# 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_spkb32122 # _entry.id spkb32122 # 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" "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 LYS 3 1 n VAL 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n ILE 8 1 n THR 9 1 n ALA 10 1 n ILE 11 1 n LEU 12 1 n ALA 13 1 n VAL 14 1 n ALA 15 1 n VAL 16 1 n GLY 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 11:23:53)" _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 97.05 _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 94.26 1 1 A LYS 2 2 94.61 1 2 A LYS 3 2 95.96 1 3 A VAL 4 2 98.52 1 4 A LEU 5 2 96.94 1 5 A LEU 6 2 97.83 1 6 A LEU 7 2 97.07 1 7 A ILE 8 2 97.75 1 8 A THR 9 2 97.53 1 9 A ALA 10 2 98.82 1 10 A ILE 11 2 97.83 1 11 A LEU 12 2 97.54 1 12 A ALA 13 2 98.87 1 13 A VAL 14 2 98.49 1 14 A ALA 15 2 98.80 1 15 A VAL 16 2 97.30 1 16 A GLY 17 2 93.10 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 LYS . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n GLY . 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 ? -11.678 0.843 3.434 1.00 98.02 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.093 -0.381 4.011 1.00 98.36 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.581 -0.222 4.171 1.00 98.39 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.896 0.180 3.234 1.00 97.70 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.372 -1.586 3.108 1.00 97.42 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.856 -1.891 3.005 1.00 93.31 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.201 -3.278 1.905 1.00 90.09 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.974 -3.373 2.067 1.00 80.76 1 A 1 ATOM 9 N N . LYS A 1 2 ? -9.059 -0.548 5.353 1.00 98.43 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -7.625 -0.425 5.633 1.00 98.54 2 A 1 ATOM 11 C C . LYS A 1 2 ? -6.814 -1.500 4.913 1.00 98.65 2 A 1 ATOM 12 O O . LYS A 1 2 ? -5.694 -1.248 4.474 1.00 98.40 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -7.388 -0.518 7.139 1.00 98.13 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -8.011 0.643 7.901 1.00 95.34 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -7.762 0.516 9.392 1.00 93.60 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -8.395 1.671 10.153 1.00 87.59 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -8.184 1.540 11.616 1.00 82.80 2 A 1 ATOM 18 N N . LYS A 1 3 ? -7.383 -2.701 4.787 1.00 98.76 3 A 1 ATOM 19 C CA . LYS A 1 3 ? -6.697 -3.819 4.133 1.00 98.82 3 A 1 ATOM 20 C C . LYS A 1 3 ? -6.331 -3.478 2.691 1.00 98.87 3 A 1 ATOM 21 O O . LYS A 1 3 ? -5.207 -3.739 2.250 1.00 98.73 3 A 1 ATOM 22 C CB . LYS A 1 3 ? -7.575 -5.067 4.181 1.00 98.67 3 A 1 ATOM 23 C CG . LYS A 1 3 ? -6.866 -6.290 3.636 1.00 97.29 3 A 1 ATOM 24 C CD . LYS A 1 3 ? -7.777 -7.511 3.631 1.00 95.20 3 A 1 ATOM 25 C CE . LYS A 1 3 ? -8.121 -7.974 5.036 1.00 91.45 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? -8.944 -9.208 5.019 1.00 85.81 3 A 1 ATOM 27 N N . VAL A 1 4 ? -7.266 -2.890 1.959 1.00 98.87 4 A 1 ATOM 28 C CA . VAL A 1 4 ? -7.028 -2.523 0.562 1.00 