# 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_spkb28479 # _entry.id spkb28479 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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 ILE 2 1 n LYS 3 1 n THR 4 1 n LEU 5 1 n PHE 6 1 n ILE 7 1 n ILE 8 1 n LEU 9 1 n LEU 10 1 n CYS 11 1 n GLY 12 1 n ILE 13 1 n LEU 14 1 n SER 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 @ 2025-07-03 00:32:53)" _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 94.46 _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 90.37 1 1 A ILE 2 2 94.17 1 2 A LYS 3 2 91.61 1 3 A THR 4 2 95.98 1 4 A LEU 5 2 94.24 1 5 A PHE 6 2 94.47 1 6 A ILE 7 2 96.42 1 7 A ILE 8 2 97.04 1 8 A LEU 9 2 95.94 1 9 A LEU 10 2 95.07 1 10 A CYS 11 2 96.59 1 11 A GLY 12 2 97.59 1 12 A ILE 13 2 95.59 1 13 A LEU 14 2 93.08 1 14 A SER 15 2 93.50 1 15 A ALA 16 2 91.28 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 ILE . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n ILE . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n SER . 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 ? -10.646 -1.353 6.722 1.00 95.76 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.345 -2.582 5.968 1.00 96.61 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.851 -2.671 5.669 1.00 96.85 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.279 -1.737 5.111 1.00 95.24 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.112 -2.618 4.655 1.00 93.50 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.622 -2.537 4.844 1.00 85.78 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.174 -0.858 5.139 1.00 83.16 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.917 -1.137 5.418 1.00 76.02 1 A 1 ATOM 9 N N . ILE A 1 2 ? -8.256 -3.801 6.033 1.00 96.81 2 A 1 ATOM 10 C CA . ILE A 1 2 ? -6.832 -3.998 5.800 1.00 97.23 2 A 1 ATOM 11 C C . ILE A 1 2 ? -6.514 -4.042 4.309 1.00 97.57 2 A 1 ATOM 12 O O . ILE A 1 2 ? -5.431 -3.648 3.884 1.00 96.84 2 A 1 ATOM 13 C CB . ILE A 1 2 ? -6.339 -5.288 6.467 1.00 96.26 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -7.059 -6.507 5.908 1.00 92.28 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? -6.515 -5.189 7.975 1.00 91.08 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -6.338 -7.794 6.206 1.00 85.29 