# 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_spkb29369 # _entry.id spkb29369 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=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" "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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 LEU 2 1 n PHE 3 1 n SER 4 1 n TYR 5 1 n LEU 6 1 n LEU 7 1 n ALA 8 1 n THR 9 1 n LEU 10 1 n PRO 11 1 n LEU 12 1 n LEU 13 1 n ALA 14 1 n ASN 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 @ 2025-07-12 16:12:10)" _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 88.17 _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 81.62 1 1 A LEU 2 2 85.61 1 2 A PHE 3 2 87.26 1 3 A SER 4 2 91.11 1 4 A TYR 5 2 87.56 1 5 A LEU 6 2 89.87 1 6 A LEU 7 2 89.92 1 7 A ALA 8 2 93.49 1 8 A THR 9 2 89.99 1 9 A LEU 10 2 90.03 1 10 A PRO 11 2 92.92 1 11 A LEU 12 2 89.86 1 12 A LEU 13 2 86.94 1 13 A ALA 14 2 91.27 1 14 A ASN 15 2 84.09 1 15 A ALA 16 2 83.30 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 LEU . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n TYR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PRO . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ASN . 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 ? 1.187 6.106 9.056 1.00 87.02 1 A 1 ATOM 2 C CA . MET A 1 1 ? 2.457 6.562 8.454 1.00 88.05 1 A 1 ATOM 3 C C . MET A 1 1 ? 2.257 6.869 6.969 1.00 88.95 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.416 6.259 6.314 1.00 87.36 1 A 1 ATOM 5 C CB . MET A 1 1 ? 3.541 5.497 8.612 1.00 82.07 1 A 1 ATOM 6 C CG . MET A 1 1 ? 4.005 5.358 10.069 1.00 77.03 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.658 4.913 11.168 1.00 74.85 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.523 4.928 12.734 1.00 67.61 1 A 1 ATOM 9 N N . LEU A 1 2 ? 3.043 7.786 6.454 1.00 85.69 2 A 1 ATOM 10 C CA . LEU A 1 2 ? 2.940 8.199 5.054 1.00 88.83 2 A 1 ATOM 11 C C . LEU A 1 2 ? 3.255 7.052 4.097 1.00 91.16 2 A 1 ATOM 12 O O . LEU A 1 2 ? 2.506 6.783 3.158 1.00 90.78 2 A 1 ATOM 13 C CB . LEU A 1 2 ? 3.881 9.379 4.785 1.00 87.32 2 A 1 ATOM 14 C CG . LEU A 1 2 ? 3.321 10.752 5.170 1.00 83.11 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? 2.088 11.058 4.340 1.00 79.87 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 2.980 10.803 6.655 1.00 78.13 2 A 1 ATOM 17 N N . PHE A 1 3 ? 