# 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_spkb13179 # _entry.id spkb13179 # 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 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" "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" # _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 ALA 2 1 n PRO 3 1 n PRO 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n SER 12 1 n GLY 13 1 n ALA 14 1 n ALA 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 @ 2025-07-09 20:40:23)" _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 89.69 _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 78.02 1 1 A ALA 2 2 87.36 1 2 A PRO 3 2 90.95 1 3 A PRO 4 2 92.81 1 4 A LEU 5 2 92.20 1 5 A LEU 6 2 92.78 1 6 A LEU 7 2 92.44 1 7 A LEU 8 2 91.70 1 8 A LEU 9 2 92.97 1 9 A LEU 10 2 92.28 1 10 A ALA 11 2 94.55 1 11 A SER 12 2 92.16 1 12 A GLY 13 2 92.14 1 13 A ALA 14 2 88.09 1 14 A ALA 15 2 86.29 1 15 A ALA 16 2 76.43 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 ALA . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n PRO . 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 LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 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 ? -4.205 9.911 0.249 1.00 83.31 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.104 8.781 0.569 1.00 83.67 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.440 7.841 1.576 1.00 83.73 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.531 7.102 1.224 1.00 81.38 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.437 8.016 -0.708 1.00 79.35 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.298 8.853 -1.628 1.00 74.32 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.765 7.963 -3.119 1.00 72.99 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.251 8.124 -4.056 1.00 65.43 1 A 1 ATOM 9 N N . ALA A 1 2 ? -4.882 7.909 2.815 1.00 84.48 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -4.318 7.068 3.873 1.00 88.04 2 A 1 ATOM 11 C C . ALA A 1 2 ? -4.914 5.656 3.880 1.00 90.76 2 A 1 ATOM 12 O O . ALA A 1 2 ? -4.179 4.674 4.021 1.00 89.21 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -4.533 7.744 5.224 1.00 84.33 2 A 1 ATOM 14 N N . PRO A 1 3 ? -6.261 5.537 3.746 1.00 91.47 3 A 1 ATOM 15 C CA . PRO A 1 3 ? -6.910 4.217 3.749 1.00 92.94 3 A 1 ATOM 16 C C . PRO A 1 3 ? -6.360 3.278 2.681 1.00 94.36 3 A 1 ATOM 17 O O . PRO A 1 3 ? -6.000 2.136 2.983 1.00 92.44 3 A 1 ATOM 18 C CB . PRO A 1 3 ? -8.392 4.543 3.498 1.00 89.72 3 A 1 ATOM 19 C CG . PRO A 1 3 ? -8.540 5.992 3.849 1.00 86.33 3 A 1 ATOM 20 C CD . PRO A 1 3 ? -7.189 6.645 3.652 1.00 89.40 3 A 1 ATOM 21 N N . PRO A 1 4 ? -6.293 3.723 1.427 1.00 93.64 4 A 1 ATOM 22 C CA . PRO A 1 4 ? -5.788 2.871 0.339 1.00 