# 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_spkb12096 # _entry.id spkb12096 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "L-PEPTIDE LINKING" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "PEPTIDE LINKING" "C6 H13 N O2" 131.173 LEU y LEUCINE CC(C)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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O3" 105.093 SER y SERINE C([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" # _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 CYS 2 1 n LEU 3 1 n PHE 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n PHE 8 1 n PRO 9 1 n TYR 10 1 n LEU 11 1 n ALA 12 1 n SER 13 1 n GLY 14 # _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 @ 2025-07-04 16:23:11)" _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 94.07 _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 85.75 1 1 A CYS 2 2 93.02 1 2 A LEU 3 2 94.10 1 3 A PHE 4 2 94.83 1 4 A LEU 5 2 95.30 1 5 A LEU 6 2 96.31 1 6 A LEU 7 2 95.90 1 7 A PHE 8 2 95.01 1 8 A PRO 9 2 97.04 1 9 A TYR 10 2 94.14 1 10 A LEU 11 2 95.56 1 11 A ALA 12 2 97.31 1 12 A SER 13 2 92.89 1 13 A GLY 14 2 87.80 1 14 # _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 CYS . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n PRO . 9 A 9 A 10 1 n TYR . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n GLY . 14 A 14 # _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 ? -10.103 2.884 3.180 1.00 92.25 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.051 2.585 4.168 1.00 92.32 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.212 1.382 3.741 1.00 91.54 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.086 1.211 4.204 1.00 90.17 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.680 2.309 5.537 1.00 88.61 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.124 3.598 6.230 1.00 82.16 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.734 4.548 6.804 1.00 79.04 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.576 5.979 7.499 1.00 69.90 1 A 1 ATOM 9 N N . CYS A 1 2 ? -8.751 0.580 2.865 1.00 94.37 2 A 1 ATOM 10 C CA . CYS A 1 2 ? -8.024 -0.596 2.384 1.00 95.53 2 A 1 ATOM 11 C C . CYS A 1 2 ? -6.748 -0.191 1.655 1.00 96.45 2 A 1 ATOM 12 O O . CYS A 1 2 ? -5.685 -0.766 1.876 1.00 95.05 2 A 1 ATOM 13 C CB . CYS A 1 2 ? -8.918 -1.425 1.463 1.00 91.48 2 A 1 ATOM 14 S SG . CYS A 1 2 ? -10.229 -2.300 2.359 1.00 85.21 2 A 1 ATOM 15 N N . LEU A 1 3 ? -6.854 0.814 0.794 1.00 95.79 3 A 1 ATOM 16 C CA . LEU A 1 3 ? -5.697 1.299 0.038 1.00 96.71 3 A 1 ATOM 17 C C . LEU A 1 3 ? -4.656 1.936 0.951 1.00 97.45 3 A 1 ATOM 18 O O . LEU A 1 3 ? -3.470 1.980 0.616 1.00 97.40 3 A 1 ATOM 19 C CB . LEU A 1 3 ? -6.155 2.311 -1.009 1.00 96.38 3 A 1 ATOM 20 C CG . LEU A 1 3 ? -6.886 1.696 -2.192 1.00 91.86 3 A 1 ATOM 21 C CD1 . LEU A 1 3 ? -7.559 2.784 -3.016 1.00 88.80 3 A 1 ATOM 22 C CD2 . LEU A 1 3 ? -5.916 