2 A 1 ATOM 17 N N . LYS A 1 3 ? -7.474 -4.549 3.544 1.00 98.04 3 A 1 ATOM 18 C CA . LYS A 1 3 ? -7.301 -4.636 2.095 1.00 98.03 3 A 1 ATOM 19 C C . LYS A 1 3 ? -7.139 -3.247 1.502 1.00 98.20 3 A 1 ATOM 20 O O . LYS A 1 3 ? -6.274 -3.014 0.656 1.00 97.89 3 A 1 ATOM 21 C CB . LYS A 1 3 ? -8.504 -5.337 1.478 1.00 97.36 3 A 1 ATOM 22 C CG . LYS A 1 3 ? -8.622 -6.779 1.914 1.00 91.74 3 A 1 ATOM 23 C CD . LYS A 1 3 ? -10.032 -7.304 1.697 1.00 87.97 3 A 1 ATOM 24 C CE . LYS A 1 3 ? -10.990 -6.703 2.701 1.00 81.76 3 A 1 ATOM 25 N NZ . LYS A 1 3 ? -12.282 -7.430 2.729 1.00 73.50 3 A 1 ATOM 26 N N . THR A 1 4 ? -7.964 -2.331 1.955 1.00 97.87 4 A 1 ATOM 27 C CA . THR A 1 4 ? -7.898 -0.952 1.486 1.00 98.05 4 A 1 ATOM 28 C C . THR A 1 4 ? -6.627 -0.292 1.996 1.00 98.14 4 A 1 ATOM 29 O O . THR A 1 4 ? -5.998 0.497 1.288 1.00 97.43 4 A 1 ATOM 30 C CB . THR A 1 4 ? -9.107 -0.144 1.966 1.00 97.64 4 A 1 ATOM 31 O OG1 . THR A 1 4 ? -10.283 -0.944 1.896 1.00 92.25 4 A 1 ATOM 32 C CG2 . THR A 1 4 ? -9.297 1.100 1.125 1.00 90.50 4 A 1 ATOM 33 N N . LEU A 1 5 ? -6.261 -0.624 3.230 1.00 97.87 5 A 1 ATOM 34 C CA . LEU A 1 5 ? -5.044 -0.087 3.820 1.00 97.81 5 A 1 ATOM 35 C C . LEU A 1 5 ? -3.822 -0.597 3.075 1.00 98.04 5 A 1 ATOM 36 O O . LEU A 1 5 ? -2.832 0.111 2.915 1.00 97.69 5 A 1 ATOM 37 C CB . LEU A 1 5 ? -4.965 -0.481 5.296 1.00 97.50 5 A 1 ATOM 38 C CG . LEU A 1 5 ? -4.991 0.691 6.260 1.00 90.79 5 A 1 ATOM 39 C CD1 . LEU A 1 5 ? -3.753 1.548 6.095 1.00 86.44 5 A 1 ATOM 40 C CD2 . LEU A 1 5 ? -6.249 1.519 6.037 1.00 87.77 5 A 1 ATOM 41 N N . PHE A 1 6 ? -3.917 -1.840 2.633 1.00 97.34 6 A 1 ATOM 42 C CA . PHE A 1 6 ? -2.820 -2.460 1.900 1.00 97.43 6 A 1 ATOM 43 C C . PHE A 1 6 ? -2.564 -1.736 0.586 1.00 97.73 6 A 1 ATOM 44 O O . PHE A 1 6 ? -1.416 -1.482 0.226 1.00 97.51 6 A 1 ATOM 45 C CB . PHE A 1 6 ? -3.133 -3.925 1.628 1.00 97.12 6 A 1 ATOM 46 C CG . PHE A 1 6 ? -1.908 -4.728 1.278 1.00 95.03 6 A 1 ATOM 47 C CD1 . PHE A 1 6 ? -0.946 -4.993 2.234 1.00 91.09 6 A 1 ATOM 48 C CD2 . PHE A 1 6 ? -1.730 -5.205 -0.010 1.00 91.92 6 A 1 ATOM 49 C CE1 . PHE A 1 6 ? 0.183 -5.729 1.918 1.00 91.10 6 A 1 ATOM 50 C CE2 . PHE A 1 6 ? -0.598 -5.943 -0.335 1.00 91.14 6 A 1 ATOM 51 C CZ . PHE A 1 6 ? 