# 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_spkb31478 # _entry.id spkb31478 # 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 ILE y ISOLEUCINE CC[C@H](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 ALA 3 1 n THR 4 1 n ILE 5 1 n LEU 6 1 n ALA 7 1 n SER 8 1 n THR 9 1 n PHE 10 1 n ALA 11 1 n ALA 12 1 n GLY 13 1 n ALA 14 1 n LEU 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 @ 2025-07-03 07:18:34)" _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 94.32 _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 85.98 1 1 A LYS 2 2 89.08 1 2 A ALA 3 2 97.26 1 3 A THR 4 2 95.30 1 4 A ILE 5 2 96.45 1 5 A LEU 6 2 96.14 1 6 A ALA 7 2 97.97 1 7 A SER 8 2 95.97 1 8 A THR 9 2 96.63 1 9 A PHE 10 2 94.29 1 10 A ALA 11 2 97.34 1 11 A ALA 12 2 97.30 1 12 A GLY 13 2 97.27 1 13 A ALA 14 2 96.90 1 14 A LEU 15 2 93.35 1 15 A ALA 16 2 89.23 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 ALA . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n LEU . 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 ? -3.469 12.713 0.294 1.00 88.93 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.064 12.921 -0.084 1.00 91.04 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.530 11.722 -0.865 1.00 92.90 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.908 10.586 -0.603 1.00 90.54 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.214 13.132 1.163 1.00 86.30 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.569 14.422 1.883 1.00 84.58 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.542 14.696 3.326 1.00 82.03 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.143 16.293 3.835 1.00 71.50 1 A 1 ATOM 9 N N . LYS A 1 2 ? -0.659 11.998 -1.822 1.00 92.94 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -0.097 10.945 -2.673 1.00 94.98 2 A 1 ATOM 11 C C . LYS A 1 2 ? 0.901 10.077 -1.907 1.00 96.00 2 A 1 ATOM 12 O O . LYS A 1 2 ? 0.862 8.852 -1.991 1.00 95.83 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 0.581 11.578 -3.884 1.00 93.18 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 1.024 10.540 -4.893 1.00 87.61 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 1.791 11.191 -6.024 1.00 86.00 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 2.276 10.142 -7.006 1.00 80.98 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 3.258 10.712 -7.954 1.00 74.19 2 A 1 ATOM 18 N N . ALA A 1 3 ? 1.786 10.697 -1.170 1.00 96.66 3 A 1 ATOM 19 C CA . ALA A 1 3 ? 2.800 9.976 -0.401 1.00 97.46 3 A 1 ATOM 20 C C . ALA A 1 3 ? 2.166 9.084 0.660 1.00 98.05 3 A 1 ATOM 21 O O . ALA A 1 3 ? 2.667 8.001 0.962 1.00 97.38 3 A 1 ATOM 22 C CB . ALA A 1 3 ? 3.757 10.963 0.250 1.00 96.73 3 A 1 ATOM 23 N N . THR A 1 4 ? 