# 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_spkb24678 # _entry.id spkb24678 # 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" "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N ? "L-PEPTIDE LINKING" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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 ARG 2 1 n LEU 3 1 n LEU 4 1 n LYS 5 1 n PHE 6 1 n VAL 7 1 n CYS 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n SER 12 1 n VAL 13 1 n ALA 14 1 n ALA 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 @ 2025-07-08 10:28:33)" _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 92.13 _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 83.31 1 1 A ARG 2 2 84.28 1 2 A LEU 3 2 93.15 1 3 A LEU 4 2 93.96 1 4 A LYS 5 2 91.32 1 5 A PHE 6 2 93.83 1 6 A VAL 7 2 95.82 1 7 A CYS 8 2 95.29 1 8 A LEU 9 2 94.02 1 9 A LEU 10 2 93.86 1 10 A ALA 11 2 96.72 1 11 A SER 12 2 94.47 1 12 A VAL 13 2 95.00 1 13 A ALA 14 2 95.66 1 14 A ALA 15 2 95.00 1 15 A ALA 16 2 85.34 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 ARG . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LYS . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 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 ? -2.676 9.937 -4.498 1.00 89.91 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.568 8.929 -3.884 1.00 91.09 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.869 8.229 -2.723 1.00 92.41 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.680 7.957 -2.799 1.00 88.91 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.964 7.893 -4.929 1.00 86.32 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.980 8.449 -5.912 1.00 80.28 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.287 7.297 -7.256 1.00 73.78 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.288 8.308 -8.332 1.00 63.80 1 A 1 ATOM 9 N N . ARG A 1 2 ? -3.603 7.991 -1.661 1.00 94.38 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -3.041 7.337 -0.477 1.00 95.24 2 A 1 ATOM 11 C C . ARG A 1 2 ? -3.611 5.932 -0.299 1.00 96.38 2 A 1 ATOM 12 O O . ARG A 1 2 ? -2.925 5.039 0.192 1.00 94.41 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -3.351 8.182 0.762 1.00 92.97 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -2.666 9.526 0.755 1.00 84.86 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -3.675 10.611 1.057 1.00 82.21 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -4.594 10.812 -0.059 1.00 75.85 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -4.433 11.748 -0.977 1.00 74.06 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -3.437 12.597 -0.917 1.00 69.15 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -5.293 11.815 -1.969 1.00 67.61 2 A 1 ATOM 20 N N . LEU A 1 3 ? -4.846 5.757 -0.683 1.00 96.11 3 A 1 ATOM 21 C CA . LEU A 1 3 ? -5.497 4.452 -0.569 1.00 96.66 3 A 1 ATOM 22 C C . LEU A 1 3 ? -4.750 3.404 -1.384 1.00 97.28 3 A 1 ATOM 23 O O . LEU A 1 3 ? -4.512 2.287 -0.922 1.00 96.12 3 A 1 ATOM 24 C CB . LEU A 1 3 ? -6.948 4.549 -1.048 1.00 96.04 3 A 1 ATOM 25 C CG . LEU A 1 3 ? -7.965 4.358 0.065 1.00 90.78 3 A 1 ATOM 26 C CD1 . LEU A 1 3 ? -8.325 5.707 0.685 1.00 86.52 3 A 1 ATOM 27 C CD2 . LEU A 1 3 ? -9.212 3.673 -0.460 1.00 85.68 3 A 1 ATOM 28 N N . LEU A 1 4 ? -4.391 3.782 -2.591 1.00 97.04 4 A 1 ATOM 29 C CA . LEU A 1 4 ? -3.661 2.872 -3.472 1.00 97.15 4 A 1 ATOM 30 C C . LEU A 1 4 ? -2.340 2.454 -2.837 1.00 97.29 4 A 1 ATOM 31 O O . LEU A 1 4 ? -1.922 1.299 -2.939 1.00 96.32 4 A 1 ATOM 32 C CB . LEU A 1 4 ? -3.403 3.551 -4.818 1.00 96.70 4 A 1 ATOM 33 C CG . LEU A 1 4 ? -4.178 2.920 -5.966 1.00 92.76 4 A 1 ATOM 34 C CD1 . LEU A 1 4 ? -5.512 3.617 -6.169 1.00 88.04 4 A 1 ATOM 35 C CD2 . LEU A 1 4 ? -3.358 2.970 -7.245 1.00 86.40 4 A 1 ATOM 36 N N . LYS A 1 5 ? -1.712 3.404 -2.184 1.00 96.74 5 A 1 ATOM 37 C CA . LYS A 1 5 ? -0.439 3.147 -1.522 1.00 96.92 5 A 1 ATOM 38 C C . LYS A 1 5 ? -0.618 2.108 -0.418 1.00 97.19 5 A 1 ATOM 39 O O . LYS A 1 5 ? 0.233 1.238 -0.237 1.00 96.78 5 A 1 ATOM 40 C CB . LYS A 1 5 ? 0.096 4.447 -0.938 1.00 96.54 5 A 1 ATOM 41 C CG . LYS A 1 5 ? 1.503 4.287 -0.416 1.00 91.73 5 A 1 ATOM 42 C CD . LYS A 1 5 ? 1.905 5.477 0.423 1.00 87.43 5 A 1 ATOM 43 C CE . LYS A 1 5 ? 3.182 5.176 1.182 1.00 82.82 5 A 1 ATOM 44 N NZ . LYS A 1 5 ? 3.334 6.096 2.335 1.00 75.74 5 A 1 ATOM 45 N N . PHE A 1 6 ? -1.716 2.222 0.294 1.00 96.48 6 A 1 ATOM 46 C CA . PHE A 1 6 ? -2.016 1.283 1.369 1.00 96.67 6 A 1 ATOM 47 C C . PHE A 1 6 ? -2.132 -0.132 0.825 1.00 97.13 6 A 1 ATOM 48 O O . PHE A 1 6 ? -1.586 -1.077 1.395 1.00 96.34 6 A 1 ATOM 49 C CB . PHE A 1 6 ? -3.322 1.685 2.052 1.00 96.31 6 A 1 ATOM 50 C CG . PHE A 1 6 ? -3.672 0.778 3.201 1.00 94.51 6 A 1 ATOM 51 C CD1 . PHE A 1 6 ? -2.921 0.792 4.363 1.00 91.32 6 A 1 ATOM 52 C CD2 . PHE A 1 6 ? -4.745 -0.094 3.104 1.00 91.47 6 A 1 ATOM 53 C CE1 . PHE A 1 6 ? -3.233 -0.051 5.417 1.00 90.70 6 A 1 ATOM 54 C CE2 . PHE A 1 6 ? -5.064 -0.944 4.158 1.00 90.69 6 A 1 ATOM 55 C CZ . PHE A 1 6 ? -4.304 -0.919 5.314 1.00 90.56 6 A 1 ATOM 56 N N . VAL A 1 7 ? -2.855 -0.263 -0.269 1.00 97.23 7 A 1 ATOM 57 C CA . VAL A 1 7 ? -3.043 -1.569 -0.897 1.00 97.18 7 A 1 ATOM 58 C C . VAL A 1 7 ? -1.706 -2.111 -1.382 1.00 97.37 7 A 1 ATOM 59 O O . VAL A 1 7 ? -1.414 -3.303 -1.250 1.00 96.67 7 A 1 ATOM 60 C CB . VAL A 1 7 ? -4.028 -1.484 -2.077 1.00 96.65 7 A 1 ATOM 61 C CG1 . VAL A 1 7 ? -4.224 -2.851 -2.718 1.00 92.89 7 A 1 ATOM 62 C CG2 . VAL A 1 7 ? -5.366 -0.927 -1.615 1.00 92.76 7 A 1 ATOM 63 N N . CYS A 1 8 ? -0.922 -1.232 -1.944 1.00 96.59 8 A 1 ATOM 64 C CA . CYS A 1 8 ? 0.390 -1.606 -2.459 1.00 96.63 8 A 1 ATOM 65 C C . CYS A 1 8 ? 1.297 -2.070 -1.323 1.00 96.61 8 A 1 ATOM 66 O O . CYS A 1 8 ? 2.071 -3.012 -1.478 1.00 95.28 8 A 1 ATOM 67 C CB . CYS A 1 8 ? 1.018 -0.416 -3.179 1.00 96.05 8 A 1 ATOM 68 S SG . CYS A 1 8 ? 2.360 -0.904 -4.277 1.00 90.56 8 A 1 ATOM 69 N N . LEU A 1 9 ? 1.187 -1.392 -0.207 1.00 96.60 9 A 1 ATOM 70 C CA . LEU A 1 9 ? 1.981 -1.737 0.966 1.00 96.55 9 A 1 ATOM 71 C C . LEU A 1 9 ? 1.656 -3.146 1.438 1.00 97.08 9 A 1 ATOM 72 O O . LEU A 1 9 ? 