98.89 4 A 1 ATOM 29 C C . VAL A 1 4 ? -5.915 -1.487 0.465 1.00 98.90 4 A 1 ATOM 30 O O . VAL A 1 4 ? -5.028 -1.581 -0.388 1.00 98.81 4 A 1 ATOM 31 C CB . VAL A 1 4 ? -8.310 -1.973 -0.084 1.00 98.81 4 A 1 ATOM 32 C CG1 . VAL A 1 4 ? -8.042 -1.524 -1.515 1.00 97.79 4 A 1 ATOM 33 C CG2 . VAL A 1 4 ? -9.402 -3.036 -0.069 1.00 97.55 4 A 1 ATOM 34 N N . LEU A 1 5 ? -5.952 -0.501 1.346 1.00 98.83 5 A 1 ATOM 35 C CA . LEU A 1 5 ? -4.948 0.555 1.357 1.00 98.83 5 A 1 ATOM 36 C C . LEU A 1 5 ? -3.563 -0.013 1.642 1.00 98.87 5 A 1 ATOM 37 O O . LEU A 1 5 ? -2.575 0.411 1.035 1.00 98.79 5 A 1 ATOM 38 C CB . LEU A 1 5 ? -5.313 1.601 2.407 1.00 98.72 5 A 1 ATOM 39 C CG . LEU A 1 5 ? -4.356 2.788 2.442 1.00 94.48 5 A 1 ATOM 40 C CD1 . LEU A 1 5 ? -4.382 3.543 1.119 1.00 93.35 5 A 1 ATOM 41 C CD2 . LEU A 1 5 ? -4.723 3.730 3.583 1.00 93.63 5 A 1 ATOM 42 N N . LEU A 1 6 ? -3.488 -0.972 2.555 1.00 98.90 6 A 1 ATOM 43 C CA . LEU A 1 6 ? -2.218 -1.597 2.919 1.00 98.89 6 A 1 ATOM 44 C C . LEU A 1 6 ? -1.613 -2.339 1.731 1.00 98.90 6 A 1 ATOM 45 O O . LEU A 1 6 ? -0.405 -2.268 1.499 1.00 98.86 6 A 1 ATOM 46 C CB . LEU A 1 6 ? -2.433 -2.568 4.083 1.00 98.81 6 A 1 ATOM 47 C CG . LEU A 1 6 ? -2.734 -1.880 5.414 1.00 96.68 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? -3.149 -2.906 6.459 1.00 95.69 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? -1.519 -1.105 5.909 1.00 95.94 6 A 1 ATOM 50 N N . LEU A 1 7 ? -2.453 -3.034 0.971 1.00 98.89 7 A 1 ATOM 51 C CA . LEU A 1 7 ? -1.990 -3.786 -0.192 1.00 98.88 7 A 1 ATOM 52 C C . LEU A 1 7 ? -1.422 -2.852 -1.256 1.00 98.92 7 A 1 ATOM 53 O O . LEU A 1 7 ? -0.348 -3.100 -1.809 1.00 98.88 7 A 1 ATOM 54 C CB . LEU A 1 7 ? -3.146 -4.602 -0.777 1.00 98.78 7 A 1 ATOM 55 C CG . LEU A 1 7 ? -3.624 -5.740 0.128 1.00 93.65 7 A 1 ATOM 56 C CD1 . LEU A 1 7 ? -4.897 -6.363 -0.435 1.00 93.86 7 A 1 ATOM 57 C CD2 . LEU A 1 7 ? -2.542 -6.805 0.271 1.00 94.68 7 A 1 ATOM 58 N N . ILE A 1 8 ? -2.141 -1.779 -1.532 1.00 98.86 8 A 1 ATOM 59 C CA . ILE A 1 8 ? -1.702 -0.806 -2.530 1.00 98.84 8 A 1 ATOM 60 C C . ILE A 1 8 ? -0.420 -0.124 -2.066 1.00 98.86 8 A 1 ATOM 61 O O . ILE A 1 8 ? 0.521 0.062 -2.845 1.00 98.83 8 A 1 ATOM 62 C CB . ILE A 1 8 ? -2.801 0.241 -2.784 1.00 98.78 8 A 1 ATOM 63 C CG1 . ILE A 1 8 ? -4.045 -0.438 -3.378 1.00 97.74 8 A 1 ATOM 64 C CG2 . ILE A 1 8 ? -2.292 1.330 -3.731 1.00 97.29 8 A 1 ATOM 65 C CD1 . ILE A 1 8 ? -5.257 0.475 -3.426 1.00 92.83 8 A 1 ATOM 66 N N . THR A 1 9 ? -0.376 0.249 -0.795 1.00 98.84 9 A 1 ATOM 67 C CA . THR A 1 9 ? 0.790 0.920 -0.229 1.00 98.81 9 A 1 ATOM 68 C C . THR A 1 9 ? 2.016 0.011 -0.282 1.00 98.85 9 A 1 ATOM 69 O O . THR A 1 9 ? 3.124 0.471 -0.571 1.00 98.73 9 A 1 ATOM 70 C CB . THR A 1 9 ? 0.524 1.330 1.224 1.00 98.57 9 A 1 ATOM 71 O OG1 . THR A 1 9 ? -0.616 2.183 1.281 1.00 94.87 9 A 1 ATOM 72 C CG2 . THR A 1 9 ? 1.714 2.086 1.798 1.00 94.03 9 A 1 ATOM 73 N N . ALA A 1 10 ? 1.823 -1.272 -0.017 1.00 98.87 10 A 1 ATOM 74 C CA . ALA A 1 10 ? 2.921 -2.236 -0.040 1.00 98.86 10 A 1 ATOM 75 C C . ALA A 1 10 ? 3.545 -2.317 -1.430 1.00 98.89 10 A 1 ATOM 76 O O . ALA A 1 10 ? 