# 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_spkb25028 # _entry.id spkb25028 # 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" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 ALA 3 1 n TYR 4 1 n ALA 5 1 n TRP 6 1 n LEU 7 1 n TYR 8 1 n CYS 9 1 n ALA 10 1 n LEU 11 1 n ALA 12 1 n LEU 13 1 n GLY 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 22:04:58)" _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 95.97 _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 87.35 1 1 A ALA 2 2 95.54 1 2 A ALA 3 2 97.86 1 3 A TYR 4 2 96.22 1 4 A ALA 5 2 98.39 1 5 A TRP 6 2 96.35 1 6 A LEU 7 2 97.39 1 7 A TYR 8 2 95.94 1 8 A CYS 9 2 98.00 1 9 A ALA 10 2 98.46 1 10 A LEU 11 2 97.62 1 11 A ALA 12 2 98.60 1 12 A LEU 13 2 96.96 1 13 A GLY 14 2 90.24 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 ALA . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n TYR . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n TRP . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n TYR . 8 A 8 A 9 1 n CYS . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n GLY . 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 ? 2.769 5.680 7.847 1.00 91.77 1 A 1 ATOM 2 C CA . MET A 1 1 ? 2.123 4.544 8.531 1.00 92.33 1 A 1 ATOM 3 C C . MET A 1 1 ? 2.366 3.241 7.767 1.00 92.83 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.214 3.200 6.545 1.00 91.01 1 A 1 ATOM 5 C CB . MET A 1 1 ? 0.623 4.778 8.640 1.00 89.23 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.249 5.655 9.831 1.00 84.59 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.886 7.318 9.681 1.00 82.68 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.112 8.070 11.115 1.00 74.34 1 A 1 ATOM 9 N N . ALA A 1 2 ? 2.714 2.188 8.499 1.00 93.26 2 A 1 ATOM 10 C CA . ALA A 1 2 ? 2.979 0.882 7.897 1.00 96.23 2 A 1 ATOM 11 C C . ALA A 1 2 ? 1.679 0.194 7.487 1.00 97.49 2 A 1 ATOM 12 O O . ALA A 1 2 ? 1.655 -0.587 6.537 1.00 96.67 2 A 1 ATOM 13 C CB . ALA A 1 2 ? 3.758 0.007 8.871 1.00 94.06 2 A 1 ATOM 14 N N . ALA A 1 3 ? 0.607 0.479 8.207 1.00 97.43 3 A 1 ATOM 15 C CA . ALA A 1 3 ? -0.703 -0.111 7.927 1.00 97.93 3 A 1 ATOM 16 C C . ALA A 1 3 ? -1.225 0.327 6.562 1.00 98.36 3 A 1 ATOM 17 O O . ALA A 1 3 ? -1.935 -0.416 5.888 1.00 98.14 3 A 1 ATOM 18 C CB . ALA A 1 3 ? -1.687 0.276 9.020 1.00 97.45 3 A 1 ATOM 19 N N . TYR A 1 4 ? -0.860 1.543 6.159 1.00 98.19 4 A 1 ATOM 20 C CA . TYR A 1 4 ? -1.296 2.076 4.870 1.00 98.30 4 A 1 ATOM 21 C C . TYR A 1 4 ? -0.317 1.723 3.757 1.00 98.49 4 A 1 ATOM 22 O O . TYR A 1 4 ? -0.607 1.943 2.580 1.00 98.30 4 A 1 ATOM 23 C CB . TYR A 1 4 ? -1.442 3.593 4.956 1.00 97.91 4 A 1 ATOM 24 C CG . TYR A 1 4 ? -2.592 4.016 5.839 1.00 96.60 4 A 1 ATOM 25 C CD1 . TYR A 1 4 ? -3.899 3.738 5.471 1.00 95.29 4 A 1 ATOM 26 C CD2 . TYR A 1 4 ? -2.361 4.694 7.022 1.00 95.06 4 A 1 ATOM 27 C CE1 . TYR A 1 4 ? -4.959 4.125 6.275 1.00 94.42 4 A 1 ATOM 28 C CE2 . TYR A 1 4 ? -3.416 5.085 7.832 1.00 94.23 4 A 1 ATOM 29 C CZ . TYR A 1 4 ? -4.711 4.797 7.453 1.00 94.41 4 A 1 ATOM 30 O OH . TYR A 1 4 ? -5.754 5.184 8.243 1.00 93.49 4 A 1 ATOM 31 N N . ALA A 1 5 ? 0.827 1.174 4.115 1.00 98.32 5 A 1 ATOM 32 C CA . ALA A 1 5 ? 1.851 0.806 3.140 1.00 98.41 5 A 1 ATOM 33 C C . ALA A 1 5 ? 1.327 -0.239 2.162 1.00 98.59 5 A 1 ATOM 34 O O . ALA A 1 5 ? 1.395 -0.055 0.947 1.00 98.46 5 A 1 ATOM 35 C CB . ALA A 1 5 ? 3.095 0.293 3.852 1.00 98.18 5 A 1 ATOM 36 N N . TRP A 1 6 ? 0.800 -1.333 2.702 1.00 97.83 6 A 1 ATOM 37 C CA . TRP A 1 6 ? 0.267 -2.405 1.865 1.00 97.91 6 A 1 ATOM 38 C C . TRP A 1 6 ? -1.052 -1.975 1.230 1.00 98.25 6 A 1 ATOM 39 O O . TRP A 1 6 ? -1.391 -2.417 0.132 1.00 98.14 6 A 1 ATOM 40 C CB . TRP A 1 6 ? 0.082 -3.672 2.698 1.00 97.67 6 A 1 ATOM 41 C CG . TRP A 1 6 ? -1.127 -3.634 3.567 1.00 96.98 6 A 1 ATOM 42 C CD1 . TRP A 1 6 ? -1.213 -3.147 4.825 1.00 95.44 6 A 1 ATOM 43 C CD2 . TRP A 1 6 ? -2.445 -4.090 3.215 1.00 96.50 6 A 1 ATOM 44 N NE1 . TRP A 1 6 ? -2.502 -3.263 5.284 1.00 94.86 6 A 1 ATOM 45 C CE2 . TRP A 1 6 ? -3.282 -3.849 4.317 1.00 95.86 6 A 1 ATOM 46 C CE3 . TRP A 1 6 ? -2.991 -4.684 2.074 1.00 95.22 6 A 1 ATOM 47 C CZ2 . TRP A 1 6 ? -4.635 -4.175 4.308 1.00 95.47 6 A 1 ATOM 48 C CZ3 . TRP A 1 6 ? -4.340 -5.015 2.067 1.00 94.51 6 A 1 ATOM 49 C CH2 . TRP A 1 6 ? -5.151 -4.755 3.179 1.00 94.27 6 A 1 ATOM 50 N N . LEU A 1 7 ? -1.782 -1.110 1.917 1.00 98.18 7 A 1 ATOM 51 C CA . LEU A 1 7 ? -3.056 -0.610 1.406 1.00 98.18 7 A 1 ATOM 52 C C . LEU A 1 7 ? -2.840 0.166 0.118 1.00 98.37 7 A 1 ATOM 53 O O . LEU A 1 7 ? -3.592 0.023 -0.848 1.00 98.25 7 A 1 ATOM 54 C CB . LEU A 1 7 ? -3.725 0.283 2.450 1.00 98.04 7 A 1 ATOM 55 C CG . LEU A 1 7 ? -5.200 0.539 2.168 1.00 96.80 7 A 1 ATOM 56 C CD1 . LEU A 1 7 ? -6.071 -0.207 3.168 1.00 95.55 7 A 1 ATOM 57 C CD2 . LEU A 1 7 ? -5.506 2.024 2.204 1.00 95.77 7 A 1 ATOM 58 N N . TYR A 1 8 ? -1.802 0.992 0.105 1.00 98.16 8 A 1 ATOM 59 C CA . TYR A 1 8 ? -1.463 1.773 -1.080 1.00 98.16 8 A 1 ATOM 60 C C . TYR A 1 8 ? -1.018 0.849 -2.211 1.00 98.35 8 A 1 ATOM 61 O O . TYR A 1 8 ? -1.323 1.095 -3.381 1.00 98.27 8 A 1 ATOM 62 C CB . TYR A 1 8 ? -0.374 2.788 -0.726 1.00 97.86 8 A 1 ATOM 63 C CG . TYR A 1 8 ? 0.823 2.733 -1.645 1.00 96.67 8 A 1 ATOM 64 C CD1 . TYR A 1 8 ? 0.768 3.310 -2.913 1.00 94.51 8 A 1 ATOM 65 C CD2 . TYR A 1 8 ? 1.997 2.116 -1.244 1.00 94.60 8 A 1 ATOM 66 C CE1 . TYR A 1 8 ? 1.866 3.259 -3.755 1.00 93.66 8 A 1 ATOM 67 C CE2 . TYR A 1 8 ? 3.094 2.062 -2.091 1.00 93.70 8 A 1 ATOM 68 C CZ . TYR A 1 8 ? 3.024 2.633 -3.342 1.00 94.13 8 A 1 ATOM 69 O OH . TYR A 1 8 ? 4.110 2.576 -4.179 1.00 93.19 8 A 1 ATOM 70 N N . CYS A 1 9 ? -0.303 -0.209 -1.860 1.00 98.27 9 A 1 ATOM 71 C CA . CYS A 1 9 ? 0.165 -1.177 -2.840 1.00 98.26 9 A 1 ATOM 72 C C . CYS A 1 9 ? -1.019 -1.884 -3.492 1.00 98.45 9 A 1 ATOM 73 O O . CYS A 1 9 ? -1.035 -2.095 -4.702 1.00 98.24 9 A 1 ATOM 74 C CB . CYS A 1 9 ? 1.092 -2.199 -2.181 1.00 97.94 9 A 1 ATOM 75 S SG . CYS A 1 9 ? 2.796 -1.623 -2.077 1.00 96.81 9 A 1 ATOM 76 N N . ALA A 1 10 ? -1.999 -2.239 -2.679 1.00 98.47 10 A 1 ATOM 77 C CA . ALA A 1 10 ? -3.192 -2.911 -3.179 1.00 98.47 10 A 1 ATOM 78 C C . ALA A 1 10 ? -3.961 -2.005 -4.133 1.00 98.63 10 A 1 ATOM 79 O O . ALA A 1 10 ? -4.517 -2.467 -5.129 1.00 98.46 10 A 1 ATOM 80 C CB . ALA A 1 10 ? -4.084 -3.318 -2.015 1.00 98.25 10 A 1 ATOM 81 N N . LEU A 1 11 ? -3.985 -0.726 -3.825 1.00 98.42 11 A 1 ATOM 82 C CA . LEU A 1 11 ? -4.661 0.255 -4.671 1.00 98.33 11 A 1 ATOM 83 C C . LEU A 1 11 ? -3.910 0.440 -5.980 1.00 98.48 11 A 1 ATOM 84 O O . LEU A 1 11 ? -4.524 0.581 -7.042 1.00 98.26 11 A 1 ATOM 85 C CB . LEU A 1 11 ? -4.773 1.592 -3.936 1.00 98.07 11 A 1 ATOM 86 C CG . LEU A 1 11 ? -5.328 2.743 -4.773 1.00 97.27 11 A 1 ATOM 87 C CD1 . LEU A 1 11 ? -6.751 2.439 -5.233 1.00 96.21 11 A 1 ATOM 88 C CD2 . LEU A 1 11 ? -5.293 4.040 -3.987 1.00 95.93 11 A 1 ATOM 89 N N . ALA A 1 12 ? -2.592 0.444 -5.903 1.00 98.70 12 A 1 ATOM 90 C CA . ALA A 1 12 ? -1.754 0.605 -7.087 1.00 98.67 12 A 1 ATOM 91 C C . ALA A 1 12 ? -1.914 -0.579 -8.030 1.00 98.72 12 A 1 ATOM 92 O O . ALA A 1 12 ? -1.963 -0.405 -9.250 1.00 98.47 12 A 1 ATOM 93 C CB . ALA A 1 12 ? -0.294 0.766 -6.683 1.00 98.44 12 A 1 ATOM 94 N N . LEU A 1 13 ? -2.015 -1.788 -7.467 1.00 98.46 13 A 1 ATOM 95 C CA . LEU A 1 13 ? -2.175 -3.004 -8.263 1.00 98.23 13 A 1 ATOM 96 C C . LEU A 1 13 ? -3.600 -3.123 -8.783 1.00 98.27 13 A 1 ATOM 97 O O . LEU A 1 13 ? -3.821 -3.341 -9.977 1.00 97.54 13 A 1 ATOM 98 C CB . LEU A 1 13 ? -1.808 -4.223 -7.419 1.00 97.73 13 A 1 ATOM 99 C CG . LEU A 1 13 ? -0.342 -4.254 -7.003 1.00 96.68 13 A 1 ATOM 100 C CD1 . LEU A 1 13 ? -0.135 -5.256 -5.877 1.00 95.04 13 A 1 ATOM 101 C CD2 . LEU A 1 13 ? 0.536 -4.608 -8.196 1.00 93.70 13 A 1 ATOM 102 N N . GLY A 1 14 ? -4.549 -2.967 -7.873 1.00 95.33 14 A 1 ATOM 103 C CA . GLY A 1 14 ? -5.964 -3.056 -8.235 1.00 92.18 14 A 1 ATOM 104 C C . GLY A 1 14 ? -6.505 -4.454 -8.048 1.00 89.61 14 A 1 ATOM 105 O O . GLY A 1 14 ? -7.721 -4.588 -7.806 1.00 85.30 14 A 1 ATOM 106 O OXT . GLY A 1 14 ? -5.756 -5.408 -8.159 1.00 88.77 14 A 1 #