data_8FD7 # _model_server_result.job_id '_V_rCmUD8vtMz-dspRHJpw' _model_server_result.datetime_utc '2024-11-04 22:33:59' _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":"P","auth_seq_id":1701}' # _entry.id 8FD7 # _exptl.entry_id 8FD7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 649.879 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl heptadecanoate' _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 9 _struct_asym.id P _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 'C34 H68 N O8 P' _chem_comp.formula_weight 649.879 _chem_comp.id WO9 _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl heptadecanoate' _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 O27 P25 WO9 doub 512 n n C40 C41 WO9 sing 513 n n C40 C39 WO9 sing 514 n n C44 C45 WO9 sing 515 n n C44 C43 WO9 sing 516 n n C41 C42 WO9 sing 517 n n C42 C43 WO9 sing 518 n n O34 C33 WO9 doub 519 n n C38 C39 WO9 sing 520 n n C38 C37 WO9 sing 521 n n O24 P25 WO9 sing 522 n n O24 C23 WO9 sing 523 n n P25 O26 WO9 sing 524 n n P25 O28 WO9 sing 525 n n C36 C37 WO9 sing 526 n n C36 C35 WO9 sing 527 n n O19 C18 WO9 doub 528 n n N31 C30 WO9 sing 529 n n C33 C35 WO9 sing 530 n n C33 O32 WO9 sing 531 n n C22 C23 WO9 sing 532 n n C22 C21 WO9 sing 533 n n C22 O32 WO9 sing 534 n n C16 C15 WO9 sing 535 n n C16 C17 WO9 sing 536 n n C29 O28 WO9 sing 537 n n C29 C30 WO9 sing 538 n n C18 C17 WO9 sing 539 n n C18 O20 WO9 sing 540 n n C21 O20 WO9 sing 541 n n C14 C15 WO9 sing 542 n n C14 C13 WO9 sing 543 n n C12 C13 WO9 sing 544 n n C12 C11 WO9 sing 545 n n C10 C11 WO9 sing 546 n n C10 C09 WO9 sing 547 n n C09 C08 WO9 sing 548 n n C08 C07 WO9 sing 549 n n C07 C06 WO9 sing 550 n n C06 C05 WO9 sing 551 n n C05 C04 WO9 sing 552 n n C04 C03 WO9 sing 553 n n C03 C02 WO9 sing 554 n n C02 H1 WO9 sing 555 n n C02 H2 WO9 sing 556 n n C02 H3 WO9 sing 557 n n C03 H4 WO9 sing 558 n n C03 H5 WO9 sing 559 n n C04 H6 WO9 sing 560 n n C04 H7 WO9 sing 561 n n C05 H8 WO9 sing 562 n n C05 H9 WO9 sing 563 n n C06 H10 WO9 sing 564 n n C06 H11 WO9 sing 565 n n C07 H12 WO9 sing 566 n n C07 H13 WO9 sing 567 n n C08 H14 WO9 sing 568 n n C08 H15 WO9 sing 569 n n C09 H16 WO9 sing 570 n n C09 H17 WO9 sing 571 n n C10 H18 WO9 sing 572 n n C10 H19 WO9 sing 573 n n C11 H20 WO9 sing 574 n n C11 H21 WO9 sing 575 n n C12 H22 WO9 sing 576 n n C12 H23 WO9 sing 577 n n C13 H24 WO9 sing 578 n n C13 H25 WO9 sing 579 n n C14 H26 WO9 sing 580 n n C14 H27 WO9 sing 581 n n C15 H28 WO9 sing 582 n n C15 H29 WO9 sing 583 n n C16 H30 WO9 sing 584 n n C16 H31 WO9 sing 585 n n C17 H32 WO9 sing 586 n n C17 H33 WO9 sing 587 n n C21 H34 WO9 sing 588 n n C21 H35 WO9 sing 589 n n C22 H36 WO9 sing 590 n n C23 H37 WO9 sing 591 n n C23 H38 WO9 sing 592 n n C29 H39 WO9 sing 593 n n C29 H40 WO9 sing 594 n n C30 H41 WO9 sing 595 n n C30 H42 WO9 sing 596 n n C35 H43 WO9 sing 597 n n C35 H44 WO9 sing 598 n n C36 H45 WO9 sing 599 n n C36 H46 WO9 sing 600 n n C37 H47 WO9 sing 601 n n C37 H48 WO9 sing 602 n n C38 H49 WO9 sing 603 n n C38 H50 WO9 sing 604 n n C39 H51 WO9 sing 605 n n C39 H52 WO9 sing 606 n n C40 H53 WO9 sing 607 n n C40 H54 WO9 sing 608 n n C41 H55 WO9 sing 609 n n C41 H56 WO9 sing 610 n n C42 H57 WO9 sing 611 n n C42 H58 WO9 sing 612 n n C43 H59 WO9 sing 613 n n C43 H60 WO9 sing 614 n n C44 H61 WO9 sing 615 n n C44 H62 WO9 sing 616 n n C45 H63 WO9 sing 617 n n C45 H64 WO9 sing 618 n n C45 H65 WO9 sing 619 n n N31 H66 WO9 sing 620 n n N31 H67 WO9 sing 621 n n O26 H69 WO9 sing 