# 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_spkb28223 # _entry.id spkb28223 # 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" "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 LEU 2 1 n THR 3 1 n THR 4 1 n ALA 5 1 n ILE 6 1 n LEU 7 1 n PHE 8 1 n THR 9 1 n SER 10 1 n LEU 11 1 n ALA 12 1 n GLY 13 1 n SER 14 1 n ALA 15 1 n TYR 16 1 n ALA 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 @ 2025-07-02 19:26:24)" _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 93.14 _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 84.87 1 1 A LEU 2 2 89.95 1 2 A THR 3 2 94.45 1 3 A THR 4 2 95.94 1 4 A ALA 5 2 97.77 1 5 A ILE 6 2 95.84 1 6 A LEU 7 2 94.44 1 7 A PHE 8 2 92.17 1 8 A THR 9 2 95.60 1 9 A SER 10 2 95.41 1 10 A LEU 11 2 94.99 1 11 A ALA 12 2 96.69 1 12 A GLY 13 2 96.31 1 13 A SER 14 2 93.73 1 14 A ALA 15 2 95.28 1 15 A TYR 16 2 89.90 1 16 A ALA 17 2 87.68 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 LEU . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n TYR . 16 A 16 A 17 1 n ALA . 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 ? -9.245 -1.203 10.361 1.00 87.06 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.965 -0.765 9.787 1.00 90.89 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.979 -0.835 8.262 1.00 92.96 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.096 -1.429 7.649 1.00 91.56 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.821 -1.642 10.307 1.00 84.40 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.586 -1.494 11.795 1.00 80.33 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.240 -2.547 12.366 1.00 80.39 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.107 -1.993 14.059 1.00 71.39 1 A 1 ATOM 9 N N . LEU A 1 2 ? -8.978 -0.233 7.659 1.00 90.28 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -9.088 -0.235 6.204 1.00 94.76 2 A 1 ATOM 11 C C . LEU A 1 2 ? -8.241 0.878 5.590 1.00 96.87 2 A 1 ATOM 12 O O . LEU A 1 2 ? -7.562 0.682 4.582 1.00 96.16 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -10.563 -0.099 5.801 1.00 92.57 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -11.308 1.035 6.498 1.00 85.28 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -11.398 2.255 5.603 1.00 83.11 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -12.701 0.582 6.896 1.00 80.58 2 A 1 ATOM 17 N N . THR A 1 3 ? -8.269 2.051 6.219 1.00 94.50 3 A 1 ATOM 18 C CA . THR A 1 3 ? -7.492 3.196 5.744 1.00 95.92 3 A 1 ATOM 19 C C . THR A 1 3 ? -5.998 2.964 5.947 1.00 96.74 3 A 1 ATOM 20 O O . THR A 1 3 ? -5.172 3.406 5.148 1.00 96.65 3 A 1 ATOM 21 C CB . THR A 1 3 ? -7.908 4.481 6.473 1.00 95.19 3 A 1 ATOM 22 O OG1 . THR A 1 3 ? -9.325 4.623 6.437 1.00 91.25 3 A 1 ATOM 23 C CG2 . THR A 1 3 ? -7.263 5.696 5.834 1.00 90.88 3 A 1 ATOM 24 N N . THR A 1 4 ? -5.655 2.254 7.012 1.00 97.15 4 A 1 ATOM 25 C CA . THR A 1 4 ? -4.257 1.956 7.330 1.00 97.35 4 A 1 ATOM 26 C C . THR A 1 4 ? -3.594 1.190 6.188 1.00 97.60 4 A 1 ATOM 27 O O . THR A 1 4 ? -2.435 1.435 5.852 1.00 97.38 4 A 1 ATOM 