# 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_spkb32238 # _entry.id spkb32238 # 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 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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" "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" "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 GLU 2 1 n THR 3 1 n PHE 4 1 n PRO 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n SER 10 1 n LEU 11 1 n GLY 12 1 n LEU 13 1 n VAL 14 1 n LEU 15 1 n ALA 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 @ 2025-07-12 21:56:12)" _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 87.53 _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 75.95 1 1 A GLU 2 2 75.90 1 2 A THR 3 2 83.62 1 3 A PHE 4 2 84.98 1 4 A PRO 5 2 90.85 1 5 A LEU 6 2 89.45 1 6 A LEU 7 2 90.41 1 7 A LEU 8 2 91.06 1 8 A LEU 9 2 90.57 1 9 A SER 10 2 90.92 1 10 A LEU 11 2 90.35 1 11 A GLY 12 2 93.89 1 12 A LEU 13 2 90.74 1 13 A VAL 14 2 92.42 1 14 A LEU 15 2 90.38 1 15 A ALA 16 2 85.53 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 GLU . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n PRO . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n ALA . 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 ? -13.370 -1.852 12.810 1.00 81.23 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.952 -1.621 12.486 1.00 83.26 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.551 -2.403 11.243 1.00 83.80 1 A 1 ATOM 4 O O . MET A 1 1 ? -11.718 -3.614 11.193 1.00 79.84 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.061 -2.058 13.644 1.00 78.34 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.315 -1.261 14.909 1.00 73.99 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.263 -1.808 16.265 1.00 67.23 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.868 -0.750 17.559 1.00 59.89 1 A 1 ATOM 9 N N . GLU A 1 2 ? -11.016 -1.726 10.242 1.00 81.35 2 A 1 ATOM 10 C CA . GLU A 1 2 ? -10.561 -2.372 9.021 1.00 84.69 2 A 1 ATOM 11 C C . GLU A 1 2 ? -9.128 -1.951 8.702 1.00 86.69 2 A 1 ATOM 12 O O . GLU A 1 2 ? -8.770 -0.785 8.846 1.00 84.04 2 A 1 ATOM 13 C CB . GLU A 1 2 ? -11.485 -2.005 7.862 1.00 79.42 2 A 1 ATOM 14 C CG . GLU A 1 2 ? -11.584 -0.510 7.632 1.00 72.19 2 A 1 ATOM 15 C CD . GLU A 1 2 ? -12.600 -0.193 6.561 1.00 68.13 2 A 1 ATOM 16 O OE1 . GLU A 1 2 ? -12.596 -0.870 5.529 1.00 61.74 2 A 1 ATOM 17 O OE2 . GLU A 1 2 ? -13.398 0.738 6.759 1.00 64.85 2 A 1 ATOM 18 N N . THR A 1 3 ? -8.305 -2.902 8.265 1.00 83.98 3 A 1 ATOM 19 C CA . THR A 1 3 ? -6.905 -2.644 7.955 1.00 87.27 3 A 1 ATOM 20 C C . THR A 1 3 ? -6.587 -3.004 6.506 1.00 89.38 3 A 1 ATOM 21 O O . THR A 1 3 ? -7.149 -3.948 5.955 1.00 87.20 3 A 1 ATOM 22 C CB . THR A 1 3 ? -5.997 -3.441 8.895 1.00 83.86 3 A 1 ATOM 23 O OG1 . THR A 1 3 ? -4.633 -3.174 8.582 1.00 77.89 3 A 1 ATOM 24 C CG2 . THR A 1 3 ? -6.259 -4.930 8.785 1.00 75.76 3 A 1 ATOM 25 N N . PHE A 1 4 ? -5.701 -2.254 5.906 1.00 88.29 4 A 1 ATOM 26 C CA . PHE A 1 4 ? -5.302 -2.490 4.521 1.00 89.30 4 A 1 ATOM 27 C C . PHE A 1 4 ? -3.781 -2.533 4.406 1.00 91.21 4 A 1 ATOM 