# 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_spkb32495 # _entry.id spkb32495 # 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" "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 VAL 3 1 n LEU 4 1 n VAL 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n VAL 9 1 n THR 10 1 n LEU 11 1 n ALA 12 1 n VAL 13 1 n VAL 14 1 n TYR 15 1 n ALA 16 # _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 @ 2025-07-02 10:59:10)" _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 95.80 _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 88.78 1 1 A LYS 2 2 91.80 1 2 A VAL 3 2 97.49 1 3 A LEU 4 2 96.07 1 4 A VAL 5 2 97.73 1 5 A LEU 6 2 96.22 1 6 A LEU 7 2 97.11 1 7 A LEU 8 2 96.04 1 8 A VAL 9 2 98.13 1 9 A THR 10 2 96.97 1 10 A LEU 11 2 96.38 1 11 A ALA 12 2 98.44 1 12 A VAL 13 2 97.98 1 13 A VAL 14 2 97.51 1 14 A TYR 15 2 94.89 1 15 A ALA 16 2 94.11 1 16 # _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 VAL . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n TYR . 15 A 15 A 16 1 n ALA . 16 A 16 # _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 ? 3.813 -5.755 12.079 1.00 93.91 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.625 -5.994 10.634 1.00 94.72 1 A 1 ATOM 3 C C . MET A 1 1 ? 4.102 -4.793 9.822 1.00 95.31 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.791 -3.653 10.154 1.00 93.40 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.153 -6.252 10.337 1.00 91.28 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.615 -7.466 11.084 1.00 86.07 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.404 -8.993 10.590 1.00 83.02 1 A 1 ATOM 8 C CE . MET A 1 1 ? 1.684 -9.210 8.971 1.00 72.55 1 A 1 ATOM 9 N N . LYS A 1 2 ? 4.856 -5.055 8.771 1.00 97.15 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 5.399 -3.984 7.931 1.00 97.46 2 A 1 ATOM 11 C C . LYS A 1 2 ? 4.644 -3.864 6.606 1.00 97.89 2 A 1 ATOM 12 O O . LYS A 1 2 ? 4.700 -2.821 5.954 1.00 97.54 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 6.881 -4.247 7.664 1.00 96.59 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 7.719 -4.250 8.925 1.00 91.75 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 9.179 -4.483 8.612 1.00 88.41 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 10.013 -4.462 9.880 1.00 82.73 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 9.629 -5.562 10.797 1.00 76.65 2 A 1 ATOM 18 N N . VAL A 1 3 ? 3.949 -4.921 6.217 1.00 98.31 3 A 1 ATOM 19 C CA . VAL A 1 3 ? 3.194 -4.921 4.968 1.00 98.48 3 A 1 ATOM 20 C C . VAL A 1 3 ? 2.103 -3.851 4.989 1.00 98.61 3 A 1 ATOM 21 O O . VAL A 1 3 ? 1.871 -3.158 3.995 1.00 98.28 3 A 1 ATOM 22 C CB . VAL A 1 3 ? 2.569 -6.304 4.710 1.00 98.12 3 A 1 ATOM 23 C CG1 . VAL A 1 3 ? 1.748 -6.279 3.431 1.00 95.46 3 A 1 ATOM 24 C CG2 . VAL A 1 3 ? 3.656 -7.364 4.614 1.00 95.15 3 A 1 ATOM 25 N N . LEU A 1 4 ? 1.436 -3.713 6.133 1.00 98.28 4 A 1 ATOM 26 C CA . LEU A 1 4 ? 0.370 -2.722 6.273 1.00 98.35 4 A 1 ATOM 27 C C . LEU A 1 4 ? 0.914 -1.313 6.081 1.00 98.47 4 A 1 ATOM 28 O O . LEU A 1 4 ? 