# 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_spkb32661 # _entry.id spkb32661 # 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" "C4 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "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 PHE 4 1 n ALA 5 1 n LEU 6 1 n THR 7 1 n THR 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n ALA 12 1 n THR 13 1 n ASP 14 1 n SER 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 @ 2025-07-12 23:49:32)" _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 88.54 _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 85.08 1 1 A LYS 2 2 86.16 1 2 A PHE 3 2 87.00 1 3 A PHE 4 2 88.60 1 4 A ALA 5 2 94.68 1 5 A LEU 6 2 90.35 1 6 A THR 7 2 93.13 1 7 A THR 8 2 92.09 1 8 A LEU 9 2 91.28 1 9 A LEU 10 2 91.82 1 10 A ALA 11 2 93.85 1 11 A ALA 12 2 93.07 1 12 A THR 13 2 89.54 1 13 A ASP 14 2 83.79 1 14 A SER 15 2 81.05 1 15 A ALA 16 2 78.84 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 PHE . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n THR . 7 A 7 A 8 1 n THR . 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 ALA . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n ASP . 14 A 14 A 15 1 n SER . 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 ? -10.918 6.753 -4.617 1.00 88.70 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.729 5.945 -4.993 1.00 91.07 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.675 4.648 -4.192 1.00 92.41 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.725 4.678 -2.969 1.00 89.30 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.471 6.743 -4.718 1.00 86.85 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.536 8.124 -5.357 1.00 82.84 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.931 8.663 -5.906 1.00 80.47 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.834 10.242 -5.083 1.00 68.97 1 A 1 ATOM 9 N N . LYS A 1 2 ? -9.571 3.523 -4.884 1.00 90.81 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -9.511 2.210 -4.221 1.00 92.27 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.088 1.650 -4.217 1.00 92.24 2 A 1 ATOM 12 O O . LYS A 1 2 ? -7.829 0.630 -3.594 1.00 92.19 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -10.460 1.244 -4.932 1.00 90.40 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -11.815 1.161 -4.256 1.00 85.60 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -12.593 -0.044 -4.736 1.00 82.70 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -13.705 -0.408 -3.775 1.00 77.18 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -14.979 0.208 -4.209 1.00 72.04 2 A 1 ATOM 18 N N . PHE A 1 3 ? -7.175 2.300 -4.892 1.00 89.04 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -5.786 1.835 -4.954 1.00 91.34 3 A 1 ATOM 20 C C . PHE A 1 3 ? -5.045 2.095 -3.648 1.00 93.77 3 A 1 ATOM 21 O O . PHE A 1 3 ? -3.897 1.692 -3.488 1.00 92.51 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -5.080 2.546 -6.106 1.00 89.74 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -5.279 1.824 -7.416 1.00 87.00 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -4.715 0.577 -7.615 1.00 85.19 