# 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_spkb38328 # _entry.id spkb38328 # 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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O3" 105.093 SER y SERINE C([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 SER 3 1 n VAL 4 1 n PRO 5 1 n LEU 6 1 n ILE 7 1 n SER 8 1 n GLY 9 1 n GLY 10 1 n LEU 11 1 n SER 12 1 n LEU 13 1 n PHE 14 1 n LEU 15 1 n SER 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 @ 2025-07-02 15:58:30)" _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 82.05 _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 73.36 1 1 A LYS 2 2 68.68 1 2 A SER 3 2 77.80 1 3 A VAL 4 2 80.91 1 4 A PRO 5 2 81.10 1 5 A LEU 6 2 80.77 1 6 A ILE 7 2 83.30 1 7 A SER 8 2 86.89 1 8 A GLY 9 2 87.28 1 9 A GLY 10 2 88.91 1 10 A LEU 11 2 85.65 1 11 A SER 12 2 86.37 1 12 A LEU 13 2 83.42 1 13 A PHE 14 2 85.47 1 14 A LEU 15 2 85.77 1 15 A SER 16 2 85.01 1 16 A ALA 17 2 82.34 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 SER . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n PRO . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n GLY . 9 A 9 A 10 1 n GLY . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n PHE . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n SER . 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 ? 14.306 -8.206 -0.886 1.00 75.91 1 A 1 ATOM 2 C CA . MET A 1 1 ? 13.595 -7.875 0.359 1.00 79.55 1 A 1 ATOM 3 C C . MET A 1 1 ? 12.986 -6.482 0.249 1.00 81.54 1 A 1 ATOM 4 O O . MET A 1 1 ? 13.704 -5.491 0.305 1.00 75.97 1 A 1 ATOM 5 C CB . MET A 1 1 ? 14.557 -7.944 1.542 1.00 73.92 1 A 1 ATOM 6 C CG . MET A 1 1 ? 13.979 -8.705 2.715 1.00 73.61 1 A 1 ATOM 7 S SD . MET A 1 1 ? 15.195 -8.929 4.014 1.00 66.95 1 A 1 ATOM 8 C CE . MET A 1 1 ? 14.219 -9.765 5.249 1.00 59.41 1 A 1 ATOM 9 N N . LYS A 1 2 ? 11.671 -6.412 0.057 1.00 73.65 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 10.978 -5.133 -0.074 1.00 76.20 2 A 1 ATOM 11 C C . LYS A 1 2 ? 9.735 -5.121 0.812 1.00 77.19 2 A 1 ATOM 12 O O . LYS A 1 2 ? 9.001 -6.105 0.865 1.00 73.88 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 10.611 -4.896 -1.537 1.00 71.91 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 10.778 -3.450 -1.957 1.00 66.91 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 10.629 -3.301 -3.473 1.00 65.46 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 11.964 -3.372 -4.184 1.00 59.58 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 11.789 -3.331 -5.659 1.00 53.32 2 A 1 ATOM 18 N N . SER A 1 3 ? 