1.048 9.537 1.207 1.00 96.05 4 A 1 ATOM 24 C CA . THR A 1 4 ? 0.333 8.789 2.239 1.00 96.35 4 A 1 ATOM 25 C C . THR A 1 4 ? -0.202 7.475 1.684 1.00 97.11 4 A 1 ATOM 26 O O . THR A 1 4 ? -0.230 6.457 2.374 1.00 96.57 4 A 1 ATOM 27 C CB . THR A 1 4 ? -0.835 9.607 2.792 1.00 96.04 4 A 1 ATOM 28 O OG1 . THR A 1 4 ? -0.378 10.911 3.144 1.00 93.03 4 A 1 ATOM 29 C CG2 . THR A 1 4 ? -1.434 8.939 4.017 1.00 91.97 4 A 1 ATOM 30 N N . ILE A 1 5 ? -0.625 7.490 0.430 1.00 97.39 5 A 1 ATOM 31 C CA . ILE A 1 5 ? -1.163 6.301 -0.220 1.00 97.30 5 A 1 ATOM 32 C C . ILE A 1 5 ? -0.082 5.235 -0.361 1.00 97.51 5 A 1 ATOM 33 O O . ILE A 1 5 ? -0.329 4.047 -0.150 1.00 97.20 5 A 1 ATOM 34 C CB . ILE A 1 5 ? -1.736 6.651 -1.601 1.00 97.42 5 A 1 ATOM 35 C CG1 . ILE A 1 5 ? -2.866 7.676 -1.463 1.00 96.18 5 A 1 ATOM 36 C CG2 . ILE A 1 5 ? -2.257 5.393 -2.292 1.00 95.58 5 A 1 ATOM 37 C CD1 . ILE A 1 5 ? -3.327 8.228 -2.796 1.00 93.06 5 A 1 ATOM 38 N N . LEU A 1 6 ? 1.106 5.658 -0.716 1.00 97.74 6 A 1 ATOM 39 C CA . LEU A 1 6 ? 2.223 4.738 -0.885 1.00 97.68 6 A 1 ATOM 40 C C . LEU A 1 6 ? 2.565 4.054 0.433 1.00 97.93 6 A 1 ATOM 41 O O . LEU A 1 6 ? 2.780 2.847 0.486 1.00 97.88 6 A 1 ATOM 42 C CB . LEU A 1 6 ? 3.452 5.483 -1.416 1.00 97.51 6 A 1 ATOM 43 C CG . LEU A 1 6 ? 3.623 5.417 -2.931 1.00 94.33 6 A 1 ATOM 44 C CD1 . LEU A 1 6 ? 3.845 3.985 -3.369 1.00 92.80 6 A 1 ATOM 45 C CD2 . LEU A 1 6 ? 2.414 6.004 -3.628 1.00 93.26 6 A 1 ATOM 46 N N . ALA A 1 7 ? 2.615 4.843 1.492 1.00 98.03 7 A 1 ATOM 47 C CA . ALA A 1 7 ? 2.936 4.312 2.810 1.00 98.01 7 A 1 ATOM 48 C C . ALA A 1 7 ? 1.834 3.389 3.319 1.00 98.21 7 A 1 ATOM 49 O O . ALA A 1 7 ? 2.110 2.359 3.938 1.00 97.88 7 A 1 ATOM 50 C CB . ALA A 1 7 ? 3.153 5.458 3.787 1.00 97.71 7 A 1 ATOM 51 N N . SER A 1 8 ? 0.585 3.747 3.036 1.00 97.53 8 A 1 ATOM 52 C CA . SER A 1 8 ? -0.563 2.968 3.482 1.00 97.21 8 A 1 ATOM 53 C C . SER A 1 8 ? -0.653 1.639 2.746 1.00 97.64 8 A 1 ATOM 54 O O . SER A 1 8 ? -0.822 0.589 3.361 1.00 97.25 8 A 1 ATOM 55 C CB . SER A 1 8 ? -1.848 3.755 3.273 1.00 96.48 8 A 1 ATOM 56 O OG . SER A 1 8 ? -2.949 3.036 3.777 1.00 89.71 8 A 1 ATOM 57 N N . THR A 1 9 ? -0.544 1.674 1.428 1.00 97.35 9 A 1 ATOM 58 C CA . THR A 1 9 ? -0.640 0.463 0.615 1.00 97.43 9 A 1 ATOM 59 C C . THR A 1 9 ? 0.546 -0.460 0.862 1.00 97.79 9 A 1 ATOM 60 O O . THR A 1 9 ? 0.406 -1.680 0.829 1.00 97.44 9 A 1 ATOM 61 C CB . THR A 1 9 ? -0.725 0.805 -0.876 1.00 97.10 9 A 1 ATOM 62 O OG1 . THR A 1 9 ? -0.974 -0.385 -1.620 1.00 95.21 9 A 1 ATOM 63 C CG2 . THR A 1 9 ? 0.559 1.427 -1.381 1.00 94.09 9 A 1 ATOM 64 N N . PHE A 1 10 ? 1.699 0.120 1.121 1.00 97.46 10 A 1 ATOM 65 C CA . PHE A 1 10 ? 2.901 -0.663 1.374 1.00 96.87 10 A 1 ATOM 66 C C . PHE A 1 10 ? 