# 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_spkb16995 # _entry.id spkb16995 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "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" # _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 SER 3 1 n LYS 4 1 n LEU 5 1 n PHE 6 1 n LEU 7 1 n ALA 8 1 n ALA 9 1 n ALA 10 1 n LEU 11 1 n LEU 12 1 n GLN 13 1 n GLY 14 1 n ALA 15 1 n LEU 16 1 n SER 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 18:03:09)" _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 94.76 _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 84.86 1 1 A ALA 2 2 95.24 1 2 A SER 3 2 95.87 1 3 A LYS 4 2 93.06 1 4 A LEU 5 2 95.68 1 5 A PHE 6 2 94.80 1 6 A LEU 7 2 95.64 1 7 A ALA 8 2 98.16 1 8 A ALA 9 2 98.04 1 9 A ALA 10 2 98.34 1 10 A LEU 11 2 97.25 1 11 A LEU 12 2 96.58 1 12 A GLN 13 2 93.49 1 13 A GLY 14 2 98.01 1 14 A ALA 15 2 98.09 1 15 A LEU 16 2 95.75 1 16 A SER 17 2 88.79 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 ALA . 2 A 2 A 3 1 n SER . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n GLN . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n SER . 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 ? -12.133 4.882 9.295 1.00 89.66 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.265 3.714 9.048 1.00 91.09 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.665 3.785 7.646 1.00 92.13 1 A 1 ATOM 4 O O . MET A 1 1 ? -11.267 3.312 6.686 1.00 90.49 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.075 2.425 9.199 1.00 85.79 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.452 2.170 10.646 1.00 80.83 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.496 0.721 10.820 1.00 78.90 1 A 1 ATOM 8 C CE . MET A 1 1 ? -13.727 0.707 12.583 1.00 70.01 1 A 1 ATOM 9 N N . ALA A 1 2 ? -9.498 4.371 7.538 1.00 92.73 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -8.819 4.537 6.252 1.00 95.98 2 A 1 ATOM 11 C C . ALA A 1 2 ? -7.464 3.823 6.245 1.00 97.08 2 A 1 ATOM 12 O O . ALA A 1 2 ? -6.471 4.356 5.743 1.00 96.12 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -8.645 6.020 5.956 1.00 94.29 2 A 1 ATOM 14 N N . SER A 1 3 ? -7.427 2.619 6.810 1.00 97.21 3 A 1 ATOM 15 C CA . SER A 1 3 ? -6.190 1.836 6.872 1.00 97.43 3 A 1 ATOM 16 C C . SER A 1 3 ? -5.701 1.446 5.480 1.00 97.95 3 A 1 ATOM 17 O O . SER A 1 3 ? -4.508 1.232 5.270 1.00 97.26 3 A 1 ATOM 18 C CB . SER A 1 3 ? -6.408 0.582 7.712 1.00 96.00 3 A 1 ATOM 19 O OG . SER A 1 3 ? -6.839 0.921 9.015 1.00 89.38 3 A 1 ATOM 20 N N . LYS A 1 4 ? -6.640 1.365 4.541 1.00 96.88 4 A 1 ATOM 21 C CA . LYS A 1 4 ? -6.307 1.017 3.159 1.00 97.62 4 A 1 ATOM 22 C C . LYS A 1 4 ? -5.329 2.027 2.559 1.00 97.91 4 A 1 ATOM 23 O O . LYS A 1 4 ? -4.405 1.651 1.834 1.00 97.63 4 A 1 ATOM 24 C CB . LYS A 1 4 ? -7.581 0.955 2.318 1.00 97.23 4 A 1 ATOM 25 C CG . LYS A 1 4 ? -7.866 -0.433 1.775 1.00 93.09 4 A 1 ATOM 26 C CD . LYS A 1 4 ? -6.968 -0.782 0.605 1.00 90.56 4 A 1 ATOM 27 C CE . LYS A 1 4 ? -7.522 -1.942 -0.201 1.00 86.43 4 A 1 ATOM 28 N