# 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_spkb13453 # _entry.id spkb13453 # 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 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" "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 LEU 2 1 n LEU 3 1 n ALA 4 1 n THR 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n GLY 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 @ 2025-07-05 17:53:00)" _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 94.95 _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 85.33 1 1 A LEU 2 2 95.55 1 2 A LEU 3 2 96.73 1 3 A ALA 4 2 98.00 1 4 A THR 5 2 96.67 1 5 A LEU 6 2 96.65 1 6 A LEU 7 2 96.46 1 7 A LEU 8 2 96.56 1 8 A LEU 9 2 97.11 1 9 A LEU 10 2 97.36 1 10 A LEU 11 2 96.50 1 11 A GLY 12 2 96.79 1 12 A GLY 13 2 95.97 1 13 A ALA 14 2 96.09 1 14 A LEU 15 2 92.31 1 15 A ALA 16 2 86.11 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 LEU . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n GLY . 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 ? 4.890 9.615 1.671 1.00 89.10 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.483 9.161 1.630 1.00 91.29 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.329 7.882 2.457 1.00 93.13 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.452 6.787 1.926 1.00 90.96 1 A 1 ATOM 5 C CB . MET A 1 1 ? 3.045 8.915 0.185 1.00 85.27 1 A 1 ATOM 6 C CG . MET A 1 1 ? 3.021 10.197 -0.637 1.00 81.29 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.499 9.863 -2.335 1.00 80.95 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.673 11.488 -3.050 1.00 70.63 1 A 1 ATOM 9 N N . LEU A 1 2 ? 3.093 8.028 3.750 1.00 95.57 2 A 1 ATOM 10 C CA . LEU A 1 2 ? 2.964 6.882 4.667 1.00 97.30 2 A 1 ATOM 11 C C . LEU A 1 2 ? 1.703 6.062 4.379 1.00 98.02 2 A 1 ATOM 12 O O . LEU A 1 2 ? 1.765 4.840 4.276 1.00 97.60 2 A 1 ATOM 13 C CB . LEU A 1 2 ? 2.966 7.405 6.109 1.00 96.93 2 A 1 ATOM 14 C CG . LEU A 1 2 ? 4.365 7.419 6.722 1.00 94.69 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? 4.538 8.604 7.655 1.00 92.81 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 4.603 6.130 7.495 1.00 91.44 2 A 1 ATOM 17 N N . LEU A 1 3 ? 0.584 6.739 4.203 1.00 97.87 3 A 1 ATOM 18 C CA . LEU A 1 3 ? -0.699 6.088 3.911 1.00 98.12 3 A 1 ATOM 19 C C . LEU A 1 3 ? -0.702 5.449 2.522 1.00 98.21 3 A 1 ATOM 20 O O . LEU A 1 3 ? -1.224 4.350 2.341 1.00 97.97 3 A 1 ATOM 21 C CB . LEU A 1 3 ? -1.817 7.128 4.049 1.00 97.99 3 A 1 ATOM 22 C CG . LEU A 1 3 ? -2.714 6.855 5.252 1.00 96.20 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? -3.217 8.161 5.842 1.00 94.02 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? -3.888 5.987 4.853 1.00 93.50 3 A 1 ATOM 25 N N . ALA A 1 4 ? -0.095 6.111 1.562 1.00 98.05 4 A 1 ATOM 26 C CA . ALA A 1 4 ? 