# 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_spkb27080 # _entry.id spkb27080 # 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" "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 ILE 3 1 n ALA 4 1 n ILE 5 1 n VAL 6 1 n LEU 7 1 n LEU 8 1 n ALA 9 1 n ILE 10 1 n VAL 11 1 n GLY 12 1 n LEU 13 1 n ALA 14 1 n ALA 15 # _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 @ 2025-07-03 19:28:05)" _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 96.44 _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 90.18 1 1 A LYS 2 2 94.03 1 2 A ILE 3 2 97.47 1 3 A ALA 4 2 98.49 1 4 A ILE 5 2 97.68 1 5 A VAL 6 2 98.43 1 6 A LEU 7 2 97.31 1 7 A LEU 8 2 96.90 1 8 A ALA 9 2 98.44 1 9 A ILE 10 2 97.53 1 10 A VAL 11 2 98.06 1 11 A GLY 12 2 98.37 1 12 A LEU 13 2 95.68 1 13 A ALA 14 2 97.54 1 14 A ALA 15 2 93.43 1 15 # _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 ILE . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 15 A 15 # _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 ? -2.315 10.102 11.830 1.00 94.27 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.284 9.767 10.838 1.00 95.17 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.847 8.830 9.778 1.00 95.79 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.341 7.754 10.098 1.00 93.49 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.082 9.102 11.517 1.00 92.10 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.061 8.828 10.573 1.00 88.42 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.499 8.121 11.385 1.00 86.30 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.075 9.534 12.311 1.00 75.89 1 A 1 ATOM 9 N N . LYS A 1 2 ? -1.779 9.244 8.508 1.00 97.22 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -2.288 8.447 7.403 1.00 97.98 2 A 1 ATOM 11 C C . LYS A 1 2 ? -1.156 7.836 6.579 1.00 98.33 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.364 7.443 5.434 1.00 98.09 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -3.207 9.285 6.511 1.00 97.43 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -2.605 10.620 6.092 1.00 94.58 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.973 11.719 7.071 1.00 92.04 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.579 13.082 6.536 1.00 88.04 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -3.003 14.156 7.465 1.00 82.52 2 A 1 ATOM 18 N N . ILE A 1 3 ? 0.026 7.747 7.155 1.00 98.20 3 A 1 ATOM 19 C CA . ILE A 1 3 ? 1.185 7.184 6.472 1.00 98.30 3 A 1 ATOM 20 C C . ILE A 1 3 ? 1.006 5.687 6.258 1.00 98.44 3 A 1 ATOM 21 O O . ILE A 1 3 ? 1.478 5.119 5.274 1.00 98.30 3 A 1 ATOM 22 C CB . ILE A 1 3 ? 2.471 7.448 7.269 1.00 98.19 3 A 1 ATOM 23 C CG1 . ILE A 1 3 ? 