# 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_spkb38306 # _entry.id spkb38306 # 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" "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" # _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 THR 3 1 n LYS 4 1 n THR 5 1 n ILE 6 1 n LEU 7 1 n THR 8 1 n ALA 9 1 n LEU 10 1 n LEU 11 1 n SER 12 1 n ALA 13 1 n ILE 14 1 n ALA 15 1 n LEU 16 1 n THR 17 1 n GLY 18 # _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 @ 2025-07-07 21:58:16)" _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 93.95 _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 85.87 1 1 A LYS 2 2 86.34 1 2 A THR 3 2 93.88 1 3 A LYS 4 2 90.42 1 4 A THR 5 2 95.08 1 5 A ILE 6 2 95.67 1 6 A LEU 7 2 93.95 1 7 A THR 8 2 96.29 1 8 A ALA 9 2 98.03 1 9 A LEU 10 2 95.77 1 10 A LEU 11 2 95.64 1 11 A SER 12 2 96.42 1 12 A ALA 13 2 98.09 1 13 A ILE 14 2 97.00 1 14 A ALA 15 2 98.44 1 15 A LEU 16 2 95.49 1 16 A THR 17 2 94.73 1 17 A GLY 18 2 89.81 1 18 # _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 THR . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n THR . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ILE . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n THR . 17 A 17 A 18 1 n GLY . 18 A 18 # _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 ? -8.874 11.398 -1.325 1.00 90.33 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.519 11.826 -0.914 1.00 93.06 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.472 11.362 -1.917 1.00 93.70 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.546 10.253 -2.422 1.00 90.00 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.187 11.254 0.455 1.00 87.89 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.797 12.095 1.553 1.00 82.78 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.549 11.388 3.173 1.00 79.19 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.181 12.704 4.190 1.00 69.99 1 A 1 ATOM 9 N N . LYS A 1 2 ? -5.545 12.228 -2.203 1.00 92.53 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -4.498 11.921 -3.186 1.00 94.69 2 A 1 ATOM 11 C C . LYS A 1 2 ? -3.326 11.192 -2.532 1.00 95.56 2 A 1 ATOM 12 O O . LYS A 1 2 ? -2.828 10.199 -3.055 1.00 93.90 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -4.033 13.229 -3.820 1.00 91.63 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -3.258 13.002 -5.102 1.00 83.07 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.786 14.326 -5.673 