# 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_spkb42894 # _entry.id spkb42894 # 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" # _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 ALA 3 1 n LEU 4 1 n ILE 5 1 n GLY 6 1 n ILE 7 1 n GLY 8 1 n LEU 9 1 n CYS 10 1 n ALA 11 1 n ALA 12 1 n LEU 13 1 n LEU 14 1 n GLY 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 @ 2025-07-05 09:53:19)" _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 92.80 _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 86.10 1 1 A LYS 2 2 88.57 1 2 A ALA 3 2 96.01 1 3 A LEU 4 2 94.11 1 4 A ILE 5 2 94.03 1 5 A GLY 6 2 96.11 1 6 A ILE 7 2 94.24 1 7 A GLY 8 2 96.31 1 8 A LEU 9 2 94.75 1 9 A CYS 10 2 95.34 1 10 A ALA 11 2 96.91 1 11 A ALA 12 2 96.87 1 12 A LEU 13 2 94.65 1 13 A LEU 14 2 92.72 1 14 A GLY 15 2 90.69 1 15 A GLY 16 2 80.54 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 ALA . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n GLY . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n GLY . 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 ? -7.013 -1.321 -6.655 1.00 90.91 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.726 -2.485 -5.796 1.00 91.41 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.277 -2.444 -5.326 1.00 92.49 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.998 -2.436 -4.131 1.00 89.81 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.984 -3.782 -6.568 1.00 88.09 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.441 -3.909 -6.980 1.00 85.91 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.752 -5.375 -7.956 1.00 80.55 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.491 -5.179 -8.254 1.00 69.65 1 A 1 ATOM 9 N N . LYS A 1 2 ? -4.377 -2.399 -6.290 1.00 94.10 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -2.954 -2.325 -5.959 1.00 94.80 2 A 1 ATOM 11 C C . LYS A 1 2 ? -2.650 -1.029 -5.225 1.00 95.42 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.768 -0.971 -4.371 1.00 94.43 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -2.130 -2.410 -7.234 1.00 92.64 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -0.634 -2.482 -6.968 1.00 87.58 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -0.253 -3.778 -6.279 1.00 84.59 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 1.253 -3.901 -6.136 1.00 79.73 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.632 -5.202 -5.527 1.00 73.85 2 A 1 ATOM 18 N N . ALA A 1 3 ? -3.399 0.008 -5.554 1.00 95.48 3 A 1 ATOM 19 C CA . ALA A 1 3 ? -3.222 1.316 -4.930 1.00 96.31 3 A 1 ATOM 20 C C . ALA A 1 3 ? -3.466 1.240 -3.430 1.00 97.10 3 A 1 ATOM 21 O O . ALA A 1 