2.638 8.948 7.536 1.00 96.99 3 A 1 ATOM 24 C CG2 . ILE A 1 3 ? 3.679 6.911 6.514 1.00 96.61 3 A 1 ATOM 25 C CD1 . ILE A 1 3 ? 2.674 9.777 6.268 1.00 94.74 3 A 1 ATOM 26 N N . ALA A 1 4 ? 0.304 5.048 7.182 1.00 98.49 4 A 1 ATOM 27 C CA . ALA A 1 4 ? 0.052 3.615 7.096 1.00 98.55 4 A 1 ATOM 28 C C . ALA A 1 4 ? -0.709 3.263 5.823 1.00 98.61 4 A 1 ATOM 29 O O . ALA A 1 4 ? -0.468 2.227 5.204 1.00 98.42 4 A 1 ATOM 30 C CB . ALA A 1 4 ? -0.729 3.155 8.319 1.00 98.38 4 A 1 ATOM 31 N N . ILE A 1 5 ? -1.633 4.137 5.425 1.00 98.57 5 A 1 ATOM 32 C CA . ILE A 1 5 ? -2.421 3.934 4.218 1.00 98.55 5 A 1 ATOM 33 C C . ILE A 1 5 ? -1.534 4.007 2.985 1.00 98.63 5 A 1 ATOM 34 O O . ILE A 1 5 ? -1.677 3.226 2.043 1.00 98.52 5 A 1 ATOM 35 C CB . ILE A 1 5 ? -3.539 4.977 4.117 1.00 98.40 5 A 1 ATOM 36 C CG1 . ILE A 1 5 ? -4.399 4.970 5.386 1.00 97.33 5 A 1 ATOM 37 C CG2 . ILE A 1 5 ? -4.394 4.706 2.885 1.00 97.03 5 A 1 ATOM 38 C CD1 . ILE A 1 5 ? -5.009 3.609 5.685 1.00 94.43 5 A 1 ATOM 39 N N . VAL A 1 6 ? -0.617 4.958 2.986 1.00 98.68 6 A 1 ATOM 40 C CA . VAL A 1 6 ? 0.311 5.135 1.871 1.00 98.73 6 A 1 ATOM 41 C C . VAL A 1 6 ? 1.215 3.916 1.734 1.00 98.77 6 A 1 ATOM 42 O O . VAL A 1 6 ? 1.437 3.412 0.631 1.00 98.68 6 A 1 ATOM 43 C CB . VAL A 1 6 ? 1.170 6.393 2.067 1.00 98.64 6 A 1 ATOM 44 C CG1 . VAL A 1 6 ? 2.158 6.544 0.922 1.00 97.93 6 A 1 ATOM 45 C CG2 . VAL A 1 6 ? 0.283 7.619 2.170 1.00 97.58 6 A 1 ATOM 46 N N . LEU A 1 7 ? 1.723 3.448 2.862 1.00 98.61 7 A 1 ATOM 47 C CA . LEU A 1 7 ? 2.605 2.287 2.874 1.00 98.55 7 A 1 ATOM 48 C C . LEU A 1 7 ? 1.886 1.055 2.341 1.00 98.64 7 A 1 ATOM 49 O O . LEU A 1 7 ? 2.432 0.304 1.534 1.00 98.61 7 A 1 ATOM 50 C CB . LEU A 1 7 ? 3.094 2.025 4.297 1.00 98.43 7 A 1 ATOM 51 C CG . LEU A 1 7 ? 4.078 3.067 4.820 1.00 95.64 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? 4.268 2.906 6.320 1.00 94.80 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? 5.412 2.932 4.110 1.00 95.20 7 A 1 ATOM 54 N N . LEU A 1 8 ? 0.658 0.861 2.788 1.00 98.58 8 A 1 ATOM 55 C CA . LEU A 1 8 ? -0.139 -0.279 2.359 1.00 98.49 8 A 1 ATOM 56 C C . LEU A 1 8 ? -0.425 -0.213 0.864 1.00 98.61 8 A 1 ATOM 57 O O . LEU A 1 8 ? -0.391 -1.228 0.170 1.00 98.41 8 A 1 ATOM 58 C CB . LEU A 1 8 ? -1.450 -0.313 3.141 1.00 98.15 8 A 1 ATOM 59 C CG . LEU A 1 8 ? -2.324 -1.525 2.849 1.00 94.75 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? -1.628 -2.804 3.274 1.00 93.93 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? -3.662 -1.394 3.557 1.00 94.30 8 A 1 ATOM 62 N N . ALA A 1 9 ? -0.711 0.982 0.373 1.00 98.50 9 A 1 ATOM 63 C CA . ALA A 1 9 ? -1.002 1.183 -1.041 1.00 98.50 9 A 1 ATOM 64 C C . ALA A 1 9 ? 