0.284 -0.472 5.438 1.00 98.30 4 A 1 ATOM 29 C CB . LEU A 1 4 ? -0.279 -2.853 7.655 1.00 98.21 4 A 1 ATOM 30 C CG . LEU A 1 4 ? -1.044 -4.161 7.855 1.00 94.26 4 A 1 ATOM 31 C CD1 . LEU A 1 4 ? -1.511 -4.269 9.293 1.00 91.24 4 A 1 ATOM 32 C CD2 . LEU A 1 4 ? -2.229 -4.239 6.912 1.00 91.49 4 A 1 ATOM 33 N N . VAL A 1 5 ? 2.082 -1.059 6.635 1.00 98.37 5 A 1 ATOM 34 C CA . VAL A 1 5 ? 2.718 0.249 6.508 1.00 98.43 5 A 1 ATOM 35 C C . VAL A 1 5 ? 3.044 0.530 5.045 1.00 98.49 5 A 1 ATOM 36 O O . VAL A 1 5 ? 2.815 1.634 4.542 1.00 98.28 5 A 1 ATOM 37 C CB . VAL A 1 5 ? 4.001 0.317 7.351 1.00 98.13 5 A 1 ATOM 38 C CG1 . VAL A 1 5 ? 4.688 1.657 7.159 1.00 96.36 5 A 1 ATOM 39 C CG2 . VAL A 1 5 ? 3.670 0.096 8.820 1.00 96.08 5 A 1 ATOM 40 N N . LEU A 1 6 ? 3.578 -0.472 4.372 1.00 98.52 6 A 1 ATOM 41 C CA . LEU A 1 6 ? 3.932 -0.330 2.963 1.00 98.48 6 A 1 ATOM 42 C C . LEU A 1 6 ? 2.690 -0.030 2.129 1.00 98.55 6 A 1 ATOM 43 O O . LEU A 1 6 ? 2.731 0.798 1.215 1.00 98.43 6 A 1 ATOM 44 C CB . LEU A 1 6 ? 4.597 -1.613 2.464 1.00 98.32 6 A 1 ATOM 45 C CG . LEU A 1 6 ? 5.051 -1.553 1.008 1.00 93.00 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? 6.125 -0.490 0.828 1.00 91.77 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? 5.581 -2.907 0.568 1.00 92.65 6 A 1 ATOM 48 N N . LEU A 1 7 ? 1.602 -0.698 2.457 1.00 98.58 7 A 1 ATOM 49 C CA . LEU A 1 7 ? 0.344 -0.496 1.747 1.00 98.56 7 A 1 ATOM 50 C C . LEU A 1 7 ? -0.133 0.944 1.901 1.00 98.66 7 A 1 ATOM 51 O O . LEU A 1 7 ? -0.574 1.571 0.934 1.00 98.57 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -0.714 -1.459 2.288 1.00 98.48 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -2.073 -1.343 1.594 1.00 95.79 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -1.953 -1.705 0.120 1.00 93.70 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -3.086 -2.253 2.271 1.00 94.57 7 A 1 ATOM 56 N N . LEU A 1 8 ? -0.049 1.461 3.116 1.00 98.43 8 A 1 ATOM 57 C CA . LEU A 1 8 ? -0.468 2.830 3.394 1.00 98.39 8 A 1 ATOM 58 C C . LEU A 1 8 ? 0.372 3.824 2.602 1.00 98.52 8 A 1 ATOM 59 O O . LEU A 1 8 ? -0.154 4.781 2.028 1.00 98.38 8 A 1 ATOM 60 C CB . LEU A 1 8 ? -0.342 3.116 4.889 1.00 98.14 8 A 1 ATOM 61 C CG . LEU A 1 8 ? -0.802 4.516 5.289 1.00 92.62 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? -2.281 4.701 4.987 1.00 91.52 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? -0.537 4.754 6.768 1.00 92.33 8 A 1 ATOM 64 N N . VAL A 1 9 ? 1.675 3.596 2.568 1.00 98.66 9 A 1 ATOM 65 C CA . VAL A 1 9 ? 2.585 4.473 1.836 1.00 98.64 9 A 1 ATOM 66 C C . VAL A 1 9 ? 2.266 4.437 0.346 1.00 98.70 9 A 1 ATOM 67 O O . VAL A 1 9 ? 2.208 5.480 -0.314 1.00 98.53 9 A 1 ATOM 68 C CB . VAL A 1 9 ? 4.048 4.062 2.072 1.00 98.38 9 A 1 ATOM 69 C CG1 . VAL A 1 9 ? 4.985 4.885 1.200 1.00 97.06 9 A 1 ATOM 70 C CG2 . VAL A 1 9 ? 4.412 4.244 3.540 1.00 96.97 9 A 1 ATOM 71 N N . THR A 1 10 ? 2.059 3.244 -0.170 1.00 98.46 10 A 1 ATOM 72 C CA . THR A 1 10 ? 1.751 3.081 -1.586 1.00 98.43 10 A 1 ATOM 73 C C . THR A 1 10 ? 0.465 3.822 -1.938 1.00 98.52 10 A 1 ATOM 74 O O . THR A 1 10 ? 0.389 4.506 -2.963 1.00 98.04 10 A 1 ATOM 75 C CB . THR A 1 10 ? 1.593 1.597 -1.933 1.00 98.02 10 A 1 ATOM 76 O OG1 . THR A 1 10 ? 