0.357 -6.206 0.628 1.00 91.78 6 A 1 ATOM 52 N N . ILE A 1 7 ? -3.640 -1.423 -0.121 1.00 98.08 7 A 1 ATOM 53 C CA . ILE A 1 7 ? -3.506 -0.721 -1.391 1.00 98.02 7 A 1 ATOM 54 C C . ILE A 1 7 ? -2.978 0.693 -1.179 1.00 98.15 7 A 1 ATOM 55 O O . ILE A 1 7 ? -2.172 1.192 -1.969 1.00 97.95 7 A 1 ATOM 56 C CB . ILE A 1 7 ? -4.838 -0.678 -2.164 1.00 97.82 7 A 1 ATOM 57 C CG1 . ILE A 1 7 ? -4.617 -0.053 -3.545 1.00 96.06 7 A 1 ATOM 58 C CG2 . ILE A 1 7 ? -5.889 0.099 -1.397 1.00 95.69 7 A 1 ATOM 59 C CD1 . ILE A 1 7 ? -5.858 0.005 -4.392 1.00 89.60 7 A 1 ATOM 60 N N . ILE A 1 8 ? -3.435 1.310 -0.106 1.00 98.14 8 A 1 ATOM 61 C CA . ILE A 1 8 ? -2.984 2.657 0.225 1.00 97.99 8 A 1 ATOM 62 C C . ILE A 1 8 ? -1.500 2.643 0.550 1.00 98.00 8 A 1 ATOM 63 O O . ILE A 1 8 ? -0.735 3.476 0.057 1.00 97.82 8 A 1 ATOM 64 C CB . ILE A 1 8 ? -3.774 3.229 1.415 1.00 97.91 8 A 1 ATOM 65 C CG1 . ILE A 1 8 ? -5.243 3.413 1.042 1.00 96.89 8 A 1 ATOM 66 C CG2 . ILE A 1 8 ? -3.175 4.568 1.849 1.00 96.67 8 A 1 ATOM 67 C CD1 . ILE A 1 8 ? -6.129 3.668 2.237 1.00 92.92 8 A 1 ATOM 68 N N . LEU A 1 9 ? -1.113 1.688 1.390 1.00 98.21 9 A 1 ATOM 69 C CA . LEU A 1 9 ? 0.284 1.550 1.771 1.00 98.03 9 A 1 ATOM 70 C C . LEU A 1 9 ? 1.125 1.163 0.571 1.00 98.12 9 A 1 ATOM 71 O O . LEU A 1 9 ? 2.248 1.640 0.404 1.00 97.88 9 A 1 ATOM 72 C CB . LEU A 1 9 ? 0.430 0.500 2.873 1.00 97.86 9 A 1 ATOM 73 C CG . LEU A 1 9 ? 0.763 1.070 4.247 1.00 93.85 9 A 1 ATOM 74 C CD1 . LEU A 1 9 ? 2.135 1.720 4.224 1.00 91.01 9 A 1 ATOM 75 C CD2 . LEU A 1 9 ? -0.296 2.082 4.661 1.00 92.59 9 A 1 ATOM 76 N N . LEU A 1 10 ? 0.563 0.291 -0.256 1.00 97.98 10 A 1 ATOM 77 C CA . LEU A 1 10 ? 1.257 -0.158 -1.454 1.00 97.73 10 A 1 ATOM 78 C C . LEU A 1 10 ? 1.550 1.017 -2.371 1.00 97.77 10 A 1 ATOM 79 O O . LEU A 1 10 ? 2.650 1.145 -2.904 1.00 97.26 10 A 1 ATOM 80 C CB . LEU A 1 10 ? 0.406 -1.188 -2.197 1.00 97.30 10 A 1 ATOM 81 C CG . LEU A 1 10 ? 1.216 -2.352 -2.764 1.00 93.58 10 A 1 ATOM 82 C CD1 . LEU A 1 10 ? 1.573 -3.327 -1.654 1.00 88.93 10 A 1 ATOM 83 C CD2 . LEU A 1 10 ? 0.433 -3.061 -3.853 1.00 89.98 10 A 1 ATOM 84 N N . CYS A 1 11 ? 0.561 1.863 -2.547 1.00 97.74 11 A 1 ATOM 85 C CA . CYS A 1 11 ? 0.713 3.040 -3.397 1.00 97.52 11 A 1 ATOM 86 C C . CYS A 1 11 ? 1.738 3.998 -2.813 1.00 97.59 11 A 1 ATOM 87 O O . CYS A 1 11 ? 