# By using this file you agree to the legally binding terms of use found at # https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. # To request access to the AlphaFold 3 model parameters, follow the process set # out at https://github.com/google-deepmind/alphafold3. You may only use these if # received directly from Google. Use is subject to terms of use available at # https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. data_spkb38764 # _entry.id spkb38764 # loop_ _atom_type.symbol C N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Google DeepMind" 1 "Isomorphic Labs" 2 # _audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic _audit_conform.dict_name mmcif_ma.dic _audit_conform.dict_version 1.4.5 # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_smiles _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.093 ALA y ALANINE C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "PEPTIDE LINKING" "C6 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 ILE y ISOLEUCINE CC[C@H](C)[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 LEU y LEUCINE CC(C)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C5 H11 N O2" 117.146 VAL y VALINE CC(C)[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" # _citation.book_publisher ? _citation.country UK _citation.id primary _citation.journal_full Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 0028-0836 _citation.journal_volume 630 _citation.page_first 493 _citation.page_last 500 _citation.pdbx_database_id_DOI 10.1038/s41586-024-07487-w _citation.pdbx_database_id_PubMed 38718835 _citation.title "Accurate structure prediction of biomolecular interactions with AlphaFold 3" _citation.year 2024 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary "Google DeepMind" 1 primary "Isomorphic Labs" 2 # _entity.id 1 _entity.pdbx_description . _entity.type polymer # _entity_poly.entity_id 1 _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 n MET 1 1 n LYS 2 1 n LEU 3 1 n VAL 4 1 n HIS 5 1 n MET 6 1 n ALA 7 1 n SER 8 1 n GLY 9 1 n LEU 10 1 n ALA 11 1 n VAL 12 1 n ALA 13 1 n ILE 14 1 n ALA 15 1 n LEU 16 1 n ALA 17 1 n ALA 18 # _ma_data.content_type "model coordinates" _ma_data.id 1 _ma_data.name Model # _ma_model_list.data_id 1 _ma_model_list.model_group_id 1 _ma_model_list.model_group_name "AlphaFold-beta-20231127 (3.0.0 @ 2025-07-09 16:21:58)" _ma_model_list.model_id 1 _ma_model_list.model_name "Top ranked model" _ma_model_list.model_type "Ab initio model" _ma_model_list.ordinal_id 1 # loop_ _ma_protocol_step.method_type _ma_protocol_step.ordinal_id _ma_protocol_step.protocol_id _ma_protocol_step.step_id "coevolution MSA" 1 1 1 "template search" 2 1 2 modeling 3 1 3 # loop_ _ma_qa_metric.id _ma_qa_metric.mode _ma_qa_metric.name _ma_qa_metric.software_group_id _ma_qa_metric.type 1 global pLDDT 1 pLDDT 2 local pLDDT 1 pLDDT # _ma_qa_metric_global.metric_id 1 _ma_qa_metric_global.metric_value 92.07 _ma_qa_metric_global.model_id 1 _ma_qa_metric_global.ordinal_id 1 # loop_ _ma_qa_metric_local.label_asym_id _ma_qa_metric_local.label_comp_id _ma_qa_metric_local.label_seq_id _ma_qa_metric_local.metric_id _ma_qa_metric_local.metric_value _ma_qa_metric_local.model_id _ma_qa_metric_local.ordinal_id A MET 1 2 86.44 1 1 A LYS 2 2 88.17 1 2 A LEU 3 2 91.26 1 3 A VAL 4 2 95.22 1 4 A HIS 5 2 88.62 1 5 A MET 6 2 89.52 1 6 A ALA 7 2 94.94 1 7 A SER 8 2 92.87 1 8 A GLY 9 2 94.17 1 9 A LEU 10 2 91.98 1 10 A ALA 11 2 95.75 1 11 A VAL 12 2 95.23 1 12 A ALA 13 2 95.80 1 13 A ILE 14 2 94.57 1 14 A ALA 15 2 96.66 1 15 A LEU 16 2 92.59 1 16 A ALA 17 2 95.66 1 17 A ALA 18 2 86.76 1 18 # _ma_software_group.group_id 1 _ma_software_group.ordinal_id 1 _ma_software_group.software_id 1 # _ma_target_entity.data_id 1 _ma_target_entity.entity_id 1 _ma_target_entity.origin . # _ma_target_entity_instance.asym_id A _ma_target_entity_instance.details . _ma_target_entity_instance.entity_id 1 # loop_ _pdbx_data_usage.details _pdbx_data_usage.id _pdbx_data_usage.type _pdbx_data_usage.url ;Non-commercial use only, by using this file you agree to the terms of use found at https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. To request access to the AlphaFold 3 model parameters, follow the process set out at https://github.com/google-deepmind/alphafold3. You may only use these if received directly from Google. Use is subject to terms of use available at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. ; 1 license https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md ;AlphaFold 3 and its output are not intended for, have not been validated for, and are not approved for clinical use. They are provided "as-is" without any warranty of any kind, whether expressed or implied. No warranty is given that use shall not infringe the rights of any third party. ; 2 disclaimer ? # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.hetero _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.seq_id A 1 1 n MET . 1 A 1 A 2 1 n LYS . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n HIS . 5 A 5 A 6 1 n MET . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n GLY . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ILE . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n ALA . 17 A 17 A 18 1 n ALA . 