1.00 82.84 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -1.921 14.113 -6.893 1.00 74.69 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -2.641 14.548 -8.094 1.00 68.12 2 A 1 ATOM 18 N N . THR A 1 3 ? -2.894 11.674 -1.408 1.00 95.45 3 A 1 ATOM 19 C CA . THR A 1 3 ? -1.755 11.092 -0.694 1.00 96.26 3 A 1 ATOM 20 C C . THR A 1 3 ? -2.141 9.800 0.016 1.00 96.84 3 A 1 ATOM 21 O O . THR A 1 3 ? -1.279 9.040 0.451 1.00 95.46 3 A 1 ATOM 22 C CB . THR A 1 3 ? -1.220 12.096 0.330 1.00 95.02 3 A 1 ATOM 23 O OG1 . THR A 1 3 ? -1.248 13.403 -0.222 1.00 89.88 3 A 1 ATOM 24 C CG2 . THR A 1 3 ? 0.214 11.765 0.713 1.00 88.23 3 A 1 ATOM 25 N N . LYS A 1 4 ? -3.431 9.550 0.111 1.00 97.27 4 A 1 ATOM 26 C CA . LYS A 1 4 ? -3.922 8.351 0.787 1.00 97.48 4 A 1 ATOM 27 C C . LYS A 1 4 ? -3.397 7.096 0.108 1.00 97.76 4 A 1 ATOM 28 O O . LYS A 1 4 ? -3.082 6.109 0.762 1.00 97.05 4 A 1 ATOM 29 C CB . LYS A 1 4 ? -5.444 8.362 0.776 1.00 96.82 4 A 1 ATOM 30 C CG . LYS A 1 4 ? -6.018 7.469 1.859 1.00 90.78 4 A 1 ATOM 31 C CD . LYS A 1 4 ? -5.676 8.016 3.229 1.00 87.08 4 A 1 ATOM 32 C CE . LYS A 1 4 ? -6.530 7.404 4.315 1.00 78.96 4 A 1 ATOM 33 N NZ . LYS A 1 4 ? -6.106 7.920 5.634 1.00 70.54 4 A 1 ATOM 34 N N . THR A 1 5 ? -3.310 7.141 -1.201 1.00 97.06 5 A 1 ATOM 35 C CA . THR A 1 5 ? -2.829 5.996 -1.972 1.00 97.34 5 A 1 ATOM 36 C C . THR A 1 5 ? -1.378 5.686 -1.624 1.00 97.54 5 A 1 ATOM 37 O O . THR A 1 5 ? -0.974 4.525 -1.592 1.00 96.81 5 A 1 ATOM 38 C CB . THR A 1 5 ? -2.940 6.295 -3.466 1.00 97.00 5 A 1 ATOM 39 O OG1 . THR A 1 5 ? -4.251 6.765 -3.753 1.00 91.33 5 A 1 ATOM 40 C CG2 . THR A 1 5 ? -2.675 5.046 -4.288 1.00 88.48 5 A 1 ATOM 41 N N . ILE A 1 6 ? -0.613 6.709 -1.365 1.00 97.98 6 A 1 ATOM 42 C CA . ILE A 1 6 ? 0.796 6.535 -1.025 1.00 97.74 6 A 1 ATOM 43 C C . ILE A 1 6 ? 0.921 5.849 0.329 1.00 97.71 6 A 1 ATOM 44 O O . ILE A 1 6 ? 1.775 4.984 0.524 1.00 97.10 6 A 1 ATOM 45 C CB . ILE A 1 6 ? 1.512 7.894 -0.993 1.00 97.68 6 A 1 ATOM 46 C CG1 . ILE A 1 6 ? 1.392 8.589 -2.353 1.00 95.12 6 A 1 ATOM 47 C CG2 . ILE A 1 6 ? 2.984 7.699 -0.631 1.00 94.34 6 A 1 ATOM 48 C CD1 . ILE A 1 6 ? 1.726 10.066 -2.277 1.00 87.67 6 A 1 ATOM 49 N N . LEU A 1 7 ? 0.063 6.239 1.240 1.00 97.59 7 A 1 ATOM 50 C CA . LEU A 1 7 ? 0.070 5.649 2.575 1.00 97.54 7 A 1 ATOM 51 C C . LEU A 1 7 ? -0.284 4.169 2.500 1.00 97.79 7 A 1 ATOM 52 O O . LEU A 1 7 ? 