2.787 0.895 -1.614 1.00 94.02 10 A 1 ATOM 77 C CG2 . THR A 1 10 ? 1.311 1.428 -3.420 1.00 93.27 10 A 1 ATOM 78 N N . LEU A 1 11 ? -0.537 3.692 -1.082 1.00 98.60 11 A 1 ATOM 79 C CA . LEU A 1 11 ? -1.814 4.355 -1.302 1.00 98.52 11 A 1 ATOM 80 C C . LEU A 1 11 ? -1.629 5.869 -1.334 1.00 98.56 11 A 1 ATOM 81 O O . LEU A 1 11 ? -2.211 6.561 -2.172 1.00 98.20 11 A 1 ATOM 82 C CB . LEU A 1 11 ? -2.789 3.976 -0.190 1.00 98.22 11 A 1 ATOM 83 C CG . LEU A 1 11 ? -4.197 4.521 -0.399 1.00 94.41 11 A 1 ATOM 84 C CD1 . LEU A 1 11 ? -4.837 3.896 -1.628 1.00 91.88 11 A 1 ATOM 85 C CD2 . LEU A 1 11 ? -5.050 4.247 0.835 1.00 92.65 11 A 1 ATOM 86 N N . ALA A 1 12 ? -0.829 6.381 -0.420 1.00 98.56 12 A 1 ATOM 87 C CA . ALA A 1 12 ? -0.565 7.814 -0.349 1.00 98.54 12 A 1 ATOM 88 C C . ALA A 1 12 ? 0.090 8.312 -1.634 1.00 98.61 12 A 1 ATOM 89 O O . ALA A 1 12 ? -0.236 9.392 -2.126 1.00 98.21 12 A 1 ATOM 90 C CB . ALA A 1 12 ? 0.332 8.115 0.845 1.00 98.26 12 A 1 ATOM 91 N N . VAL A 1 13 ? 1.006 7.529 -2.176 1.00 98.65 13 A 1 ATOM 92 C CA . VAL A 1 13 ? 1.700 7.897 -3.407 1.00 98.59 13 A 1 ATOM 93 C C . VAL A 1 13 ? 0.724 7.956 -4.577 1.00 98.65 13 A 1 ATOM 94 O O . VAL A 1 13 ? 0.767 8.885 -5.390 1.00 98.25 13 A 1 ATOM 95 C CB . VAL A 1 13 ? 2.830 6.905 -3.714 1.00 98.21 13 A 1 ATOM 96 C CG1 . VAL A 1 13 ? 3.452 7.207 -5.068 1.00 96.66 13 A 1 ATOM 97 C CG2 . VAL A 1 13 ? 3.890 6.966 -2.629 1.00 96.84 13 A 1 ATOM 98 N N . VAL A 1 14 ? -0.147 6.968 -4.656 1.00 98.54 14 A 1 ATOM 99 C CA . VAL A 1 14 ? -1.132 6.910 -5.734 1.00 98.51 14 A 1 ATOM 100 C C . VAL A 1 14 ? -2.114 8.072 -5.648 1.00 98.57 14 A 1 ATOM 101 O O . VAL A 1 14 ? -2.524 8.633 -6.670 1.00 98.13 14 A 1 ATOM 102 C CB . VAL A 1 14 ? -1.897 5.580 -5.693 1.00 98.01 14 A 1 ATOM 103 C CG1 . VAL A 1 14 ? -3.000 5.571 -6.738 1.00 95.22 14 A 1 ATOM 104 C CG2 . VAL A 1 14 ? -0.943 4.425 -5.933 1.00 95.59 14 A 1 ATOM 105 N N . TYR A 1 15 ? -2.498 8.417 -4.434 1.00 98.40 15 A 1 ATOM 106 C CA . TYR A 1 15 ? -3.451 9.499 -4.215 1.00 98.31 15 A 1 ATOM 107 C C . TYR A 1 15 ? -2.757 10.849 -4.052 1.00 98.28 15 A 1 ATOM 108 O O . TYR A 1 15 ? -3.392 11.833 -3.675 1.00 97.63 15 A 1 ATOM 109 C CB . TYR A 1 15 ? -4.298 9.199 -2.968 1.00 97.83 15 A 1 ATOM 110 C CG . TYR A 1 15 ? -5.389 8.186 -3.241 1.00 94.81 15 A 1 ATOM 111 C CD1 . TYR A 1 15 ? -5.088 6.850 -3.438 1.00 92.95 15 A 1 ATOM 112 C CD2 . TYR A 1 15 ? -6.719 8.583 -3.301 1.00 92.37 15 A 1 ATOM 113 C CE1 . TYR A 1 15 ? -6.083 5.920 -3.696 1.00 92.54 15 A 1 ATOM 114 C CE2 . TYR A 1 15 ? -7.725 7.660 -3.553 1.00 92.29 15 A 1 ATOM 115 C CZ . TYR A 1 15 ? -7.400 6.329 -3.751 1.00 92.39 15 A 1 ATOM 116 O OH . TYR A 1 15 ? -8.390 5.413 -4.003 1.00 90.90 15 A 1 ATOM 117 N N . ALA A 1 16 ? -1.471 10.919 -4.356 1.00 97.33 16 A 1 ATOM 118 C CA . ALA A 1 16 ? -0.703 12.149 -4.200 1.00 96.50 16 A 1 ATOM 119 C C . ALA A 1 16 ? -1.228 13.240 -5.145 1.00 95.83 16 A 1 ATOM 120 O O . ALA A 1 16 ? -1.079 14.427 -4.820 1.00 93.12 16 A 1 ATOM 121 C CB . ALA A 1 16 ? 0.775 11.867 -4.459 1.00 94.74 16 A 1 ATOM 122 O OXT . ALA A 1 16 ? -1.769 12.937 -6.201 1.00 87.11 16 A 1 #