data_6NT3 # _model_server_result.job_id petqKho7GCuOcpU-Z_2dcA _model_server_result.datetime_utc '2024-11-04 22:41:42' _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 6nt3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1617}' # _entry.id 6NT3 # _exptl.entry_id 6NT3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 742.018 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate' _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 90 _cell.entry_id 6NT3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NT3 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 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 ? 6 J N N ? 6 K N N ? 6 L N N ? 6 M N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O3 HO3 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O3 HO3 . sing 3 ? 2 4 3 BMA BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 BMA BMA C1 O1 . O6 HO6 . sing 5 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . 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 2 n B NAG 1 B 1 NAG A 1601 NAG 2 n B NAG 2 B 2 NAG A 1603 NAG 2 n B BMA 3 B 3 BMA A 1605 BMA 2 n B BMA 4 B 4 BMA A 1602 BMA 2 n B BMA 5 B 5 BMA A 1604 BMA 3 n C NAG 1 C 1 NAG A 1614 NAG 3 n C NAG 2 C 2 NAG A 1615 NAG 3 n D NAG 1 D 1 NAG A 1619 NAG 3 n D NAG 2 D 2 NAG A 1620 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 342 A CYS 288 1_555 A SG CYS 391 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 382 A CYS 328 1_555 A SG CYS 397 A CYS 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf3 A SG CYS 763 A CYS 709 1_555 A SG CYS 771 A CYS 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 1065 A CYS 1011 1_555 A SG CYS 1084 A CYS 1030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 1422 A CYS 1368 1_555 A SG CYS 1435 A CYS 1381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 354 A ASN 300 1_555 H C1 NAG . A NAG 1613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 362 A ASN 308 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 366 A ASN 312 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 A ND2 ASN 384 A ASN 330 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 A ND2 ASN 1069 A ASN 1015 1_555 G C1 NAG . A NAG 1608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale6 A ND2 ASN 1082 A ASN 1028 1_555 E C1 NAG . A NAG 1606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 B O3 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale8 B O3 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale9 B O3 BMA . B BMA 3 1_555 B C1 BMA . B BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale10 B O6 BMA . B BMA 3 1_555 B C1 BMA . B BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale11 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale12 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _chem_comp.formula 'C41 H76 N O8 P' _chem_comp.formula_weight 742.018 _chem_comp.id 76F _chem_comp.mon_nstd_flag . _chem_comp.name '(7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate' _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 C47 C46 76F sing 1 n n C46 C45 76F sing 2 n n C22 C21 76F doub 3 e n C45 C44 76F sing 4 n n C21 C20 76F sing 5 n n C44 C43 76F sing 6 n n C20 C19 76F sing 7 n n C43 C42 76F sing 8 n n C19 C18 76F doub 9 z n C42 