94.03 4 A 1 ATOM 23 C C . PRO A 1 4 ? -4.295 2.601 0.465 1.00 95.00 4 A 1 ATOM 24 O O . PRO A 1 4 ? -3.748 1.760 -0.249 1.00 93.28 4 A 1 ATOM 25 C CB . PRO A 1 4 ? -6.096 3.679 -0.932 1.00 91.52 4 A 1 ATOM 26 C CG . PRO A 1 4 ? -6.184 5.096 -0.467 1.00 89.72 4 A 1 ATOM 27 C CD . PRO A 1 4 ? -6.720 5.039 0.941 1.00 92.50 4 A 1 ATOM 28 N N . LEU A 1 5 ? -3.643 3.292 1.370 1.00 93.67 5 A 1 ATOM 29 C CA . LEU A 1 5 ? -2.203 3.112 1.581 1.00 94.17 5 A 1 ATOM 30 C C . LEU A 1 5 ? -1.900 1.651 1.906 1.00 95.09 5 A 1 ATOM 31 O O . LEU A 1 5 ? -0.861 1.117 1.520 1.00 93.98 5 A 1 ATOM 32 C CB . LEU A 1 5 ? -1.744 3.999 2.737 1.00 93.32 5 A 1 ATOM 33 C CG . LEU A 1 5 ? -0.244 3.903 2.969 1.00 90.92 5 A 1 ATOM 34 C CD1 . LEU A 1 5 ? 0.512 4.490 1.780 1.00 88.79 5 A 1 ATOM 35 C CD2 . LEU A 1 5 ? 0.137 4.664 4.239 1.00 87.69 5 A 1 ATOM 36 N N . LEU A 1 6 ? -2.825 1.014 2.600 1.00 94.07 6 A 1 ATOM 37 C CA . LEU A 1 6 ? -2.653 -0.395 2.965 1.00 94.25 6 A 1 ATOM 38 C C . LEU A 1 6 ? -2.534 -1.259 1.712 1.00 95.16 6 A 1 ATOM 39 O O . LEU A 1 6 ? -1.713 -2.174 1.648 1.00 94.67 6 A 1 ATOM 40 C CB . LEU A 1 6 ? -3.851 -0.853 3.799 1.00 93.93 6 A 1 ATOM 41 C CG . LEU A 1 6 ? -3.677 -2.275 4.316 1.00 91.29 6 A 1 ATOM 42 C CD1 . LEU A 1 6 ? -2.498 -2.347 5.282 1.00 89.56 6 A 1 ATOM 43 C CD2 . LEU A 1 6 ? -4.947 -2.728 5.028 1.00 89.34 6 A 1 ATOM 44 N N . LEU A 1 7 ? -3.366 -0.955 0.713 1.00 94.46 7 A 1 ATOM 45 C CA . LEU A 1 7 ? -3.345 -1.708 -0.543 1.00 94.25 7 A 1 ATOM 46 C C . LEU A 1 7 ? -2.014 -1.493 -1.252 1.00 94.96 7 A 1 ATOM 47 O O . LEU A 1 7 ? -1.436 -2.425 -1.810 1.00 94.34 7 A 1 ATOM 48 C CB . LEU A 1 7 ? -4.495 -1.240 -1.442 1.00 93.41 7 A 1 ATOM 49 C CG . LEU A 1 7 ? -5.866 -1.425 -0.792 1.00 90.20 7 A 1 ATOM 50 C CD1 . LEU A 1 7 ? -6.957 -1.016 -1.773 1.00 89.18 7 A 1 ATOM 51 C CD2 . LEU A 1 7 ? -6.065 -2.878 -0.372 1.00 88.72 7 A 1 ATOM 52 N N . LEU A 1 8 ? -1.540 -0.267 -1.222 1.00 94.29 8 A 1 ATOM 53 C CA . LEU A 1 8 ? -0.263 0.066 -1.859 1.00 93.88 8 A 1 ATOM 54 C C . LEU A 1 8 ? 0.873 -0.689 -1.175 1.00 94.57 8 A 1 ATOM 55 O O . LEU A 1 8 ? 1.772 -1.213 -1.830 1.00 93.74 8 A 1 ATOM 56 C CB . LEU A 1 8 ? -0.023 1.571 -1.757 1.00 93.21 8 A 1 ATOM 57 C CG . LEU A 1 8 ? 1.250 1.999 -2.484 1.00 88.47 8 A 1 ATOM 58 C CD1 . LEU A 1 8 ? 1.091 1.793 -3.989 1.00 87.66 8 A 1 ATOM 59 C CD2 . LEU A 1 8 ? 1.552 3.466 -2.198 1.00 87.78 8 A 1 ATOM 60 N N . LEU A 1 9 ? 0.814 -0.738 0.139 1.00 94.51 9 A 1 ATOM 61 C CA . LEU A 1 9 ? 1.843 -1.441 0.912 1.00 94.33 9 A 1 ATOM 62 C C . LEU A 1 9 ? 1.836 -2.929 0.571 1.00 95.07 9 A 1 ATOM 63 O O . LEU A 1 9 ? 2.888 -3.550 0.411 1.00 94.42 9 A 1 ATOM 64 C CB . LEU A 1 9 ? 1.569 -1.246 2.403 1.00 94.13 9 A 1 ATOM 65 C CG . LEU A 1 9 ? 