NZ . LYS A 1 4 ? -6.662 -2.249 -1.378 1.00 80.17 4 A 1 ATOM 29 N N . LEU A 1 5 ? -5.522 3.291 2.865 1.00 97.27 5 A 1 ATOM 30 C CA . LEU A 1 5 ? -4.654 4.349 2.355 1.00 97.62 5 A 1 ATOM 31 C C . LEU A 1 5 ? -3.242 4.216 2.916 1.00 97.88 5 A 1 ATOM 32 O O . LEU A 1 5 ? -2.258 4.402 2.199 1.00 97.60 5 A 1 ATOM 33 C CB . LEU A 1 5 ? -5.240 5.713 2.716 1.00 97.46 5 A 1 ATOM 34 C CG . LEU A 1 5 ? -6.582 6.006 2.053 1.00 94.90 5 A 1 ATOM 35 C CD1 . LEU A 1 5 ? -7.267 7.176 2.740 1.00 91.47 5 A 1 ATOM 36 C CD2 . LEU A 1 5 ? -6.380 6.318 0.574 1.00 91.24 5 A 1 ATOM 37 N N . PHE A 1 6 ? -3.154 3.890 4.195 1.00 97.80 6 A 1 ATOM 38 C CA . PHE A 1 6 ? -1.858 3.729 4.851 1.00 97.73 6 A 1 ATOM 39 C C . PHE A 1 6 ? -1.106 2.534 4.284 1.00 97.97 6 A 1 ATOM 40 O O . PHE A 1 6 ? 0.097 2.613 4.019 1.00 97.47 6 A 1 ATOM 41 C CB . PHE A 1 6 ? -2.058 3.553 6.353 1.00 97.31 6 A 1 ATOM 42 C CG . PHE A 1 6 ? -2.738 4.736 6.990 1.00 95.11 6 A 1 ATOM 43 C CD1 . PHE A 1 6 ? -4.114 4.777 7.105 1.00 92.19 6 A 1 ATOM 44 C CD2 . PHE A 1 6 ? -1.985 5.797 7.469 1.00 92.61 6 A 1 ATOM 45 C CE1 . PHE A 1 6 ? -4.740 5.869 7.689 1.00 91.60 6 A 1 ATOM 46 C CE2 . PHE A 1 6 ? -2.607 6.890 8.056 1.00 91.42 6 A 1 ATOM 47 C CZ . PHE A 1 6 ? -3.984 6.924 8.165 1.00 91.56 6 A 1 ATOM 48 N N . LEU A 1 7 ? -1.821 1.436 4.090 1.00 97.86 7 A 1 ATOM 49 C CA . LEU A 1 7 ? -1.216 0.229 3.534 1.00 97.78 7 A 1 ATOM 50 C C . LEU A 1 7 ? -0.765 0.463 2.096 1.00 98.12 7 A 1 ATOM 51 O O . LEU A 1 7 ? 0.301 0.004 1.686 1.00 98.06 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -2.212 -0.929 3.589 1.00 97.42 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -2.040 -1.818 4.816 1.00 93.05 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -2.919 -1.345 5.961 1.00 91.06 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -2.352 -3.263 4.471 1.00 91.79 7 A 1 ATOM 56 N N . ALA A 1 8 ? -1.586 1.181 1.335 1.00 98.01 8 A 1 ATOM 57 C CA . ALA A 1 8 ? -1.263 1.483 -0.058 1.00 98.16 8 A 1 ATOM 58 C C . ALA A 1 8 ? 0.017 2.311 -0.142 1.00 98.41 8 A 1 ATOM 59 O O . ALA A 1 8 ? 0.872 2.068 -0.997 1.00 98.25 8 A 1 ATOM 60 C CB . ALA A 1 8 ? -2.422 2.231 -0.706 1.00 97.95 8 A 1 ATOM 61 N N . ALA A 1 9 ? 0.153 3.274 0.748 1.00 98.10 9 A 1 ATOM 62 C CA . ALA A 1 9 ? 1.337 4.126 0.782 1.00 98.08 9 A 1 ATOM 63 C C . ALA A 1 9 ? 2.575 3.315 1.141 1.00 98.33 9 A 1 ATOM 64 O O . ALA A 1 9 ? 3.653 3.533 0.586 1.00 98.03 9 A 1 ATOM 65 C CB . ALA A 1 9 ? 1.133 5.249 1.791 1.00 97.65 9 A 1 ATOM 66 N N . ALA A 1 10 ? 2.419 2.373 2.062 1.00 98.45 10 A 1 ATOM 67 C CA . ALA A 1 10 ? 3.527 1.518 2.482 1.00 98.40 10 A 1 ATOM 68 C C . ALA A 1 10 ? 4.012 0.649 1.331 1.00 98.58 10 A 1 ATOM 69 O O . ALA A 1 10 ? 5.213 0.427 1.179 1.00 98.20 10 A 1 ATOM 70 C CB . ALA A 1 10 ? 3.088 0.643 3.646 1.00 98.05 10 A 1 ATOM 71 N N . LEU A 1 11 ? 3.077 0.161 0.527 1.00 98.49 11 A 1 ATOM 72 C CA . LEU A 1 11 ? 3.413 -0.679 -0.623 1.00 98.41 11 A 1 ATOM 73 C C . LEU A 1 11 ? 4.223 0.111 -1.643 1.00 98.50 11 A 1 ATOM 74 O O . LEU A 1 11 ? 