18 A 18 # _software.classification other _software.date ? _software.description "Structure prediction" _software.name AlphaFold _software.pdbx_ordinal 1 _software.type package _software.version "AlphaFold-beta-20231127 (9ceee3b5f7825b611ab42eaad843248507ced2da1e745fa3b3d93c6c4ad3ca74)" # _struct_asym.entity_id 1 _struct_asym.id A # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . MET A 1 1 ? -12.242 3.035 3.393 1.00 91.49 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.446 2.660 4.579 1.00 92.33 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.080 3.346 4.541 1.00 92.85 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.299 3.131 3.619 1.00 89.77 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.254 1.151 4.625 1.00 88.50 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.563 0.424 4.889 1.00 85.39 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.396 -1.360 4.770 1.00 80.64 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.086 -1.850 5.053 1.00 70.55 1 A 1 ATOM 9 N N . LYS A 1 2 ? -9.823 4.168 5.539 1.00 92.81 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -8.563 4.912 5.611 1.00 94.16 2 A 1 ATOM 11 C C . LYS A 1 2 ? -7.378 3.978 5.869 1.00 95.01 2 A 1 ATOM 12 O O . LYS A 1 2 ? -6.275 4.226 5.384 1.00 94.22 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -8.659 5.966 6.715 1.00 92.23 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -7.515 6.950 6.679 1.00 86.83 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -7.702 8.058 7.713 1.00 84.97 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -8.596 9.155 7.186 1.00 79.12 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -8.817 10.212 8.207 1.00 74.21 2 A 1 ATOM 18 N N . LEU A 1 3 ? -7.616 2.911 6.622 1.00 92.89 3 A 1 ATOM 19 C CA . LEU A 1 3 ? -6.562 1.950 6.959 1.00 94.24 3 A 1 ATOM 20 C C . LEU A 1 3 ? -6.031 1.265 5.704 1.00 95.12 3 A 1 ATOM 21 O O . LEU A 1 3 ? -4.821 1.110 5.525 1.00 93.03 3 A 1 ATOM 22 C CB . LEU A 1 3 ? -7.107 0.906 7.941 1.00 93.26 3 A 1 ATOM 23 C CG . LEU A 1 3 ? -6.078 0.381 8.940 1.00 90.24 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? -4.878 -0.220 8.229 1.00 86.88 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? -5.645 1.486 9.885 1.00 84.46 3 A 1 ATOM 26 N N . VAL A 1 4 ? -6.948 0.850 4.833 1.00 96.52 4 A 1 ATOM 27 C CA . VAL A 1 4 ? -6.575 0.176 3.589 1.00 96.51 4 A 1 ATOM 28 C C . VAL A 1 4 ? -5.773 1.107 2.689 1.00 96.53 4 A 1 ATOM 29 O O . VAL A 1 4 ? -4.783 0.699 2.071 1.00 95.75 4 A 1 ATOM 30 C CB . VAL A 1 4 ? -7.821 -0.321 2.841 1.00 95.80 4 A 1 ATOM 31 C CG1 . VAL A 1 4 ? -7.429 -1.005 1.543 1.00 92.91 4 A 1 ATOM 32 C CG2 . VAL A 1 4 ? -8.619 -1.270 3.719 1.00 92.51 4 A 1 ATOM 33 N N . HIS A 1 5 ? -6.210 2.351 2.614 1.00 92.17 5 A 1 ATOM 34 C CA . HIS A 1 5 ? -5.531 3.338 1.779 1.00 92.64 5 A 1 ATOM 35 C C . HIS A 1 5 ? -4.136 3.642 2.321 1.00 93.25 5 A 1 ATOM 36 O O . HIS A 1 5 ? -3.180 3.802 1.558 1.00 91.69 5 A 1 ATOM 37 C CB . HIS A 1 5 ? -6.357 4.621 1.713 1.00 91.65 5 A 