2.515 4.610 -3.542 1.00 96.42 11 A 1 ATOM 88 C CB . CYS A 1 11 ? -0.632 3.746 -3.551 1.00 96.64 11 A 1 ATOM 89 S SG . CYS A 1 11 ? -0.588 5.039 -4.794 1.00 93.65 11 A 1 ATOM 90 N N . GLY A 1 12 ? 1.724 4.112 -1.493 1.00 97.62 12 A 1 ATOM 91 C CA . GLY A 1 12 ? 2.661 4.993 -0.814 1.00 97.52 12 A 1 ATOM 92 C C . GLY A 1 12 ? 4.084 4.488 -0.884 1.00 97.89 12 A 1 ATOM 93 O O . GLY A 1 12 ? 4.997 5.235 -1.222 1.00 97.32 12 A 1 ATOM 94 N N . ILE A 1 13 ? 4.266 3.214 -0.557 1.00 97.57 13 A 1 ATOM 95 C CA . ILE A 1 13 ? 5.596 2.618 -0.582 1.00 97.52 13 A 1 ATOM 96 C C . ILE A 1 13 ? 6.118 2.494 -2.005 1.00 97.70 13 A 1 ATOM 97 O O . ILE A 1 13 ? 7.314 2.629 -2.246 1.00 96.83 13 A 1 ATOM 98 C CB . ILE A 1 13 ? 5.602 1.233 0.085 1.00 96.89 13 A 1 ATOM 99 C CG1 . ILE A 1 13 ? 4.620 0.294 -0.604 1.00 94.81 13 A 1 ATOM 100 C CG2 . ILE A 1 13 ? 5.285 1.376 1.564 1.00 93.77 13 A 1 ATOM 101 C CD1 . ILE A 1 13 ? 4.770 -1.139 -0.164 1.00 89.65 13 A 1 ATOM 102 N N . LEU A 1 14 ? 5.217 2.228 -2.934 1.00 97.16 14 A 1 ATOM 103 C CA . LEU A 1 14 ? 5.604 2.105 -4.336 1.00 96.67 14 A 1 ATOM 104 C C . LEU A 1 14 ? 6.083 3.438 -4.878 1.00 96.82 14 A 1 ATOM 105 O O . LEU A 1 14 ? 6.927 3.487 -5.776 1.00 95.45 14 A 1 ATOM 106 C CB . LEU A 1 14 ? 4.424 1.602 -5.163 1.00 95.67 14 A 1 ATOM 107 C CG . LEU A 1 14 ? 4.275 0.086 -5.166 1.00 91.78 14 A 1 ATOM 108 C CD1 . LEU A 1 14 ? 2.969 -0.310 -5.828 1.00 85.84 14 A 1 ATOM 109 C CD2 . LEU A 1 14 ? 5.453 -0.548 -5.892 1.00 85.24 14 A 1 ATOM 110 N N . SER A 1 15 ? 5.553 4.509 -4.337 1.00 96.51 15 A 1 ATOM 111 C CA . SER A 1 15 ? 5.955 5.853 -4.745 1.00 96.17 15 A 1 ATOM 112 C C . SER A 1 15 ? 7.399 6.131 -4.348 1.00 96.24 15 A 1 ATOM 113 O O . SER A 1 15 ? 8.084 6.933 -4.978 1.00 93.83 15 A 1 ATOM 114 C CB . SER A 1 15 ? 5.041 6.894 -4.119 1.00 93.69 15 A 1 ATOM 115 O OG . SER A 1 15 ? 3.764 6.831 -4.692 1.00 84.55 15 A 1 ATOM 116 N N . ALA A 1 16 ? 7.836 5.461 -3.292 1.00 95.82 16 A 1 ATOM 117 C CA . ALA A 1 16 ? 9.187 5.644 -2.802 1.00 94.72 16 A 1 ATOM 118 C C . ALA A 1 16 ? 9.838 4.295 -2.496 1.00 93.76 16 A 1 ATOM 119 O O . ALA A 1 16 ? 9.122 3.346 -2.141 1.00 89.29 16 A 1 ATOM 120 C CB . ALA A 1 16 ? 9.191 6.523 -1.561 1.00 91.93 16 A 1 ATOM 121 O OXT . ALA A 1 16 ? 11.059 4.170 -2.585 1.00 82.16 16 A 1 #