# 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_spkb31897 # _entry.id spkb31897 # 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" "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" "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C5 H11 N O2" 117.146 VAL y VALINE CC(C)[C@@H](C(=O)O)N ? "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 SER 2 1 n PRO 3 1 n CYS 4 1 n LYS 5 1 n LEU 6 1 n LEU 7 1 n PRO 8 1 n PHE 9 1 n CYS 10 1 n VAL 11 1 n ALA 12 1 n LEU 13 1 n ALA 14 1 n LEU 15 1 n THR 16 1 n GLY 17 # _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 @ 2025-07-11 14:13:06)" _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 91.79 _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 81.12 1 1 A SER 2 2 88.28 1 2 A PRO 3 2 94.33 1 3 A CYS 4 2 93.39 1 4 A LYS 5 2 88.85 1 5 A LEU 6 2 94.78 1 6 A LEU 7 2 93.03 1 7 A PRO 8 2 96.07 1 8 A PHE 9 2 91.96 1 9 A CYS 10 2 94.78 1 10 A VAL 11 2 94.54 1 11 A ALA 12 2 96.12 1 12 A LEU 13 2 92.64 1 13 A ALA 14 2 94.44 1 14 A LEU 15 2 92.64 1 15 A THR 16 2 90.85 1 16 A GLY 17 2 83.84 1 17 # _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 SER . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n CYS . 4 A 4 A 5 1 n LYS . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PRO . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n THR . 16 A 16 A 17 1 n GLY . 17 A 17 # _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 ? -9.956 2.746 -5.270 1.00 85.94 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.903 1.795 -4.850 1.00 86.79 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.000 1.542 -3.354 1.00 88.52 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.494 2.394 -2.625 1.00 84.84 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.516 2.351 -5.196 1.00 83.16 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.233 2.257 -6.684 1.00 79.11 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.580 2.833 -7.079 1.00 74.18 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.436 2.252 -8.761 1.00 66.43 1 A 1 ATOM 9 N N . SER A 1 2 ? -8.532 0.398 -2.914 1.00 87.49 2 A 1 ATOM 10 C CA . SER A 1 2 ? -8.548 0.042 -1.494 1.00 90.54 2 A 1 ATOM 11 C C . SER A 1 2 ? -7.640 0.983 -0.686 1.00 92.72 2 A 1 ATOM 12 O O . SER A 1 2 ? -6.712 1.568 -1.244 1.00 91.91 2 A 1 ATOM 13 C CB . SER A 1 2 ? -8.089 -1.401 -1.331 1.00 88.15 2 A 1 ATOM 14 O OG . SER A 1 2 ? -8.952 -2.271 -2.017 1.00 78.89 2 A 1 ATOM 15 N N . PRO A 1 3 ? -7.882 1.123 0.611 1.00 94.99 3 A 1 ATOM 16 C CA . PRO A 1 3 ? -7.075 1.999 1.469 1.00 95.76 3 A 1 ATOM 17 C C . PRO A 1 3 ? -5.680 1.408 1.725 1.00 96.38 3 A 1 ATOM 18 O O . PRO A 1 3 ? -5.396 0.872 2.792 1.00 94.51 3 A 1 ATOM 19 C CB . PRO A 1 3 ? -7.913 2.117 2.747 1.00 94.24 3 A 1 ATOM 20 C CG . PRO A 1 3 ? -8.711 0.845 2.793 1.00 91.07 3 A 1 ATOM 21 C CD . PRO A 1 3 ? -8.973 0.503 1.336 1.00 93.35 3 A 1 ATOM 22 N N . CYS A 1 4 ? -4.805 1.517 0.728 1.00 93.95 4 A 1 ATOM 23 C CA . CYS A 1 4 ? -3.437 1.009 0.824 1.00 94.64 4 A 1 ATOM 24 C C . CYS A 1 4 ? -2.629 1.706 1.913 1.00 95.23 4 A 1 ATOM 25 O O . CYS A 1 4 ? -1.713 1.116 2.469 1.00 93.09 4 A 1 ATOM 26 C CB . CYS A 1 4 ? -2.744 1.176 -0.524 1.00 92.99 4 A 1 ATOM 27 S SG . CYS A 1 4 ? -3.369 0.031 -1.769 1.00 90.47 4 A 1 ATOM 28 N N . LYS A 1 5 ? -2.989 2.941 2.219 1.00 93.62 5 A 1 ATOM 29 C CA . LYS A 1 5 ? -2.304 3.687 3.283 1.00 94.06 5 A 1 ATOM 30 C C . LYS A 1 5 ? -2.502 3.046 4.661 1.00 95.21 5 A 1 ATOM 31 O O . LYS A 1 5 ? -1.656 3.208 5.535 1.00 94.85 5 A 1 ATOM 32 C CB . LYS A 1 5 ? -2.799 5.130 3.307 1.00 93.50 5 A 1 ATOM 33 C CG . LYS A 1 5 ? -2.120 5.968 2.233 1.00 87.72 5 A 1 ATOM 34 C CD . LYS A 1 5 ? -2.405 7.440 2.445 1.00 85.10 5 A 1 ATOM 35 C CE . LYS A 1 5 ? -1.558 8.292 1.520 1.00 80.61 5 A 1 ATOM 36 N NZ . LYS A 1 5 ? -1.634 9.725 1.890 1.00 74.94 5 A 1 ATOM 37 N N . LEU A 1 6 ? -3.602 2.324 4.818 1.00 95.81 6 A 1 ATOM 38 C CA . LEU A 1 6 ? -3.893 1.653 6.085 1.00 96.33 6 A 1 ATOM 39 C C . LEU A 1 6 ? -3.268 0.260 6.147 1.00 97.02 6 A 1 ATOM 40 O O . LEU A 1 6 ? -3.067 -0.279 7.235 1.00 96.40 6 A 1 ATOM 41 C CB . LEU A 1 6 ? -5.410 1.572 6.263 1.00 96.31 6 A 1 ATOM 42 C CG . LEU A 1 6 ? -6.046 2.925 6.576 1.00 93.69 6 A 1 ATOM 43 C CD1 . LEU A 1 6 ? -7.538 2.885 6.303 1.00 91.60 6 A 1 ATOM 44 C CD2 . LEU A 1 6 ? -5.814 3.295 8.042 1.00 91.06 6 A 1 ATOM 45 N N . LEU A 1 7 ? -2.948 -0.309 4.987 1.00 95.46 7 A 1 ATOM 46 C CA . LEU A 1 7 ? -2.386 -1.652 4.913 1.00 95.36 7 A 1 ATOM 47 C C . LEU A 1 7 ? -0.917 -1.590 4.490 1.00 96.13 7 A 1 ATOM 48 O O . LEU A 1 7 ? -0.624 -1.230 3.350 1.00 95.55 7 A 1 ATOM 49 C CB . LEU A 1 7 ? -3.213 -2.485 3.930 1.00 94.68 7 A 1 ATOM 50 C CG . LEU A 1 7 ? -4.625 -2.788 4.424 1.00 91.29 7 A 1 ATOM 51 C CD1 . LEU A 1 7 ? -5.480 -3.288 3.267 1.00 88.26 7 A 1 ATOM 52 C CD2 . LEU A 1 7 ? -4.596 -3.846 5.526 1.00 87.49 7 A 1 ATOM 53 N N . PRO A 1 8 ? 