# 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_spkb29803 # _entry.id spkb29803 # 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" "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 LYS 2 1 n PHE 3 1 n PHE 4 1 n ALA 5 1 n VAL 6 1 n PHE 7 1 n ALA 8 1 n LEU 9 1 n CYS 10 1 n VAL 11 1 n ALA 12 1 n SER 13 1 n VAL 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 @ 2025-07-12 18:56:40)" _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 88.82 _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 81.00 1 1 A LYS 2 2 82.23 1 2 A PHE 3 2 87.21 1 3 A PHE 4 2 87.71 1 4 A ALA 5 2 93.38 1 5 A VAL 6 2 92.86 1 6 A PHE 7 2 89.92 1 7 A ALA 8 2 92.03 1 8 A LEU 9 2 90.69 1 9 A CYS 10 2 93.15 1 10 A VAL 11 2 91.83 1 11 A ALA 12 2 94.26 1 12 A SER 13 2 92.44 1 13 A VAL 14 2 89.46 1 14 A SER 15 2 88.01 1 15 A ALA 16 2 82.55 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 LYS . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n VAL . 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 ? -9.892 -6.768 2.546 1.00 86.12 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.434 -6.784 2.332 1.00 87.76 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.755 -5.629 3.063 1.00 89.29 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.844 -4.482 2.638 1.00 85.57 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.111 -6.679 0.845 1.00 82.67 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.306 -8.001 0.119 1.00 78.33 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.726 -7.948 -0.967 1.00 74.24 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.406 -9.571 -0.683 1.00 64.04 1 A 1 ATOM 9 N N . LYS A 1 2 ? -7.085 -5.949 4.149 1.00 89.56 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -6.399 -4.935 4.947 1.00 90.38 2 A 1 ATOM 11 C C . LYS A 1 2 ? -5.045 -4.582 4.334 1.00 90.88 2 A 1 ATOM 12 O O . LYS A 1 2 ? -4.553 -3.466 4.493 1.00 89.61 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -6.221 -5.449 6.377 1.00 87.70 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -6.688 -4.460 7.429 1.00 81.22 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -5.539 -3.657 7.989 1.00 76.84 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -6.028 -2.675 9.041 1.00 70.43 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -4.896 -2.061 9.782 1.00 63.46 2 A 1 ATOM 18 N N . PHE A 1 3 ? -4.462 -5.530 3.625 1.00 89.76 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -3.167 -5.328 2.982 1.00 90.78 3 A 1 ATOM 20 C C . PHE A 1 3 ? -3.267 -4.370 1.802 1.00 92.62 3 A 1 ATOM 21 O O . PHE A 1 3 ? -2.326 -3.642 1.504 1.00 91.24 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -2.608 -6.673 2.514 1.00 89.39 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -1.491 -7.173 3.394 1.00 87.22 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -1.720 -7.484 4.720 1.00 84.72 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -0.214 -7.322 2.877 1.00 84.50 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -0.692 -7.933 5.531 1.00 83.21 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? 