# 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_spkb00142 # _entry.id spkb00142 # 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 "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C4 H9 N O2" 103.120 UNK y UNKNOWN CC[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 CYS 1 1 n ASN 2 1 n TYR 3 1 n UNK 4 1 n PRO 5 1 n UNK 6 1 n GLY 7 1 n ASN 8 1 n UNK 9 1 n UNK 10 1 n UNK 11 1 n UNK 12 1 n UNK 13 1 n PRO 14 1 n TYR 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 @ 2025-06-25 12:36:43)" _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 85.26 _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 CYS 1 2 84.60 1 1 A ASN 2 2 83.24 1 2 A TYR 3 2 83.52 1 3 A UNK 4 2 86.88 1 4 A PRO 5 2 86.95 1 5 A UNK 6 2 87.69 1 6 A GLY 7 2 87.91 1 7 A ASN 8 2 82.19 1 8 A UNK 9 2 87.87 1 9 A UNK 10 2 86.49 1 10 A UNK 11 2 86.25 1 11 A UNK 12 2 86.05 1 12 A UNK 13 2 86.47 1 13 A PRO 14 2 85.84 1 14 A TYR 15 2 84.94 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 CYS . 1 A 1 A 2 1 n ASN . 2 A 2 A 3 1 n TYR . 3 A 3 A 4 1 n UNK . 4 A 4 A 5 1 n PRO . 5 A 5 A 6 1 n UNK . 6 A 6 A 7 1 n GLY . 7 A 7 A 8 1 n ASN . 8 A 8 A 9 1 n UNK . 9 A 9 A 10 1 n UNK . 10 A 10 A 11 1 n UNK . 11 A 11 A 12 1 n UNK . 12 A 12 A 13 1 n UNK . 13 A 13 A 14 1 n PRO . 14 A 14 A 15 1 n TYR . 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 . CYS A 1 1 ? -4.349 4.715 -4.987 1.00 83.77 1 A 1 ATOM 2 C CA . CYS A 1 1 ? -2.950 4.509 -4.593 1.00 87.13 1 A 1 ATOM 3 C C . CYS A 1 1 ? -2.865 4.060 -3.138 1.00 88.56 1 A 1 ATOM 4 O O . CYS A 1 1 ? -2.952 4.868 -2.221 1.00 85.70 1 A 1 ATOM 5 C CB . CYS A 1 1 ? -2.161 5.806 -4.779 1.00 82.27 1 A 1 ATOM 6 S SG . CYS A 1 1 ? -2.179 6.426 -6.486 1.00 80.15 1 A 1 ATOM 7 N N . ASN A 1 2 ? -2.702 2.756 -2.922 1.00 83.73 2 A 1 ATOM 8 C CA . ASN A 1 2 ? -2.597 2.211 -1.572 1.00 86.30 2 A 1 ATOM 9 C C . ASN A 1 2 ? -1.227 1.584 -1.325 1.00 86.70 2 A 1 ATOM 10 O O . ASN A 1 2 ? -0.594 1.064 -2.249 1.00 83.97 2 A 1 ATOM 11 C CB . ASN A 1 2 ? -3.692 1.167 -1.350 1.00 83.69 2 A 1 ATOM 12 C CG . ASN A 1 2 ? -5.082 1.753 -1.514 1.00 82.16 2 A 1 ATOM 13 O OD1 . ASN A 1 2 ? -5.317 2.929 -1.255 1.00 80.02 2 A 1 ATOM 14 N ND2 . ASN A 1 2 ? -6.028 0.940 -1.955 1.00 79.35 2 A 1 ATOM 15 N N . TYR A 1 3 ? -0.789 1.630 -0.073 1.00 86.65 3 A 1 ATOM 16 C CA . TYR A 1 3 ? 0.496 1.045 0.294 1.00 86.50 3 A 1 ATOM 17 C C . TYR A 1 3 ? 0.293 -0.247 1.085 1.00 86.69 3 A 1 ATOM 18 O O . TYR A 1 3 ? -0.265 -0.231 2.185 1.00 83.38 3 A 1 ATOM 19 C CB . TYR A 1 3 ? 1.296 2.046 1.124 1.00 84.89 3 A 1 ATOM 20 C CG . TYR A 1 3 ? 2.722 1.600 1.357 1.00 83.43 3 A 1 ATOM 21 C CD1 . TYR A 1 3 ? 3.697 1.811 0.391 1.00 83.32 3 A 1 ATOM 22 C CD2 . TYR A 1 3 ? 3.091 0.978 2.546 1.00 83.52 3 A 1 ATOM 23 C CE1 . TYR A 1 3 ? 5.006 1.410 0.602 1.00 82.27 3 A 1 ATOM 24 C CE2 . TYR A 1 3 ? 4.399 0.569 2.761 1.00 81.65 3 A 1 ATOM 25 C CZ . TYR A 1 3 ? 5.352 0.793 1.790 1.00 81.29 3 A 1 ATOM 26 O OH . TYR A 1 3 ? 6.647 0.391 2.000 1.00 78.63 3 A 1 HETATM 27 N N . UNK A 1 4 ? 0.725 -1.344 0.525 1.00 87.45 4 A 1 HETATM 28 C CA . UNK A 1 4 ? 0.584 -2.628 1.199 1.00 86.33 4 A 1 HETATM 29 C C . UNK A 1 4 ? -0.822 -3.201 1.066 1.00 87.24 4 A 1 HETATM 30 O O . UNK A 1 4 ? -1.752 -2.504 0.638 1.00 86.52 4 A 1 ATOM 31 N N . PRO A 1 5 ? -0.999 -4.463 1.430 1.00 87.51 5 A 1 ATOM 32 C CA . PRO A 1 5 ? -2.303 -5.131 1.354 1.00 87.94 5 A 1 ATOM 33 C C . PRO A 1 5 ? -3.338 -4.501 2.283 1.00 87.96 5 A 1 ATOM 34 O O . PRO A 1 5 ? -4.532 -4.771 2.154 1.00 85.15 5 A 1 ATOM 35 C CB . PRO A 1 5 ? -1.991 -6.575 1.779 1.00 85.70 5 A 1 ATOM 36 C CG . PRO A 1 5 ? -0.756 -6.452 2.622 1.00 85.69 5 A 1 ATOM 37 C CD . PRO A 1 5 ? 0.039 -5.327 2.001 1.00 88.68 5 A 1 HETATM 38 N N . UNK A 1 6 ? -2.920 -3.666 3.203 1.00 88.47 6 A 1 HETATM 39 C CA . UNK A 1 6 ? -3.828 -3.001 4.127 1.00 87.70 6 A 1 HETATM 40 C C . UNK A 1 6 ? -4.804 -2.095 3.405 1.00 89.15 6 A 1 HETATM 41 O O . UNK A 1 6 ? -5.960 -1.958 3.807 1.00 85.42 6 A 1 ATOM 42 N N . GLY A 1 7 ? -4.357 -1.472 2.339 1.00 87.95 7 A 1 ATOM 43 C CA . GLY A 1 7 ? -5.220 -0.579 1.573 1.00 87.65 7 A 1 ATOM 44 C C . GLY A 1 7 ? -5.196 0.840 2.108 1.00 88.81 7 A 1 ATOM 45 O O . GLY A 1 7 ? -6.212 1.529 2.092 1.00 87.21 7 A 1 ATOM 46 N N . ASN A 1 8 ? -4.050 1.284 2.580 1.00 85.33 8 A 1 ATOM 47 C CA . ASN A 1 8 ? -3.921 2.642 3.107 1.00 85.63 8 A 1 ATOM 48 C C . ASN A 1 8 ? -3.305 3.567 2.065 1.00 85.75 8 A 1 ATOM 49 O O . ASN A 1 8 ? -2.252 3.269 1.503 1.00 82.43 8 A 1 ATOM 50 C CB . ASN A 1 8 ? -3.064 2.649 4.371 1.00 82.64 8 A 1 ATOM 51 C CG . ASN A 1 8 ? -3.869 2.234 5.587 1.00 80.58 8 A 1 ATOM 52 O OD1 . ASN A 1 8 ? -4.682 1.315 5.526 1.00 77.64 8 A 1 ATOM 53 N ND2 . ASN A 1 8 ? -3.648 2.902 6.702 1.00 77.50 8 A 1 HETATM 54 N N . UNK A 1 9 ? -3.964 4.682 1.796 1.00 88.46 9 A 1 HETATM 55 C CA . UNK A 1 9 ? -3.476 5.643 0.812 1.00 88.31 9 A 1 HETATM 56 C C . UNK A 1 9 ? -2.379 6.506 1.398 1.00 88.97 9 A 1 HETATM 57 O O . UNK A 1 9 ? -2.655 7.582 1.915 1.00 85.72 9 A 1 HETATM 58 N N . UNK A 1 10 ? -1.155 6.050 1.317 1.00 87.52 10 A 1 HETATM 59 C CA . UNK A 1 10 ? -0.019 6.806 1.831 1.00 86.79 10 A 1 HETATM 60 C C . UNK A 1 10 ? 