0.005 -1.969 5.367 1.00 96.39 8 A 1 ATOM 54 C CA . PRO A 1 8 ? 1.438 -1.930 5.048 1.00 96.68 8 A 1 ATOM 55 C C . PRO A 1 8 ? 1.801 -2.851 3.881 1.00 97.02 8 A 1 ATOM 56 O O . PRO A 1 8 ? 2.733 -2.575 3.130 1.00 96.02 8 A 1 ATOM 57 C CB . PRO A 1 8 ? 2.124 -2.369 6.349 1.00 95.63 8 A 1 ATOM 58 C CG . PRO A 1 8 ? 1.089 -3.157 7.091 1.00 94.57 8 A 1 ATOM 59 C CD . PRO A 1 8 ? -0.228 -2.515 6.705 1.00 96.16 8 A 1 ATOM 60 N N . PHE A 1 9 ? 1.034 -3.911 3.701 1.00 94.91 9 A 1 ATOM 61 C CA . PHE A 1 9 ? 1.253 -4.847 2.604 1.00 94.62 9 A 1 ATOM 62 C C . PHE A 1 9 ? 0.951 -4.204 1.251 1.00 95.30 9 A 1 ATOM 63 O O . PHE A 1 9 ? 1.659 -4.437 0.273 1.00 93.79 9 A 1 ATOM 64 C CB . PHE A 1 9 ? 0.374 -6.077 2.832 1.00 93.91 9 A 1 ATOM 65 C CG . PHE A 1 9 ? 1.083 -7.361 2.492 1.00 92.20 9 A 1 ATOM 66 C CD1 . PHE A 1 9 ? 2.049 -7.879 3.355 1.00 89.89 9 A 1 ATOM 67 C CD2 . PHE A 1 9 ? 0.783 -8.039 1.316 1.00 89.80 9 A 1 ATOM 68 C CE1 . PHE A 1 9 ? 2.713 -9.065 3.050 1.00 89.20 9 A 1 ATOM 69 C CE2 . PHE A 1 9 ? 1.443 -9.229 0.997 1.00 88.74 9 A 1 ATOM 70 C CZ . PHE A 1 9 ? 2.409 -9.741 1.867 1.00 89.16 9 A 1 ATOM 71 N N . CYS A 1 10 ? -0.060 -3.369 1.195 1.00 95.47 10 A 1 ATOM 72 C CA . CYS A 1 10 ? -0.413 -2.671 -0.044 1.00 95.64 10 A 1 ATOM 73 C C . CYS A 1 10 ? 0.645 -1.629 -0.407 1.00 95.91 10 A 1 ATOM 74 O O . CYS A 1 10 ? 0.944 -1.427 -1.579 1.00 94.14 10 A 1 ATOM 75 C CB . CYS A 1 10 ? -1.786 -2.024 0.107 1.00 94.60 10 A 1 ATOM 76 S SG . CYS A 1 10 ? -2.510 -1.696 -1.518 1.00 92.92 10 A 1 ATOM 77 N N . VAL A 1 11 ? 1.231 -0.999 0.575 1.00 95.76 11 A 1 ATOM 78 C CA . VAL A 1 11 ? 2.302 -0.017 0.361 1.00 95.57 11 A 1 ATOM 79 C C . VAL A 1 11 ? 3.526 -0.696 -0.250 1.00 95.99 11 A 1 ATOM 80 O O . VAL A 1 11 ? 4.130 -0.172 -1.186 1.00 95.18 11 A 1 ATOM 81 C CB . VAL A 1 11 ? 2.670 0.680 1.679 1.00 94.85 11 A 1 ATOM 82 C CG1 . VAL A 1 11 ? 3.806 1.674 1.479 1.00 91.93 11 A 1 ATOM 83 C CG2 . VAL A 1 11 ? 1.467 1.417 2.251 1.00 92.49 11 A 1 ATOM 84 N N . ALA A 1 12 ? 3.872 -1.863 0.243 1.00 96.28 12 A 1 ATOM 85 C CA . ALA A 1 12 ? 4.995 -2.627 -0.295 1.00 96.31 12 A 1 ATOM 86 C C . ALA A 1 12 ? 