0.819 -7.776 3.679 1.00 83.84 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? 0.580 -8.082 5.006 1.00 82.00 3 A 1 ATOM 29 N N . PHE A 1 4 ? -4.408 -4.377 1.140 1.00 91.31 4 A 1 ATOM 30 C CA . PHE A 1 4 ? -4.620 -3.519 -0.020 1.00 91.85 4 A 1 ATOM 31 C C . PHE A 1 4 ? -4.594 -2.050 0.386 1.00 93.35 4 A 1 ATOM 32 O O . PHE A 1 4 ? -4.095 -1.197 -0.345 1.00 92.22 4 A 1 ATOM 33 C CB . PHE A 1 4 ? -5.958 -3.859 -0.680 1.00 90.99 4 A 1 ATOM 34 C CG . PHE A 1 4 ? -5.877 -3.818 -2.186 1.00 87.31 4 A 1 ATOM 35 C CD1 . PHE A 1 4 ? -5.650 -2.625 -2.847 1.00 84.06 4 A 1 ATOM 36 C CD2 . PHE A 1 4 ? -6.024 -4.979 -2.932 1.00 84.12 4 A 1 ATOM 37 C CE1 . PHE A 1 4 ? -5.563 -2.582 -4.230 1.00 83.01 4 A 1 ATOM 38 C CE2 . PHE A 1 4 ? -5.946 -4.941 -4.317 1.00 83.75 4 A 1 ATOM 39 C CZ . PHE A 1 4 ? -5.715 -3.740 -4.966 1.00 82.79 4 A 1 ATOM 40 N N . ALA A 1 5 ? -5.128 -1.764 1.556 1.00 93.14 5 A 1 ATOM 41 C CA . ALA A 1 5 ? -5.161 -0.391 2.056 1.00 93.55 5 A 1 ATOM 42 C C . ALA A 1 5 ? -3.748 0.148 2.267 1.00 94.68 5 A 1 ATOM 43 O O . ALA A 1 5 ? -3.442 1.277 1.888 1.00 93.16 5 A 1 ATOM 44 C CB . ALA A 1 5 ? -5.946 -0.339 3.361 1.00 92.36 5 A 1 ATOM 45 N N . VAL A 1 6 ? -2.899 -0.666 2.870 1.00 94.04 6 A 1 ATOM 46 C CA . VAL A 1 6 ? -1.511 -0.280 3.126 1.00 94.32 6 A 1 ATOM 47 C C . VAL A 1 6 ? -0.721 -0.211 1.824 1.00 94.81 6 A 1 ATOM 48 O O . VAL A 1 6 ? 0.134 0.661 1.646 1.00 93.61 6 A 1 ATOM 49 C CB . VAL A 1 6 ? -0.837 -1.271 4.089 1.00 93.48 6 A 1 ATOM 50 C CG1 . VAL A 1 6 ? 0.583 -0.823 4.408 1.00 89.55 6 A 1 ATOM 51 C CG2 . VAL A 1 6 ? -1.648 -1.402 5.369 1.00 90.18 6 A 1 ATOM 52 N N . PHE A 1 7 ? -1.018 -1.127 0.926 1.00 92.42 7 A 1 ATOM 53 C CA . PHE A 1 7 ? -0.335 -1.176 -0.366 1.00 91.87 7 A 1 ATOM 54 C C . PHE A 1 7 ? -0.630 0.077 -1.179 1.00 93.22 7 A 1 ATOM 55 O O . PHE A 1 7 ? 0.258 0.642 -1.815 1.00 92.57 7 A 1 ATOM 56 C CB . PHE A 1 7 ? -0.775 -2.420 -1.140 1.00 91.86 7 A 1 ATOM 57 C CG . PHE A 1 7 ? 0.054 -2.659 -2.376 1.00 90.26 7 A 1 ATOM 58 C CD1 . PHE A 1 7 ? 1.382 -3.036 -2.272 1.00 87.57 7 A 1 ATOM 59 C CD2 . PHE A 1 7 ? -0.504 -2.499 -3.633 1.00 88.27 7 A 1 ATOM 60 C CE1 . PHE A 1 7 ? 2.152 -3.250 -3.406 1.00 86.95 7 A 1 ATOM 61 C CE2 . PHE A 1 7 ? 0.264 -2.711 -4.774 1.00 87.16 7 A 1 ATOM 62 C CZ . PHE A 1 7 ? 1.590 -3.086 -4.660 1.00 86.99 7 A 1 ATOM 63 N N . ALA A 1 8 ? -1.879 0.502 -1.154 1.00 92.06 8 A 1 ATOM 64 C CA . ALA A 1 8 ? -2.294 1.693 -1.894 1.00 91.90 8 A 1 ATOM 65 C C . ALA A 1 8 ? -1.530 2.924 -1.415 1.00 93.37 8 A 1 ATOM 66 O O . ALA A 1 8 ? -1.099 3.752 -2.216 1.00 91.86 8 A 1 ATOM 67 C CB . ALA A 1 8 ? -3.792 1.906 -1.720 1.00 90.98 8 A 1 ATOM 68 N N . LEU A 1 9 ? -1.367 3.035 -0.109 1.00 94.14 9 A 1 ATOM 69 C CA . LEU A 1 9 ? -0.644 4.164 0.478 1.00 94.04 9 A 1 ATOM 70 C C . LEU A 1 9 ? 0.843 4.085 0.158 1.00 95.42 9 A 1 ATOM 71 O O . LEU A 1 9 ? 