0.009 5.596 0.198 1.00 98.12 4 A 1 ATOM 27 C C . ALA A 1 4 ? 0.829 4.303 0.147 1.00 98.21 4 A 1 ATOM 28 O O . ALA A 1 4 ? 0.492 3.382 -0.591 1.00 97.80 4 A 1 ATOM 29 C CB . ALA A 1 4 ? 0.625 6.676 -0.688 1.00 97.82 4 A 1 ATOM 30 N N . THR A 1 5 ? 1.857 4.220 0.958 1.00 97.91 5 A 1 ATOM 31 C CA . THR A 1 5 ? 2.691 3.020 1.060 1.00 97.79 5 A 1 ATOM 32 C C . THR A 1 5 ? 1.884 1.838 1.591 1.00 97.88 5 A 1 ATOM 33 O O . THR A 1 5 ? 2.028 0.721 1.098 1.00 97.43 5 A 1 ATOM 34 C CB . THR A 1 5 ? 3.892 3.282 1.974 1.00 97.38 5 A 1 ATOM 35 O OG1 . THR A 1 5 ? 4.495 4.514 1.633 1.00 94.87 5 A 1 ATOM 36 C CG2 . THR A 1 5 ? 4.950 2.211 1.827 1.00 93.40 5 A 1 ATOM 37 N N . LEU A 1 6 ? 1.012 2.088 2.552 1.00 97.80 6 A 1 ATOM 38 C CA . LEU A 1 6 ? 0.142 1.061 3.118 1.00 97.70 6 A 1 ATOM 39 C C . LEU A 1 6 ? -0.830 0.519 2.065 1.00 97.83 6 A 1 ATOM 40 O O . LEU A 1 6 ? -1.040 -0.690 1.976 1.00 97.67 6 A 1 ATOM 41 C CB . LEU A 1 6 ? -0.622 1.650 4.306 1.00 97.64 6 A 1 ATOM 42 C CG . LEU A 1 6 ? -0.987 0.590 5.343 1.00 95.99 6 A 1 ATOM 43 C CD1 . LEU A 1 6 ? 0.124 0.457 6.382 1.00 94.10 6 A 1 ATOM 44 C CD2 . LEU A 1 6 ? -2.282 0.957 6.044 1.00 94.45 6 A 1 ATOM 45 N N . LEU A 1 7 ? -1.381 1.406 1.260 1.00 97.70 7 A 1 ATOM 46 C CA . LEU A 1 7 ? -2.287 1.034 0.171 1.00 97.59 7 A 1 ATOM 47 C C . LEU A 1 7 ? -1.569 0.206 -0.890 1.00 97.82 7 A 1 ATOM 48 O O . LEU A 1 7 ? -2.106 -0.795 -1.364 1.00 97.74 7 A 1 ATOM 49 C CB . LEU A 1 7 ? -2.873 2.306 -0.446 1.00 97.42 7 A 1 ATOM 50 C CG . LEU A 1 7 ? -4.058 2.854 0.342 1.00 95.33 7 A 1 ATOM 51 C CD1 . LEU A 1 7 ? -4.213 4.344 0.104 1.00 93.91 7 A 1 ATOM 52 C CD2 . LEU A 1 7 ? -5.344 2.149 -0.078 1.00 94.15 7 A 1 ATOM 53 N N . LEU A 1 8 ? -0.354 0.595 -1.224 1.00 97.66 8 A 1 ATOM 54 C CA . LEU A 1 8 ? 0.477 -0.145 -2.174 1.00 97.46 8 A 1 ATOM 55 C C . LEU A 1 8 ? 0.811 -1.539 -1.655 1.00 97.79 8 A 1 ATOM 56 O O . LEU A 1 8 ? 0.793 -2.503 -2.418 1.00 97.56 8 A 1 ATOM 57 C CB . LEU A 1 8 ? 1.758 0.651 -2.430 1.00 97.02 8 A 1 ATOM 58 C CG . LEU A 1 8 ? 1.618 1.634 -3.589 1.00 95.50 8 A 1 ATOM 59 C CD1 . LEU A 1 8 ? 2.537 2.826 -3.401 1.00 94.72 8 A 1 ATOM 60 C CD2 . LEU A 1 8 ? 1.963 0.941 -4.905 1.00 94.74 8 A 1 ATOM 61 N N . LEU A 1 9 ? 1.079 -1.642 -0.365 1.00 97.64 9 A 1 ATOM 62 C CA . LEU A 1 9 ? 1.379 -2.919 0.273 1.00 97.71 9 A 1 ATOM 63 C C . LEU A 1 9 ? 0.168 -3.853 0.229 1.00 98.05 9 A 1 ATOM 64 O O . LEU A 1 9 ? 0.311 -5.038 -0.070 1.00 97.86 9 A 1 ATOM 65 C CB . LEU A 1 9 ? 1.813 -2.666 1.720 1.00 97.57 9 A 1 ATOM 66 C CG . LEU A 1 9 ? 2.798 -3.715 2.224 1.00 96.75 9 A 1 ATOM 67 C CD1 . LEU A 1 9 ? 4.233 -3.266 1.965 1.00 95.71 9 A 1 ATOM 68 C CD2 . LEU A 1 9 ? 