# 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_spkb34478 # _entry.id spkb34478 # 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" "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C5 H11 N O2" 117.146 VAL y VALINE CC(C)[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 ILE 3 1 n VAL 4 1 n ALA 5 1 n PHE 6 1 n THR 7 1 n LEU 8 1 n VAL 9 1 n ALA 10 1 n PHE 11 1 n VAL 12 1 n ALA 13 1 n LEU 14 1 n ALA 15 1 n GLY 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 @ 2025-07-12 00:28:43)" _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 95.25 _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 87.71 1 1 A LYS 2 2 90.92 1 2 A ILE 3 2 96.12 1 3 A VAL 4 2 97.36 1 4 A ALA 5 2 98.10 1 5 A PHE 6 2 95.56 1 6 A THR 7 2 97.15 1 7 A LEU 8 2 96.19 1 8 A VAL 9 2 97.70 1 9 A ALA 10 2 98.25 1 10 A PHE 11 2 95.72 1 11 A VAL 12 2 97.63 1 12 A ALA 13 2 98.23 1 13 A LEU 14 2 94.87 1 14 A ALA 15 2 96.94 1 15 A GLY 16 2 94.54 1 16 A ALA 17 2 89.87 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 LYS . 2 A 2 A 3 1 n ILE . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n THR . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n GLY . 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 ? 0.462 1.876 13.149 1.00 93.12 1 A 1 ATOM 2 C CA . MET A 1 1 ? -0.626 1.787 12.156 1.00 93.82 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.198 0.922 10.965 1.00 94.36 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.281 1.428 9.955 1.00 90.65 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.001 3.174 11.655 1.00 89.52 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.814 3.948 12.685 1.00 86.08 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.812 4.598 14.004 1.00 82.47 1 A 1 ATOM 8 C CE . MET A 1 1 ? -2.041 5.494 14.943 1.00 71.65 1 A 1 ATOM 9 N N . LYS A 1 2 ? -0.374 -0.374 11.114 1.00 96.15 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 0.007 -1.300 10.051 1.00 96.70 2 A 1 ATOM 11 C C . LYS A 1 2 ? -1.078 -1.369 8.980 1.00 97.28 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.803 -1.699 7.830 1.00 96.91 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 0.273 -2.682 10.649 1.00 95.31 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 1.480 -2.676 11.574 1.00 90.45 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 1.712 -4.010 12.227 