4.360 6.368 4.339 1.00 89.73 3 A 1 ATOM 18 C CA . PHE A 1 3 ? 4.771 5.257 3.481 1.00 90.08 3 A 1 ATOM 19 C C . PHE A 1 3 ? 3.807 4.079 3.593 1.00 92.11 3 A 1 ATOM 20 O O . PHE A 1 3 ? 3.695 3.270 2.677 1.00 91.73 3 A 1 ATOM 21 C CB . PHE A 1 3 ? 6.184 4.811 3.860 1.00 89.17 3 A 1 ATOM 22 C CG . PHE A 1 3 ? 6.810 3.938 2.814 1.00 87.30 3 A 1 ATOM 23 C CD1 . PHE A 1 3 ? 7.293 4.490 1.639 1.00 84.63 3 A 1 ATOM 24 C CD2 . PHE A 1 3 ? 6.908 2.574 3.008 1.00 84.58 3 A 1 ATOM 25 C CE1 . PHE A 1 3 ? 7.870 3.694 0.663 1.00 84.49 3 A 1 ATOM 26 C CE2 . PHE A 1 3 ? 7.480 1.764 2.030 1.00 83.06 3 A 1 ATOM 27 C CZ . PHE A 1 3 ? 7.959 2.327 0.859 1.00 83.02 3 A 1 ATOM 28 N N . SER A 1 4 ? 3.106 3.987 4.700 1.00 92.28 4 A 1 ATOM 29 C CA . SER A 1 4 ? 2.149 2.906 4.918 1.00 92.80 4 A 1 ATOM 30 C C . SER A 1 4 ? 0.987 2.997 3.933 1.00 93.39 4 A 1 ATOM 31 O O . SER A 1 4 ? 0.428 1.983 3.520 1.00 91.88 4 A 1 ATOM 32 C CB . SER A 1 4 ? 1.619 2.951 6.354 1.00 91.23 4 A 1 ATOM 33 O OG . SER A 1 4 ? 2.678 2.902 7.287 1.00 85.10 4 A 1 ATOM 34 N N . TYR A 1 5 ? 0.632 4.197 3.544 1.00 90.75 5 A 1 ATOM 35 C CA . TYR A 1 5 ? -0.469 4.414 2.614 1.00 91.05 5 A 1 ATOM 36 C C . TYR A 1 5 ? -0.086 3.973 1.204 1.00 92.19 5 A 1 ATOM 37 O O . TYR A 1 5 ? -0.876 3.327 0.508 1.00 91.39 5 A 1 ATOM 38 C CB . TYR A 1 5 ? -0.864 5.890 2.608 1.00 90.65 5 A 1 ATOM 39 C CG . TYR A 1 5 ? -1.533 6.320 3.897 1.00 88.22 5 A 1 ATOM 40 C CD1 . TYR A 1 5 ? -0.787 6.578 5.036 1.00 85.99 5 A 1 ATOM 41 C CD2 . TYR A 1 5 ? -2.915 6.463 3.963 1.00 85.37 5 A 1 ATOM 42 C CE1 . TYR A 1 5 ? -1.399 6.960 6.224 1.00 84.31 5 A 1 ATOM 43 C CE2 . TYR A 1 5 ? -3.536 6.849 5.146 1.00 83.84 5 A 1 ATOM 44 C CZ . TYR A 1 5 ? -2.770 7.095 6.272 1.00 84.41 5 A 1 ATOM 45 O OH . TYR A 1 5 ? -3.380 7.475 7.442 1.00 82.52 5 A 1 ATOM 46 N N . LEU A 1 6 ? 1.117 4.303 0.794 1.00 92.46 6 A 1 ATOM 47 C CA . LEU A 1 6 ? 1.599 3.923 -0.531 1.00 92.47 6 A 1 ATOM 48 C C . LEU A 1 6 ? 1.734 2.410 -0.648 1.00 93.53 6 A 1 ATOM 49 O O . LEU A 1 6 ? 1.451 1.828 -1.694 1.00 93.82 6 A 1 ATOM 50 C CB . LEU A 1 6 ? 2.949 4.586 -0.816 1.00 92.10 6 A 1 ATOM 51 C CG . LEU A 1 6 ? 2.849 6.071 -1.155 1.00 86.71 6 A 1 ATOM 52 C CD1 . LEU A 1 6 ? 2.786 6.914 0.115 1.00 84.16 6 A 1 ATOM 53 C CD2 . LEU A 1 6 ? 4.030 6.504 -2.008 1.00 83.69 6 A 1 ATOM 54 N N . LEU A 1 7 ? 