2.606 -3.946 3.713 1.00 95.62 9 A 1 ATOM 69 N N . LEU A 1 10 ? -1.005 -3.311 0.499 1.00 97.97 10 A 1 ATOM 70 C CA . LEU A 1 10 ? -2.257 -4.064 0.437 1.00 98.00 10 A 1 ATOM 71 C C . LEU A 1 10 ? -2.542 -4.547 -0.978 1.00 98.12 10 A 1 ATOM 72 O O . LEU A 1 10 ? -2.902 -5.709 -1.169 1.00 97.81 10 A 1 ATOM 73 C CB . LEU A 1 10 ? -3.402 -3.184 0.949 1.00 97.94 10 A 1 ATOM 74 C CG . LEU A 1 10 ? -3.616 -3.313 2.455 1.00 97.25 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? -4.289 -2.070 3.004 1.00 95.98 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? -4.481 -4.532 2.763 1.00 95.84 10 A 1 ATOM 77 N N . LEU A 1 11 ? -2.341 -3.684 -1.953 1.00 97.81 11 A 1 ATOM 78 C CA . LEU A 1 11 ? -2.525 -4.032 -3.361 1.00 97.72 11 A 1 ATOM 79 C C . LEU A 1 11 ? -1.548 -5.113 -3.799 1.00 97.71 11 A 1 ATOM 80 O O . LEU A 1 11 ? -1.949 -6.080 -4.442 1.00 96.68 11 A 1 ATOM 81 C CB . LEU A 1 11 ? -2.359 -2.769 -4.212 1.00 97.40 11 A 1 ATOM 82 C CG . LEU A 1 11 ? -3.684 -2.054 -4.461 1.00 96.38 11 A 1 ATOM 83 C CD1 . LEU A 1 11 ? -3.469 -0.564 -4.651 1.00 94.49 11 A 1 ATOM 84 C CD2 . LEU A 1 11 ? -4.363 -2.627 -5.695 1.00 93.78 11 A 1 ATOM 85 N N . GLY A 1 12 ? -0.301 -4.974 -3.427 1.00 97.01 12 A 1 ATOM 86 C CA . GLY A 1 12 ? 0.717 -5.965 -3.760 1.00 96.74 12 A 1 ATOM 87 C C . GLY A 1 12 ? 0.459 -7.305 -3.093 1.00 97.10 12 A 1 ATOM 88 O O . GLY A 1 12 ? 0.611 -8.350 -3.723 1.00 96.29 12 A 1 ATOM 89 N N . GLY A 1 13 ? 0.042 -7.292 -1.838 1.00 96.07 13 A 1 ATOM 90 C CA . GLY A 1 13 ? -0.289 -8.507 -1.099 1.00 95.80 13 A 1 ATOM 91 C C . GLY A 1 13 ? -1.544 -9.188 -1.612 1.00 96.49 13 A 1 ATOM 92 O O . GLY A 1 13 ? -1.589 -10.414 -1.701 1.00 95.53 13 A 1 ATOM 93 N N . ALA A 1 14 ? -2.553 -8.416 -1.980 1.00 96.27 14 A 1 ATOM 94 C CA . ALA A 1 14 ? -3.800 -8.950 -2.528 1.00 96.41 14 A 1 ATOM 95 C C . ALA A 1 14 ? -3.615 -9.498 -3.944 1.00 96.90 14 A 1 ATOM 96 O O . ALA A 1 14 ? -4.307 -10.435 -4.333 1.00 95.49 14 A 1 ATOM 97 C CB . ALA A 1 14 ? -4.865 -7.855 -2.509 1.00 95.38 14 A 1 ATOM 98 N N . LEU A 1 15 ? -2.707 -8.919 -4.696 1.00 95.50 15 A 1 ATOM 99 C CA . LEU A 1 15 ? -2.409 -9.356 -6.057 1.00 95.34 15 A 1 ATOM 100 C C . LEU A 1 15 ? -1.675 -10.691 -6.068 1.00 95.56 15 A 1 ATOM 101 O O . LEU A 1 15 ? -1.867 -11.489 -6.984 1.00 93.21 15 A 1 ATOM 102 C CB . LEU A 1 15 ? -1.575 -8.280 -6.761 1.00 93.89 15 A 1 ATOM 103 C CG . LEU A 1 15 ? -1.660 -8.341 -8.279 1.00 91.50 15 A 1 ATOM 104 C CD1 . LEU A 1 15 ? -2.827 -7.510 -8.787 1.00 88.58 15 A 1 ATOM 105 C CD2 . LEU A 1 15 ? -0.372 -7.836 -8.901 1.00 84.91 15 A 1 ATOM 106 N N . ALA A 1 16 ? -0.853 -10.927 -5.061 1.00 92.42 16 A 1 ATOM 107 C CA . ALA A 1 16 ? -0.087 -12.166 -4.936 1.00 90.00 16 A 1 ATOM 108 C C . ALA A 1 16 ? -0.991 -13.339 -4.577 1.00 88.47 16 A 1 ATOM 109 O O . ALA A 1 16 ? -0.890 -14.391 -5.236 1.00 83.39 16 A 1 ATOM 110 C CB . ALA A 1 16 ? 1.012 -11.978 -3.893 1.00 85.12 16 A 1 ATOM 111 O OXT . ALA A 1 16 ? -1.785 -13.192 -3.638 1.00 77.26 16 A 1 #