1.00 87.41 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 2.922 -3.944 13.143 1.00 81.58 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 3.126 -5.231 13.857 1.00 76.53 2 A 1 ATOM 18 N N . ILE A 1 3 ? -2.290 -1.052 9.365 1.00 97.42 3 A 1 ATOM 19 C CA . ILE A 1 3 ? -3.409 -1.040 8.423 1.00 97.84 3 A 1 ATOM 20 C C . ILE A 1 3 ? -3.191 0.039 7.370 1.00 98.23 3 A 1 ATOM 21 O O . ILE A 1 3 ? -3.483 -0.153 6.185 1.00 97.96 3 A 1 ATOM 22 C CB . ILE A 1 3 ? -4.736 -0.802 9.157 1.00 97.50 3 A 1 ATOM 23 C CG1 . ILE A 1 3 ? -4.970 -1.882 10.216 1.00 95.31 3 A 1 ATOM 24 C CG2 . ILE A 1 3 ? -5.891 -0.798 8.155 1.00 94.49 3 A 1 ATOM 25 C CD1 . ILE A 1 3 ? -6.121 -1.547 11.143 1.00 90.20 3 A 1 ATOM 26 N N . VAL A 1 4 ? -2.675 1.167 7.815 1.00 98.05 4 A 1 ATOM 27 C CA . VAL A 1 4 ? -2.399 2.287 6.917 1.00 98.12 4 A 1 ATOM 28 C C . VAL A 1 4 ? -1.342 1.895 5.894 1.00 98.32 4 A 1 ATOM 29 O O . VAL A 1 4 ? -1.456 2.212 4.708 1.00 98.16 4 A 1 ATOM 30 C CB . VAL A 1 4 ? -1.929 3.522 7.704 1.00 97.75 4 A 1 ATOM 31 C CG1 . VAL A 1 4 ? -1.656 4.689 6.767 1.00 95.61 4 A 1 ATOM 32 C CG2 . VAL A 1 4 ? -2.965 3.912 8.748 1.00 95.54 4 A 1 ATOM 33 N N . ALA A 1 5 ? -0.315 1.209 6.369 1.00 97.94 5 A 1 ATOM 34 C CA . ALA A 1 5 ? 0.769 0.769 5.497 1.00 98.17 5 A 1 ATOM 35 C C . ALA A 1 5 ? 0.264 -0.222 4.453 1.00 98.36 5 A 1 ATOM 36 O O . ALA A 1 5 ? 0.616 -0.134 3.277 1.00 98.15 5 A 1 ATOM 37 C CB . ALA A 1 5 ? 1.880 0.142 6.328 1.00 97.88 5 A 1 ATOM 38 N N . PHE A 1 6 ? -0.561 -1.158 4.900 1.00 97.91 6 A 1 ATOM 39 C CA . PHE A 1 6 ? -1.115 -2.167 4.004 1.00 97.98 6 A 1 ATOM 40 C C . PHE A 1 6 ? -2.036 -1.528 2.974 1.00 98.27 6 A 1 ATOM 41 O O . PHE A 1 6 ? -1.999 -1.871 1.792 1.00 97.98 6 A 1 ATOM 42 C CB . PHE A 1 6 ? -1.875 -3.209 4.817 1.00 97.69 6 A 1 ATOM 43 C CG . PHE A 1 6 ? -1.660 -4.607 4.302 1.00 95.70 6 A 1 ATOM 44 C CD1 . PHE A 1 6 ? -0.478 -5.278 4.566 1.00 93.52 6 A 1 ATOM 45 C CD2 . PHE A 1 6 ? -2.642 -5.239 3.558 1.00 93.82 6 A 1 ATOM 46 C CE1 . PHE A 1 6 ? -0.272 -6.564 4.095 1.00 92.86 6 A 1 ATOM 47 C CE2 . PHE A 1 6 ? -2.444 -6.527 3.079 1.00 92.94 6 A 1 ATOM 48 C CZ . PHE A 1 6 ? -1.259 -7.193 3.348 1.00 92.50 6 A 1 ATOM 49 N N . THR A 1 7 ? -2.837 -0.590 3.433 1.00 98.08 7 A 1 ATOM 50 C CA . THR A 1 7 ? -3.762 0.119 2.549 1.00 98.19 7 A 1 ATOM 51 C C . THR A 1 7 ? -2.994 0.937 1.517 1.00 