3 ? -2.806 1.929 -2.651 1.00 95.80 3 A 1 ATOM 22 C CB . ALA A 1 3 ? -4.167 2.326 -5.565 1.00 95.34 3 A 1 ATOM 23 N N . LEU A 1 4 ? -4.409 0.391 -3.022 1.00 96.19 4 A 1 ATOM 24 C CA . LEU A 1 4 ? -4.729 0.226 -1.608 1.00 96.71 4 A 1 ATOM 25 C C . LEU A 1 4 ? -3.496 -0.222 -0.835 1.00 97.04 4 A 1 ATOM 26 O O . LEU A 1 4 ? -3.233 0.244 0.272 1.00 96.21 4 A 1 ATOM 27 C CB . LEU A 1 4 ? -5.849 -0.805 -1.447 1.00 96.37 4 A 1 ATOM 28 C CG . LEU A 1 4 ? -7.162 -0.381 -2.097 1.00 93.11 4 A 1 ATOM 29 C CD1 . LEU A 1 4 ? -8.187 -1.497 -1.984 1.00 89.27 4 A 1 ATOM 30 C CD2 . LEU A 1 4 ? -7.687 0.891 -1.455 1.00 87.99 4 A 1 ATOM 31 N N . ILE A 1 5 ? -2.738 -1.122 -1.437 1.00 96.48 5 A 1 ATOM 32 C CA . ILE A 1 5 ? -1.508 -1.608 -0.823 1.00 96.30 5 A 1 ATOM 33 C C . ILE A 1 5 ? -0.501 -0.470 -0.729 1.00 96.47 5 A 1 ATOM 34 O O . ILE A 1 5 ? 0.215 -0.330 0.265 1.00 96.03 5 A 1 ATOM 35 C CB . ILE A 1 5 ? -0.920 -2.766 -1.637 1.00 96.03 5 A 1 ATOM 36 C CG1 . ILE A 1 5 ? -1.919 -3.926 -1.700 1.00 93.04 5 A 1 ATOM 37 C CG2 . ILE A 1 5 ? 0.396 -3.225 -1.022 1.00 92.15 5 A 1 ATOM 38 C CD1 . ILE A 1 5 ? -1.475 -5.051 -2.617 1.00 85.73 5 A 1 ATOM 39 N N . GLY A 1 6 ? -0.466 0.338 -1.769 1.00 95.82 6 A 1 ATOM 40 C CA . GLY A 1 6 ? 0.441 1.478 -1.791 1.00 95.92 6 A 1 ATOM 41 C C . GLY A 1 6 ? 0.156 2.454 -0.666 1.00 96.55 6 A 1 ATOM 42 O O . GLY A 1 6 ? 1.073 3.023 -0.074 1.00 96.13 6 A 1 ATOM 43 N N . ILE A 1 7 ? -1.120 2.646 -0.372 1.00 96.32 7 A 1 ATOM 44 C CA . ILE A 1 7 ? -1.525 3.556 0.699 1.00 96.22 7 A 1 ATOM 45 C C . ILE A 1 7 ? -0.959 3.084 2.032 1.00 96.57 7 A 1 ATOM 46 O O . ILE A 1 7 ? -0.400 3.872 2.799 1.00 96.04 7 A 1 ATOM 47 C CB . ILE A 1 7 ? -3.056 3.643 0.787 1.00 95.95 7 A 1 ATOM 48 C CG1 . ILE A 1 7 ? -3.620 4.235 -0.507 1.00 93.47 7 A 1 ATOM 49 C CG2 . ILE A 1 7 ? -3.460 4.502 1.983 1.00 92.47 7 A 1 ATOM 50 C CD1 . ILE A 1 7 ? -5.134 4.153 -0.582 1.00 86.88 7 A 1 ATOM 51 N N . GLY A 1 8 ? -1.113 1.798 2.300 1.00 96.00 8 A 1 ATOM 52 C CA . GLY A 1 8 ? -0.599 1.240 3.545 1.00 96.16 8 A 1 ATOM 53 C C . GLY A 1 8 ? 0.912 1.343 3.621 1.00 96.72 8 A 1 ATOM 54 O O . GLY A 1 8 ? 1.473 1.692 4.661 1.00 96.34 8 A 1 ATOM 55 N N . LEU A 1 9 ? 1.565 1.046 2.506 1.00 96.69 9 A 1 ATOM 56 C CA . LEU A 1 9 ? 3.021 1.110 2.449 1.00 96.74 9 A 1 ATOM 57 C C . LEU A 1 9 ? 3.498 2.540 2.648 1.00 97.32 9 A 1 ATOM 58 O O . LEU A 1 9 ? 4.459 2.790 3.378 1.00 97.00 9 A 1 ATOM 59 C CB . LEU A 1 9 ? 3.510 0.583 1.103 1.00 96.33 9 A 1 ATOM 60 C CG . LEU A 1 9 ? 5.032 0.565 0.982 1.00 92.77 9 A 1 ATOM 61 C CD1 . LEU A 1 9 ? 5.638 -0.369 2.012 1.00 90.53 9 A 1 ATOM 62 C CD2 . LEU A 1 9 ? 