C41 76F sing 10 n n C18 C17 76F sing 11 n n C41 C40 76F doub 12 e n C17 C16 76F sing 13 n n C40 C39 76F sing 14 n n C16 C15 76F sing 15 n n C39 C38 76F sing 16 n n C15 C14 76F sing 17 n n C38 C37 76F sing 18 n n C14 C13 76F sing 19 n n C37 C36 76F sing 20 n n C13 C12 76F sing 21 n n C36 C35 76F sing 22 n n C12 C11 76F sing 23 n n C35 C34 76F sing 24 n n C11 C10 76F sing 25 n n C34 C33 76F sing 26 n n O4 C10 76F doub 27 n n C10 O2 76F sing 28 n n C33 C32 76F sing 29 n n O2 C2 76F sing 30 n n C32 C31 76F sing 31 n n C2 C3 76F sing 32 n n C2 C1 76F sing 33 n n C31 C30 76F sing 34 n n C3 O3 76F sing 35 n n C1 O3P 76F sing 36 n n C30 O3 76F sing 37 n n C30 O5 76F doub 38 n n O3P P 76F sing 39 n n O1P P 76F doub 40 n n O2P P 76F sing 41 n n P O4P 76F sing 42 n n O4P C4 76F sing 43 n n C4 C5 76F sing 44 n n C5 N 76F sing 45 n n C2 H1 76F sing 46 n n C1 H2 76F sing 47 n n C1 H3 76F sing 48 n n N H4 76F sing 49 n n N H5 76F sing 50 n n C3 H7 76F sing 51 n n C3 H8 76F sing 52 n n C4 H9 76F sing 53 n n C4 H10 76F sing 54 n n C5 H11 76F sing 55 n n C5 H12 76F sing 56 n n C11 H13 76F sing 57 n n C11 H14 76F sing 58 n n C12 H15 76F sing 59 n n C12 H16 76F sing 60 n n C13 H17 76F sing 61 n n C13 H18 76F sing 62 n n C14 H19 76F sing 63 n n C14 H20 76F sing 64 n n C15 H21 76F sing 65 n n C15 H22 76F sing 66 n n C16 H23 76F sing 67 n n C16 H24 76F sing 68 n n C17 H25 76F sing 69 n n C17 H26 76F sing 70 n n C18 H27 76F sing 71 n n C19 H29 76F sing 72 n n C20 H31 76F sing 73 n n C20 H32 76F sing 74 n n C21 H33 76F sing 75 n n C22 H35 76F sing 76 n n C31 H38 76F sing 77 n n C31 H39 76F sing 78 n n C32 H40 76F sing 79 n n C32 H41 76F sing 80 n n C33 H42 76F sing 81 n n C33 H43 76F sing 82 n n C34 H44 76F sing 83 n n C34 H45 76F sing 84 n n C35 H46 76F sing 85 n n C35 H47 76F sing 86 n n C36 H48 76F sing 87 n n C36 H49 76F sing 88 n n C37 H50 76F sing 89 n n C37 H51 76F sing 90 n n C38 H52 76F sing 91 n n C38 H53 76F sing 92 n n C39 H54 76F sing 93 n n C39 H55 76F sing 94 n n C40 H56 76F sing 95 n n C41 H58 76F sing 96 n n C42 H60 76F sing 97 n n C42 H61 76F sing 98 n n C43 H62 76F sing 99 n n C43 H63 76F sing 100 n n C44 H64 76F sing 101 n n C44 H65 76F sing 102 n n C45 H66 76F sing 103 n n C45 H67 76F sing 104 n n C46 H68 76F sing 105 n n C46 H69 76F sing 106 n n C47 H70 76F sing 107 n n C47 H71 76F sing 108 n n C47 H72 76F sing 109 n n O2P H73 76F sing 110 n n C22 C23 76F sing 111 n n C23 C24 76F sing 112 n n C24 C25 76F sing 113 n n C25 C26 76F sing 114 n n C26 C27 76F sing 115 n n C23 H6 76F sing 116 n n C23 H28 76F sing 117 n n C24 H30 76F sing 118 n n C24 H34 76F sing 119 n n C25 H36 76F sing 120 n n C25 H37 76F sing 121 n n C26 H57 76F sing 122 n n C26 H59 76F sing 123 n n C27 H74 76F sing 124 n n C27 H75 76F sing 125 n n C27 H76 76F sing 126 n n # _atom_sites.entry_id 6NT3 _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 4 NAG A 1 1606 1607 NAG NAG . F 4 NAG A 1 1607 1609 NAG NAG . G 4 NAG A 1 1608 1612 NAG NAG . H 4 NAG A 1 1613 1624 NAG NAG . I 5 Y01 A 1 1614 1 Y01 CHS . J 6 76F A 1 1615 1 76F PEE . K 6 76F A 1 1616 3 76F PEE . L 6 76F A 1 1617 4 76F PEE . M 6 76F A 1 1618 5 76F PEE . N 7 LHG A 1 1619 1 LHG LHG . O 8 AJP A 1 1620 1 AJP DIG . # 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 