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -6.026 2.401 -8.430 1.00 84.25 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -4.891 -0.095 -8.816 1.00 82.47 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -6.204 1.734 -9.634 1.00 81.67 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -5.636 0.487 -9.825 1.00 80.06 3 A 1 ATOM 29 N N . PHE A 1 4 ? -5.698 2.754 -2.715 1.00 90.85 4 A 1 ATOM 30 C CA . PHE A 1 4 ? -5.078 3.044 -1.420 1.00 92.25 4 A 1 ATOM 31 C C . PHE A 1 4 ? -4.790 1.746 -0.666 1.00 94.39 4 A 1 ATOM 32 O O . PHE A 1 4 ? -3.836 1.661 0.101 1.00 93.80 4 A 1 ATOM 33 C CB . PHE A 1 4 ? -6.010 3.936 -0.598 1.00 91.51 4 A 1 ATOM 34 C CG . PHE A 1 4 ? -5.372 4.383 0.695 1.00 88.23 4 A 1 ATOM 35 C CD1 . PHE A 1 4 ? -4.014 4.642 0.768 1.00 85.57 4 A 1 ATOM 36 C CD2 . PHE A 1 4 ? -6.144 4.539 1.836 1.00 85.89 4 A 1 ATOM 37 C CE1 . PHE A 1 4 ? -3.423 5.052 1.960 1.00 84.18 4 A 1 ATOM 38 C CE2 . PHE A 1 4 ? -5.559 4.952 3.030 1.00 84.56 4 A 1 ATOM 39 C CZ . PHE A 1 4 ? -4.200 5.205 3.091 1.00 83.35 4 A 1 ATOM 40 N N . ALA A 1 5 ? -5.613 0.738 -0.891 1.00 94.09 5 A 1 ATOM 41 C CA . ALA A 1 5 ? -5.419 -0.552 -0.221 1.00 94.81 5 A 1 ATOM 42 C C . ALA A 1 5 ? -4.257 -1.323 -0.848 1.00 95.68 5 A 1 ATOM 43 O O . ALA A 1 5 ? -3.607 -2.125 -0.186 1.00 94.85 5 A 1 ATOM 44 C CB . ALA A 1 5 ? -6.702 -1.365 -0.311 1.00 93.96 5 A 1 ATOM 45 N N . LEU A 1 6 ? -3.988 -1.067 -2.116 1.00 93.24 6 A 1 ATOM 46 C CA . LEU A 1 6 ? -2.900 -1.753 -2.818 1.00 93.77 6 A 1 ATOM 47 C C . LEU A 1 6 ? -1.546 -1.246 -2.336 1.00 94.95 6 A 1 ATOM 48 O O . LEU A 1 6 ? -0.615 -2.021 -2.136 1.00 94.61 6 A 1 ATOM 49 C CB . LEU A 1 6 ? -3.057 -1.536 -4.322 1.00 92.75 6 A 1 ATOM 50 C CG . LEU A 1 6 ? -2.896 -2.826 -5.120 1.00 85.48 6 A 1 ATOM 51 C CD1 . LEU A 1 6 ? -3.527 -2.663 -6.503 1.00 84.72 6 A 1 ATOM 52 C CD2 . LEU A 1 6 ? -1.427 -3.178 -5.272 1.00 83.31 6 A 1 ATOM 53 N N . THR A 1 7 ? -1.441 0.033 -2.140 1.00 93.93 7 A 1 ATOM 54 C CA . THR A 1 7 ? -0.181 0.630 -1.683 1.00 94.42 7 A 1 ATOM 55 C C . THR A 1 7 ? 0.077 0.278 -0.221 1.00 95.23 7 A 1 ATOM 56 O O . THR A 1 7 ? 1.222 0.253 0.221 1.00 94.81 7 A 1 ATOM 57 C CB . THR A 1 7 ? -0.232 2.148 -1.866 1.00 93.84 7 A 1 ATOM 58 O OG1 . THR A 1 7 ? 1.070 2.675 -1.616 1.00 90.14 7 A 1 ATOM 59 C CG2 . THR A 1 7 ? -1.204 2.785 -0.897 1.00 89.54 7 A 1 ATOM 60 N N . THR A 1 8 ? -0.971 -0.000 0.520 1.00 93.52 8 A 1 ATOM 61 C CA . THR A 1 8 ? -0.826 -0.352 1.938 1.00 93.24 8 A 1 ATOM 62 C C . THR A 1 8 ? -0.164 -1.722 2.076 1.00 94.04 8 A 1 ATOM 63 O O . THR A 1 8 ? 0.679 -1.929 2.947 1.00 93.32 8 A 1 ATOM 64 C CB . THR A 1 8 ? -2.200 -0.368 2.609 1.00 92.64 8 A 1 ATOM 65 O OG1 . THR A 1 8 ? -2.750 0.941 2.565 1.00 89.50 8 A 1 ATOM 66 C CG2 . THR A 1 8 ? -2.085 -0.784 4.071 1.00 88.37 8 A 1 ATOM 67 N N . LEU A 1 9 ? -0.532 -2.655 1.221 1.00 93.93 9 A 1 ATOM 68 C CA . LEU A 1 9 ? 0.047 -4.001 1.269 1.00 93.89 9 A 1 ATOM 69 C C . LEU A 1 9 ? 1.525 -3.960 0.886 1.00 94.64 9 A 1 ATOM 70 O O . LEU A 1 9 ? 