# 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_spkb24033 # _entry.id spkb24033 # 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 LYS 2 1 n PHE 3 1 n LEU 4 1 n THR 5 1 n LEU 6 1 n ALA 7 1 n LEU 8 1 n SER 9 1 n ALA 10 1 n THR 11 1 n ALA 12 1 n THR 13 1 n ALA 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 @ 2025-07-07 02:48:43)" _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 90.15 _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 85.09 1 1 A LYS 2 2 88.00 1 2 A PHE 3 2 89.97 1 3 A LEU 4 2 92.72 1 4 A THR 5 2 92.42 1 5 A LEU 6 2 89.92 1 6 A ALA 7 2 95.08 1 7 A LEU 8 2 91.51 1 8 A SER 9 2 92.25 1 9 A ALA 10 2 94.95 1 10 A THR 11 2 92.77 1 11 A ALA 12 2 92.52 1 12 A THR 13 2 88.43 1 13 A ALA 14 2 79.68 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 LYS . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n ALA . 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 ? -6.343 7.486 8.727 1.00 89.53 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.414 7.682 7.593 1.00 90.87 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.554 6.543 6.585 1.00 92.24 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.290 5.391 6.905 1.00 90.38 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.973 7.739 8.092 1.00 86.76 1 A 1 ATOM 6 C CG . MET A 1 1 ? -3.719 8.945 8.979 1.00 82.68 1 A 1 ATOM 7 S SD . MET A 1 1 ? -2.041 8.967 9.620 1.00 79.43 1 A 1 ATOM 8 C CE . MET A 1 1 ? -2.090 10.488 10.562 1.00 68.84 1 A 1 ATOM 9 N N . LYS A 1 2 ? -5.981 6.890 5.365 1.00 92.10 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -6.201 5.900 4.306 1.00 93.39 2 A 1 ATOM 11 C C . LYS A 1 2 ? -4.988 5.796 3.382 1.00 94.61 2 A 1 ATOM 12 O O . LYS A 1 2 ? -4.568 4.704 3.015 1.00 94.41 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -7.451 6.299 3.513 1.00 91.89 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -7.835 5.274 2.458 1.00 87.32 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -8.541 4.079 3.073 1.00 84.72 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -9.042 3.147 1.985 1.00 79.70 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -9.772 1.991 2.555 1.00 73.89 2 A 1 ATOM 18 N N . PHE A 1 3 ? -4.421 6.928 3.004 1.00 91.60 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -3.266 6.973 2.109 1.00 93.21 3 A 1 ATOM 20 C C . PHE A 1 3 ? -2.040 6.289 2.724 1.00 95.16 3 A 1 ATOM 21 O O . PHE A 1 3 ? -1.160 5.824 1.997 1.00 93.63 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -2.943 8.421 1.743 1.00 92.16 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -2.905 