28 O O . PHE A 1 4 ? -3.149 -1.534 4.043 1.00 90.43 4 A 1 ATOM 29 C CB . PHE A 1 4 ? -5.857 -1.396 3.621 1.00 87.78 4 A 1 ATOM 30 C CG . PHE A 1 4 ? -7.351 -1.269 3.699 1.00 84.78 4 A 1 ATOM 31 C CD1 . PHE A 1 4 ? -7.923 -0.367 4.578 1.00 82.32 4 A 1 ATOM 32 C CD2 . PHE A 1 4 ? -8.161 -2.052 2.907 1.00 81.64 4 A 1 ATOM 33 C CE1 . PHE A 1 4 ? -9.298 -0.240 4.666 1.00 80.00 4 A 1 ATOM 34 C CE2 . PHE A 1 4 ? -9.540 -1.936 2.981 1.00 79.76 4 A 1 ATOM 35 C CZ . PHE A 1 4 ? -10.110 -1.029 3.862 1.00 79.27 4 A 1 ATOM 36 N N . PRO A 1 5 ? -3.154 -3.677 4.710 1.00 91.01 5 A 1 ATOM 37 C CA . PRO A 1 5 ? -1.694 -3.835 4.644 1.00 92.35 5 A 1 ATOM 38 C C . PRO A 1 5 ? -1.145 -3.633 3.238 1.00 93.04 5 A 1 ATOM 39 O O . PRO A 1 5 ? -0.060 -3.075 3.059 1.00 90.96 5 A 1 ATOM 40 C CB . PRO A 1 5 ? -1.463 -5.271 5.127 1.00 90.40 5 A 1 ATOM 41 C CG . PRO A 1 5 ? -2.762 -5.965 4.892 1.00 88.00 5 A 1 ATOM 42 C CD . PRO A 1 5 ? -3.829 -4.926 5.088 1.00 90.22 5 A 1 ATOM 43 N N . LEU A 1 6 ? -1.896 -4.086 2.238 1.00 91.98 6 A 1 ATOM 44 C CA . LEU A 1 6 ? -1.472 -3.947 0.846 1.00 92.09 6 A 1 ATOM 45 C C . LEU A 1 6 ? -1.359 -2.477 0.457 1.00 92.84 6 A 1 ATOM 46 O O . LEU A 1 6 ? -0.479 -2.090 -0.311 1.00 91.27 6 A 1 ATOM 47 C CB . LEU A 1 6 ? -2.468 -4.650 -0.072 1.00 90.95 6 A 1 ATOM 48 C CG . LEU A 1 6 ? -2.528 -6.159 0.125 1.00 87.64 6 A 1 ATOM 49 C CD1 . LEU A 1 6 ? -3.624 -6.754 -0.739 1.00 84.83 6 A 1 ATOM 50 C CD2 . LEU A 1 6 ? -1.186 -6.793 -0.212 1.00 83.99 6 A 1 ATOM 51 N N . LEU A 1 7 ? -2.245 -1.671 1.002 1.00 92.38 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -2.238 -0.237 0.725 1.00 92.65 7 A 1 ATOM 53 C C . LEU A 1 7 ? -0.948 0.396 1.239 1.00 93.61 7 A 1 ATOM 54 O O . LEU A 1 7 ? -0.326 1.212 0.560 1.00 92.57 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -3.446 0.426 1.391 1.00 92.09 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -3.694 1.855 0.929 1.00 88.71 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -4.158 1.873 -0.519 1.00 85.93 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -4.737 2.521 1.815 1.00 85.32 7 A 1 ATOM 59 N N . LEU A 1 8 ? -0.553 0.014 2.445 1.00 92.06 8 A 1 ATOM 60 C CA . LEU A 1 8 ? 0.677 0.520 3.051 1.00 92.73 8 A 1 ATOM 61 C C . LEU A 1 8 ? 1.890 0.116 2.219 1.00 93.49 8 A 1 ATOM 62 O O . LEU A 1 8 ? 2.775 0.930 1.947 1.00 92.73 8 A 1 ATOM 63 C CB . LEU A 1 8 ? 0.815 -0.026 4.474 1.00 92.07 8 A 1 ATOM 64 C CG . LEU A 1 8 ? 2.031 0.503 5.218 1.00 90.00 8 A 1 ATOM 65 C CD1 . LEU A 1 8 ? 1.869 1.988 5.516 1.00 88.04 8 A 1 ATOM 66 C CD2 . LEU A 1 8 ? 2.238 -0.269 6.512 1.00 87.39 8 A 1 ATOM 67 N N . LEU A 1 9 ? 1.925 -1.150 1.809 1.00 92.17 9 A 1 ATOM 68 C CA . LEU A 1 9 ? 3.028 -1.671 1.007 1.00 92.44 9 A 1 ATOM 69 C C . LEU A 1 9 ? 3.106 -0.949 -0.335 1.00 93.69 9 A 1 ATOM 70 O O . LEU A 1 9 ? 4.187 -0.620 -0.818 1.00 93.02 9 A 1 ATOM 71 C CB . LEU A 1 9 ? 2.851 -3.180 0.791 1.00 91.70 9 A 1 ATOM 72 C CG . LEU A 1 9 ? 3.670 -4.048 1.740 1.00 88.60 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? 5.150 -3.897 1.439 1.00 86.44 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? 