2.336 -4.707 1.430 1.00 93.83 9 A 1 ATOM 71 C CB . LEU A 1 9 ? -0.721 -4.912 0.313 1.00 93.26 9 A 1 ATOM 72 C CG . LEU A 1 9 ? -2.094 -5.326 0.833 1.00 88.12 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? -2.868 -6.044 -0.272 1.00 86.42 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? -1.948 -6.264 2.035 1.00 86.13 9 A 1 ATOM 75 N N . LEU A 1 10 ? 1.865 -3.101 -0.038 1.00 95.50 10 A 1 ATOM 76 C CA . LEU A 1 10 ? 3.256 -2.975 -0.479 1.00 94.86 10 A 1 ATOM 77 C C . LEU A 1 10 ? 4.104 -2.307 0.596 1.00 95.10 10 A 1 ATOM 78 O O . LEU A 1 10 ? 5.240 -2.702 0.839 1.00 94.39 10 A 1 ATOM 79 C CB . LEU A 1 10 ? 3.297 -2.168 -1.775 1.00 94.13 10 A 1 ATOM 80 C CG . LEU A 1 10 ? 3.931 -2.947 -2.926 1.00 88.33 10 A 1 ATOM 81 C CD1 . LEU A 1 10 ? 3.590 -2.289 -4.260 1.00 86.18 10 A 1 ATOM 82 C CD2 . LEU A 1 10 ? 5.438 -3.012 -2.755 1.00 86.05 10 A 1 ATOM 83 N N . ALA A 1 11 ? 3.561 -1.319 1.243 1.00 94.65 11 A 1 ATOM 84 C CA . ALA A 1 11 ? 4.286 -0.604 2.298 1.00 94.19 11 A 1 ATOM 85 C C . ALA A 1 11 ? 4.461 -1.483 3.531 1.00 94.49 11 A 1 ATOM 86 O O . ALA A 1 11 ? 5.433 -1.341 4.265 1.00 92.93 11 A 1 ATOM 87 C CB . ALA A 1 11 ? 3.525 0.663 2.665 1.00 93.00 11 A 1 ATOM 88 N N . ALA A 1 12 ? 3.526 -2.382 3.763 1.00 94.01 12 A 1 ATOM 89 C CA . ALA A 1 12 ? 3.591 -3.269 4.927 1.00 93.46 12 A 1 ATOM 90 C C . ALA A 1 12 ? 4.710 -4.293 4.762 1.00 93.75 12 A 1 ATOM 91 O O . ALA A 1 12 ? 5.304 -4.732 5.744 1.00 91.70 12 A 1 ATOM 92 C CB . ALA A 1 12 ? 2.252 -3.970 5.108 1.00 92.41 12 A 1 ATOM 93 N N . THR A 1 13 ? 5.007 -4.681 3.540 1.00 92.70 13 A 1 ATOM 94 C CA . THR A 1 13 ? 6.060 -5.664 3.274 1.00 92.36 13 A 1 ATOM 95 C C . THR A 1 13 ? 7.350 -4.997 2.808 1.00 91.52 13 A 1 ATOM 96 O O . THR A 1 13 ? 8.325 -5.669 2.496 1.00 89.02 13 A 1 ATOM 97 C CB . THR A 1 13 ? 5.582 -6.663 2.218 1.00 90.47 13 A 1 ATOM 98 O OG1 . THR A 1 13 ? 6.554 -7.703 2.089 1.00 86.17 13 A 1 ATOM 99 C CG2 . THR A 1 13 ? 5.411 -5.985 0.869 1.00 84.57 13 A 1 ATOM 100 N N . ASP A 1 14 ? 7.357 -3.697 2.779 1.00 87.14 14 A 1 ATOM 101 C CA . ASP A 1 14 ? 8.550 -2.957 2.339 1.00 88.56 14 A 1 ATOM 102 C C . ASP A 1 14 ? 9.698 -3.144 3.323 1.00 88.79 14 A 1 ATOM 103 O O . ASP A 1 14 ? 10.870 -3.088 2.954 1.00 85.62 14 A 1 ATOM 104 C CB . ASP A 1 14 ? 8.221 -1.474 2.215 1.00 84.81 14 A 1 ATOM 105 C CG . ASP A 1 14 ? 8.952 -0.855 1.041 1.00 80.29 14 A 1 ATOM 106 O OD1 . ASP A 1 14 ? 10.046 -1.320 0.707 1.00 77.59 14 A 1 ATOM 107 O OD2 . ASP A 1 14 ? 8.420 0.101 0.454 1.00 77.50 14 A 1 ATOM 108 N N . SER A 1 15 ? 9.383 -3.376 4.567 1.00 85.46 15 A 1 ATOM 109 C CA . SER A 1 15 ? 10.393 -3.570 5.613 1.00 85.00 15 A 1 ATOM 110 C C . SER A 1 15 ? 10.682 -5.048 5.845 1.00 84.41 15 A 1 ATOM 111 O O . SER A 1 15 ? 11.633 -5.396 6.550 1.00 79.54 15 A 1 ATOM 112 C CB . SER A 1 15 ? 9.920 -2.930 6.916 1.00 80.55 15 A 1 ATOM 113 O OG . SER A 1 15 ? 10.458 -1.628 7.060 1.00 71.33 15 A 1 ATOM 114 N N . ALA A 1 16 ? 9.862 -5.898 5.266 1.00 85.00 16 A 1 ATOM 115 C CA . ALA A 1 16 ? 10.021 -7.346 5.428 1.00 83.78 16 A 1 ATOM 116 C C . ALA A 1 16 ? 10.735 -7.926 4.211 1.00 80.75 16 A 1 ATOM 117 O O . ALA A 1 16 ? 10.510 -9.090 3.859 1.00 75.55 16 A 1 ATOM 118 C CB . ALA A 1 16 ? 8.664 -7.999 5.632 1.00 77.87 16 A 1 ATOM 119 O OXT . ALA A 1 16 ? 11.539 -7.213 3.579 1.00 70.12 16 A 1 #