622 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 C02 WO9 . . . P 9 175.325 201.626 193.456 1 0 ? C02 WO9 1701 K 1 HETATM 2 C C03 WO9 . . . P 9 174.262 201.852 194.635 1 0 ? C03 WO9 1701 K 1 HETATM 3 C C04 WO9 . . . P 9 174.631 200.898 195.87 1 0 ? C04 WO9 1701 K 1 HETATM 4 C C05 WO9 . . . P 9 173.595 201.148 197.069 1 0 ? C05 WO9 1701 K 1 HETATM 5 C C06 WO9 . . . P 9 173.859 200.061 198.218 1 0 ? C06 WO9 1701 K 1 HETATM 6 C C07 WO9 . . . P 9 172.869 200.32 199.452 1 0 ? C07 WO9 1701 K 1 HETATM 7 C C08 WO9 . . . P 9 173.14 199.209 200.579 1 0 ? C08 WO9 1701 K 1 HETATM 8 C C09 WO9 . . . P 9 172.2 199.481 201.85 1 0 ? C09 WO9 1701 K 1 HETATM 9 C C10 WO9 . . . P 9 172.417 198.307 202.923 1 0 ? C10 WO9 1701 K 1 HETATM 10 C C11 WO9 . . . P 9 173.989 198.037 203.097 1 0 ? C11 WO9 1701 K 1 HETATM 11 C C12 WO9 . . . P 9 174.304 196.478 202.892 1 0 ? C12 WO9 1701 K 1 HETATM 12 C C13 WO9 . . . P 9 175.882 196.288 202.697 1 0 ? C13 WO9 1701 K 1 HETATM 13 C C14 WO9 . . . P 9 176.276 194.75 202.913 1 0 ? C14 WO9 1701 K 1 HETATM 14 C C15 WO9 . . . P 9 177.873 194.616 202.923 1 0 ? C15 WO9 1701 K 1 HETATM 15 C C16 WO9 . . . P 9 178.291 193.155 203.432 1 0 ? C16 WO9 1701 K 1 HETATM 16 C C17 WO9 . . . P 9 178.307 192.14 202.192 1 0 ? C17 WO9 1701 K 1 HETATM 17 C C18 WO9 . . . P 9 179.33 190.947 202.509 1 0 ? C18 WO9 1701 K 1 HETATM 18 C C21 WO9 . . . P 9 180.628 189.01 201.707 1 0 ? C21 WO9 1701 K 1 HETATM 19 C C22 WO9 . . . P 9 180.543 187.919 202.877 1 0 ? C22 WO9 1701 K 1 HETATM 20 C C23 WO9 . . . P 9 181.693 186.82 202.674 1 0 ? C23 WO9 1701 K 1 HETATM 21 C C29 WO9 . . . P 9 179.076 184.289 201.347 1 0 ? C29 WO9 1701 K 1 HETATM 22 C C30 WO9 . . . P 9 178.401 183.162 202.264 1 0 ? C30 WO9 1701 K 1 HETATM 23 C C33 WO9 . . . P 9 178.316 187.721 203.894 1 0 ? C33 WO9 1701 K 1 HETATM 24 C C35 WO9 . . . P 9 176.889 188.352 203.525 1 0 ? C35 WO9 1701 K 1 HETATM 25 C C36 WO9 . . . P 9 176.553 189.553 204.536 1 0 ? C36 WO9 1701 K 1 HETATM 26 C C37 WO9 . . . P 9 175.415 190.492 203.903 1 0 ? C37 WO9 1701 K 1 HETATM 27 C C38 WO9 . . . P 9 174.728 191.356 205.069 1 0 ? C38 WO9 1701 K 1 HETATM 28 C C39 WO9 . . . P 9 173.711 192.42 204.432 1 0 ? C39 WO9 1701 K 1 HETATM 29 C C40 WO9 . . . P 9 172.625 192.833 205.539 1 0 ? C40 WO9 1701 K 1 HETATM 30 C C41 WO9 . . . P 9 171.845 194.154 205.076 1 0 ? C41 WO9 1701 K 1 HETATM 31 C C42 WO9 . . . P 9 170.741 194.524 206.181 1 0 ? C42 WO9 1701 K 1 HETATM 32 C C43 WO9 . . . P 9 170.172 195.998 205.907 1 0 ? C43 WO9 1701 K 1 HETATM 33 C C44 WO9 . . . P 9 168.673 195.897 205.34 1 0 ? C44 WO9 1701 K 1 HETATM 34 C C45 WO9 . . . P 9 167.865 197.228 205.73 1 0 ? C45 WO9 1701 K 1 HETATM 35 N N31 WO9 . . . P 9 177.077 183.678 202.81 1 0 ? N31 WO9 1701 K 1 HETATM 36 O O19 WO9 . . . P 9 180.098 191.035 203.483 1 0 ? O19 WO9 1701 K 1 HETATM 37 O O20 WO9 . . . P 9 179.364 189.758 201.646 1 0 ? O20 WO9 1701 K 1 HETATM 38 O O24 WO9 . . . P 9 181.29 185.563 203.316 1 0 ? O24 WO9 1701 K 1 HETATM 39 O O26 WO9 . . . P 9 183.037 183.989 202.003 1 0 ? O26 WO9 1701 K 1 HETATM 40 O O27 WO9 . . . P 9 181.475 182.872 203.391 1 0 ? O27 WO9 1701 K 1 HETATM 41 O O28 WO9 . . . P 9 180.489 183.962 201.127 1 0 ? O28 WO9 1701 K 1 HETATM 42 O O32 WO9 . . . P 9 179.223 187.278 202.83 1 0 ? O32 WO9 1701 K 1 HETATM 43 O O34 WO9 . . . P 9 178.655 187.607 205.084 1 0 ? O34 WO9 1701 K 1 HETATM 44 P P25 WO9 . . . P 9 181.578 184.087 202.463 1 0 ? P25 WO9 1701 K 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #