# 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_spkb08765 # _entry.id spkb08765 # 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 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" "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 LYS 2 1 n THR 3 1 n ILE 4 1 n ILE 5 1 n ALA 6 1 n LEU 7 1 n SER 8 1 n TYR 9 1 n ILE 10 1 n PHE 11 1 n CYS 12 1 n LEU 13 1 n ALA 14 1 n LEU 15 1 n GLY 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 13:58:36)" _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 96.18 _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 92.17 1 1 A LYS 2 2 92.05 1 2 A THR 3 2 96.79 1 3 A ILE 4 2 97.15 1 4 A ILE 5 2 97.22 1 5 A ALA 6 2 98.60 1 6 A LEU 7 2 96.98 1 7 A SER 8 2 97.59 1 8 A TYR 9 2 96.01 1 9 A ILE 10 2 97.63 1 10 A PHE 11 2 96.86 1 11 A CYS 12 2 98.04 1 12 A LEU 13 2 97.24 1 13 A ALA 14 2 98.58 1 14 A LEU 15 2 95.67 1 15 A GLY 16 2 91.68 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 THR . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n TYR . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n CYS . 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 GLY . 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 ? -7.681 9.846 8.724 1.00 97.18 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.794 8.695 8.995 1.00 97.42 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.588 8.732 8.067 1.00 97.56 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.747 8.638 6.856 1.00 96.07 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.548 7.378 8.796 1.00 95.66 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.018 6.779 10.105 1.00 91.42 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.967 5.275 9.849 1.00 85.86 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.999 4.626 11.512 1.00 76.21 1 A 1 ATOM 9 N N . LYS A 1 2 ? -4.407 8.890 8.629 1.00 97.29 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -3.168 8.923 7.840 1.00 97.73 2 A 1 ATOM 11 C C . LYS A 1 2 ? -2.487 7.551 7.819 1.00 98.06 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.567 7.331 7.042 1.00 97.30 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -2.233 9.988 8.412 1.00 96.83 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -2.756 11.398 8.172 1.00 92.03 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -1.808 12.442 8.733 1.00 88.94 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.307 13.840 8.415 1.00 83.58 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -1.417 14.877 8.994 1.00 76.65 2 A 1 ATOM 18 N N . THR A 1 3 ? -2.950 6.636 8.636 1.00 98.22 3 A 1 ATOM 19 C CA . THR A 1 3 ? -2.372 5.295 8.728 1.00 98.35 3 A 1 ATOM 20 C C . THR A 1 3 ? -2.643 4.494 7.454 1.00 98.47 3 A 1 ATOM 21 O O . THR A 1 3 ? -1.800 3.719 7.009 1.00 97.99 3 A 1 ATOM 22 C CB . THR A 1 3 ? -2.949 4.547 9.934 1.00 98.03 3 A 1 ATOM 23 O OG1 . THR A 1 3 ? -3.239 5.460 10.987 1.00 93.89 3 A 1 ATOM 24 C CG2 . THR A 1 3 ? -1.972 3.508 10.446 1.00 92.58 3 A 1 ATOM 25 N N . ILE A 1 4 ? -3.807 4.702 6.855 1.00 98.51 4 A 1 ATOM 26 C CA . ILE A 1 4 ? -4.178 4.000 5.624 1.00 98.52 4 A 1 ATOM 27 C C . ILE A 1 4 ? -3.247 4.403 4.484 1.00 98.55 4 A 1 ATOM 28 O O . ILE A 1 4 ? -2.868 3.574 3.653 1.00 98.29 4 A 1 ATOM 29 C CB . ILE A 1 4 ? -5.642 4.297 5.261 1.00 98.41 4 A 1 ATOM 30 C CG1 . ILE A 1 4 ? -6.578 3.867 6.400 1.00 96.68 4 A 1 ATOM 31 C CG2 . ILE A 1 4 ? -6.024 3.567 3.967 1.00 96.45 4 A 1 ATOM 32 C CD1 . ILE A 1 4 ? -7.997 4.384 6.222 1.00 91.78 4 A 1 ATOM 33 N N . ILE A 1 5 ? -2.868 5.659 4.454 1.00 98.54 5 A 1 ATOM 34 C CA . ILE A 1 5 ? -1.967 6.171 3.424 1.00 98.44 5 A 1 ATOM 35 C C . ILE A 1 5 ? -0.601 5.501 3.535 1.00 98.40 5 A 1 ATOM 36 O O . ILE A 1 5 ? 0.012 5.149 2.528 1.00 98.23 5 A 1 ATOM 37 C CB . ILE A 1 5 ? -1.828 7.698 3.553 1.00 98.34 5 A 1 ATOM 38 C CG1 . ILE A 1 5 ? -3.208 8.379 3.569 1.00 96.50 5 A 1 ATOM 39 C CG2 . ILE A 1 5 ? -0.974 8.255 2.411 1.00 96.32 5 A 1 ATOM 40 C CD1 . ILE A 1 5 ? -4.034 8.109 2.313 1.00 92.98 5 A 1 ATOM 41 N N . ALA A 1 6 ? -0.134 5.319 4.749 1.00 98.69 6 A 1 ATOM 42 C CA . ALA A 1 6 ? 1.157 4.682 4.989 1.00 98.67 6 A 1 ATOM 43 C C . ALA A 1 6 ? 1.140 3.218 4.543 1.00 98.69 6 A 1 ATOM 44 O O . ALA A 1 6 ? 2.068 2.755 3.888 1.00 98.42 6 A 1 ATOM 45 C CB . ALA A 1 6 ? 1.501 4.788 6.469 1.00 98.54 6 A 1 ATOM 46 N N . LEU A 1 7 ? 0.072 2.500 4.872 1.00 98.70 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -0.065 1.100 4.473 1.00 98.63 7 A 1 ATOM 48 C C . LEU A 1 7 ? -0.165 0.972 2.958 1.00 98.67 7 A 1 ATOM 49 O O . LEU A 1 7 ? 0.452 0.093 2.360 1.00 98.51 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -1.303 0.484 5.130 1.00 98.48 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -0.966 -0.342 6.369 1.00 96.32 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -1.107 0.500 7.633 1.00 92.55 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -1.872 -1.561 6.460 1.00 93.99 7 A 1 ATOM 54 N N . SER A 1 8 ? -0.935 1.852 2.340 1.00 98.61 8 A 1 ATOM 55 C CA . SER A 1 8 ? -1.100 1.848 0.888 1.00 98.58 8 A 1 ATOM 56 C C . SER A 1 8 ? 0.230 2.124 0.186 1.00 98.67 8 A 1 ATOM 57 O O . SER A 1 8 ? 0.533 1.522 -0.843 1.00 98.51 8 A 1 ATOM 58 C CB . SER A 1 8 ? -2.136 2.891 0.492 1.00 98.32 8 A 1 ATOM 59 O OG . SER A 1 8 ? -2.501 2.716 -0.851 1.00 92.86 8 A 1 ATOM 60 N N . TYR A 1 9 ? 1.026 2.996 0.752 1.00 98.28 9 A 1 ATOM 61 C CA . TYR A 1 9 ? 2.331 3.337 0.192 1.00 98.35 9 A 1 ATOM 62 C C . TYR A 1 9 ? 3.264 2.123 0.205 1.00 98.52 9 A 1 ATOM 63 O O . TYR A 1 9 ? 3.946 1.848 -0.781 1.00 98.39 9 A 1 ATOM 64 C CB . TYR A 1 9 ? 2.934 4.484 0.998 1.00 98.18 9 A 1 ATOM 65 C CG . TYR A 1 9 ? 4.113 5.102 0.292 1.00 96.31 9 A 1 ATOM 66 C CD1 . TYR A 1 9 ? 5.409 4.645 0.542 1.00 94.33 9 A 1 ATOM 67 C CD2 . TYR A 1 9 ? 3.918 6.132 -0.630 1.00 94.63 9 A 1 ATOM 68 C CE1 . TYR A 1 9 ? 6.494 5.209 -0.120 1.00 93.34 9 A 1 ATOM 69 C CE2 . TYR A 1 9 ? 5.004 6.701 -1.293 1.00 93.75 9 A 1 ATOM 70 C CZ . TYR A 1 9 ? 6.288 6.232 -1.036 1.00 94.61 9 A 1 ATOM 71 O OH . TYR A 1 9 ? 7.359 6.783 -1.688 1.00 93.45 9 A 1 ATOM 72 N N . ILE A 1 10 ? 3.274 1.389 1.302 1.00 98.62 10 A 1 ATOM 73 C CA . ILE A 1 10 ? 4.111 0.192 1.424 1.00 98.57 10 A 1 ATOM 74 C C . ILE A 1 10 ? 3.669 -0.870 0.420 1.00 98.63 10 A 1 ATOM 75 O O . ILE A 1 10 ? 4.497 -1.534 -0.204 1.00 98.38 10 A 1 ATOM 76 C CB . ILE A 1 10 ? 4.038 -0.366 2.855 1.00 98.38 10 A 1 ATOM 77 C CG1 . ILE A 1 10 ? 4.588 0.657 3.860 1.00 97.34 10 A 1 ATOM 78 C CG2 . ILE A 1 10 ? 4.834 -1.672 2.959 1.00 97.09 10 A 1 ATOM 79 C CD1 . ILE A 1 10 ? 4.196 0.347 5.290 1.00 94.00 10 A 1 ATOM 80 N N . PHE A 1 11 ? 2.360 -1.029 0.264 1.00 98.51 11 A 1 ATOM 81 C CA . PHE A 1 11 ? 1.810 -2.007 -0.670 1.00 98.43 11 A 1 ATOM 82 C C . PHE A 1 11 ? 2.188 -1.655 -2.108 1.00 98.51 11 A 1 ATOM 83 O O . PHE A 1 11 ? 2.566 -2.530 -2.886 1.00 98.27 11 A 1 ATOM 84 C CB . PHE A 1 11 ? 0.291 -2.056 -0.507 1.00 98.23 11 A 1 ATOM 85 C CG . PHE A 1 11 ? -0.276 -3.395 -0.907 1.00 97.44 11 A 1 ATOM 86 C CD1 . PHE A 1 11 ? -0.654 -3.644 -2.220 1.00 94.95 11 A 1 ATOM 87 C CD2 . PHE A 1 11 ? -0.418 -4.400 0.046 1.00 95.75 11 A 1 ATOM 88 C CE1 . PHE A 1 11 ? -1.167 -4.885 -2.587 1.00 95.03 11 A 1 ATOM 89 C CE2 . PHE A 1 11 ? -0.933 -5.644 -0.316 1.00 94.94 11 A 1 ATOM 90 C CZ . PHE A 1 11 ? -1.307 -5.887 -1.633 1.00 95.37 11 A 1 ATOM 91 N N . CYS A 1 12 ? 2.104 -0.387 -2.457 1.00 98.61 12 A 1 ATOM 92 C CA . CYS A 1 12 ? 2.471 0.066 -3.797 1.00 98.63 12 A 1 ATOM 93 C C . CYS A 1 12 ? 3.969 -0.105 -4.046 1.00 98.72 12 A 1 ATOM 94 O O . CYS A 1 12 ? 4.377 -0.450 -5.146 1.00 98.54 12 A 1 ATOM 95 C CB . CYS A 1 12 ? 2.070 1.531 -3.971 1.00 98.31 12 A 1 ATOM 96 S SG . CYS A 1 12 ? 0.349 1.677 -4.475 1.00 95.45 12 A 1 ATOM 97 N N . LEU A 1 13 ? 4.764 0.117 -3.035 1.00 98.70 13 A 1 ATOM 98 C CA . LEU A 1 13 ? 6.215 -0.008 -3.155 1.00 98.65 13 A 1 ATOM 99 C C . LEU A 1 13 ? 6.635 -1.467 -3.305 1.00 98.72 13 A 1 ATOM 100 O O . LEU A 1 13 ? 7.618 -1.767 -3.981 1.00 98.48 13 A 1 ATOM 101 C CB . LEU A 1 13 ? 6.869 0.629 -1.928 1.00 98.40 13 A 1 ATOM 102 C CG . LEU A 1 13 ? 8.373 0.798 -2.092 1.00 96.59 13 A 1 ATOM 103 C CD1 . LEU A 1 13 ? 8.788 2.213 -1.718 1.00 94.05 13 A 1 ATOM 104 C CD2 . LEU A 1 13 ? 9.123 -0.201 -1.232 1.00 94.31 13 A 1 ATOM 105 N N . ALA A 1 14 ? 5.898 -2.381 -2.686 1.00 98.65 14 A 1 ATOM 106 C CA . ALA A 1 14 ? 6.207 -3.808 -2.761 1.00 98.67 14 A 1 ATOM 107 C C . ALA A 1 14 ? 5.913 -4.380 -4.150 1.00 98.72 14 A 1 ATOM 108 O O . ALA A 1 14 ? 6.657 -5.225 -4.642 1.00 98.40 14 A 1 ATOM 109 C CB . ALA A 1 14 ? 5.409 -4.554 -1.693 1.00 98.47 14 A 1 ATOM 110 N N . LEU A 1 15 ? 4.840 -3.934 -4.772 1.00 98.31 15 A 1 ATOM 111 C CA . LEU A 1 15 ? 4.431 -4.416 -6.095 1.00 98.05 15 A 1 ATOM 112 C C . LEU A 1 15 ? 5.015 -3.570 -7.223 1.00 97.97 15 A 1 ATOM 113 O O . LEU A 1 15 ? 5.529 -4.109 -8.203 1.00 96.88 15 A 1 ATOM 114 C CB . LEU A 1 15 ? 2.900 -4.425 -6.177 1.00 97.52 15 A 1 ATOM 115 C CG . LEU A 1 15 ? 2.249 -5.509 -5.323 1.00 95.53 15 A 1 ATOM 116 C CD1 . LEU A 1 15 ? 0.756 -5.235 -5.189 1.00 91.41 15 A 1 ATOM 117 C CD2 . LEU A 1 15 ? 2.456 -6.883 -5.955 1.00 89.69 15 A 1 ATOM 118 N N . GLY A 1 16 ? 4.898 -2.269 -7.089 1.00 95.89 16 A 1 ATOM 119 C CA . GLY A 1 16 ? 5.347 -1.324 -8.104 1.00 93.42 16 A 1 ATOM 120 C C . GLY A 1 16 ? 6.473 -0.443 -7.608 1.00 91.38 16 A 1 ATOM 121 O O . GLY A 1 16 ? 6.305 0.189 -6.553 1.00 88.28 16 A 1 ATOM 122 O OXT . GLY A 1 16 ? 7.492 -0.363 -8.296 1.00 89.44 16 A 1 #