9.349 2.934 1.00 90.68 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -1.758 9.452 3.708 1.00 87.77 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -4.016 10.104 3.274 1.00 87.64 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -1.714 10.299 4.804 1.00 86.36 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -3.980 10.953 4.378 1.00 86.21 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -2.828 11.049 5.140 1.00 85.23 3 A 1 ATOM 29 N N . LEU A 1 4 ? -1.970 6.219 4.031 1.00 95.16 4 A 1 ATOM 30 C CA . LEU A 1 4 ? -0.845 5.587 4.720 1.00 95.54 4 A 1 ATOM 31 C C . LEU A 1 4 ? -0.767 4.099 4.386 1.00 96.60 4 A 1 ATOM 32 O O . LEU A 1 4 ? 0.314 3.552 4.176 1.00 96.07 4 A 1 ATOM 33 C CB . LEU A 1 4 ? -0.975 5.795 6.237 1.00 95.07 4 A 1 ATOM 34 C CG . LEU A 1 4 ? -0.071 6.891 6.800 1.00 89.41 4 A 1 ATOM 35 C CD1 . LEU A 1 4 ? 1.389 6.492 6.662 1.00 87.20 4 A 1 ATOM 36 C CD2 . LEU A 1 4 ? -0.330 8.208 6.092 1.00 86.69 4 A 1 ATOM 37 N N . THR A 1 5 ? -1.920 3.455 4.322 1.00 93.36 5 A 1 ATOM 38 C CA . THR A 1 5 ? -1.984 2.028 3.999 1.00 93.73 5 A 1 ATOM 39 C C . THR A 1 5 ? -1.544 1.785 2.554 1.00 94.67 5 A 1 ATOM 40 O O . THR A 1 5 ? -0.840 0.817 2.262 1.00 93.78 5 A 1 ATOM 41 C CB . THR A 1 5 ? -3.410 1.500 4.199 1.00 93.06 5 A 1 ATOM 42 O OG1 . THR A 1 5 ? -3.843 1.791 5.523 1.00 90.11 5 A 1 ATOM 43 C CG2 . THR A 1 5 ? -3.465 -0.006 3.990 1.00 88.20 5 A 1 ATOM 44 N N . LEU A 1 6 ? -1.939 2.659 1.647 1.00 93.83 6 A 1 ATOM 45 C CA . LEU A 1 6 ? -1.579 2.547 0.236 1.00 93.98 6 A 1 ATOM 46 C C . LEU A 1 6 ? -0.084 2.791 0.041 1.00 95.31 6 A 1 ATOM 47 O O . LEU A 1 6 ? 0.575 2.118 -0.747 1.00 94.17 6 A 1 ATOM 48 C CB . LEU A 1 6 ? -2.391 3.551 -0.590 1.00 92.71 6 A 1 ATOM 49 C CG . LEU A 1 6 ? -3.650 2.957 -1.211 1.00 83.71 6 A 1 ATOM 50 C CD1 . LEU A 1 6 ? -3.283 1.917 -2.260 1.00 83.48 6 A 1 ATOM 51 C CD2 . LEU A 1 6 ? -4.540 2.340 -0.149 1.00 82.15 6 A 1 ATOM 52 N N . ALA A 1 7 ? 0.449 3.766 0.752 1.00 94.76 7 A 1 ATOM 53 C CA . ALA A 1 7 ? 1.867 4.099 0.659 1.00 95.04 7 A 1 ATOM 54 C C . ALA A 1 7 ? 2.738 2.952 1.174 1.00 96.04 7 A 1 ATOM 55 O O . ALA A 1 7 ? 3.827 2.711 0.652 1.00 95.17 7 A 1 ATOM 56 C CB . ALA A 1 7 ? 2.151 5.371 1.450 1.00 94.41 7 A 1 ATOM 57 N N . LEU A 1 8 ? 2.258 2.241 2.170 1.00 94.70 8 A 1 ATOM 58 C CA . LEU A 1 8 ? 3.004 1.118 2.745 1.00 94.36 8 A 1 ATOM 59 C C . LEU A 1 8 ? 3.127 -0.028 1.744 1.00 95.55 8 A 1 ATOM 60 O O . LEU A 1 8 ? 4.206 -0.590 1.567 1.00 94.71 8 A 1 ATOM 61 C CB . LEU A 1 8 ? 2.300 0.630 4.008 1.00 93.59 8 A 1 ATOM 62 C CG . LEU A 1 8 ? 3.130 -0.368 4.818 1.00 87.29 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? 4.200 0.355 5.616 1.00 86.02 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? 2.236 -1.170 5.755 1.00 85.85 8 A 1 ATOM 65 N N . SER A 1 9 ? 2.036 -0.368 1.085 1.00 94.63 9 A 1 ATOM 66 C CA . SER A 1 9 ? 2.012 -1.460 0.111 1.00 94.09 9 A 1 ATOM 67 C C . SER A 1 9 ? 2.666 -1.064 -1.207 1.00 94.59 9 A 1 ATOM 68 O O . SER A 1 9 ? 3.191 -1.916 -1.925 1.00 93.52 9 A 1 ATOM 69 C CB . SER A 1 9 ? 0.571 -1.897 -0.137 1.00 92.65 9 A 1 ATOM 70 O OG . SER A 1 9 ? 0.540 -3.018 -0.990 1.00 84.04 9 A 1 ATOM 71 N N . ALA A 1 10 ? 2.635 0.213 -1.529 1.00 95.65 10 A 1 ATOM 72 C CA . ALA A 1 10 ? 3.208 0.713 -2.781 1.00 95.22 10 A 1 ATOM 73 C C . ALA A 1 10 ? 4.727 0.856 -2.701 1.00 96.03 10 A 1 ATOM 74 O O . ALA A 1 10 ? 5.428 0.619 -3.682 1.00 94.37 10 A 1 ATOM 75 C CB . ALA A 1 10 ? 2.576 2.053 -3.137 1.00 93.47 10 A 1 ATOM 76 N N . THR A 1 11 ? 5.235 1.253 -1.551 1.00 95.80 11 A 1 ATOM 77 C CA . THR A 1 11 ? 6.675 1.460 -1.383 1.00 95.26 11 A 1 ATOM 78 C C . THR A 1 11 ? 7.401 0.182 -0.974 1.00 95.31 11 A 1 ATOM 79 O O . THR A 1 11 ? 8.548 -0.033 -1.363 1.00 93.35 11 A 1 ATOM 80 C CB . THR A 1 11 ? 6.936 2.555 -0.341 1.00 93.57 11 A 1 ATOM 81 O OG1 . THR A 1 11 ? 8.323 2.896 -0.357 1.00 88.33 11 A 1 ATOM 82 C CG2 . THR A 1 11 ? 6.574 2.085 1.056 1.00 87.78 11 A 1 ATOM 83 N N . ALA A 1 12 ? 6.752 -0.670 -0.215 1.00 93.72 12 A 1 ATOM 84 C CA . ALA A 1 12 ? 7.359 -1.912 0.265 1.00 92.67 12 A 1 ATOM 85 C C . ALA A 1 12 ? 6.823 -3.133 -0.480 1.00 93.95 12 A 1 ATOM 86 O O . ALA A 1 12 ? 6.459 -4.139 0.125 1.00 91.74 12 A 1 ATOM 87 C CB . ALA A 1 12 ? 7.119 -2.049 1.764 1.00 90.52 12 A 1 ATOM 88 N N . THR A 1 13 ? 6.790 -3.053 -1.797 1.00 91.99 13 A 1 ATOM 89 C CA . THR A 1 13 ? 6.280 -4.152 -2.621 1.00 91.69 13 A 1 ATOM 90 C C . THR A 1 13 ? 7.426 -4.912 -3.283 1.00 91.63 13 A 1 ATOM 91 O O . THR A 1 13 ? 8.427 -4.321 -3.690 1.00 88.09 13 A 1 ATOM 92 C CB . THR A 1 13 ? 5.323 -3.616 -3.692 1.00 89.62 13 A 1 ATOM 93 O OG1 . THR A 1 13 ? 4.685 -4.721 -4.340 1.00 83.64 13 A 1 ATOM 94 C CG2 . THR A 1 13 ? 6.051 -2.786 -4.728 1.00 82.32 13 A 1 ATOM 95 N N . ALA A 1 14 ? 7.293 -6.240 -3.391 1.00 87.24 14 A 1 ATOM 96 C CA . ALA A 1 14 ? 8.322 -7.075 -4.015 1.00 83.96 14 A 1 ATOM 97 C C . ALA A 1 14 ? 7.765 -8.455 -4.326 1.00 82.09 14 A 1 ATOM 98 O O . ALA A 1 14 ? 7.993 -8.950 -5.449 1.00 76.07 14 A 1 ATOM 99 C CB . ALA A 1 14 ? 9.537 -7.190 -3.100 1.00 77.89 14 A 1 ATOM 100 O OXT . ALA A 1 14 ? 7.127 -9.054 -3.458 1.00 70.84 14 A 1 #