28 C CB . THR A 1 4 ? -4.154 1.127 8.614 1.00 96.73 4 A 1 ATOM 29 O OG1 . THR A 1 4 ? -4.884 1.775 9.660 1.00 92.97 4 A 1 ATOM 30 C CG2 . THR A 1 4 ? -2.705 0.974 9.035 1.00 92.43 4 A 1 ATOM 31 N N . ALA A 1 5 ? -4.335 0.270 5.587 1.00 97.58 5 A 1 ATOM 32 C CA . ALA A 1 5 ? -3.815 -0.525 4.477 1.00 97.87 5 A 1 ATOM 33 C C . ALA A 1 5 ? -3.478 0.365 3.285 1.00 98.17 5 A 1 ATOM 34 O O . ALA A 1 5 ? -2.465 0.167 2.610 1.00 97.80 5 A 1 ATOM 35 C CB . ALA A 1 5 ? -4.838 -1.584 4.077 1.00 97.42 5 A 1 ATOM 36 N N . ILE A 1 6 ? -4.330 1.339 3.035 1.00 97.48 6 A 1 ATOM 37 C CA . ILE A 1 6 ? -4.130 2.274 1.932 1.00 97.37 6 A 1 ATOM 38 C C . ILE A 1 6 ? -2.891 3.133 2.173 1.00 97.50 6 A 1 ATOM 39 O O . ILE A 1 6 ? -2.079 3.347 1.269 1.00 97.31 6 A 1 ATOM 40 C CB . ILE A 1 6 ? -5.362 3.176 1.749 1.00 97.31 6 A 1 ATOM 41 C CG1 . ILE A 1 6 ? -6.606 2.330 1.471 1.00 95.30 6 A 1 ATOM 42 C CG2 . ILE A 1 6 ? -5.122 4.160 0.604 1.00 94.26 6 A 1 ATOM 43 C CD1 . ILE A 1 6 ? -7.891 3.138 1.501 1.00 90.22 6 A 1 ATOM 44 N N . LEU A 1 7 ? -2.748 3.610 3.397 1.00 96.85 7 A 1 ATOM 45 C CA . LEU A 1 7 ? -1.604 4.449 3.752 1.00 96.54 7 A 1 ATOM 46 C C . LEU A 1 7 ? -0.298 3.667 3.641 1.00 97.09 7 A 1 ATOM 47 O O . LEU A 1 7 ? 0.704 4.173 3.133 1.00 97.20 7 A 1 ATOM 48 C CB . LEU A 1 7 ? -1.775 4.978 5.176 1.00 96.27 7 A 1 ATOM 49 C CG . LEU A 1 7 ? -2.941 5.948 5.351 1.00 91.65 7 A 1 ATOM 50 C CD1 . LEU A 1 7 ? -3.160 6.245 6.829 1.00 90.08 7 A 1 ATOM 51 C CD2 . LEU A 1 7 ? -2.680 7.241 4.595 1.00 89.84 7 A 1 ATOM 52 N N . PHE A 1 8 ? -0.332 2.428 4.103 1.00 95.39 8 A 1 ATOM 53 C CA . PHE A 1 8 ? 0.851 1.576 4.072 1.00 95.42 8 A 1 ATOM 54 C C . PHE A 1 8 ? 1.267 1.263 2.642 1.00 96.55 8 A 1 ATOM 55 O O . PHE A 1 8 ? 2.442 1.368 2.287 1.00 96.44 8 A 1 ATOM 56 C CB . PHE A 1 8 ? 0.576 0.281 4.831 1.00 94.84 8 A 1 ATOM 57 C CG . PHE A 1 8 ? 1.807 -0.571 4.984 1.00 91.48 8 A 1 ATOM 58 C CD1 . PHE A 1 8 ? 2.785 -0.230 5.905 1.00 89.37 8 A 1 ATOM 59 C CD2 . PHE A 1 8 ? 1.979 -1.708 4.212 1.00 89.35 8 A 1 ATOM 60 C CE1 . PHE A 1 8 ? 3.923 -1.008 6.052 1.00 88.52 8 A 1 ATOM 61 C CE2 . PHE A 1 8 ? 3.121 -2.491 4.351 1.00 88.09 8 A 1 ATOM 62 C CZ . PHE A 1 8 ? 4.095 -2.143 5.273 1.00 88.39 8 A 1 ATOM 63 N N . THR A 1 9 ? 0.302 0.882 1.815 1.00 96.81 9 A 1 ATOM 64 C CA . THR A 1 9 ? 0.595 0.545 0.421 1.00 96.80 9 A 1 ATOM 65 C C . THR A 1 9 ? 1.060 1.778 -0.351 1.00 97.31 9 A 1 ATOM 66 O O . THR A 1 9 ? 1.914 1.682 -1.234 1.00 96.88 9 A 1 ATOM 67 C CB . THR A 1 9 ? -0.630 -0.084 -0.264 1.00 96.30 9 A 1 ATOM 68 O OG1 . THR A 1 9 ? -0.229 -0.641 -1.519 1.00 93.15 9 A 1 ATOM 69 C CG2 . THR A 1 9 ? -1.719 0.935 -0.518 1.00 91.94 9 A 1 ATOM 70 N N . SER A 1 10 ? 0.510 2.935 0.000 1.00 96.93 10 A 1 ATOM 71 C CA . SER A 1 10 ? 0.885 4.190 -0.642 1.00 96.78 10 A 1 ATOM 72 C C . SER A 1 10 ? 2.337 4.539 -0.323 1.00 97.22 10 A 1 ATOM 73 O O . SER A 1 10 ? 3.098 4.937 -1.206 1.00 96.64 10 A 1 ATOM 74 C CB . SER A 1 10 ? -0.032 5.324 -0.179 1.00 96.23 10 A 1 ATOM 75 O OG . SER A 1 10 ? 