2.556 -3.940 1.720 1.00 96.69 9 A 1 ATOM 73 C CB . LEU A 1 9 ? 1.703 -0.739 2.087 1.00 96.37 9 A 1 ATOM 74 C CG . LEU A 1 9 ? 2.872 -0.577 3.042 1.00 90.99 9 A 1 ATOM 75 C CD1 . LEU A 1 9 ? 3.763 0.576 2.587 1.00 88.74 9 A 1 ATOM 76 C CD2 . LEU A 1 9 ? 2.383 -0.334 4.454 1.00 89.14 9 A 1 ATOM 77 N N . LEU A 1 10 ? 0.385 -3.426 1.520 1.00 97.00 10 A 1 ATOM 78 C CA . LEU A 1 10 ? -0.072 -4.742 1.950 1.00 96.90 10 A 1 ATOM 79 C C . LEU A 1 10 ? 0.428 -5.820 1.004 1.00 97.12 10 A 1 ATOM 80 O O . LEU A 1 10 ? 0.913 -6.870 1.433 1.00 96.50 10 A 1 ATOM 81 C CB . LEU A 1 10 ? -1.597 -4.773 2.003 1.00 96.32 10 A 1 ATOM 82 C CG . LEU A 1 10 ? -2.138 -5.567 3.184 1.00 90.89 10 A 1 ATOM 83 C CD1 . LEU A 1 10 ? -2.391 -4.638 4.363 1.00 88.13 10 A 1 ATOM 84 C CD2 . LEU A 1 10 ? -3.415 -6.294 2.808 1.00 87.99 10 A 1 ATOM 85 N N . ALA A 1 11 ? 0.287 -5.548 -0.274 1.00 97.18 11 A 1 ATOM 86 C CA . ALA A 1 11 ? 0.719 -6.494 -1.293 1.00 97.01 11 A 1 ATOM 87 C C . ALA A 1 11 ? 2.231 -6.671 -1.261 1.00 97.27 11 A 1 ATOM 88 O O . ALA A 1 11 ? 2.742 -7.768 -1.484 1.00 95.87 11 A 1 ATOM 89 C CB . ALA A 1 11 ? 0.271 -6.006 -2.664 1.00 96.27 11 A 1 ATOM 90 N N . SER A 1 12 ? 2.929 -5.597 -0.983 1.00 97.00 12 A 1 ATOM 91 C CA . SER A 1 12 ? 4.384 -5.620 -0.921 1.00 96.94 12 A 1 ATOM 92 C C . SER A 1 12 ? 4.866 -6.537 0.195 1.00 97.12 12 A 1 ATOM 93 O O . SER A 1 12 ? 5.797 -7.319 0.011 1.00 95.93 12 A 1 ATOM 94 C CB . SER A 1 12 ? 4.922 -4.212 -0.697 1.00 95.81 12 A 1 ATOM 95 O OG . SER A 1 12 ? 6.315 -4.190 -0.859 1.00 84.01 12 A 1 ATOM 96 N N . VAL A 1 13 ? 4.227 -6.438 1.335 1.00 97.10 13 A 1 ATOM 97 C CA . VAL A 1 13 ? 4.583 -7.265 2.483 1.00 96.93 13 A 1 ATOM 98 C C . VAL A 1 13 ? 4.324 -8.733 2.189 1.00 97.23 13 A 1 ATOM 99 O O . VAL A 1 13 ? 5.134 -9.599 2.529 1.00 95.90 13 A 1 ATOM 100 C CB . VAL A 1 13 ? 3.792 -6.845 3.724 1.00 95.76 13 A 1 ATOM 101 C CG1 . VAL A 1 13 ? 4.142 -7.737 4.902 1.00 90.96 13 A 1 ATOM 102 C CG2 . VAL A 1 13 ? 4.071 -5.395 4.058 1.00 91.12 13 A 1 ATOM 103 N N . ALA A 1 14 ? 3.192 -8.994 1.585 1.00 96.43 14 A 1 ATOM 104 C CA . ALA A 1 14 ? 2.819 -10.362 1.246 1.00 96.16 14 A 1 ATOM 105 C C . ALA A 1 14 ? 3.694 -10.911 0.132 1.00 96.34 14 A 1 ATOM 106 O O . ALA A 1 14 ? 4.045 -12.092 0.128 1.00 94.56 14 A 1 ATOM 107 C CB . ALA A 1 14 ? 1.357 -10.411 0.825 1.00 94.80 14 A 1 ATOM 108 N N . ALA A 1 15 ? 4.014 -10.056 -0.812 1.00 96.34 15 A 1 ATOM 109 C CA . ALA A 1 15 ? 4.836 -10.455 -1.945 1.00 95.89 15 A 1 ATOM 110 C C . ALA A 1 15 ? 6.257 -10.764 -1.507 1.00 96.09 15 A 1 ATOM 111 O O . ALA A 1 15 ? 6.873 -11.718 -1.989 1.00 92.74 15 A 1 ATOM 112 C CB . ALA A 1 15 ? 4.841 -9.354 -2.997 1.00 93.94 15 A 1 ATOM 113 N N . ALA A 1 16 ? 6.771 -9.956 -0.598 1.00 92.14 16 A 1 ATOM 114 C CA . ALA A 1 16 ? 8.130 -10.129 -0.097 1.00 89.82 16 A 1 ATOM 115 C C . ALA A 1 16 ? 8.272 -11.454 0.645 1.00 88.03 16 A 1 ATOM 116 O O . ALA A 1 16 ? 8.925 -12.372 0.123 1.00 80.63 16 A 1 ATOM 117 C CB . ALA A 1 16 ? 8.492 -8.969 0.819 1.00 85.20 16 A 1 ATOM 118 O OXT . ALA A 1 16 ? 7.744 -11.559 1.735 1.00 76.20 16 A 1 #