2.150 1.773 0.429 1.00 92.88 7 A 1 ATOM 55 C CA . LEU A 1 7 ? 2.323 0.322 0.442 1.00 92.88 7 A 1 ATOM 56 C C . LEU A 1 7 ? 0.972 -0.389 0.440 1.00 93.40 7 A 1 ATOM 57 O O . LEU A 1 7 ? 0.870 -1.546 0.039 1.00 93.11 7 A 1 ATOM 58 C CB . LEU A 1 7 ? 3.130 -0.091 1.677 1.00 91.76 7 A 1 ATOM 59 C CG . LEU A 1 7 ? 3.635 -1.532 1.639 1.00 86.54 7 A 1 ATOM 60 C CD1 . LEU A 1 7 ? 4.771 -1.665 0.630 1.00 84.71 7 A 1 ATOM 61 C CD2 . LEU A 1 7 ? 4.112 -1.964 3.017 1.00 84.06 7 A 1 ATOM 62 N N . ALA A 1 8 ? -0.061 0.289 0.883 1.00 93.47 8 A 1 ATOM 63 C CA . ALA A 1 8 ? -1.401 -0.284 0.938 1.00 93.60 8 A 1 ATOM 64 C C . ALA A 1 8 ? -2.205 0.031 -0.321 1.00 94.64 8 A 1 ATOM 65 O O . ALA A 1 8 ? -3.276 -0.532 -0.540 1.00 93.13 8 A 1 ATOM 66 C CB . ALA A 1 8 ? -2.126 0.240 2.173 1.00 92.62 8 A 1 ATOM 67 N N . THR A 1 9 ? -1.689 0.919 -1.146 1.00 92.25 9 A 1 ATOM 68 C CA . THR A 1 9 ? -2.378 1.313 -2.372 1.00 91.92 9 A 1 ATOM 69 C C . THR A 1 9 ? -1.930 0.477 -3.566 1.00 92.60 9 A 1 ATOM 70 O O . THR A 1 9 ? -2.738 0.125 -4.423 1.00 90.66 9 A 1 ATOM 71 C CB . THR A 1 9 ? -2.132 2.795 -2.678 1.00 90.58 9 A 1 ATOM 72 O OG1 . THR A 1 9 ? -0.745 3.077 -2.606 1.00 86.30 9 A 1 ATOM 73 C CG2 . THR A 1 9 ? -2.877 3.672 -1.696 1.00 85.65 9 A 1 ATOM 74 N N . LEU A 1 10 ? -0.650 0.157 -3.625 1.00 92.55 10 A 1 ATOM 75 C CA . LEU A 1 10 ? -0.106 -0.639 -4.724 1.00 92.89 10 A 1 ATOM 76 C C . LEU A 1 10 ? -0.676 -2.060 -4.742 1.00 93.91 10 A 1 ATOM 77 O O . LEU A 1 10 ? -1.104 -2.536 -5.795 1.00 92.68 10 A 1 ATOM 78 C CB . LEU A 1 10 ? 1.422 -0.680 -4.627 1.00 91.64 10 A 1 ATOM 79 C CG . LEU A 1 10 ? 2.099 0.668 -4.835 1.00 88.14 10 A 1 ATOM 80 C CD1 . LEU A 1 10 ? 3.557 0.599 -4.417 1.00 84.78 10 A 1 ATOM 81 C CD2 . LEU A 1 10 ? 1.988 1.098 -6.291 1.00 83.69 10 A 1 ATOM 82 N N . PRO A 1 11 ? -0.688 -2.759 -3.607 1.00 94.02 11 A 1 ATOM 83 C CA . PRO A 1 11 ? -1.217 -4.132 -3.551 1.00 93.55 11 A 1 ATOM 84 C C . PRO A 1 11 ? -2.682 -4.204 -3.945 1.00 94.00 11 A 1 ATOM 85 O O . PRO A 1 11 ? -3.148 -5.225 -4.446 1.00 92.09 11 A 1 ATOM 86 C CB . PRO A 1 11 ? -1.040 -4.530 -2.083 1.00 92.03 11 A 1 ATOM 87 C CG . PRO A 1 11 ? 