9.519 -4.016 1.480 1.00 77.69 3 A 1 ATOM 19 C CA . SER A 1 3 ? 8.370 -3.867 2.366 1.00 80.25 3 A 1 ATOM 20 C C . SER A 1 3 ? 7.142 -3.429 1.569 1.00 82.22 3 A 1 ATOM 21 O O . SER A 1 3 ? 7.116 -2.339 0.999 1.00 79.33 3 A 1 ATOM 22 C CB . SER A 1 3 ? 8.687 -2.861 3.466 1.00 77.15 3 A 1 ATOM 23 O OG . SER A 1 3 ? 9.321 -3.494 4.555 1.00 70.14 3 A 1 ATOM 24 N N . VAL A 1 4 ? 6.150 -4.294 1.517 1.00 81.18 4 A 1 ATOM 25 C CA . VAL A 1 4 ? 4.911 -3.999 0.800 1.00 83.13 4 A 1 ATOM 26 C C . VAL A 1 4 ? 3.711 -4.134 1.738 1.00 85.79 4 A 1 ATOM 27 O O . VAL A 1 4 ? 3.148 -5.217 1.874 1.00 83.53 4 A 1 ATOM 28 C CB . VAL A 1 4 ? 4.746 -4.912 -0.426 1.00 79.78 4 A 1 ATOM 29 C CG1 . VAL A 1 4 ? 5.271 -4.234 -1.676 1.00 75.46 4 A 1 ATOM 30 C CG2 . VAL A 1 4 ? 5.429 -6.254 -0.226 1.00 77.52 4 A 1 ATOM 31 N N . PRO A 1 5 ? 3.326 -3.047 2.378 1.00 80.61 5 A 1 ATOM 32 C CA . PRO A 1 5 ? 2.182 -3.056 3.285 1.00 82.08 5 A 1 ATOM 33 C C . PRO A 1 5 ? 0.874 -3.231 2.514 1.00 84.33 5 A 1 ATOM 34 O O . PRO A 1 5 ? 0.392 -2.302 1.872 1.00 82.08 5 A 1 ATOM 35 C CB . PRO A 1 5 ? 2.258 -1.694 3.976 1.00 78.15 5 A 1 ATOM 36 C CG . PRO A 1 5 ? 3.024 -0.816 3.054 1.00 78.35 5 A 1 ATOM 37 C CD . PRO A 1 5 ? 3.946 -1.725 2.279 1.00 82.11 5 A 1 ATOM 38 N N . LEU A 1 6 ? 0.319 -4.421 2.570 1.00 83.60 6 A 1 ATOM 39 C CA . LEU A 1 6 ? -0.928 -4.732 1.877 1.00 84.78 6 A 1 ATOM 40 C C . LEU A 1 6 ? -2.111 -4.032 2.538 1.00 87.00 6 A 1 ATOM 41 O O . LEU A 1 6 ? -3.025 -3.572 1.858 1.00 84.26 6 A 1 ATOM 42 C CB . LEU A 1 6 ? -1.128 -6.246 1.869 1.00 81.31 6 A 1 ATOM 43 C CG . LEU A 1 6 ? -0.091 -6.998 1.042 1.00 77.48 6 A 1 ATOM 44 C CD1 . LEU A 1 6 ? 0.116 -8.394 1.602 1.00 75.73 6 A 1 ATOM 45 C CD2 . LEU A 1 6 ? -0.544 -7.077 -0.412 1.00 71.96 6 A 1 ATOM 46 N N . ILE A 1 7 ? -2.065 -3.951 3.855 1.00 86.25 7 A 1 ATOM 47 C CA . ILE A 1 7 ? -3.127 -3.299 4.619 1.00 85.61 7 A 1 ATOM 48 C C . ILE A 1 7 ? -3.113 -1.792 4.389 1.00 86.54 7 A 1 ATOM 49 O O . ILE A 1 7 ? -4.151 -1.180 4.116 1.00 85.02 7 A 1 ATOM 50 C CB . ILE A 1 7 ? -2.984 -3.625 6.123 1.00 84.71 7 