0.321 3.336 3.169 1.00 97.67 7 A 1 ATOM 53 C CB . LEU A 1 7 ? -0.941 6.378 3.457 1.00 97.19 7 A 1 ATOM 54 C CG . LEU A 1 7 ? -0.390 6.675 4.846 1.00 90.57 7 A 1 ATOM 55 C CD1 . LEU A 1 7 ? 0.335 8.010 4.848 1.00 86.59 7 A 1 ATOM 56 C CD2 . LEU A 1 7 ? -1.507 6.692 5.872 1.00 86.64 7 A 1 ATOM 57 N N . THR A 1 8 ? -1.265 3.859 1.682 1.00 98.19 8 A 1 ATOM 58 C CA . THR A 1 8 ? -1.707 2.476 1.511 1.00 97.93 8 A 1 ATOM 59 C C . THR A 1 8 ? -0.608 1.643 0.866 1.00 97.99 8 A 1 ATOM 60 O O . THR A 1 8 ? -0.392 0.492 1.242 1.00 97.74 8 A 1 ATOM 61 C CB . THR A 1 8 ? -2.959 2.439 0.635 1.00 97.65 8 A 1 ATOM 62 O OG1 . THR A 1 8 ? -3.950 3.285 1.196 1.00 93.44 8 A 1 ATOM 63 C CG2 . THR A 1 8 ? -3.525 1.028 0.559 1.00 91.10 8 A 1 ATOM 64 N N . ALA A 1 9 ? 0.066 2.216 -0.103 1.00 98.20 9 A 1 ATOM 65 C CA . ALA A 1 9 ? 1.147 1.519 -0.797 1.00 98.12 9 A 1 ATOM 66 C C . ALA A 1 9 ? 2.272 1.184 0.176 1.00 98.25 9 A 1 ATOM 67 O O . ALA A 1 9 ? 2.845 0.098 0.123 1.00 97.69 9 A 1 ATOM 68 C CB . ALA A 1 9 ? 1.671 2.397 -1.923 1.00 97.91 9 A 1 ATOM 69 N N . LEU A 1 10 ? 2.565 2.105 1.053 1.00 98.17 10 A 1 ATOM 70 C CA . LEU A 1 10 ? 3.619 1.908 2.047 1.00 97.99 10 A 1 ATOM 71 C C . LEU A 1 10 ? 3.239 0.782 2.995 1.00 98.13 10 A 1 ATOM 72 O O . LEU A 1 10 ? 4.066 -0.058 3.347 1.00 97.68 10 A 1 ATOM 73 C CB . LEU A 1 10 ? 3.828 3.210 2.819 1.00 97.67 10 A 1 ATOM 74 C CG . LEU A 1 10 ? 5.213 3.313 3.438 1.00 94.64 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? 5.775 4.714 3.248 1.00 90.53 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? 5.166 2.984 4.920 1.00 91.31 10 A 1 ATOM 77 N N . LEU A 1 11 ? 1.995 0.766 3.396 1.00 97.86 11 A 1 ATOM 78 C CA . LEU A 1 11 ? 1.498 -0.276 4.291 1.00 97.82 11 A 1 ATOM 79 C C . LEU A 1 11 ? 1.559 -1.634 3.611 1.00 98.04 11 A 1 ATOM 80 O O . LEU A 1 11 ? 1.871 -2.642 4.241 1.00 97.64 11 A 1 ATOM 81 C CB . LEU A 1 11 ? 0.056 0.043 4.683 1.00 97.48 11 A 1 ATOM 82 C CG . LEU A 1 11 ? -0.354 -0.636 5.984 1.00 94.73 11 A 1 ATOM 83 C CD1 . LEU A 1 11 ? 0.069 0.224 7.170 1.00 90.49 11 A 1 ATOM 84 C CD2 . LEU A 1 11 ? -1.853 -0.860 6.029 1.00 91.04 11 A 1 ATOM 85 N N . SER A 1 12 ? 1.255 -1.658 2.339 1.00 97.98 12 A 1 ATOM 86 C CA . SER A 1 12 ? 1.277 -2.894 1.559 1.00 97.89 12 A 1 ATOM 87 C C . SER A 1 12 ? 2.686 -3.471 1.508 1.00 98.21 12 A 1 ATOM 88 O O . SER A 1 12 ? 2.869 -4.683 1.598 1.00 97.68 12 A 1 ATOM 89 C CB . SER A 1 12 ? 0.778 -2.616 0.147 1.00 97.04 12 A 1 ATOM 90 O OG . SER A 1 12 ? 0.624 -3.815 -0.559 1.00 89.72 12 A 1 ATOM 91 N N . ALA A 1 13 ? 