3.378 -3.690 3.184 1.00 86.50 9 A 1 ATOM 75 N N . SER A 1 10 ? 1.953 -0.711 -0.928 1.00 92.19 10 A 1 ATOM 76 C CA . SER A 1 10 ? 1.884 -0.025 -2.212 1.00 92.90 10 A 1 ATOM 77 C C . SER A 1 10 ? 2.477 1.377 -2.112 1.00 93.66 10 A 1 ATOM 78 O O . SER A 1 10 ? 3.249 1.801 -2.972 1.00 91.81 10 A 1 ATOM 79 C CB . SER A 1 10 ? 0.435 0.060 -2.686 1.00 91.41 10 A 1 ATOM 80 O OG . SER A 1 10 ? 0.366 0.699 -3.937 1.00 83.56 10 A 1 ATOM 81 N N . LEU A 1 11 ? 2.119 2.079 -1.053 1.00 92.68 11 A 1 ATOM 82 C CA . LEU A 1 11 ? 2.618 3.435 -0.836 1.00 93.02 11 A 1 ATOM 83 C C . LEU A 1 11 ? 4.138 3.440 -0.703 1.00 94.19 11 A 1 ATOM 84 O O . LEU A 1 11 ? 4.825 4.258 -1.316 1.00 92.61 11 A 1 ATOM 85 C CB . LEU A 1 11 ? 1.979 4.019 0.423 1.00 91.81 11 A 1 ATOM 86 C CG . LEU A 1 11 ? 2.403 5.450 0.732 1.00 88.11 11 A 1 ATOM 87 C CD1 . LEU A 1 11 ? 1.937 6.396 -0.367 1.00 85.17 11 A 1 ATOM 88 C CD2 . LEU A 1 11 ? 1.841 5.888 2.074 1.00 85.18 11 A 1 ATOM 89 N N . GLY A 1 12 ? 4.652 2.527 0.106 1.00 93.20 12 A 1 ATOM 90 C CA . GLY A 1 12 ? 6.093 2.427 0.313 1.00 93.70 12 A 1 ATOM 91 C C . GLY A 1 12 ? 6.829 2.053 -0.957 1.00 94.92 12 A 1 ATOM 92 O O . GLY A 1 12 ? 7.900 2.585 -1.250 1.00 93.74 12 A 1 ATOM 93 N N . LEU A 1 13 ? 6.257 1.134 -1.718 1.00 92.93 13 A 1 ATOM 94 C CA . LEU A 1 13 ? 6.859 0.671 -2.965 1.00 93.64 13 A 1 ATOM 95 C C . LEU A 1 13 ? 6.989 1.810 -3.971 1.00 94.50 13 A 1 ATOM 96 O O . LEU A 1 13 ? 8.020 1.955 -4.627 1.00 92.20 13 A 1 ATOM 97 C CB . LEU A 1 13 ? 6.017 -0.458 -3.559 1.00 92.42 13 A 1 ATOM 98 C CG . LEU A 1 13 ? 6.603 -1.066 -4.826 1.00 88.92 13 A 1 ATOM 99 C CD1 . LEU A 1 13 ? 7.945 -1.718 -4.537 1.00 86.01 13 A 1 ATOM 100 C CD2 . LEU A 1 13 ? 5.636 -2.077 -5.417 1.00 85.28 13 A 1 ATOM 101 N N . VAL A 1 14 ? 5.951 2.608 -4.091 1.00 93.86 14 A 1 ATOM 102 C CA . VAL A 1 14 ? 5.959 3.735 -5.022 1.00 94.15 14 A 1 ATOM 103 C C . VAL A 1 14 ? 7.031 4.750 -4.633 1.00 94.72 14 A 1 ATOM 104 O O . VAL A 1 14 ? 7.737 5.287 -5.493 1.00 92.65 14 A 1 ATOM 105 C CB . VAL A 1 14 ? 4.581 4.416 -5.065 1.00 92.48 14 A 1 ATOM 106 C CG1 . VAL A 1 14 ? 4.636 5.686 -5.901 1.00 89.67 14 A 1 ATOM 107 C CG2 . VAL A 1 14 ? 3.540 3.467 -5.635 1.00 89.44 14 A 1 ATOM 108 N N . LEU A 1 15 ? 7.152 5.019 -3.345 1.00 92.51 15 A 1 ATOM 109 C CA . LEU A 1 15 ? 8.130 5.977 -2.840 1.00 93.08 15 A 1 ATOM 110 C C . LEU A 1 15 ? 9.552 5.442 -2.956 1.00 93.72 15 A 1 ATOM 111 O O . LEU A 1 15 ? 10.504 6.214 -3.051 1.00 91.89 15 A 1 ATOM 112 C CB . LEU A 1 15 ? 7.815 6.315 -1.384 1.00 91.64 15 A 1 ATOM 113 C CG . LEU A 1 15 ? 6.492 7.056 -1.186 1.00 89.22 15 A 1 ATOM 114 C CD1 . LEU A 1 15 ? 6.192 7.218 0.295 1.00 86.03 15 A 1 ATOM 115 C CD2 . LEU A 1 15 ? 6.532 8.410 -1.873 1.00 84.96 15 A 1 ATOM 116 N N . ALA A 1 16 ? 9.701 4.116 -2.944 1.00 91.90 16 A 1 ATOM 117 C CA . ALA A 1 16 ? 11.007 3.474 -3.025 1.00 90.20 16 A 1 ATOM 118 C C . ALA A 1 16 ? 11.676 3.725 -4.378 1.00 87.78 16 A 1 ATOM 119 O O . ALA A 1 16 ? 11.007 4.166 -5.325 1.00 82.97 16 A 1 ATOM 120 C CB . ALA A 1 16 ? 10.876 1.979 -2.759 1.00 84.24 16 A 1 ATOM 121 O OXT . ALA A 1 16 ? 12.880 3.482 -4.503 1.00 76.11 16 A 1 #