C2 76F . . . L 6 144.787 105.144 135.586 1 94.54 ? C2 76F 1617 A 1 HETATM 2 C C1 76F . . . L 6 146.042 105.333 136.433 1 94.54 ? C1 76F 1617 A 1 HETATM 3 N N 76F . . . L 6 147.64 104.322 143.639 1 94.54 ? N 76F 1617 A 1 HETATM 4 C C3 76F . . . L 6 144.271 103.721 135.766 1 94.54 ? C3 76F 1617 A 1 HETATM 5 C C4 76F . . . L 6 146.429 104.333 141.517 1 94.54 ? C4 76F 1617 A 1 HETATM 6 C C5 76F . . . L 6 147.789 104.477 142.201 1 94.54 ? C5 76F 1617 A 1 HETATM 7 C C10 76F . . . L 6 143.251 106.863 135.031 1 94.54 ? C10 76F 1617 A 1 HETATM 8 C C11 76F . . . L 6 143.35 106.512 133.55 1 94.54 ? C11 76F 1617 A 1 HETATM 9 C C12 76F . . . L 6 141.981 106.702 132.907 1 94.54 ? C12 76F 1617 A 1 HETATM 10 C C13 76F . . . L 6 142.109 107.591 131.677 1 94.54 ? C13 76F 1617 A 1 HETATM 11 C C14 76F . . . L 6 141.136 108.758 131.799 1 94.54 ? C14 76F 1617 A 1 HETATM 12 C C15 76F . . . L 6 140.167 108.702 130.626 1 94.54 ? C15 76F 1617 A 1 HETATM 13 C C16 76F . . . L 6 139.383 110.005 130.538 1 94.54 ? C16 76F 1617 A 1 HETATM 14 C C17 76F . . . L 6 138.697 110.045 129.178 1 94.54 ? C17 76F 1617 A 1 HETATM 15 C C18 76F . . . L 6 138.091 111.421 128.93 1 94.54 ? C18 76F 1617 A 1 HETATM 16 C C19 76F . . . L 6 138.006 111.635 127.424 1 94.54 ? C19 76F 1617 A 1 HETATM 17 C C20 76F . . . L 6 137.006 112.741 127.113 1 94.54 ? C20 76F 1617 A 1 HETATM 18 C C21 76F . . . L 6 137.008 113.011 125.612 1 94.54 ? C21 76F 1617 A 1 HETATM 19 C C22 76F . . . L 6 135.907 114.004 125.258 1 94.54 ? C22 76F 1617 A 1 HETATM 20 C C30 76F . . . L 6 142.218 102.859 136.569 1 94.54 ? C30 76F 1617 A 1 HETATM 21 C C31 76F . . . L 6 141.769 102.481 135.158 1 94.54 ? C31 76F 1617 A 1 HETATM 22 C C32 76F . . . L 6 140.279 102.771 134.999 1 94.54 ? C32 76F 1617 A 1 HETATM 23 C C33 76F . . . L 6 140.005 103.219 133.568 1 94.54 ? C33 76F 1617 A 1 HETATM 24 C C34 76F . . . L 6 139.569 102.012 132.75 1 94.54 ? C34 76F 1617 A 1 HETATM 25 C C35 76F . . . L 6 138.111 102.187 132.338 1 94.54 ? C35 76F 1617 A 1 HETATM 26 C C36 76F . . . L 6 137.967 103.451 131.499 1 94.54 ? C36 76F 1617 A 1 HETATM 27 C C37 76F . . . L 6 136.865 103.233 130.468 1 94.54 ? C37 76F 1617 A 1 HETATM 28 C C38 76F . . . L 6 136.784 104.454 129.557 1 94.54 ? C38 76F 1617 A 1 HETATM 29 C C39 76F . . . L 6 135.407 104.529 128.902 1 94.54 ? C39 76F 1617 A 1 HETATM 30 O O4 76F . . . L 6 142.711 107.866 135.349 1 94.54 ? O4 76F 1617 A 1 HETATM 31 O O5 76F . . . L 6 141.65 102.412 137.506 1 94.54 ? O5 76F 1617 A 1 HETATM 32 O O2 76F . . . L 6 143.795 106.03 136.017 1 94.54 ? O2 76F 1617 A 1 HETATM 33 O O3 76F . . . L 6 143.298 103.728 136.769 1 94.54 ? O3 76F 1617 A 1 HETATM 34 O O1P 76F . . . L 6 147.26 106.239 139.014 1 94.54 -1 O1P 76F 1617 A 1 HETATM 35 O O2P 76F . . . L 6 144.886 105.832 139.462 1 94.54 ? O2P 76F 1617 A 1 HETATM 36 O O3P 76F . . . L 6 145.999 104.503 137.56 1 94.54 ? O3P 76F 1617 A 1 HETATM 37 O O4P 76F . . . L 6 146.6 104.036 140.158 1 94.54 ? O4P 76F 1617 A 1 HETATM 38 P P 76F . . . L 6 146.184 105.184 139.052 1 94.54 ? P 76F 1617 A 1 HETATM 39 C C23 76F . . . L 6 136.307 114.773 124.005 1 94.54 ? C23 76F 1617 A 1 HETATM 40 C C24 76F . . . L 6 135.287 115.871 123.722 1 94.54 ? C24 76F 1617 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 40 #