A 1 ATOM 51 C CG1 . ILE A 1 7 ? -2.946 -5.137 6.366 1.00 82.74 7 A 1 ATOM 52 C CG2 . ILE A 1 7 ? -4.144 -3.004 6.905 1.00 80.71 7 A 1 ATOM 53 C CD1 . ILE A 1 7 ? -2.059 -5.525 7.527 1.00 74.78 7 A 1 ATOM 54 N N . SER A 1 8 ? -1.935 -1.204 4.485 1.00 88.97 8 A 1 ATOM 55 C CA . SER A 1 8 ? -1.767 0.233 4.290 1.00 88.98 8 A 1 ATOM 56 C C . SER A 1 8 ? -1.950 0.617 2.824 1.00 89.46 8 A 1 ATOM 57 O O . SER A 1 8 ? -2.496 1.675 2.510 1.00 87.29 8 A 1 ATOM 58 C CB . SER A 1 8 ? -0.391 0.664 4.791 1.00 87.01 8 A 1 ATOM 59 O OG . SER A 1 8 ? -0.368 2.034 5.069 1.00 79.65 8 A 1 ATOM 60 N N . GLY A 1 9 ? -1.493 -0.250 1.928 1.00 87.34 9 A 1 ATOM 61 C CA . GLY A 1 9 ? -1.620 -0.015 0.496 1.00 86.39 9 A 1 ATOM 62 C C . GLY A 1 9 ? -3.068 0.052 0.053 1.00 88.51 9 A 1 ATOM 63 O O . GLY A 1 9 ? -3.434 0.856 -0.802 1.00 86.88 9 A 1 ATOM 64 N N . GLY A 1 10 ? -3.891 -0.793 0.649 1.00 87.98 10 A 1 ATOM 65 C CA . GLY A 1 10 ? -5.314 -0.810 0.337 1.00 89.02 10 A 1 ATOM 66 C C . GLY A 1 10 ? -6.001 0.486 0.723 1.00 90.22 10 A 1 ATOM 67 O O . GLY A 1 10 ? -6.886 0.965 0.015 1.00 88.40 10 A 1 ATOM 68 N N . LEU A 1 11 ? -5.584 1.063 1.837 1.00 88.50 11 A 1 ATOM 69 C CA . LEU A 1 11 ? -6.134 2.333 2.309 1.00 88.71 11 A 1 ATOM 70 C C . LEU A 1 11 ? -5.797 3.466 1.345 1.00 90.08 11 A 1 ATOM 71 O O . LEU A 1 11 ? -6.626 4.337 1.090 1.00 87.59 11 A 1 ATOM 72 C CB . LEU A 1 11 ? -5.589 2.646 3.705 1.00 86.90 11 A 1 ATOM 73 C CG . LEU A 1 11 ? -6.598 2.445 4.823 1.00 83.62 11 A 1 ATOM 74 C CD1 . LEU A 1 11 ? -6.583 1.007 5.306 1.00 80.02 11 A 1 ATOM 75 C CD2 . LEU A 1 11 ? -6.303 3.389 5.974 1.00 79.78 11 A 1 ATOM 76 N N . SER A 1 12 ? -4.591 3.440 0.817 1.00 87.85 12 A 1 ATOM 77 C CA . SER A 1 12 ? -4.141 4.452 -0.137 1.00 88.34 12 A 1 ATOM 78 C C . SER A 1 12 ? -4.980 4.406 -1.411 1.00 89.12 12 A 1 ATOM 79 O O . SER A 1 12 ? -5.336 5.440 -1.973 1.00 87.00 12 A 1 ATOM 80 C CB . SER A 1 12 ? -2.666 4.242 -0.468 1.00 86.02 12 A 1 ATOM 81 O OG . SER A 1 12 ? -1.843 4.910 0.461 1.00 79.91 12 A 1 ATOM 82 N N . LEU A 1 13 ? -5.304 3.195 -1.844 1.00 84.77 13 A 1 ATOM 83 C CA . LEU A 1 13 ? -6.126 3.005 -3.036 1.00 86.23 13 A 1 ATOM 84 C C . LEU A 1 13 ? -7.555 3.478 -2.789 1.00 87.86 13 A 1 ATOM 85 O O . LEU A 1 13 ? -8.194 4.046 -3.676 1.00 85.63 13 A 1 ATOM 86 C CB . LEU A 1 13 ? -6.104 