# 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_spkb25256 # _entry.id spkb25256 # 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" "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" "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 SER 4 1 n LEU 5 1 n ALA 6 1 n THR 7 1 n ILE 8 1 n ALA 9 1 n LEU 10 1 n ALA 11 1 n ALA 12 1 n ALA 13 1 n VAL 14 1 n ALA 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 @ 2025-07-05 01:33:14)" _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 94.58 _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 85.03 1 1 A LYS 2 2 89.15 1 2 A PHE 3 2 91.00 1 3 A SER 4 2 95.93 1 4 A LEU 5 2 95.40 1 5 A ALA 6 2 97.80 1 6 A THR 7 2 96.63 1 7 A ILE 8 2 96.10 1 8 A ALA 9 2 97.92 1 9 A LEU 10 2 96.00 1 10 A ALA 11 2 97.73 1 11 A ALA 12 2 97.82 1 12 A ALA 13 2 98.11 1 13 A VAL 14 2 96.99 1 14 A ALA 15 2 97.81 1 15 A ALA 16 2 94.07 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 SER . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n THR . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 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 ? -7.655 3.263 10.308 1.00 89.03 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.924 3.312 9.025 1.00 90.32 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.962 1.954 8.335 1.00 92.07 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.122 1.097 8.589 1.00 89.70 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.468 3.701 9.271 1.00 85.66 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.328 5.145 9.686 1.00 83.54 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.632 5.603 10.033 1.00 79.73 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.617 5.430 11.802 1.00 70.19 1 A 1 ATOM 9 N N . LYS A 1 2 ? -7.942 1.755 7.488 1.00 92.63 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -8.079 0.486 6.774 1.00 94.63 2 A 1 ATOM 11 C C . LYS A 1 2 ? -7.655 0.672 5.321 1.00 95.42 2 A 1 ATOM 12 O O . LYS A 1 2 ? -8.382 1.259 4.522 1.00 94.77 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -9.532 0.014 6.852 1.00 92.47 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -9.727 -1.380 6.278 1.00 88.27 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -8.922 -2.402 7.065 1.00 86.50 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -9.102 -3.799 6.508 1.00 81.19 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -10.476 -4.282 6.733 1.00 76.44 2 A 1 ATOM 18 N N . PHE A 1 3 ? -6.472 0.183 4.980 1.00 93.87 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -5.957 0.305 3.617 1.00 94.84 3 A 1 ATOM 20 C C . PHE A 1 3 ? -6.199 -0.967 2.820 1.00 96.24 3 A 1 ATOM 21 O O . PHE A 1 3 ? -6.068 -2.073 3.345 1.00 95.18 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -4.465 0.598 3.655 1.00 93.88 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -4.139 1.849 