1.490 5.106 -0.080 1.00 93.93 9 A 1 ATOM 72 C CB . LEU A 1 9 ? -0.855 4.178 1.993 1.00 93.46 9 A 1 ATOM 73 C CG . LEU A 1 9 ? -0.419 5.472 2.675 1.00 87.39 9 A 1 ATOM 74 C CD1 . LEU A 1 9 ? -1.327 6.625 2.275 1.00 83.21 9 A 1 ATOM 75 C CD2 . LEU A 1 9 ? -0.423 5.301 4.187 1.00 83.95 9 A 1 ATOM 76 N N . CYS A 1 10 ? 1.379 2.882 0.155 1.00 94.88 10 A 1 ATOM 77 C CA . CYS A 1 10 ? 2.789 2.662 -0.139 1.00 95.10 10 A 1 ATOM 78 C C . CYS A 1 10 ? 3.109 3.028 -1.586 1.00 95.68 10 A 1 ATOM 79 O O . CYS A 1 10 ? 4.095 3.708 -1.864 1.00 93.81 10 A 1 ATOM 80 C CB . CYS A 1 10 ? 3.154 1.201 0.128 1.00 93.56 10 A 1 ATOM 81 S SG . CYS A 1 10 ? 4.547 1.030 1.264 1.00 85.88 10 A 1 ATOM 82 N N . VAL A 1 11 ? 2.273 2.572 -2.490 1.00 94.18 11 A 1 ATOM 83 C CA . VAL A 1 11 ? 2.460 2.848 -3.912 1.00 93.76 11 A 1 ATOM 84 C C . VAL A 1 11 ? 2.293 4.338 -4.197 1.00 94.47 11 A 1 ATOM 85 O O . VAL A 1 11 ? 2.992 4.908 -5.033 1.00 93.36 11 A 1 ATOM 86 C CB . VAL A 1 11 ? 1.463 2.042 -4.759 1.00 92.30 11 A 1 ATOM 87 C CG1 . VAL A 1 11 ? 1.614 2.386 -6.233 1.00 86.35 11 A 1 ATOM 88 C CG2 . VAL A 1 11 ? 1.673 0.553 -4.549 1.00 88.39 11 A 1 ATOM 89 N N . ALA A 1 12 ? 1.363 4.959 -3.499 1.00 95.03 12 A 1 ATOM 90 C CA . ALA A 1 12 ? 1.107 6.388 -3.673 1.00 94.62 12 A 1 ATOM 91 C C . ALA A 1 12 ? 2.339 7.209 -3.301 1.00 95.68 12 A 1 ATOM 92 O O . ALA A 1 12 ? 2.660 8.194 -3.963 1.00 93.04 12 A 1 ATOM 93 C CB . ALA A 1 12 ? -0.082 6.804 -2.816 1.00 92.94 12 A 1 ATOM 94 N N . SER A 1 13 ? 3.027 6.800 -2.249 1.00 95.48 13 A 1 ATOM 95 C CA . SER A 1 13 ? 4.228 7.487 -1.784 1.00 95.27 13 A 1 ATOM 96 C C . SER A 1 13 ? 5.364 7.367 -2.796 1.00 95.29 13 A 1 ATOM 97 O O . SER A 1 13 ? 6.061 8.340 -3.087 1.00 92.68 13 A 1 ATOM 98 C CB . SER A 1 13 ? 4.673 6.922 -0.437 1.00 93.65 13 A 1 ATOM 99 O OG . SER A 1 13 ? 5.705 7.704 0.111 1.00 82.26 13 A 1 ATOM 100 N N . VAL A 1 14 ? 5.548 6.167 -3.327 1.00 93.93 14 A 1 ATOM 101 C CA . VAL A 1 14 ? 6.596 5.913 -4.319 1.00 92.97 14 A 1 ATOM 102 C C . VAL A 1 14 ? 6.242 6.529 -5.668 1.00 93.71 14 A 1 ATOM 103 O O . VAL A 1 14 ? 7.119 6.982 -6.409 1.00 89.97 14 A 1 ATOM 104 C CB . VAL A 1 14 ? 6.831 4.403 -4.485 1.00 89.77 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? 7.936 4.146 -5.499 1.00 81.91 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? 7.180 3.775 -3.150 1.00 83.99 14 A 1 ATOM 107 N N . SER A 1 15 ? 4.966 6.532 -5.975 1.00 92.14 15 A 1 ATOM 108 C CA . SER A 1 15 ? 4.479 7.074 -7.244 1.00 91.74 15 A 1 ATOM 109 C C . SER A 1 15 ? 4.400 8.601 -7.218 1.00 90.94 15 A 1 ATOM 110 O O . SER A 1 15 ? 4.305 9.247 -8.260 1.00 87.08 15 A 1 ATOM 111 C CB . SER A 1 15 ? 3.102 6.494 -7.573 1.00 88.73 15 A 1 ATOM 112 O OG . SER A 1 15 ? 2.857 6.547 -8.960 1.00 77.42 15 A 1 ATOM 113 N N . ALA A 1 16 ? 4.448 9.174 -6.026 1.00 90.37 16 A 1 ATOM 114 C CA . ALA A 1 16 ? 4.350 10.627 -5.845 1.00 87.16 16 A 1 ATOM 115 C C . ALA A 1 16 ? 5.635 11.336 -6.275 1.00 86.03 16 A 1 ATOM 116 O O . ALA A 1 16 ? 6.237 12.060 -5.477 1.00 79.07 16 A 1 ATOM 117 C CB . ALA A 1 16 ? 4.022 10.942 -4.396 1.00 80.26 16 A 1 ATOM 118 O OXT . ALA A 1 16 ? 6.049 11.200 -7.426 1.00 72.43 16 A 1 #