0.020 -3.623 -1.567 1.00 91.27 11 A 1 ATOM 88 C CD . PRO A 1 11 ? -0.140 -2.333 -2.329 1.00 93.47 11 A 1 ATOM 89 N N . LEU A 1 12 ? -3.412 -3.135 -3.730 1.00 92.28 12 A 1 ATOM 90 C CA . LEU A 1 12 ? -4.833 -3.083 -4.054 1.00 92.17 12 A 1 ATOM 91 C C . LEU A 1 12 ? -5.055 -3.266 -5.548 1.00 92.69 12 A 1 ATOM 92 O O . LEU A 1 12 ? -6.041 -3.867 -5.976 1.00 90.68 12 A 1 ATOM 93 C CB . LEU A 1 12 ? -5.409 -1.748 -3.588 1.00 91.08 12 A 1 ATOM 94 C CG . LEU A 1 12 ? -6.827 -1.845 -3.043 1.00 89.04 12 A 1 ATOM 95 C CD1 . LEU A 1 12 ? -7.204 -0.563 -2.333 1.00 86.39 12 A 1 ATOM 96 C CD2 . LEU A 1 12 ? -7.821 -2.147 -4.151 1.00 84.55 12 A 1 ATOM 97 N N . LEU A 1 13 ? -4.143 -2.763 -6.346 1.00 92.09 13 A 1 ATOM 98 C CA . LEU A 1 13 ? -4.235 -2.884 -7.799 1.00 90.98 13 A 1 ATOM 99 C C . LEU A 1 13 ? -3.996 -4.318 -8.246 1.00 91.52 13 A 1 ATOM 100 O O . LEU A 1 13 ? -4.601 -4.781 -9.214 1.00 89.71 13 A 1 ATOM 101 C CB . LEU A 1 13 ? -3.209 -1.968 -8.466 1.00 89.18 13 A 1 ATOM 102 C CG . LEU A 1 13 ? -3.385 -1.829 -9.973 1.00 84.46 13 A 1 ATOM 103 C CD1 . LEU A 1 13 ? -4.568 -0.927 -10.287 1.00 79.41 13 A 1 ATOM 104 C CD2 . LEU A 1 13 ? -2.120 -1.276 -10.604 1.00 78.15 13 A 1 ATOM 105 N N . ALA A 1 14 ? -3.120 -5.023 -7.555 1.00 92.06 14 A 1 ATOM 106 C CA . ALA A 1 14 ? -2.796 -6.407 -7.891 1.00 91.54 14 A 1 ATOM 107 C C . ALA A 1 14 ? -3.777 -7.389 -7.261 1.00 92.22 14 A 1 ATOM 108 O O . ALA A 1 14 ? -3.904 -8.525 -7.711 1.00 90.51 14 A 1 ATOM 109 C CB . ALA A 1 14 ? -1.376 -6.731 -7.441 1.00 90.01 14 A 1 ATOM 110 N N . ASN A 1 15 ? -4.455 -6.959 -6.219 1.00 87.92 15 A 1 ATOM 111 C CA . ASN A 1 15 ? -5.419 -7.809 -5.523 1.00 87.57 15 A 1 ATOM 112 C C . ASN A 1 15 ? -6.758 -7.818 -6.238 1.00 88.11 15 A 1 ATOM 113 O O . ASN A 1 15 ? -7.345 -8.876 -6.477 1.00 86.30 15 A 1 ATOM 114 C CB . ASN A 1 15 ? -5.607 -7.329 -4.089 1.00 84.84 15 A 1 ATOM 115 C CG . ASN A 1 15 ? -6.363 -8.339 -3.261 1.00 82.04 15 A 1 ATOM 116 O OD1 . ASN A 1 15 ? -5.793 -8.971 -2.379 1.00 78.67 15 A 1 ATOM 117 N ND2 . ASN A 1 15 ? -7.648 -8.499 -3.504 1.00 77.30 15 A 1 ATOM 118 N N . ALA A 1 16 ? -7.237 -6.660 -6.576 1.00 89.39 16 A 1 ATOM 119 C CA . ALA A 1 16 ? -8.529 -6.523 -7.256 1.00 86.98 16 A 1 ATOM 120 C C . ALA A 1 16 ? -8.380 -6.690 -8.766 1.00 85.06 16 A 1 ATOM 121 O O . ALA A 1 16 ? -8.416 -5.693 -9.496 1.00 80.97 16 A 1 ATOM 122 C CB . ALA A 1 16 ? -9.148 -5.184 -6.915 1.00 82.18 16 A 1 ATOM 123 O OXT . ALA A 1 16 ? -8.214 -7.850 -9.205 1.00 75.24 16 A 1 #