4.426 1.00 91.80 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -4.619 3.074 4.001 1.00 88.38 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -3.355 1.791 5.565 1.00 88.05 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -4.321 4.236 4.701 1.00 86.48 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -3.051 2.947 6.273 1.00 86.61 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -3.539 4.172 5.841 1.00 85.70 3 A 1 ATOM 29 N N . SER A 1 4 ? -6.545 -0.804 1.561 1.00 96.96 4 A 1 ATOM 30 C CA . SER A 1 4 ? -6.788 -1.944 0.688 1.00 97.26 4 A 1 ATOM 31 C C . SER A 1 4 ? -5.469 -2.434 0.088 1.00 97.88 4 A 1 ATOM 32 O O . SER A 1 4 ? -4.480 -1.708 0.077 1.00 97.59 4 A 1 ATOM 33 C CB . SER A 1 4 ? -7.749 -1.551 -0.428 1.00 96.38 4 A 1 ATOM 34 O OG . SER A 1 4 ? -8.124 -2.686 -1.173 1.00 89.49 4 A 1 ATOM 35 N N . LEU A 1 5 ? -5.465 -3.666 -0.413 1.00 97.12 5 A 1 ATOM 36 C CA . LEU A 1 5 ? -4.257 -4.238 -1.010 1.00 97.52 5 A 1 ATOM 37 C C . LEU A 1 5 ? -3.756 -3.361 -2.153 1.00 97.92 5 A 1 ATOM 38 O O . LEU A 1 5 ? -2.550 -3.216 -2.365 1.00 97.61 5 A 1 ATOM 39 C CB . LEU A 1 5 ? -4.555 -5.643 -1.534 1.00 97.09 5 A 1 ATOM 40 C CG . LEU A 1 5 ? -3.317 -6.349 -2.071 1.00 93.90 5 A 1 ATOM 41 C CD1 . LEU A 1 5 ? -2.329 -6.607 -0.945 1.00 91.35 5 A 1 ATOM 42 C CD2 . LEU A 1 5 ? -3.709 -7.662 -2.736 1.00 90.69 5 A 1 ATOM 43 N N . ALA A 1 6 ? -4.681 -2.771 -2.889 1.00 97.77 6 A 1 ATOM 44 C CA . ALA A 1 6 ? -4.336 -1.896 -4.010 1.00 97.85 6 A 1 ATOM 45 C C . ALA A 1 6 ? -3.572 -0.670 -3.526 1.00 98.14 6 A 1 ATOM 46 O O . ALA A 1 6 ? -2.637 -0.204 -4.180 1.00 97.82 6 A 1 ATOM 47 C CB . ALA A 1 6 ? -5.605 -1.473 -4.734 1.00 97.44 6 A 1 ATOM 48 N N . THR A 1 7 ? -3.959 -0.157 -2.368 1.00 97.54 7 A 1 ATOM 49 C CA . THR A 1 7 ? -3.307 1.017 -1.797 1.00 97.63 7 A 1 ATOM 50 C C . THR A 1 7 ? -1.859 0.700 -1.432 1.00 97.95 7 A 1 ATOM 51 O O . THR A 1 7 ? -0.951 1.488 -1.691 1.00 97.71 7 A 1 ATOM 52 C CB . THR A 1 7 ? -4.047 1.491 -0.542 1.00 97.26 7 A 1 ATOM 53 O OG1 . THR A 1 7 ? -5.429 1.664 -0.837 1.00 94.94 7 A 1 ATOM 54 C CG2 . THR A 1 7 ? -3.473 2.816 -0.059 1.00 93.36 7 A 1 ATOM 55 N N . ILE A 1 8 ? -1.647 -0.459 -0.822 1.00 97.82 8 A 1 ATOM 56 C CA . ILE A 1 8 ? -0.308 -0.881 -0.426 1.00 97.65 8 A 1 ATOM 57 C C . ILE A 1 8 ? 0.567 -1.096 -1.655 1.00 97.87 8 A 1 ATOM 58 O O . ILE A 1 8 ? 1.737 -0.707 -1.682 1.00 97.71 8 A 1 ATOM 59 C CB . ILE A 1 8 ? -0.373 -2.173 0.399 1.00 97.41 8 A 1 ATOM 60 C CG1 . ILE A 1 8 ? -1.263 -1.975 1.633 1.00 95.45 8 A 1 ATOM 61 C CG2 . ILE A 1 8 ? 1.040 -2.584 0.822 1.00 94.68 8 A 1 ATOM 62 C CD1 . ILE A 1 8 ? -0.791 -0.831 2.513 1.00 90.22 8 A 1 ATOM 63 N N . ALA A 1 9 ? 0.005 -1.724 -2.671 1.00 97.89 9 A 1 ATOM 64 C CA . ALA A 1 9 ? 0.743 -1.990 -3.902 1.00 97.92 9 A 1 ATOM 65 C C . ALA A 1 9 ? 1.163 -0.687 -4.576 1.00 98.22 9 A 1 ATOM 66 O O . ALA A 1 9 ? 