1 ATOM 38 C CG . HIS A 1 5 ? -7.533 4.501 0.789 1.00 91.43 5 A 1 ATOM 39 N ND1 . HIS A 1 5 ? -8.651 3.767 1.083 1.00 82.49 5 A 1 ATOM 40 C CD2 . HIS A 1 5 ? -7.749 5.034 -0.439 1.00 81.75 5 A 1 ATOM 41 C CE1 . HIS A 1 5 ? -9.499 3.858 0.066 1.00 84.00 5 A 1 ATOM 42 N NE2 . HIS A 1 5 ? -8.984 4.623 -0.870 1.00 85.09 5 A 1 ATOM 43 N N . MET A 1 6 ? -4.022 3.721 3.629 1.00 94.47 6 A 1 ATOM 44 C CA . MET A 1 6 ? -2.736 3.989 4.270 1.00 94.62 6 A 1 ATOM 45 C C . MET A 1 6 ? -1.759 2.837 4.052 1.00 95.26 6 A 1 ATOM 46 O O . MET A 1 6 ? -0.596 3.055 3.723 1.00 93.99 6 A 1 ATOM 47 C CB . MET A 1 6 ? -2.943 4.216 5.763 1.00 93.69 6 A 1 ATOM 48 C CG . MET A 1 6 ? -3.315 5.655 6.077 1.00 89.09 6 A 1 ATOM 49 S SD . MET A 1 6 ? -2.393 6.283 7.468 1.00 81.86 6 A 1 ATOM 50 C CE . MET A 1 6 ? -3.555 7.474 8.111 1.00 73.18 6 A 1 ATOM 51 N N . ALA A 1 7 ? -2.252 1.621 4.239 1.00 94.87 7 A 1 ATOM 52 C CA . ALA A 1 7 ? -1.418 0.437 4.075 1.00 94.97 7 A 1 ATOM 53 C C . ALA A 1 7 ? -0.954 0.283 2.632 1.00 95.79 7 A 1 ATOM 54 O O . ALA A 1 7 ? 0.210 -0.022 2.374 1.00 94.93 7 A 1 ATOM 55 C CB . ALA A 1 7 ? -2.191 -0.799 4.512 1.00 94.13 7 A 1 ATOM 56 N N . SER A 1 8 ? -1.869 0.493 1.694 1.00 94.46 8 A 1 ATOM 57 C CA . SER A 1 8 ? -1.554 0.373 0.274 1.00 94.46 8 A 1 ATOM 58 C C . SER A 1 8 ? -0.559 1.439 -0.160 1.00 95.37 8 A 1 ATOM 59 O O . SER A 1 8 ? 0.409 1.152 -0.864 1.00 94.53 8 A 1 ATOM 60 C CB . SER A 1 8 ? -2.827 0.487 -0.558 1.00 93.12 8 A 1 ATOM 61 O OG . SER A 1 8 ? -3.660 -0.630 -0.344 1.00 85.29 8 A 1 ATOM 62 N N . GLY A 1 9 ? -0.808 2.668 0.264 1.00 93.19 9 A 1 ATOM 63 C CA . GLY A 1 9 ? 0.081 3.773 -0.079 1.00 93.71 9 A 1 ATOM 64 C C . GLY A 1 9 ? 1.460 3.596 0.524 1.00 95.22 9 A 1 ATOM 65 O O . GLY A 1 9 ? 2.473 3.886 -0.112 1.00 94.55 9 A 1 ATOM 66 N N . LEU A 1 10 ? 1.489 3.103 1.750 1.00 94.51 10 A 1 ATOM 67 C CA . LEU A 1 10 ? 2.753 2.881 2.447 1.00 94.44 10 A 1 ATOM 68 C C . LEU A 1 10 ? 3.570 1.800 1.758 1.00 95.76 10 A 1 ATOM 69 O O . LEU A 1 10 ? 4.795 1.887 1.679 1.00 94.89 10 A 1 ATOM 70 C CB . LEU A 1 10 ? 2.481 2.475 3.892 1.00 93.37 10 A 1 ATOM 71 C CG . LEU A 1 10 ? 3.687 2.659 4.803 1.00 88.98 10 A 1 ATOM 72 C CD1 . LEU A 1 10 ? 3.885 4.124 5.129 1.00 86.81 10 A 1 ATOM 73 C CD2 . LEU A 1 10 ? 3.520 1.842 6.074 1.00 87.11 10 A 1 ATOM 74 N N . ALA A 1 11 ? 2.888 0.775 1.256 1.00 95.41 11 A 1 ATOM 75 C CA . ALA A 1 11 ? 3.555 -0.324 0.566 1.00 95.82 11 A 1 ATOM 76 C C . ALA A 1 11 ? 4.337 0.190 -0.637 1.00 96.81 11 A 1 ATOM 77 O O . ALA A 1 11 ? 5.434 -0.288 -0.930 1.00 95.76 11 A 1 ATOM 78 C CB . ALA A 1 11 ? 2.524 -1.351 0.118 1.00 94.95 11 A 1 ATOM 79 N N . VAL A 1 12 ? 3.774 1.164 -1.329 1.00 95.45 12 A 1 ATOM 80 C CA . VAL A 1 12 ? 4.429 1.757 -2.493 1.00 96.08 12 A 1 ATOM 81 C C . VAL A 1 12 ? 