98.45 7 A 1 ATOM 52 O O . THR A 1 7 ? -3.367 0.984 0.342 1.00 98.30 7 A 1 ATOM 53 C CB . THR A 1 7 ? -4.672 1.050 3.358 1.00 97.99 7 A 1 ATOM 54 O OG1 . THR A 1 7 ? -5.339 0.304 4.364 1.00 95.22 7 A 1 ATOM 55 C CG2 . THR A 1 7 ? -5.717 1.700 2.461 1.00 93.83 7 A 1 ATOM 56 N N . LEU A 1 8 ? -1.925 1.565 1.965 1.00 98.25 8 A 1 ATOM 57 C CA . LEU A 1 8 ? -1.097 2.377 1.080 1.00 98.26 8 A 1 ATOM 58 C C . LEU A 1 8 ? -0.448 1.507 0.012 1.00 98.48 8 A 1 ATOM 59 O O . LEU A 1 8 ? -0.457 1.844 -1.172 1.00 98.45 8 A 1 ATOM 60 C CB . LEU A 1 8 ? -0.014 3.101 1.883 1.00 98.07 8 A 1 ATOM 61 C CG . LEU A 1 8 ? 0.447 4.399 1.230 1.00 93.58 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? -0.228 5.591 1.886 1.00 91.61 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? 1.960 4.544 1.314 1.00 92.84 8 A 1 ATOM 64 N N . VAL A 1 9 ? 0.119 0.390 0.444 1.00 98.18 9 A 1 ATOM 65 C CA . VAL A 1 9 ? 0.773 -0.537 -0.479 1.00 98.23 9 A 1 ATOM 66 C C . VAL A 1 9 ? -0.233 -1.084 -1.486 1.00 98.43 9 A 1 ATOM 67 O O . VAL A 1 9 ? 0.072 -1.216 -2.674 1.00 98.31 9 A 1 ATOM 68 C CB . VAL A 1 9 ? 1.436 -1.691 0.292 1.00 97.86 9 A 1 ATOM 69 C CG1 . VAL A 1 9 ? 1.979 -2.739 -0.665 1.00 96.54 9 A 1 ATOM 70 C CG2 . VAL A 1 9 ? 2.559 -1.159 1.169 1.00 96.35 9 A 1 ATOM 71 N N . ALA A 1 10 ? -1.418 -1.400 -1.000 1.00 98.30 10 A 1 ATOM 72 C CA . ALA A 1 10 ? -2.471 -1.925 -1.863 1.00 98.31 10 A 1 ATOM 73 C C . ALA A 1 10 ? -2.865 -0.895 -2.918 1.00 98.45 10 A 1 ATOM 74 O O . ALA A 1 10 ? -3.088 -1.236 -4.079 1.00 98.17 10 A 1 ATOM 75 C CB . ALA A 1 10 ? -3.685 -2.307 -1.026 1.00 98.04 10 A 1 ATOM 76 N N . PHE A 1 11 ? -2.939 0.359 -2.502 1.00 98.00 11 A 1 ATOM 77 C CA . PHE A 1 11 ? -3.284 1.443 -3.414 1.00 97.92 11 A 1 ATOM 78 C C . PHE A 1 11 ? -2.220 1.604 -4.490 1.00 98.26 11 A 1 ATOM 79 O O . PHE A 1 11 ? -2.535 1.764 -5.670 1.00 97.96 11 A 1 ATOM 80 C CB . PHE A 1 11 ? -3.437 2.746 -2.632 1.00 97.49 11 A 1 ATOM 81 C CG . PHE A 1 11 ? -3.760 3.920 -3.517 1.00 95.81 11 A 1 ATOM 82 C CD1 . PHE A 1 11 ? -4.987 3.999 -4.153 1.00 93.94 11 A 1 ATOM 83 C CD2 . PHE A 1 11 ? -2.834 4.935 -3.705 1.00 94.27 11 A 1 ATOM 84 C CE1 . PHE A 1 11 ? -5.288 5.078 -4.970 1.00 93.09 11 A 1 ATOM 85 C CE2 . PHE A 1 11 ? -3.129 6.016 -4.526 1.00 92.96 11 A 1 ATOM 86 C CZ . PHE A 1 11 ? -4.358 6.087 -5.160 1.00 93.18 11 A 1 ATOM 87 N N . VAL A 1 12 ? -0.962 1.553 -4.069 1.00 98.34 12 A 1 ATOM 88 C CA . VAL A 1 12 ? 