197.048 183.9 1 0.5 ? C06 YSW 1702 K 1 HETATM 7 C C07 YSW . . . Q 10 158.75 198.466 183.493 1 0.5 ? C07 YSW 1702 K 1 HETATM 8 C C08 YSW . . . Q 10 159.117 198.631 182.108 1 0.5 ? C08 YSW 1702 K 1 HETATM 9 C C09 YSW . . . Q 10 160.422 198.066 181.869 1 0.5 ? C09 YSW 1702 K 1 HETATM 10 C C10 YSW . . . Q 10 160.707 197.907 180.418 1 0.5 ? C10 YSW 1702 K 1 HETATM 11 C C11 YSW . . . Q 10 160.579 199.166 179.737 1 0.5 ? C11 YSW 1702 K 1 HETATM 12 C C12 YSW . . . Q 10 160.399 198.99 178.311 1 0.5 ? C12 YSW 1702 K 1 HETATM 13 C C15 YSW . . . Q 10 162.289 198.852 176.974 1 0.5 ? C15 YSW 1702 K 1 HETATM 14 C C16 YSW . . . Q 10 163.486 197.948 176.795 1 0.5 ? C16 YSW 1702 K 1 HETATM 15 C C17 YSW . . . Q 10 163.671 197.582 175.336 1 0.5 ? C17 YSW 1702 K 1 HETATM 16 C C23 YSW . . . Q 10 167.699 196.232 172.894 1 0.5 ? C23 YSW 1702 K 1 HETATM 17 C C24 YSW . . . Q 10 168.693 196.945 172.035 1 0.5 ? C24 YSW 1702 K 1 HETATM 18 C C27 YSW . . . Q 10 164.956 199.782 177.538 1 0.5 ? C27 YSW 1702 K 1 HETATM 19 C C29 YSW . . . Q 10 165.18 200.272 178.945 1 0.5 ? C29 YSW 1702 K 1 HETATM 20 C C30 YSW . . . Q 10 164.403 199.544 180.017 1 0.5 ? C30 YSW 1702 K 1 HETATM 21 C C31 YSW . . . Q 10 164.458 200.249 181.372 1 0.5 ? C31 YSW 1702 K 1 HETATM 22 C C32 YSW . . . Q 10 163.625 199.695 182.489 1 0.5 ? C32 YSW 1702 K 1 HETATM 23 C C33 YSW . . . Q 10 164.2 198.473 183.126 1 0.5 ? C33 YSW 1702 K 1 HETATM 24 C C34 YSW . . . Q 10 164.628 198.655 184.538 1 0.5 ? C34 YSW 1702 K 1 HETATM 25 C C35 YSW . . . Q 10 164.514 197.414 185.334 1 0.5 ? C35 YSW 1702 K 1 HETATM 26 C C36 YSW . . . Q 10 163.599 197.452 186.517 1 0.5 ? C36 YSW 1702 K 1 HETATM 27 C C37 YSW . . . Q 10 164.182 196.809 187.745 1 0.5 ? C37 YSW 1702 K 1 HETATM 28 C C38 YSW . . . Q 10 163.168 196.185 188.634 1 0.5 ? C38 YSW 1702 K 1 HETATM 29 C C39 YSW . . . Q 10 163.602 195.561 189.936 1 0.5 ? C39 YSW 1702 K 1 HETATM 30 N N25 YSW . . . Q 10 169.589 195.977 171.377 1 0.5 ? N25 YSW 1702 K 1 HETATM 31 O O13 YSW . . . Q 10 159.562 199.478 177.665 1 0.5 ? O13 YSW 1702 K 1 HETATM 32 O O14 YSW . . . Q 10 161.32 198.201 177.814 1 0.5 ? O14 YSW 1702 K 1 HETATM 33 O O18 YSW . . . Q 10 164.743 198.194 174.564 1 0.5 ? O18 YSW 1702 K 1 HETATM 34 O O20 YSW . . . Q 10 165.865 196.172 175.242 1 0.5 ? O20 YSW 1702 K 1 HETATM 35 O O21 YSW . . . Q 10 166.956 198.502 175.429 1 0.5 ? O21 YSW 1702 K 1 HETATM 36 O O22 YSW . . . Q 10 166.635 197.178 173.144 1 0.5 ? O22 YSW 1702 K 1 HETATM 37 O O26 YSW . . . Q 10 164.732 198.463 177.368 1 0.5 ? O26 YSW 1702 K 1 HETATM 38 O O28 YSW . . . Q 10 164.98 200.508 176.597 1 0.5 ? O28 YSW 1702 K 1 HETATM 39 P P19 YSW . . . Q 10 166.177 197.492 174.644 1 0.5 ? P19 YSW 1702 K 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 95 _model_server_stats.query_time_ms 421 _model_server_stats.encode_time_ms 56 _model_server_stats.element_count 39 #