4.737 -3.041 -1.749 1.00 96.72 12 A 1 ATOM 87 O O . ALA A 1 12 ? 5.636 -2.970 -2.585 1.00 95.46 12 A 1 ATOM 88 C CB . ALA A 1 12 ? 5.234 -3.850 0.590 1.00 95.82 12 A 1 ATOM 89 N N . LEU A 1 13 ? 3.510 -3.432 -2.052 1.00 95.45 13 A 1 ATOM 90 C CA . LEU A 1 13 ? 3.125 -3.801 -3.414 1.00 94.84 13 A 1 ATOM 91 C C . LEU A 1 13 ? 3.154 -2.595 -4.349 1.00 95.28 13 A 1 ATOM 92 O O . LEU A 1 13 ? 3.581 -2.718 -5.498 1.00 94.33 13 A 1 ATOM 93 C CB . LEU A 1 13 ? 1.730 -4.433 -3.373 1.00 94.05 13 A 1 ATOM 94 C CG . LEU A 1 13 ? 1.787 -5.948 -3.179 1.00 90.48 13 A 1 ATOM 95 C CD1 . LEU A 1 13 ? 0.499 -6.450 -2.542 1.00 88.35 13 A 1 ATOM 96 C CD2 . LEU A 1 13 ? 1.982 -6.637 -4.529 1.00 88.33 13 A 1 ATOM 97 N N . ALA A 1 14 ? 2.747 -1.446 -3.873 1.00 95.18 14 A 1 ATOM 98 C CA . ALA A 1 14 ? 2.764 -0.218 -4.667 1.00 94.80 14 A 1 ATOM 99 C C . ALA A 1 14 ? 4.193 0.190 -5.040 1.00 95.32 14 A 1 ATOM 100 O O . ALA A 1 14 ? 4.424 0.723 -6.120 1.00 93.27 14 A 1 ATOM 101 C CB . ALA A 1 14 ? 2.074 0.891 -3.879 1.00 93.64 14 A 1 ATOM 102 N N . LEU A 1 15 ? 5.150 -0.074 -4.171 1.00 95.25 15 A 1 ATOM 103 C CA . LEU A 1 15 ? 6.563 0.209 -4.436 1.00 94.78 15 A 1 ATOM 104 C C . LEU A 1 15 ? 7.161 -0.772 -5.440 1.00 94.97 15 A 1 ATOM 105 O O . LEU A 1 15 ? 8.101 -0.434 -6.159 1.00 93.12 15 A 1 ATOM 106 C CB . LEU A 1 15 ? 7.329 0.158 -3.107 1.00 93.88 15 A 1 ATOM 107 C CG . LEU A 1 15 ? 7.517 1.548 -2.500 1.00 92.02 15 A 1 ATOM 108 C CD1 . LEU A 1 15 ? 7.577 1.470 -0.979 1.00 89.10 15 A 1 ATOM 109 C CD2 . LEU A 1 15 ? 8.794 2.184 -3.021 1.00 88.03 15 A 1 ATOM 110 N N . THR A 1 16 ? 6.635 -1.973 -5.479 1.00 93.87 16 A 1 ATOM 111 C CA . THR A 1 16 ? 7.132 -3.010 -6.388 1.00 93.67 16 A 1 ATOM 112 C C . THR A 1 16 ? 6.570 -2.843 -7.804 1.00 93.54 16 A 1 ATOM 113 O O . THR A 1 16 ? 7.177 -3.319 -8.764 1.00 89.58 16 A 1 ATOM 114 C CB . THR A 1 16 ? 6.780 -4.397 -5.825 1.00 92.09 16 A 1 ATOM 115 O OG1 . THR A 1 16 ? 7.113 -4.466 -4.443 1.00 87.07 16 A 1 ATOM 116 C CG2 . THR A 1 16 ? 7.566 -5.505 -6.512 1.00 86.14 16 A 1 ATOM 117 N N . GLY A 1 17 ? 5.451 -2.189 -7.934 1.00 89.22 17 A 1 ATOM 118 C CA . GLY A 1 17 ? 4.813 -1.973 -9.242 1.00 86.74 17 A 1 ATOM 119 C C . GLY A 1 17 ? 5.282 -0.702 -9.902 1.00 83.18 17 A 1 ATOM 120 O O . GLY A 1 17 ? 5.982 -0.784 -10.927 1.00 77.57 17 A 1 ATOM 121 O OXT . GLY A 1 17 ? 4.929 0.366 -9.409 1.00 82.49 17 A 1 #