1.278 6.380 1.172 1.00 87.87 10 A 1 HETATM 61 O O . UNK A 1 10 ? 2.081 5.692 1.783 1.00 83.78 10 A 1 HETATM 62 N N . UNK A 1 11 ? 1.497 6.784 -0.074 1.00 86.87 11 A 1 HETATM 63 C CA . UNK A 1 11 ? 2.724 6.461 -0.789 1.00 86.61 11 A 1 HETATM 64 C C . UNK A 1 11 ? 2.439 6.041 -2.209 1.00 87.54 11 A 1 HETATM 65 O O . UNK A 1 11 ? 1.278 5.950 -2.627 1.00 83.98 11 A 1 HETATM 66 N N . UNK A 1 12 ? 3.497 5.782 -2.966 1.00 86.66 12 A 1 HETATM 67 C CA . UNK A 1 12 ? 3.363 5.369 -4.356 1.00 86.23 12 A 1 HETATM 68 C C . UNK A 1 12 ? 3.459 3.864 -4.500 1.00 87.31 12 A 1 HETATM 69 O O . UNK A 1 12 ? 3.914 3.383 -5.528 1.00 83.98 12 A 1 HETATM 70 N N . UNK A 1 13 ? 3.038 3.101 -3.505 1.00 86.51 13 A 1 HETATM 71 C CA . UNK A 1 13 ? 3.087 1.644 -3.554 1.00 86.41 13 A 1 HETATM 72 C C . UNK A 1 13 ? 2.050 1.091 -4.517 1.00 87.26 13 A 1 HETATM 73 O O . UNK A 1 13 ? 0.971 1.663 -4.659 1.00 85.70 13 A 1 ATOM 74 N N . PRO A 1 14 ? 2.382 -0.010 -5.204 1.00 86.89 14 A 1 ATOM 75 C CA . PRO A 1 14 ? 1.461 -0.650 -6.155 1.00 86.77 14 A 1 ATOM 76 C C . PRO A 1 14 ? 0.255 -1.272 -5.459 1.00 87.24 14 A 1 ATOM 77 O O . PRO A 1 14 ? -0.722 -1.625 -6.116 1.00 84.37 14 A 1 ATOM 78 C CB . PRO A 1 14 ? 2.321 -1.715 -6.836 1.00 83.98 14 A 1 ATOM 79 C CG . PRO A 1 14 ? 3.405 -2.000 -5.846 1.00 84.30 14 A 1 ATOM 80 C CD . PRO A 1 14 ? 3.671 -0.698 -5.132 1.00 87.31 14 A 1 ATOM 81 N N . TYR A 1 15 ? 0.298 -1.453 -4.172 1.00 88.40 15 A 1 ATOM 82 C CA . TYR A 1 15 ? -0.848 -1.904 -3.381 1.00 88.30 15 A 1 ATOM 83 C C . TYR A 1 15 ? -0.698 -1.513 -1.932 1.00 86.51 15 A 1 ATOM 84 O O . TYR A 1 15 ? -1.744 -1.516 -1.235 1.00 84.07 15 A 1 ATOM 85 C CB . TYR A 1 15 ? -1.065 -3.405 -3.447 1.00 85.09 15 A 1 ATOM 86 C CG . TYR A 1 15 ? 0.174 -4.269 -3.381 1.00 85.57 15 A 1 ATOM 87 C CD1 . TYR A 1 15 ? 1.103 -4.163 -2.353 1.00 85.34 15 A 1 ATOM 88 C CD2 . TYR A 1 15 ? 0.380 -5.258 -4.350 1.00 85.66 15 A 1 ATOM 89 C CE1 . TYR A 1 15 ? 2.207 -4.996 -2.298 1.00 85.34 15 A 1 ATOM 90 C CE2 . TYR A 1 15 ? 1.469 -6.086 -4.294 1.00 85.83 15 A 1 ATOM 91 C CZ . TYR A 1 15 ? 2.382 -5.959 -3.275 1.00 84.00 15 A 1 ATOM 92 O OH . TYR A 1 15 ? 3.479 -6.790 -3.230 1.00 79.74 15 A 1 ATOM 93 O OXT . TYR A 1 15 ? 0.254 -0.965 -1.578 1.00 80.38 15 A 1 #