0.316 6.534 -0.816 1.00 88.68 10 A 1 ATOM 76 N N . LEU A 1 11 ? 2.706 4.369 0.936 1.00 97.32 11 A 1 ATOM 77 C CA . LEU A 1 11 ? 4.071 4.650 1.373 1.00 97.12 11 A 1 ATOM 78 C C . LEU A 1 11 ? 5.055 3.697 0.711 1.00 97.37 11 A 1 ATOM 79 O O . LEU A 1 11 ? 6.124 4.107 0.257 1.00 97.00 11 A 1 ATOM 80 C CB . LEU A 1 11 ? 4.170 4.520 2.894 1.00 96.77 11 A 1 ATOM 81 C CG . LEU A 1 11 ? 5.551 4.845 3.457 1.00 92.45 11 A 1 ATOM 82 C CD1 . LEU A 1 11 ? 5.909 6.300 3.210 1.00 90.63 11 A 1 ATOM 83 C CD2 . LEU A 1 11 ? 5.600 4.533 4.946 1.00 91.25 11 A 1 ATOM 84 N N . ALA A 1 12 ? 4.688 2.423 0.654 1.00 97.39 12 A 1 ATOM 85 C CA . ALA A 1 12 ? 5.533 1.410 0.031 1.00 96.99 12 A 1 ATOM 86 C C . ALA A 1 12 ? 5.734 1.712 -1.447 1.00 96.99 12 A 1 ATOM 87 O O . ALA A 1 12 ? 6.838 1.566 -1.974 1.00 95.99 12 A 1 ATOM 88 C CB . ALA A 1 12 ? 4.904 0.034 0.206 1.00 96.11 12 A 1 ATOM 89 N N . GLY A 1 13 ? 4.669 2.140 -2.111 1.00 96.33 13 A 1 ATOM 90 C CA . GLY A 1 13 ? 4.747 2.490 -3.523 1.00 95.85 13 A 1 ATOM 91 C C . GLY A 1 13 ? 5.640 3.686 -3.762 1.00 96.75 13 A 1 ATOM 92 O O . GLY A 1 13 ? 6.402 3.723 -4.731 1.00 96.30 13 A 1 ATOM 93 N N . SER A 1 14 ? 5.569 4.666 -2.871 1.00 95.96 14 A 1 ATOM 94 C CA . SER A 1 14 ? 6.388 5.870 -2.968 1.00 95.92 14 A 1 ATOM 95 C C . SER A 1 14 ? 7.866 5.533 -2.817 1.00 96.39 14 A 1 ATOM 96 O O . SER A 1 14 ? 8.710 6.056 -3.544 1.00 94.43 14 A 1 ATOM 97 C CB . SER A 1 14 ? 5.982 6.881 -1.897 1.00 94.23 14 A 1 ATOM 98 O OG . SER A 1 14 ? 6.739 8.059 -2.018 1.00 85.48 14 A 1 ATOM 99 N N . ALA A 1 15 ? 8.179 4.643 -1.875 1.00 95.53 15 A 1 ATOM 100 C CA . ALA A 1 15 ? 9.557 4.216 -1.639 1.00 95.40 15 A 1 ATOM 101 C C . ALA A 1 15 ? 10.081 3.393 -2.807 1.00 96.16 15 A 1 ATOM 102 O O . ALA A 1 15 ? 11.254 3.483 -3.169 1.00 95.20 15 A 1 ATOM 103 C CB . ALA A 1 15 ? 9.640 3.404 -0.352 1.00 94.13 15 A 1 ATOM 104 N N . TYR A 1 16 ? 9.198 2.574 -3.386 1.00 94.46 16 A 1 ATOM 105 C CA . TYR A 1 16 ? 9.558 1.733 -4.522 1.00 94.68 16 A 1 ATOM 106 C C . TYR A 1 16 ? 9.779 2.569 -5.774 1.00 95.00 16 A 1 ATOM 107 O O . TYR A 1 16 ? 10.665 2.273 -6.581 1.00 93.35 16 A 1 ATOM 108 C CB . TYR A 1 16 ? 8.455 0.699 -4.771 1.00 92.99 16 A 1 ATOM 109 C CG . TYR A 1 16 ? 8.693 -0.139 -6.006 1.00 89.61 16 A 1 ATOM 110 C CD1 . TYR A 1 16 ? 8.169 0.239 -7.233 1.00 88.27 16 A 1 ATOM 111 C CD2 . TYR A 1 16 ? 9.451 -1.300 -5.940 1.00 87.12 16 A 1 ATOM 112 C CE1 . TYR A 1 16 ? 8.395 -0.519 -8.369 1.00 86.45 16 A 1 ATOM 113 C CE2 . TYR A 1 16 ? 9.683 -2.066 -7.074 1.00 85.91 16 A 1 ATOM 114 C CZ . TYR A 1 16 ? 9.150 -1.669 -8.283 1.00 85.82 16 A 1 ATOM 115 O OH . TYR A 1 16 ? 9.377 -2.421 -9.409 1.00 85.14 16 A 1 ATOM 116 N N . ALA A 1 17 ? 8.972 3.602 -5.923 1.00 92.56 17 A 1 ATOM 117 C CA . ALA A 1 17 ? 9.053 4.484 -7.084 1.00 91.04 17 A 1 ATOM 118 C C . ALA A 1 17 ? 10.401 5.198 -7.112 1.00 89.34 17 A 1 ATOM 119 O O . ALA A 1 17 ? 11.022 5.255 -8.192 1.00 85.95 17 A 1 ATOM 120 C CB . ALA A 1 17 ? 7.908 5.487 -7.063 1.00 86.89 17 A 1 ATOM 121 O OXT . ALA A 1 17 ? 10.820 5.714 -6.067 1.00 80.30 17 A 1 #