5.443 0.142 -0.421 1.00 90.66 9 A 1 ATOM 63 N N . CYS A 1 10 ? 2.814 3.474 2.001 1.00 96.48 10 A 1 ATOM 64 C CA . CYS A 1 10 ? 3.163 4.884 2.130 1.00 96.46 10 A 1 ATOM 65 C C . CYS A 1 10 ? 3.030 5.324 3.580 1.00 96.94 10 A 1 ATOM 66 O O . CYS A 1 10 ? 3.867 6.061 4.103 1.00 96.08 10 A 1 ATOM 67 C CB . CYS A 1 10 ? 2.250 5.733 1.249 1.00 95.19 10 A 1 ATOM 68 S SG . CYS A 1 10 ? 2.692 7.474 1.314 1.00 90.92 10 A 1 ATOM 69 N N . ALA A 1 11 ? 1.973 4.868 4.227 1.00 96.96 11 A 1 ATOM 70 C CA . ALA A 1 11 ? 1.740 5.193 5.628 1.00 97.00 11 A 1 ATOM 71 C C . ALA A 1 11 ? 2.834 4.601 6.502 1.00 97.53 11 A 1 ATOM 72 O O . ALA A 1 11 ? 3.240 5.207 7.493 1.00 96.84 11 A 1 ATOM 73 C CB . ALA A 1 11 ? 0.382 4.665 6.065 1.00 96.23 11 A 1 ATOM 74 N N . ALA A 1 12 ? 3.311 3.427 6.135 1.00 96.91 12 A 1 ATOM 75 C CA . ALA A 1 12 ? 4.372 2.765 6.887 1.00 97.00 12 A 1 ATOM 76 C C . ALA A 1 12 ? 5.637 3.611 6.879 1.00 97.48 12 A 1 ATOM 77 O O . ALA A 1 12 ? 6.317 3.738 7.896 1.00 96.48 12 A 1 ATOM 78 C CB . ALA A 1 12 ? 4.657 1.391 6.298 1.00 96.49 12 A 1 ATOM 79 N N . LEU A 1 13 ? 5.938 4.200 5.726 1.00 96.93 13 A 1 ATOM 80 C CA . LEU A 1 13 ? 7.114 5.055 5.597 1.00 96.55 13 A 1 ATOM 81 C C . LEU A 1 13 ? 6.967 6.275 6.486 1.00 96.85 13 A 1 ATOM 82 O O . LEU A 1 13 ? 7.935 6.735 7.102 1.00 95.69 13 A 1 ATOM 83 C CB . LEU A 1 13 ? 7.277 5.490 4.142 1.00 96.15 13 A 1 ATOM 84 C CG . LEU A 1 13 ? 7.533 4.326 3.187 1.00 94.06 13 A 1 ATOM 85 C CD1 . LEU A 1 13 ? 7.564 4.831 1.749 1.00 91.09 13 A 1 ATOM 86 C CD2 . LEU A 1 13 ? 8.836 3.625 3.530 1.00 89.85 13 A 1 ATOM 87 N N . LEU A 1 14 ? 5.747 6.791 6.548 1.00 96.15 14 A 1 ATOM 88 C CA . LEU A 1 14 ? 5.443 7.935 7.395 1.00 95.78 14 A 1 ATOM 89 C C . LEU A 1 14 ? 5.234 7.492 8.833 1.00 96.09 14 A 1 ATOM 90 O O . LEU A 1 14 ? 5.286 8.309 9.754 1.00 94.26 14 A 1 ATOM 91 C CB . LEU A 1 14 ? 4.180 8.633 6.882 1.00 94.61 14 A 1 ATOM 92 C CG . LEU A 1 14 ? 3.822 9.897 7.652 1.00 91.83 14 A 1 ATOM 93 C CD1 . LEU A 1 14 ? 4.858 10.980 7.406 1.00 87.50 14 A 1 ATOM 94 C CD2 . LEU A 1 14 ? 2.442 10.388 7.250 1.00 85.56 14 A 1 ATOM 95 N N . GLY A 1 15 ? 5.003 6.200 9.028 1.00 93.29 15 A 1 ATOM 96 C CA . GLY A 1 15 ? 4.738 5.615 10.342 1.00 91.22 15 A 1 ATOM 97 C C . GLY A 1 15 ? 5.437 6.334 11.472 1.00 91.12 15 A 1 ATOM 98 O O . GLY A 1 15 ? 4.791 6.896 12.350 1.00 87.13 15 A 1 ATOM 99 N N . GLY A 1 16 ? 6.770 6.346 11.451 1.00 88.72 16 A 1 ATOM 100 C CA . GLY A 1 16 ? 7.491 7.055 12.497 1.00 84.03 16 A 1 ATOM 101 C C . GLY A 1 16 ? 7.089 6.603 13.897 1.00 80.37 16 A 1 ATOM 102 O O . GLY A 1 16 ? 7.268 7.371 14.850 1.00 72.31 16 A 1 ATOM 103 O OXT . GLY A 1 16 ? 6.607 5.492 14.085 1.00 77.27 16 A 1 #