5.221 -0.382 -2.174 1.00 98.22 11 A 1 ATOM 75 C CB . LEU A 1 11 ? 2.131 -1.223 -1.257 1.00 98.25 11 A 1 ATOM 76 C CG . LEU A 1 11 ? 2.365 -2.358 -2.253 1.00 96.94 11 A 1 ATOM 77 C CD1 . LEU A 1 11 ? 1.303 -3.437 -2.087 1.00 94.72 11 A 1 ATOM 78 C CD2 . LEU A 1 11 ? 2.356 -1.846 -3.677 1.00 94.50 11 A 1 ATOM 79 N N . LEU A 1 12 ? 3.792 1.330 -1.909 1.00 98.33 12 A 1 ATOM 80 C CA . LEU A 1 12 ? 4.485 2.190 -2.864 1.00 98.22 12 A 1 ATOM 81 C C . LEU A 1 12 ? 5.866 2.565 -2.345 1.00 98.23 12 A 1 ATOM 82 O O . LEU A 1 12 ? 6.845 2.582 -3.096 1.00 97.84 12 A 1 ATOM 83 C CB . LEU A 1 12 ? 3.648 3.447 -3.120 1.00 97.97 12 A 1 ATOM 84 C CG . LEU A 1 12 ? 3.467 3.783 -4.596 1.00 96.24 12 A 1 ATOM 85 C CD1 . LEU A 1 12 ? 2.246 4.663 -4.795 1.00 93.23 12 A 1 ATOM 86 C CD2 . LEU A 1 12 ? 4.707 4.466 -5.149 1.00 92.60 12 A 1 ATOM 87 N N . GLN A 1 13 ? 5.946 2.858 -1.070 1.00 98.43 13 A 1 ATOM 88 C CA . GLN A 1 13 ? 7.215 3.215 -0.440 1.00 98.22 13 A 1 ATOM 89 C C . GLN A 1 13 ? 8.146 2.016 -0.359 1.00 98.31 13 A 1 ATOM 90 O O . GLN A 1 13 ? 9.355 2.148 -0.556 1.00 97.37 13 A 1 ATOM 91 C CB . GLN A 1 13 ? 6.945 3.770 0.954 1.00 97.46 13 A 1 ATOM 92 C CG . GLN A 1 13 ? 6.542 5.232 0.924 1.00 93.13 13 A 1 ATOM 93 C CD . GLN A 1 13 ? 7.751 6.145 0.829 1.00 90.39 13 A 1 ATOM 94 O OE1 . GLN A 1 13 ? 8.601 5.994 -0.037 1.00 84.98 13 A 1 ATOM 95 N NE2 . GLN A 1 13 ? 7.848 7.100 1.731 1.00 83.15 13 A 1 ATOM 96 N N . GLY A 1 14 ? 7.586 0.855 -0.079 1.00 98.03 14 A 1 ATOM 97 C CA . GLY A 1 14 ? 8.374 -0.370 0.006 1.00 97.93 14 A 1 ATOM 98 C C . GLY A 1 14 ? 9.026 -0.714 -1.311 1.00 98.26 14 A 1 ATOM 99 O O . GLY A 1 14 ? 10.197 -1.093 -1.357 1.00 97.80 14 A 1 ATOM 100 N N . ALA A 1 15 ? 8.274 -0.576 -2.399 1.00 98.25 15 A 1 ATOM 101 C CA . ALA A 1 15 ? 8.791 -0.860 -3.737 1.00 98.27 15 A 1 ATOM 102 C C . ALA A 1 15 ? 9.844 0.166 -4.143 1.00 98.38 15 A 1 ATOM 103 O O . ALA A 1 15 ? 10.806 -0.159 -4.838 1.00 97.70 15 A 1 ATOM 104 C CB . ALA A 1 15 ? 7.646 -0.867 -4.744 1.00 97.85 15 A 1 ATOM 105 N N . LEU A 1 16 ? 9.643 1.400 -3.725 1.00 98.15 16 A 1 ATOM 106 C CA . LEU A 1 16 ? 10.579 2.478 -4.035 1.00 97.79 16 A 1 ATOM 107 C C . LEU A 1 16 ? 11.825 2.401 -3.160 1.00 97.60 16 A 1 ATOM 108 O O . LEU A 1 16 ? 12.896 2.875 -3.548 1.00 96.50 16 A 1 ATOM 109 C CB . LEU A 1 16 ? 9.891 3.833 -3.842 1.00 97.21 16 A 1 ATOM 110 C CG . LEU A 1 16 ? 9.928 4.723 -5.077 1.00 95.48 16 A 1 ATOM 111 C CD1 . LEU A 1 16 ? 8.525 5.069 -5.540 1.00 92.46 16 A 1 ATOM 112 C CD2 . LEU A 1 16 ? 10.725 5.987 -4.794 1.00 90.80 16 A 1 ATOM 113 N N . SER A 1 17 ? 11.681 1.796 -1.999 1.00 95.59 17 A 1 ATOM 114 C CA . SER A 1 17 ? 12.782 1.680 -1.044 1.00 93.58 17 A 1 ATOM 115 C C . SER A 1 17 ? 13.764 0.589 -1.470 1.00 90.98 17 A 1 ATOM 116 O O . SER A 1 17 ? 14.980 0.847 -1.502 1.00 84.51 17 A 1 ATOM 117 C CB . SER A 1 17 ? 12.237 1.391 0.355 1.00 89.40 17 A 1 ATOM 118 O OG . SER A 1 17 ? 12.871 2.202 1.317 1.00 83.22 17 A 1 ATOM 119 O OXT . SER A 1 17 ? 13.291 -0.519 -1.749 1.00 84.25 17 A 1 #