0.911 -3.067 1.00 88.38 3 A 1 ATOM 23 N N . PHE A 1 4 ? -5.109 2.436 2.088 1.00 97.21 4 A 1 ATOM 24 C CA . PHE A 1 4 ? -4.213 3.074 3.056 1.00 97.28 4 A 1 ATOM 25 C C . PHE A 1 4 ? -3.171 2.073 3.550 1.00 97.61 4 A 1 ATOM 26 O O . PHE A 1 4 ? -2.030 2.439 3.838 1.00 97.38 4 A 1 ATOM 27 C CB . PHE A 1 4 ? -5.018 3.616 4.241 1.00 97.00 4 A 1 ATOM 28 C CG . PHE A 1 4 ? -4.395 4.843 4.856 1.00 95.11 4 A 1 ATOM 29 C CD1 . PHE A 1 4 ? -3.158 4.778 5.472 1.00 92.33 4 A 1 ATOM 30 C CD2 . PHE A 1 4 ? -5.059 6.065 4.816 1.00 92.35 4 A 1 ATOM 31 C CE1 . PHE A 1 4 ? -2.575 5.912 6.035 1.00 92.18 4 A 1 ATOM 32 C CE2 . PHE A 1 4 ? -4.485 7.199 5.383 1.00 91.75 4 A 1 ATOM 33 C CZ . PHE A 1 4 ? -3.243 7.123 5.992 1.00 92.90 4 A 1 ATOM 34 N N . LEU A 1 5 ? -3.558 0.820 3.635 1.00 97.53 5 A 1 ATOM 35 C CA . LEU A 1 5 ? -2.653 -0.237 4.092 1.00 97.63 5 A 1 ATOM 36 C C . LEU A 1 5 ? -1.508 -0.422 3.099 1.00 97.86 5 A 1 ATOM 37 O O . LEU A 1 5 ? -0.406 -0.824 3.477 1.00 97.64 5 A 1 ATOM 38 C CB . LEU A 1 5 ? -3.428 -1.551 4.253 1.00 97.49 5 A 1 ATOM 39 C CG . LEU A 1 5 ? -4.389 -1.574 5.441 1.00 93.17 5 A 1 ATOM 40 C CD1 . LEU A 1 5 ? -5.382 -2.720 5.297 1.00 90.10 5 A 1 ATOM 41 C CD2 . LEU A 1 5 ? -3.624 -1.712 6.749 1.00 90.95 5 A 1 ATOM 42 N N . LEU A 1 6 ? -1.769 -0.118 1.835 1.00 97.92 6 A 1 ATOM 43 C CA . LEU A 1 6 ? -0.770 -0.237 0.781 1.00 97.84 6 A 1 ATOM 44 C C . LEU A 1 6 ? 0.075 1.032 0.687 1.00 97.87 6 A 1 ATOM 45 O O . LEU A 1 6 ? 1.140 1.037 0.064 1.00 97.50 6 A 1 ATOM 46 C CB . LEU A 1 6 ? -1.460 -0.516 -0.562 1.00 97.75 6 A 1 ATOM 47 C CG . LEU A 1 6 ? -1.717 -1.989 -0.874 1.00 95.30 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? -0.407 -2.741 -1.026 1.00 92.66 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? -2.576 -2.632 0.197 1.00 93.63 6 A 1 ATOM 50 N N . LEU A 1 7 ? -0.397 2.098 1.303 1.00 97.61 7 A 1 ATOM 51 C CA . LEU A 1 7 ? 0.305 3.381 1.285 1.00 97.45 7 A 1 ATOM 52 C C . LEU A 1 7 ? 1.605 3.315 2.084 1.00 97.52 7 A 1 ATOM 53 O O . LEU A 1 7 ? 2.625 3.867 1.671 1.00 97.22 7 A 1 ATOM 54 C CB . LEU A 1 7 ? -0.604 4.475 1.855 1.00 97.32 7 A 1 ATOM 55 C CG . LEU A 1 7 ? -0.025 5.882 1.755 1.00 95.05 7 A 1 ATOM 56 C CD1 . LEU A 1 7 ? -0.202 6.433 0.340 1.00 92.14 7 A 1 ATOM 57 C CD2 . LEU A 1 7 ? -0.710 6.805 2.754 1.00 92.88 7 A 1 ATOM 58 N N . PHE A 1 8 ? 1.559 2.647 3.219 1.00 97.29 8 A 1 ATOM 59 C CA . PHE A 1 8 ? 2.740 2.522 4.079 1.00 97.22 8 A 1 ATOM 60 C C . PHE A 1 8 ? 3.902 1.833 3.353 1.00 97.39 8 A 1 ATOM 61 O O . PHE A 1 8 ? 4.998 2.393 3.270 1.00 96.91 8 A 1 ATOM 62 C CB . PHE A 1 8 ? 2.369 1.758 5.357 1.00 96.85 8 A 1 ATOM 63 C CG . PHE A 1 8 ? 3.499 1.668 6.353 1.00 95.64 8 A 1 ATOM 64 C CD1 . PHE A 1 8 ? 4.066 2.817 6.881 1.00 92.94 8 A 1 ATOM 65 C CD2 . PHE A 1 8 ? 3.979 0.431 6.755 1.00 93.15 8 A 1 ATOM 66 C CE1 . PHE A 1 8 ? 5.105 2.740 7.798 1.00 92.37 8 A 1 ATOM 67 C CE2 . PHE A 1 8 ? 