2.770 -1.423 2.685 1.00 97.33 10 A 1 ATOM 67 O O . PHE A 1 10 ? 3.067 -2.616 2.757 1.00 96.75 10 A 1 ATOM 68 C CB . PHE A 1 10 ? 4.121 0.250 1.427 1.00 96.19 10 A 1 ATOM 69 C CG . PHE A 1 10 ? 5.405 -0.488 1.158 1.00 94.42 10 A 1 ATOM 70 C CD1 . PHE A 1 10 ? 5.833 -0.703 -0.143 1.00 92.00 10 A 1 ATOM 71 C CD2 . PHE A 1 10 ? 6.178 -0.966 2.204 1.00 92.66 10 A 1 ATOM 72 C CE1 . PHE A 1 10 ? 7.013 -1.383 -0.399 1.00 91.45 10 A 1 ATOM 73 C CE2 . PHE A 1 10 ? 7.359 -1.653 1.958 1.00 91.12 10 A 1 ATOM 74 C CZ . PHE A 1 10 ? 7.777 -1.862 0.652 1.00 90.91 10 A 1 ATOM 75 N N . ALA A 1 11 ? 2.311 -0.739 3.712 1.00 97.58 11 A 1 ATOM 76 C CA . ALA A 1 11 ? 2.125 -1.361 5.016 1.00 97.39 11 A 1 ATOM 77 C C . ALA A 1 11 ? 1.008 -2.393 4.974 1.00 97.80 11 A 1 ATOM 78 O O . ALA A 1 11 ? 1.122 -3.468 5.562 1.00 97.31 11 A 1 ATOM 79 C CB . ALA A 1 11 ? 1.816 -0.298 6.059 1.00 96.62 11 A 1 ATOM 80 N N . ALA A 1 12 ? -0.068 -2.076 4.271 1.00 97.53 12 A 1 ATOM 81 C CA . ALA A 1 12 ? -1.201 -2.984 4.143 1.00 97.37 12 A 1 ATOM 82 C C . ALA A 1 12 ? -0.831 -4.207 3.318 1.00 97.91 12 A 1 ATOM 83 O O . ALA A 1 12 ? -1.261 -5.318 3.614 1.00 97.30 12 A 1 ATOM 84 C CB . ALA A 1 12 ? -2.376 -2.261 3.503 1.00 96.39 12 A 1 ATOM 85 N N . GLY A 1 13 ? -0.034 -4.008 2.279 1.00 96.98 13 A 1 ATOM 86 C CA . GLY A 1 13 ? 0.402 -5.105 1.426 1.00 96.95 13 A 1 ATOM 87 C C . GLY A 1 13 ? 1.327 -6.051 2.150 1.00 97.72 13 A 1 ATOM 88 O O . GLY A 1 13 ? 1.265 -7.264 1.962 1.00 97.45 13 A 1 ATOM 89 N N . ALA A 1 14 ? 2.188 -5.508 2.989 1.00 96.96 14 A 1 ATOM 90 C CA . ALA A 1 14 ? 3.124 -6.318 3.762 1.00 97.12 14 A 1 ATOM 91 C C . ALA A 1 14 ? 2.387 -7.167 4.786 1.00 97.61 14 A 1 ATOM 92 O O . ALA A 1 14 ? 2.724 -8.331 4.998 1.00 96.64 14 A 1 ATOM 93 C CB . ALA A 1 14 ? 4.138 -5.425 4.462 1.00 96.17 14 A 1 ATOM 94 N N . LEU A 1 15 ? 1.380 -6.587 5.423 1.00 96.36 15 A 1 ATOM 95 C CA . LEU A 1 15 ? 0.582 -7.299 6.416 1.00 96.19 15 A 1 ATOM 96 C C . LEU A 1 15 ? -0.464 -8.172 5.746 1.00 96.72 15 A 1 ATOM 97 O O . LEU A 1 15 ? -0.645 -9.332 6.120 1.00 95.88 15 A 1 ATOM 98 C CB . LEU A 1 15 ? -0.095 -6.297 7.357 1.00 94.90 15 A 1 ATOM 99 C CG . LEU A 1 15 ? -0.759 -6.939 8.569 1.00 90.89 15 A 1 ATOM 100 C CD1 . LEU A 1 15 ? 0.262 -7.633 9.446 1.00 88.46 15 A 1 ATOM 101 C CD2 . LEU A 1 15 ? -1.516 -5.893 9.374 1.00 87.40 15 A 1 ATOM 102 N N . ALA A 1 16 ? -1.161 -7.583 4.746 1.00 93.43 16 A 1 ATOM 103 C CA . ALA A 1 16 ? -2.181 -8.261 3.945 1.00 92.37 16 A 1 ATOM 104 C C . ALA A 1 16 ? -3.145 -9.084 4.804 1.00 91.46 16 A 1 ATOM 105 O O . ALA A 1 16 ? -2.709 -9.917 5.590 1.00 87.90 16 A 1 ATOM 106 C CB . ALA A 1 16 ? -1.525 -9.159 2.909 1.00 88.60 16 A 1 ATOM 107 O OXT . ALA A 1 16 ? -4.338 -8.911 4.649 1.00 81.60 16 A 1 #