2.682 -1.825 3.275 1.00 91.03 9 A 1 ATOM 66 C CD1 . LEU A 1 9 ? 3.972 -1.032 3.086 1.00 90.12 9 A 1 ATOM 67 C CD2 . LEU A 1 9 ? 2.271 -1.788 4.745 1.00 90.14 9 A 1 ATOM 68 N N . LEU A 1 10 ? 0.642 -3.485 0.465 1.00 95.20 10 A 1 ATOM 69 C CA . LEU A 1 10 ? 0.495 -4.906 0.140 1.00 94.52 10 A 1 ATOM 70 C C . LEU A 1 10 ? 1.070 -5.184 -1.242 1.00 94.74 10 A 1 ATOM 71 O O . LEU A 1 10 ? 1.804 -6.157 -1.442 1.00 93.16 10 A 1 ATOM 72 C CB . LEU A 1 10 ? -0.985 -5.290 0.204 1.00 93.60 10 A 1 ATOM 73 C CG . LEU A 1 10 ? -1.199 -6.809 0.231 1.00 89.95 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? -2.560 -7.131 0.831 1.00 88.78 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? -1.110 -7.393 -1.169 1.00 88.26 10 A 1 ATOM 76 N N . ALA A 1 11 ? 0.731 -4.320 -2.196 1.00 95.63 11 A 1 ATOM 77 C CA . ALA A 1 11 ? 1.224 -4.482 -3.562 1.00 95.06 11 A 1 ATOM 78 C C . ALA A 1 11 ? 2.745 -4.367 -3.590 1.00 95.27 11 A 1 ATOM 79 O O . ALA A 1 11 ? 3.420 -5.112 -4.299 1.00 92.97 11 A 1 ATOM 80 C CB . ALA A 1 11 ? 0.594 -3.421 -4.456 1.00 93.84 11 A 1 ATOM 81 N N . SER A 1 12 ? 3.267 -3.441 -2.809 1.00 94.84 12 A 1 ATOM 82 C CA . SER A 1 12 ? 4.712 -3.236 -2.747 1.00 94.42 12 A 1 ATOM 83 C C . SER A 1 12 ? 5.402 -4.481 -2.208 1.00 94.57 12 A 1 ATOM 84 O O . SER A 1 12 ? 6.435 -4.907 -2.722 1.00 91.65 12 A 1 ATOM 85 C CB . SER A 1 12 ? 5.032 -2.046 -1.847 1.00 92.01 12 A 1 ATOM 86 O OG . SER A 1 12 ? 6.420 -1.851 -1.804 1.00 85.47 12 A 1 ATOM 87 N N . GLY A 1 13 ? 4.819 -5.064 -1.172 1.00 92.85 13 A 1 ATOM 88 C CA . GLY A 1 13 ? 5.394 -6.269 -0.584 1.00 92.11 13 A 1 ATOM 89 C C . GLY A 1 13 ? 5.356 -7.432 -1.552 1.00 92.70 13 A 1 ATOM 90 O O . GLY A 1 13 ? 6.302 -8.214 -1.645 1.00 90.92 13 A 1 ATOM 91 N N . ALA A 1 14 ? 4.250 -7.552 -2.281 1.00 89.54 14 A 1 ATOM 92 C CA . ALA A 1 14 ? 4.100 -8.632 -3.258 1.00 88.58 14 A 1 ATOM 93 C C . ALA A 1 14 ? 5.054 -8.433 -4.427 1.00 89.66 14 A 1 ATOM 94 O O . ALA A 1 14 ? 5.621 -9.395 -4.946 1.00 86.98 14 A 1 ATOM 95 C CB . ALA A 1 14 ? 2.661 -8.675 -3.759 1.00 85.71 14 A 1 ATOM 96 N N . ALA A 1 15 ? 5.217 -7.185 -4.849 1.00 87.58 15 A 1 ATOM 97 C CA . ALA A 1 15 ? 6.111 -6.858 -5.960 1.00 87.06 15 A 1 ATOM 98 C C . ALA A 1 15 ? 7.567 -7.062 -5.568 1.00 88.35 15 A 1 ATOM 99 O O . ALA A 1 15 ? 8.411 -7.368 -6.409 1.00 84.37 15 A 1 ATOM 100 C CB . ALA A 1 15 ? 5.886 -5.416 -6.394 1.00 84.09 15 A 1 ATOM 101 N N . ALA A 1 16 ? 7.872 -6.892 -4.285 1.00 84.40 16 A 1 ATOM 102 C CA . ALA A 1 16 ? 9.237 -7.039 -3.791 1.00 80.97 16 A 1 ATOM 103 C C . ALA A 1 16 ? 9.789 -8.427 -4.084 1.00 78.01 16 A 1 ATOM 104 O O . ALA A 1 16 ? 9.016 -9.394 -4.134 1.00 72.07 16 A 1 ATOM 105 C CB . ALA A 1 16 ? 9.271 -6.758 -2.293 1.00 74.14 16 A 1 ATOM 106 O OXT . ALA A 1 16 ? 11.024 -8.547 -4.248 1.00 69.01 16 A 1 #