1.526 -3.424 1.00 84.40 13 A 1 ATOM 87 C CG . LEU A 1 13 ? -5.190 1.235 -4.609 1.00 81.98 13 A 1 ATOM 88 C CD1 . LEU A 1 13 ? -4.431 -0.062 -4.396 1.00 78.74 13 A 1 ATOM 89 C CD2 . LEU A 1 13 ? -6.012 1.162 -5.888 1.00 77.74 13 A 1 ATOM 90 N N . PHE A 1 14 ? -8.034 3.251 -1.583 1.00 87.06 14 A 1 ATOM 91 C CA . PHE A 1 14 ? -9.376 3.664 -1.195 1.00 86.65 14 A 1 ATOM 92 C C . PHE A 1 14 ? -9.517 5.181 -1.252 1.00 88.50 14 A 1 ATOM 93 O O . PHE A 1 14 ? -10.560 5.697 -1.651 1.00 87.12 14 A 1 ATOM 94 C CB . PHE A 1 14 ? -9.670 3.150 0.214 1.00 86.19 14 A 1 ATOM 95 C CG . PHE A 1 14 ? -11.098 3.363 0.632 1.00 85.29 14 A 1 ATOM 96 C CD1 . PHE A 1 14 ? -12.115 2.644 0.026 1.00 83.08 14 A 1 ATOM 97 C CD2 . PHE A 1 14 ? -11.410 4.283 1.621 1.00 84.10 14 A 1 ATOM 98 C CE1 . PHE A 1 14 ? -13.438 2.839 0.405 1.00 83.60 14 A 1 ATOM 99 C CE2 . PHE A 1 14 ? -12.733 4.483 2.001 1.00 83.87 14 A 1 ATOM 100 C CZ . PHE A 1 14 ? -13.746 3.759 1.394 1.00 84.75 14 A 1 ATOM 101 N N . LEU A 1 15 ? -8.467 5.881 -0.865 1.00 88.62 15 A 1 ATOM 102 C CA . LEU A 1 15 ? -8.462 7.342 -0.897 1.00 88.38 15 A 1 ATOM 103 C C . LEU A 1 15 ? -8.444 7.856 -2.336 1.00 89.45 15 A 1 ATOM 104 O O . LEU A 1 15 ? -9.017 8.906 -2.632 1.00 87.19 15 A 1 ATOM 105 C CB . LEU A 1 15 ? -7.242 7.864 -0.132 1.00 86.96 15 A 1 ATOM 106 C CG . LEU A 1 15 ? -7.565 8.430 1.247 1.00 85.44 15 A 1 ATOM 107 C CD1 . LEU A 1 15 ? -7.522 7.345 2.306 1.00 80.51 15 A 1 ATOM 108 C CD2 . LEU A 1 15 ? -6.595 9.544 1.596 1.00 79.63 15 A 1 ATOM 109 N N . SER A 1 16 ? -7.790 7.112 -3.213 1.00 88.24 16 A 1 ATOM 110 C CA . SER A 1 16 ? -7.693 7.472 -4.629 1.00 87.17 16 A 1 ATOM 111 C C . SER A 1 16 ? -8.962 7.108 -5.397 1.00 87.37 16 A 1 ATOM 112 O O . SER A 1 16 ? -9.200 7.626 -6.490 1.00 84.86 16 A 1 ATOM 113 C CB . SER A 1 16 ? -6.479 6.789 -5.258 1.00 84.39 16 A 1 ATOM 114 O OG . SER A 1 16 ? -5.329 7.602 -5.165 1.00 78.02 16 A 1 ATOM 115 N N . ALA A 1 17 ? -9.753 6.222 -4.838 1.00 88.96 17 A 1 ATOM 116 C CA . ALA A 1 17 ? -10.985 5.768 -5.470 1.00 86.54 17 A 1 ATOM 117 C C . ALA A 1 17 ? -12.071 6.849 -5.456 1.00 83.15 17 A 1 ATOM 118 O O . ALA A 1 17 ? -11.943 7.841 -4.716 1.00 81.57 17 A 1 ATOM 119 C CB . ALA A 1 17 ? -11.469 4.495 -4.787 1.00 81.03 17 A 1 ATOM 120 O OXT . ALA A 1 17 ? -13.062 6.697 -6.196 1.00 72.78 17 A 1 #