5.022 0.347 7.674 1.00 92.35 8 A 1 ATOM 68 C CZ . PHE A 1 8 ? 5.586 1.502 8.195 1.00 93.03 8 A 1 ATOM 69 N N . PRO A 1 9 ? 3.695 0.637 2.838 1.00 97.57 9 A 1 ATOM 70 C CA . PRO A 1 9 ? 4.758 -0.084 2.122 1.00 97.27 9 A 1 ATOM 71 C C . PRO A 1 9 ? 5.105 0.566 0.788 1.00 97.35 9 A 1 ATOM 72 O O . PRO A 1 9 ? 6.212 0.385 0.279 1.00 96.69 9 A 1 ATOM 73 C CB . PRO A 1 9 ? 4.166 -1.486 1.918 1.00 96.63 9 A 1 ATOM 74 C CG . PRO A 1 9 ? 2.698 -1.287 1.954 1.00 96.27 9 A 1 ATOM 75 C CD . PRO A 1 9 ? 2.460 -0.152 2.924 1.00 97.51 9 A 1 ATOM 76 N N . TYR A 1 10 ? 4.167 1.313 0.234 1.00 97.01 10 A 1 ATOM 77 C CA . TYR A 1 10 ? 4.378 1.997 -1.044 1.00 97.00 10 A 1 ATOM 78 C C . TYR A 1 10 ? 5.455 3.072 -0.905 1.00 97.26 10 A 1 ATOM 79 O O . TYR A 1 10 ? 6.331 3.202 -1.766 1.00 96.43 10 A 1 ATOM 80 C CB . TYR A 1 10 ? 3.061 2.624 -1.505 1.00 96.60 10 A 1 ATOM 81 C CG . TYR A 1 10 ? 3.161 3.225 -2.888 1.00 94.39 10 A 1 ATOM 82 C CD1 . TYR A 1 10 ? 3.628 4.521 -3.071 1.00 91.89 10 A 1 ATOM 83 C CD2 . TYR A 1 10 ? 2.787 2.482 -4.005 1.00 92.00 10 A 1 ATOM 84 C CE1 . TYR A 1 10 ? 3.724 5.071 -4.343 1.00 91.45 10 A 1 ATOM 85 C CE2 . TYR A 1 10 ? 2.882 3.031 -5.281 1.00 92.04 10 A 1 ATOM 86 C CZ . TYR A 1 10 ? 3.351 4.322 -5.439 1.00 92.71 10 A 1 ATOM 87 O OH . TYR A 1 10 ? 3.447 4.866 -6.696 1.00 90.95 10 A 1 ATOM 88 N N . LEU A 1 11 ? 5.391 3.832 0.164 1.00 97.41 11 A 1 ATOM 89 C CA . LEU A 1 11 ? 6.362 4.896 0.418 1.00 97.36 11 A 1 ATOM 90 C C . LEU A 1 11 ? 7.645 4.343 1.029 1.00 97.50 11 A 1 ATOM 91 O O . LEU A 1 11 ? 8.734 4.862 0.772 1.00 96.75 11 A 1 ATOM 92 C CB . LEU A 1 11 ? 5.751 5.946 1.356 1.00 96.95 11 A 1 ATOM 93 C CG . LEU A 1 11 ? 6.489 7.281 1.354 1.00 95.10 11 A 1 ATOM 94 C CD1 . LEU A 1 11 ? 6.212 8.040 0.061 1.00 91.86 11 A 1 ATOM 95 C CD2 . LEU A 1 11 ? 6.065 8.122 2.550 1.00 91.55 11 A 1 ATOM 96 N N . ALA A 1 12 ? 7.524 3.323 1.843 1.00 97.86 12 A 1 ATOM 97 C CA . ALA A 1 12 ? 8.678 2.703 2.494 1.00 97.61 12 A 1 ATOM 98 C C . ALA A 1 12 ? 9.541 1.941 1.492 1.00 97.47 12 A 1 ATOM 99 O O . ALA A 1 12 ? 10.762 1.901 1.629 1.00 96.77 12 A 1 ATOM 100 C CB . ALA A 1 12 ? 8.209 1.763 3.602 1.00 96.86 12 A 1 ATOM 101 N N . SER A 1 13 ? 8.905 1.355 0.490 1.00 96.54 13 A 1 ATOM 102 C CA . SER A 1 13 ? 9.615 0.577 -0.526 1.00 95.75 13 A 1 ATOM 103 C C . SER A 1 13 ? 10.542 1.462 -1.352 1.00 94.80 13 A 1 ATOM 104 O O . SER A 1 13 ? 11.726 1.155 -1.515 1.00 90.62 13 A 1 ATOM 105 C CB . SER A 1 13 ? 8.623 -0.136 -1.442 1.00 93.63 13 A 1 ATOM 106 O OG . SER A 1 13 ? 9.286 -1.124 -2.191 1.00 86.00 13 A 1 ATOM 107 N N . GLY A 1 14 ? 9.999 2.554 -1.860 1.00 93.37 14 A 1 ATOM 108 C CA . GLY A 1 14 ? 10.774 3.497 -2.678 1.00 89.97 14 A 1 ATOM 109 C C . GLY A 1 14 ? 9.863 4.424 -3.446 1.00 87.59 14 A 1 ATOM 110 O O . GLY A 1 14 ? 10.114 5.641 -3.426 1.00 81.94 14 A 1 ATOM 111 O OXT . GLY A 1 14 ? 8.911 3.960 -4.064 1.00 86.15 14 A 1 #