5.701 2.479 -2.073 1.00 97.05 12 A 1 ATOM 82 O O . VAL A 1 12 ? 6.728 2.402 -2.751 1.00 96.68 12 A 1 ATOM 83 C CB . VAL A 1 12 ? 3.493 2.741 -3.204 1.00 95.27 12 A 1 ATOM 84 C CG1 . VAL A 1 12 ? 4.185 3.349 -4.417 1.00 93.10 12 A 1 ATOM 85 C CG2 . VAL A 1 12 ? 2.212 2.044 -3.616 1.00 92.98 12 A 1 ATOM 86 N N . ALA A 1 13 ? 5.622 3.176 -0.952 1.00 95.65 13 A 1 ATOM 87 C CA . ALA A 1 13 ? 6.770 3.912 -0.433 1.00 95.78 13 A 1 ATOM 88 C C . ALA A 1 13 ? 7.898 2.959 -0.047 1.00 96.79 13 A 1 ATOM 89 O O . ALA A 1 13 ? 9.074 3.255 -0.261 1.00 96.03 13 A 1 ATOM 90 C CB . ALA A 1 13 ? 6.350 4.743 0.774 1.00 94.77 13 A 1 ATOM 91 N N . ILE A 1 14 ? 7.528 1.820 0.516 1.00 95.66 14 A 1 ATOM 92 C CA . ILE A 1 14 ? 8.507 0.817 0.926 1.00 95.73 14 A 1 ATOM 93 C C . ILE A 1 14 ? 9.238 0.261 -0.287 1.00 96.37 14 A 1 ATOM 94 O O . ILE A 1 14 ? 10.467 0.135 -0.292 1.00 95.88 14 A 1 ATOM 95 C CB . ILE A 1 14 ? 7.821 -0.323 1.690 1.00 95.56 14 A 1 ATOM 96 C CG1 . ILE A 1 14 ? 7.218 0.207 2.993 1.00 94.01 14 A 1 ATOM 97 C CG2 . ILE A 1 14 ? 8.833 -1.429 1.999 1.00 93.08 14 A 1 ATOM 98 C CD1 . ILE A 1 14 ? 6.236 -0.758 3.623 1.00 90.26 14 A 1 ATOM 99 N N . ALA A 1 15 ? 8.476 -0.082 -1.318 1.00 96.75 15 A 1 ATOM 100 C CA . ALA A 1 15 ? 9.055 -0.617 -2.547 1.00 96.71 15 A 1 ATOM 101 C C . ALA A 1 15 ? 9.928 0.430 -3.233 1.00 97.27 15 A 1 ATOM 102 O O . ALA A 1 15 ? 10.959 0.106 -3.825 1.00 96.24 15 A 1 ATOM 103 C CB . ALA A 1 15 ? 7.943 -1.074 -3.485 1.00 96.35 15 A 1 ATOM 104 N N . LEU A 1 16 ? 9.505 1.673 -3.159 1.00 95.53 16 A 1 ATOM 105 C CA . LEU A 1 16 ? 10.249 2.777 -3.763 1.00 95.42 16 A 1 ATOM 106 C C . LEU A 1 16 ? 11.553 3.029 -3.016 1.00 96.15 16 A 1 ATOM 107 O O . LEU A 1 16 ? 12.573 3.367 -3.622 1.00 95.76 16 A 1 ATOM 108 C CB . LEU A 1 16 ? 9.392 4.045 -3.747 1.00 94.64 16 A 1 ATOM 109 C CG . LEU A 1 16 ? 9.851 5.106 -4.746 1.00 88.96 16 A 1 ATOM 110 C CD1 . LEU A 1 16 ? 9.346 4.771 -6.142 1.00 87.37 16 A 1 ATOM 111 C CD2 . LEU A 1 16 ? 9.365 6.483 -4.327 1.00 86.91 16 A 1 ATOM 112 N N . ALA A 1 17 ? 11.516 2.864 -1.702 1.00 95.97 17 A 1 ATOM 113 C CA . ALA A 1 17 ? 12.692 3.076 -0.861 1.00 95.76 17 A 1 ATOM 114 C C . ALA A 1 17 ? 13.733 1.986 -1.068 1.00 96.38 17 A 1 ATOM 115 O O . ALA A 1 17 ? 14.917 2.188 -0.790 1.00 95.55 17 A 1 ATOM 116 C CB . ALA A 1 17 ? 12.279 3.127 0.607 1.00 94.62 17 A 1 ATOM 117 N N . ALA A 1 18 ? 13.300 0.821 -1.549 1.00 92.39 18 A 1 ATOM 118 C CA . ALA A 1 18 ? 14.192 -0.311 -1.760 1.00 90.21 18 A 1 ATOM 119 C C . ALA A 1 18 ? 15.273 -0.002 -2.796 1.00 87.86 18 A 1 ATOM 120 O O . ALA A 1 18 ? 15.117 0.948 -3.581 1.00 85.07 18 A 1 ATOM 121 C CB . ALA A 1 18 ? 13.388 -1.540 -2.172 1.00 85.87 18 A 1 ATOM 122 O OXT . ALA A 1 18 ? 16.283 -0.723 -2.836 1.00 79.16 18 A 1 #