0.156 1.680 -5.004 1.00 98.24 12 A 1 ATOM 89 C C . VAL A 1 12 ? 0.157 0.517 -5.988 1.00 98.42 12 A 1 ATOM 90 O O . VAL A 1 12 ? 0.410 0.701 -7.181 1.00 98.19 12 A 1 ATOM 91 C CB . VAL A 1 12 ? 1.497 1.734 -4.253 1.00 97.82 12 A 1 ATOM 92 C CG1 . VAL A 1 12 ? 2.668 1.753 -5.229 1.00 96.04 12 A 1 ATOM 93 C CG2 . VAL A 1 12 ? 1.551 2.963 -3.360 1.00 96.34 12 A 1 ATOM 94 N N . ALA A 1 13 ? -0.121 -0.669 -5.480 1.00 98.42 13 A 1 ATOM 95 C CA . ALA A 1 13 ? -0.157 -1.864 -6.317 1.00 98.35 13 A 1 ATOM 96 C C . ALA A 1 13 ? -1.263 -1.760 -7.365 1.00 98.46 13 A 1 ATOM 97 O O . ALA A 1 13 ? -1.072 -2.132 -8.523 1.00 97.94 13 A 1 ATOM 98 C CB . ALA A 1 13 ? -0.366 -3.099 -5.451 1.00 97.97 13 A 1 ATOM 99 N N . LEU A 1 14 ? -2.406 -1.251 -6.950 1.00 98.09 14 A 1 ATOM 100 C CA . LEU A 1 14 ? -3.536 -1.082 -7.860 1.00 97.70 14 A 1 ATOM 101 C C . LEU A 1 14 ? -3.241 -0.017 -8.901 1.00 97.89 14 A 1 ATOM 102 O O . LEU A 1 14 ? -3.598 -0.161 -10.074 1.00 97.19 14 A 1 ATOM 103 C CB . LEU A 1 14 ? -4.778 -0.697 -7.060 1.00 97.13 14 A 1 ATOM 104 C CG . LEU A 1 14 ? -5.449 -1.879 -6.367 1.00 91.97 14 A 1 ATOM 105 C CD1 . LEU A 1 14 ? -6.363 -1.403 -5.256 1.00 89.35 14 A 1 ATOM 106 C CD2 . LEU A 1 14 ? -6.225 -2.703 -7.385 1.00 89.62 14 A 1 ATOM 107 N N . ALA A 1 15 ? -2.595 1.049 -8.467 1.00 97.74 15 A 1 ATOM 108 C CA . ALA A 1 15 ? -2.239 2.143 -9.367 1.00 97.36 15 A 1 ATOM 109 C C . ALA A 1 15 ? -1.155 1.715 -10.346 1.00 97.45 15 A 1 ATOM 110 O O . ALA A 1 15 ? -1.073 2.232 -11.460 1.00 95.78 15 A 1 ATOM 111 C CB . ALA A 1 15 ? -1.771 3.349 -8.559 1.00 96.35 15 A 1 ATOM 112 N N . GLY A 1 16 ? -0.321 0.776 -9.927 1.00 95.92 16 A 1 ATOM 113 C CA . GLY A 1 16 ? 0.759 0.274 -10.772 1.00 94.51 16 A 1 ATOM 114 C C . GLY A 1 16 ? 0.353 -0.925 -11.605 1.00 94.84 16 A 1 ATOM 115 O O . GLY A 1 16 ? 1.202 -1.699 -12.040 1.00 92.91 16 A 1 ATOM 116 N N . ALA A 1 17 ? -0.927 -1.082 -11.822 1.00 95.60 17 A 1 ATOM 117 C CA . ALA A 1 17 ? -1.440 -2.202 -12.595 1.00 93.85 17 A 1 ATOM 118 C C . ALA A 1 17 ? -1.657 -1.802 -14.059 1.00 92.58 17 A 1 ATOM 119 O O . ALA A 1 17 ? -1.544 -0.611 -14.388 1.00 86.40 17 A 1 ATOM 120 C CB . ALA A 1 17 ? -2.736 -2.713 -11.971 1.00 90.00 17 A 1 ATOM 121 O OXT . ALA A 1 17 ? -1.934 -2.683 -14.882 1.00 80.78 17 A 1 #