4.768 -2.306 -1.575 1.00 98.76 10 A 1 ATOM 77 C CB . ALA A 1 10 ? 2.417 -3.609 0.392 1.00 98.73 10 A 1 ATOM 78 N N . ILE A 1 11 ? 2.703 -2.390 -2.453 1.00 98.88 11 A 1 ATOM 79 C CA . ILE A 1 11 ? 3.177 -2.457 -3.835 1.00 98.86 11 A 1 ATOM 80 C C . ILE A 1 11 ? 3.893 -1.164 -4.205 1.00 98.88 11 A 1 ATOM 81 O O . ILE A 1 11 ? 4.952 -1.183 -4.843 1.00 98.74 11 A 1 ATOM 82 C CB . ILE A 1 11 ? 2.005 -2.707 -4.800 1.00 98.75 11 A 1 ATOM 83 C CG1 . ILE A 1 11 ? 1.361 -4.068 -4.500 1.00 97.37 11 A 1 ATOM 84 C CG2 . ILE A 1 11 ? 2.489 -2.654 -6.249 1.00 97.04 11 A 1 ATOM 85 C CD1 . ILE A 1 11 ? 0.039 -4.271 -5.219 1.00 94.13 11 A 1 ATOM 86 N N . LEU A 1 12 ? 3.315 -0.046 -3.804 1.00 98.92 12 A 1 ATOM 87 C CA . LEU A 1 12 ? 3.900 1.261 -4.094 1.00 98.89 12 A 1 ATOM 88 C C . LEU A 1 12 ? 5.263 1.398 -3.428 1.00 98.91 12 A 1 ATOM 89 O O . LEU A 1 12 ? 6.199 1.945 -4.020 1.00 98.79 12 A 1 ATOM 90 C CB . LEU A 1 12 ? 2.962 2.364 -3.608 1.00 98.74 12 A 1 ATOM 91 C CG . LEU A 1 12 ? 3.444 3.773 -3.938 1.00 96.68 12 A 1 ATOM 92 C CD1 . LEU A 1 12 ? 3.515 3.985 -5.442 1.00 94.50 12 A 1 ATOM 93 C CD2 . LEU A 1 12 ? 2.517 4.810 -3.311 1.00 94.87 12 A 1 ATOM 94 N N . ALA A 1 13 ? 5.384 0.909 -2.201 1.00 98.92 13 A 1 ATOM 95 C CA . ALA A 1 13 ? 6.643 0.976 -1.462 1.00 98.91 13 A 1 ATOM 96 C C . ALA A 1 13 ? 7.744 0.201 -2.181 1.00 98.93 13 A 1 ATOM 97 O O . ALA A 1 13 ? 8.881 0.666 -2.273 1.00 98.79 13 A 1 ATOM 98 C CB . ALA A 1 13 ? 6.449 0.425 -0.055 1.00 98.79 13 A 1 ATOM 99 N N . VAL A 1 14 ? 7.414 -0.975 -2.707 1.00 98.94 14 A 1 ATOM 100 C CA . VAL A 1 14 ? 8.380 -1.794 -3.440 1.00 98.93 14 A 1 ATOM 101 C C . VAL A 1 14 ? 8.780 -1.117 -4.740 1.00 98.95 14 A 1 ATOM 102 O O . VAL A 1 14 ? 9.947 -1.158 -5.143 1.00 98.82 14 A 1 ATOM 103 C CB . VAL A 1 14 ? 7.805 -3.183 -3.732 1.00 98.82 14 A 1 ATOM 104 C CG1 . VAL A 1 14 ? 8.768 -3.999 -4.586 1.00 97.23 14 A 1 ATOM 105 C CG2 . VAL A 1 14 ? 7.516 -3.904 -2.430 1.00 97.75 14 A 1 ATOM 106 N N . ALA A 1 15 ? 7.819 -0.496 -5.406 1.00 98.90 15 A 1 ATOM 107 C CA . ALA A 1 15 ? 8.072 0.187 -6.672 1.00 98.88 15 A 1 ATOM 108 C C . ALA A 1 15 ? 9.013 1.371 -6.487 1.00 98.89 15 A 1 ATOM 109 O O . ALA A 1 15 ? 9.897 1.606 -7.313 1.00 98.62 15 A 1 ATOM 110 C CB . ALA A 1 15 ? 6.756 0.662 -7.282 1.00 98.71 15 A 1 ATOM 111 N N . VAL A 1 16 ? 8.810 2.126 -5.409 1.00 98.73 16 A 1 ATOM 112 C CA . VAL A 1 16 ? 9.633 3.302 -5.125 1.00 98.66 16 A 1 ATOM 113 C C . VAL A 1 16 ? 10.975 2.912 -4.522 1.00 98.66 16 A 1 ATOM 114 O O . VAL A 1 16 ? 12.024 3.429 -4.930 1.00 97.98 16 A 1 ATOM 115 C CB . VAL A 1 16 ? 8.901 4.265 -4.180 1.00 98.14 16 A 1 ATOM 116 C CG1 . VAL A 1 16 ? 9.795 5.450 -3.821 1.00 93.84 16 A 1 ATOM 117 C CG2 . VAL A 1 16 ? 7.623 4.770 -4.826 1.00 95.06 16 A 1 ATOM 118 N N . GLY A 1 17 ? 10.957 2.040 -3.536 1.00 96.71 17 A 1 ATOM 119 C CA . GLY A 1 17 ? 12.171 1.601 -2.840 1.00 95.36 17 A 1 ATOM 120 C C . GLY A 1 17 ? 12.727 0.332 -3.418 1.00 93.85 17 A 1 ATOM 121 O O . GLY A 1 17 ? 13.833 0.374 -3.985 1.00 86.71 17 A 1 ATOM 122 O OXT . GLY A 1 17 ? 12.075 -0.697 -3.250 1.00 92.89 17 A 1 #