0.213 0.857 -1.905 1.00 98.63 9 A 1 ATOM 65 O O . ALA A 1 9 ? 0.086 0.227 -2.955 1.00 98.37 9 A 1 ATOM 66 C CB . ALA A 1 9 ? -1.441 2.621 -1.280 1.00 98.22 9 A 1 ATOM 67 N N . ILE A 1 10 ? 1.381 1.283 -1.465 1.00 98.59 10 A 1 ATOM 68 C CA . ILE A 1 10 ? 2.622 1.041 -2.197 1.00 98.53 10 A 1 ATOM 69 C C . ILE A 1 10 ? 2.907 -0.452 -2.290 1.00 98.59 10 A 1 ATOM 70 O O . ILE A 1 10 ? 3.225 -0.974 -3.360 1.00 98.36 10 A 1 ATOM 71 C CB . ILE A 1 10 ? 3.806 1.755 -1.521 1.00 98.33 10 A 1 ATOM 72 C CG1 . ILE A 1 10 ? 3.615 3.272 -1.584 1.00 97.08 10 A 1 ATOM 73 C CG2 . ILE A 1 10 ? 5.119 1.366 -2.200 1.00 96.84 10 A 1 ATOM 74 C CD1 . ILE A 1 10 ? 4.562 4.029 -0.682 1.00 93.94 10 A 1 ATOM 75 N N . VAL A 1 11 ? 2.792 -1.136 -1.161 1.00 98.69 11 A 1 ATOM 76 C CA . VAL A 1 11 ? 3.043 -2.574 -1.112 1.00 98.61 11 A 1 ATOM 77 C C . VAL A 1 11 ? 2.034 -3.322 -1.969 1.00 98.65 11 A 1 ATOM 78 O O . VAL A 1 11 ? 2.387 -4.248 -2.702 1.00 98.34 11 A 1 ATOM 79 C CB . VAL A 1 11 ? 2.983 -3.091 0.332 1.00 98.26 11 A 1 ATOM 80 C CG1 . VAL A 1 11 ? 3.166 -4.600 0.371 1.00 96.71 11 A 1 ATOM 81 C CG2 . VAL A 1 11 ? 4.051 -2.415 1.173 1.00 97.18 11 A 1 ATOM 82 N N . GLY A 1 12 ? 0.781 -2.920 -1.878 1.00 98.41 12 A 1 ATOM 83 C CA . GLY A 1 12 ? -0.273 -3.563 -2.650 1.00 98.35 12 A 1 ATOM 84 C C . GLY A 1 12 ? -0.058 -3.427 -4.142 1.00 98.51 12 A 1 ATOM 85 O O . GLY A 1 12 ? -0.286 -4.368 -4.902 1.00 98.21 12 A 1 ATOM 86 N N . LEU A 1 13 ? 0.381 -2.257 -4.572 1.00 98.03 13 A 1 ATOM 87 C CA . LEU A 1 13 ? 0.639 -1.998 -5.987 1.00 97.94 13 A 1 ATOM 88 C C . LEU A 1 13 ? 1.863 -2.761 -6.473 1.00 98.24 13 A 1 ATOM 89 O O . LEU A 1 13 ? 1.880 -3.280 -7.593 1.00 97.70 13 A 1 ATOM 90 C CB . LEU A 1 13 ? 0.844 -0.499 -6.218 1.00 97.35 13 A 1 ATOM 91 C CG . LEU A 1 13 ? 1.078 -0.115 -7.677 1.00 94.13 13 A 1 ATOM 92 C CD1 . LEU A 1 13 ? -0.156 -0.401 -8.506 1.00 91.51 13 A 1 ATOM 93 C CD2 . LEU A 1 13 ? 1.461 1.350 -7.780 1.00 90.54 13 A 1 ATOM 94 N N . ALA A 1 14 ? 2.889 -2.830 -5.641 1.00 97.86 14 A 1 ATOM 95 C CA . ALA A 1 14 ? 4.130 -3.519 -5.983 1.00 97.75 14 A 1 ATOM 96 C C . ALA A 1 14 ? 4.009 -5.030 -5.847 1.00 97.94 14 A 1 ATOM 97 O O . ALA A 1 14 ? 4.869 -5.770 -6.322 1.00 97.17 14 A 1 ATOM 98 C CB . ALA A 1 14 ? 5.269 -3.017 -5.098 1.00 96.99 14 A 1 ATOM 99 N N . ALA A 1 15 ? 2.940 -5.500 -5.204 1.00 97.04 15 A 1 ATOM 100 C CA . ALA A 1 15 ? 2.727 -6.920 -4.970 1.00 96.00 15 A 1 ATOM 101 C C . ALA A 1 15 ? 2.731 -7.714 -6.276 1.00 95.33 15 A 1 ATOM 102 O O . ALA A 1 15 ? 2.435 -7.142 -7.341 1.00 92.23 15 A 1 ATOM 103 C CB . ALA A 1 15 ? 1.418 -7.139 -4.218 1.00 93.74 15 A 1 ATOM 104 O OXT . ALA A 1 15 ? 3.025 -8.927 -6.235 1.00 86.26 15 A 1 #