2.283 -0.569 -5.081 1.00 97.96 9 A 1 ATOM 67 C CB . ALA A 1 9 ? -0.124 -2.811 -4.849 1.00 97.61 9 A 1 ATOM 68 N N . LEU A 1 10 ? 0.273 0.282 -4.570 1.00 97.59 10 A 1 ATOM 69 C CA . LEU A 1 10 ? 0.556 1.579 -5.184 1.00 97.59 10 A 1 ATOM 70 C C . LEU A 1 10 ? 1.704 2.266 -4.453 1.00 98.08 10 A 1 ATOM 71 O O . LEU A 1 10 ? 2.632 2.793 -5.074 1.00 97.88 10 A 1 ATOM 72 C CB . LEU A 1 10 ? -0.705 2.447 -5.158 1.00 97.07 10 A 1 ATOM 73 C CG . LEU A 1 10 ? -0.632 3.677 -6.065 1.00 94.47 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? -2.038 4.153 -6.410 1.00 92.31 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? 0.137 4.807 -5.406 1.00 92.98 10 A 1 ATOM 76 N N . ALA A 1 11 ? 1.646 2.264 -3.127 1.00 97.56 11 A 1 ATOM 77 C CA . ALA A 1 11 ? 2.690 2.884 -2.318 1.00 97.71 11 A 1 ATOM 78 C C . ALA A 1 11 ? 4.031 2.191 -2.536 1.00 98.15 11 A 1 ATOM 79 O O . ALA A 1 11 ? 5.075 2.841 -2.604 1.00 97.98 11 A 1 ATOM 80 C CB . ALA A 1 11 ? 2.302 2.822 -0.847 1.00 97.25 11 A 1 ATOM 81 N N . ALA A 1 12 ? 4.005 0.869 -2.638 1.00 97.92 12 A 1 ATOM 82 C CA . ALA A 1 12 ? 5.227 0.093 -2.848 1.00 97.85 12 A 1 ATOM 83 C C . ALA A 1 12 ? 5.856 0.421 -4.196 1.00 98.20 12 A 1 ATOM 84 O O . ALA A 1 12 ? 7.079 0.515 -4.317 1.00 97.84 12 A 1 ATOM 85 C CB . ALA A 1 12 ? 4.909 -1.394 -2.769 1.00 97.29 12 A 1 ATOM 86 N N . ALA A 1 13 ? 5.032 0.594 -5.211 1.00 98.27 13 A 1 ATOM 87 C CA . ALA A 1 13 ? 5.519 0.913 -6.553 1.00 98.23 13 A 1 ATOM 88 C C . ALA A 1 13 ? 6.215 2.271 -6.574 1.00 98.44 13 A 1 ATOM 89 O O . ALA A 1 13 ? 7.248 2.441 -7.226 1.00 97.93 13 A 1 ATOM 90 C CB . ALA A 1 13 ? 4.358 0.903 -7.542 1.00 97.70 13 A 1 ATOM 91 N N . VAL A 1 14 ? 5.652 3.233 -5.864 1.00 98.13 14 A 1 ATOM 92 C CA . VAL A 1 14 ? 6.230 4.576 -5.800 1.00 98.09 14 A 1 ATOM 93 C C . VAL A 1 14 ? 7.522 4.573 -4.990 1.00 98.32 14 A 1 ATOM 94 O O . VAL A 1 14 ? 8.498 5.237 -5.348 1.00 97.99 14 A 1 ATOM 95 C CB . VAL A 1 14 ? 5.236 5.568 -5.178 1.00 97.30 14 A 1 ATOM 96 C CG1 . VAL A 1 14 ? 5.866 6.949 -5.056 1.00 94.26 14 A 1 ATOM 97 C CG2 . VAL A 1 14 ? 3.973 5.640 -6.022 1.00 94.84 14 A 1 ATOM 98 N N . ALA A 1 15 ? 7.526 3.836 -3.893 1.00 98.10 15 A 1 ATOM 99 C CA . ALA A 1 15 ? 8.699 3.757 -3.021 1.00 97.97 15 A 1 ATOM 100 C C . ALA A 1 15 ? 9.843 2.993 -3.683 1.00 98.17 15 A 1 ATOM 101 O O . ALA A 1 15 ? 11.015 3.322 -3.493 1.00 97.66 15 A 1 ATOM 102 C CB . ALA A 1 15 ? 8.321 3.085 -1.707 1.00 97.14 15 A 1 ATOM 103 N N . ALA A 1 16 ? 9.509 1.953 -4.446 1.00 97.23 16 A 1 ATOM 104 C CA . ALA A 1 16 ? 10.512 1.126 -5.102 1.00 96.42 16 A 1 ATOM 105 C C . ALA A 1 16 ? 11.022 1.771 -6.386 1.00 95.82 16 A 1 ATOM 106 O O . ALA A 1 16 ? 10.309 2.589 -6.979 1.00 92.70 16 A 1 ATOM 107 C CB . ALA A 1 16 ? 9.933 -0.254 -5.392 1.00 94.68 16 A 1 ATOM 108 O OXT . ALA A 1 16 ? 12.141 1.426 -6.826 1.00 87.58 16 A 1 #