3.656 -2.610 1.367 1.00 98.16 13 A 1 ATOM 92 C CA . ALA A 1 13 ? 5.053 -3.039 1.309 1.00 98.19 13 A 1 ATOM 93 C C . ALA A 1 13 ? 5.472 -3.686 2.625 1.00 98.47 13 A 1 ATOM 94 O O . ALA A 1 13 ? 6.182 -4.690 2.633 1.00 97.94 13 A 1 ATOM 95 C CB . ALA A 1 13 ? 5.939 -1.839 1.010 1.00 97.71 13 A 1 ATOM 96 N N . ILE A 1 14 ? 5.028 -3.121 3.721 1.00 98.39 14 A 1 ATOM 97 C CA . ILE A 1 14 ? 5.354 -3.655 5.043 1.00 98.30 14 A 1 ATOM 98 C C . ILE A 1 14 ? 4.674 -5.002 5.253 1.00 98.45 14 A 1 ATOM 99 O O . ILE A 1 14 ? 5.265 -5.925 5.810 1.00 98.02 14 A 1 ATOM 100 C CB . ILE A 1 14 ? 4.909 -2.672 6.137 1.00 97.90 14 A 1 ATOM 101 C CG1 . ILE A 1 14 ? 5.622 -1.329 5.969 1.00 96.12 14 A 1 ATOM 102 C CG2 . ILE A 1 14 ? 5.216 -3.256 7.516 1.00 95.71 14 A 1 ATOM 103 C CD1 . ILE A 1 14 ? 4.936 -0.208 6.717 1.00 93.12 14 A 1 ATOM 104 N N . ALA A 1 15 ? 3.437 -5.093 4.816 1.00 98.62 15 A 1 ATOM 105 C CA . ALA A 1 15 ? 2.675 -6.332 4.959 1.00 98.61 15 A 1 ATOM 106 C C . ALA A 1 15 ? 3.305 -7.452 4.139 1.00 98.64 15 A 1 ATOM 107 O O . ALA A 1 15 ? 3.352 -8.596 4.578 1.00 98.08 15 A 1 ATOM 108 C CB . ALA A 1 15 ? 1.235 -6.099 4.516 1.00 98.27 15 A 1 ATOM 109 N N . LEU A 1 16 ? 3.773 -7.127 2.951 1.00 98.24 16 A 1 ATOM 110 C CA . LEU A 1 16 ? 4.409 -8.111 2.077 1.00 97.97 16 A 1 ATOM 111 C C . LEU A 1 16 ? 5.731 -8.582 2.663 1.00 98.01 16 A 1 ATOM 112 O O . LEU A 1 16 ? 6.030 -9.775 2.663 1.00 96.90 16 A 1 ATOM 113 C CB . LEU A 1 16 ? 4.641 -7.503 0.696 1.00 97.60 16 A 1 ATOM 114 C CG . LEU A 1 16 ? 3.725 -8.096 -0.369 1.00 94.80 16 A 1 ATOM 115 C CD1 . LEU A 1 16 ? 2.369 -7.423 -0.354 1.00 90.30 16 A 1 ATOM 116 C CD2 . LEU A 1 16 ? 4.366 -7.961 -1.741 1.00 90.07 16 A 1 ATOM 117 N N . THR A 1 17 ? 6.506 -7.651 3.161 1.00 97.69 17 A 1 ATOM 118 C CA . THR A 1 17 ? 7.806 -7.974 3.758 1.00 97.15 17 A 1 ATOM 119 C C . THR A 1 17 ? 7.624 -8.783 5.033 1.00 97.00 17 A 1 ATOM 120 O O . THR A 1 17 ? 8.336 -9.760 5.266 1.00 94.02 17 A 1 ATOM 121 C CB . THR A 1 17 ? 8.568 -6.684 4.071 1.00 95.86 17 A 1 ATOM 122 O OG1 . THR A 1 17 ? 8.639 -5.887 2.893 1.00 90.79 17 A 1 ATOM 123 C CG2 . THR A 1 17 ? 9.975 -7.001 4.533 1.00 90.63 17 A 1 ATOM 124 N N . GLY A 1 18 ? 6.666 -8.369 5.840 1.00 96.07 18 A 1 ATOM 125 C CA . GLY A 1 18 ? 6.393 -9.070 7.098 1.00 92.70 18 A 1 ATOM 126 C C . GLY A 1 18 ? 7.476 -8.814 8.111 1.00 89.15 18 A 1 ATOM 127 O O . GLY A 1 18 ? 7.165 -8.283 9.191 1.00 82.31 18 A 1 ATOM 128 O OXT . GLY A 1 18 ? 8.612 -9.139 7.826 1.00 88.83 18 A 1 #