# 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_spkb26001 # _entry.id spkb26001 # 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 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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" "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" "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 HIS 1 1 n PHE 2 1 n LYS 3 1 n PRO 4 1 n ILE 5 1 n LEU 6 1 n VAL 7 1 n LEU 8 1 n CYS 9 1 n LEU 10 1 n ALA 11 1 n THR 12 1 n LEU 13 1 n ALA 14 1 n LEU 15 1 n GLY 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 @ 2025-07-06 20:59:16)" _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 95.05 _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 HIS 1 2 88.07 1 1 A PHE 2 2 92.04 1 2 A LYS 3 2 92.13 1 3 A PRO 4 2 97.44 1 4 A ILE 5 2 96.62 1 5 A LEU 6 2 96.07 1 6 A VAL 7 2 97.68 1 7 A LEU 8 2 96.12 1 8 A CYS 9 2 97.75 1 9 A LEU 10 2 96.24 1 10 A ALA 11 2 98.21 1 11 A THR 12 2 97.17 1 12 A LEU 13 2 96.60 1 13 A ALA 14 2 98.31 1 14 A LEU 15 2 95.31 1 15 A GLY 16 2 90.57 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 HIS . 1 A 1 A 2 1 n PHE . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n CYS . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n GLY . 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 . HIS A 1 1 ? -8.346 -9.745 4.565 1.00 92.12 1 A 1 ATOM 2 C CA . HIS A 1 1 ? -6.887 -9.700 4.410 1.00 93.64 1 A 1 ATOM 3 C C . HIS A 1 1 ? -6.361 -8.264 4.501 1.00 92.10 1 A 1 ATOM 4 O O . HIS A 1 1 ? -7.006 -7.339 4.009 1.00 88.71 1 A 1 ATOM 5 C CB . HIS A 1 1 ? -6.481 -10.309 3.060 1.00 91.73 1 A 1 ATOM 6 C CG . HIS A 1 1 ? -5.442 -11.396 3.187 1.00 87.38 1 A 1 ATOM 7 N ND1 . HIS A 1 1 ? -4.104 -11.156 3.229 1.00 82.24 1 A 1 ATOM 8 C CD2 . HIS A 1 1 ? -5.594 -12.735 3.271 1.00 81.24 1 A 1 ATOM 9 C CE1 . HIS A 1 1 ? -3.462 -12.327 3.342 1.00 85.23 1 A 1 ATOM 10 N NE2 . HIS A 1 1 ? -4.349 -13.295 3.370 1.00 86.33 1 A 1 ATOM 11 N N . PHE A 1 2 ? -5.211 -8.106 5.124 1.00 94.55 2 A 1 ATOM 12 C CA . PHE A 1 2 ? -4.589 -6.797 5.304 1.00 95.87 2 A 1 ATOM 13 C C . PHE A 1 2 ? -3.653 -6.450 4.142 1.00 96.72 2 A 1 ATOM 14 O O . PHE A 1 2 ? -3.005 -5.397 4.157 1.00 95.71 2 A 1 ATOM 15 C CB . PHE A 1 2 ? -3.819 -6.766 6.624 1.00 94.40 2 A 1 ATOM 16 C CG . PHE A 1 2 ? -2.618 -7.684 6.639 1.00 92.16 2 A 1 ATOM 17 C CD1 . PHE A 1 2 ? -1.368 -7.203 6.276 1.00 89.74 2 A 1 ATOM 18 C CD2 . PHE A 1 2 ? -2.748 -9.009 7.010 1.00 88.90 2 A 1 ATOM 19 C CE1 . PHE A 1 2 ? -0.260 -8.034 6.281 1.00 88.23 2 A 1 ATOM 20 C CE2 . PHE A 1 2 ? -1.638 -9.852 7.015 1.00 88.14 2 A 1 ATOM 21 C CZ . PHE A 1 2 ? -0.401 -9.362 6.650 1.00 88.06 2 A 1 ATOM 22 N N . LYS A 1 3 ? -3.584 -7.317 3.179 1.00 96.84 3 A 1 ATOM 23 C CA . LYS A 1 3 ? -2.691 -7.144 2.035 1.00 97.27 3 A 1 ATOM 24 C C . LYS A 1 3 ? -2.941 -5.821 1.299 1.00 97.88 3 A 1 ATOM 25 O O . LYS A 1 3 ? -1.996 -5.065 1.065 1.00 97.69 3 A 1 ATOM 26 C CB . LYS A 1 3 ? -2.822 -8.337 1.084 1.00 96.46 3 A 1 ATOM 27 C CG . LYS A 1 3 ? -1.523 -8.682 0.375 1.00 91.56 3 A 1 ATOM 28 C CD . LYS A 1 3 ? -1.697 -9.878 -0.535 1.00 88.88 3 A 1 ATOM 29 C CE . LYS A 1 3 ? -0.362 -10.378 -1.062 1.00 84.75 3 A 1 ATOM 30 N NZ . LYS A 1 3 ? 0.295 -9.370 -1.940 1.00 77.87 3 A 1 ATOM 31 N N . PRO A 1 4 ? -4.193 -5.533 0.924 1.00 97.83 4 A 1 ATOM 32 C CA . PRO A 1 4 ? -4.480 -4.265 0.233 1.00 98.08 4 A 1 ATOM 33 C C . PRO A 1 4 ? -4.179 -3.054 1.110 1.00 98.28 4 A 1 ATOM 34 O O . PRO A 1 4 ? -3.794 -1.998 0.613 1.00 97.85 4 A 1 ATOM 35 C CB . PRO A 1 4 ? -5.977 -4.362 -0.089 1.00 97.32 4 A 1 ATOM 36 C CG . PRO A 1 4 ? -6.510 -5.357 0.879 1.00 95.72 4 A 1 ATOM 37 C CD . PRO A 1 4 ? -5.394 -6.329 1.118 1.00 97.02 4 A 1 ATOM 38 N N . ILE A 1 5 ? -4.348 -3.214 2.409 1.00 98.12 5 A 1 ATOM 39 C CA . ILE A 1 5 ? -4.072 -2.141 3.358 1.00 98.05 5 A 1 ATOM 40 C C . ILE A 1 5 ? -2.578 -1.846 3.407 1.00 98.18 5 A 1 ATOM 41 O O . ILE A 1 5 ? -2.166 -0.687 3.488 1.00 97.67 5 A 1 ATOM 42 C CB . ILE A 1 5 ? -4.587 -2.505 4.760 1.00 97.71 5 A 1 ATOM 43 C CG1 . ILE A 1 5 ? -6.088 -2.806 4.711 1.00 95.91 5 A 1 ATOM 44 C CG2 . ILE A 1 5 ? -4.305 -1.366 5.740 1.00 95.63 5 A 1 ATOM 45 C CD1 . ILE A 1 5 ? -6.634 -3.293 6.039 1.00 91.69 5 A 1 ATOM 46 N N . LEU A 1 6 ? -1.783 -2.893 3.349 1.00 98.10 6 A 1 ATOM 47 C CA . LEU A 1 6 ? -0.330 -2.745 3.374 1.00 98.05 6 A 1 ATOM 48 C C . LEU A 1 6 ? 0.153 -1.954 2.162 1.00 98.19 6 A 1 ATOM 49 O O . LEU A 1 6 ? 0.989 -1.056 2.283 1.00 98.05 6 A 1 ATOM 50 C CB . LEU A 1 6 ? 0.333 -4.121 3.401 1.00 97.86 6 A 1 ATOM 51 C CG . LEU A 1 6 ? 1.850 -4.078 3.537 1.00 93.70 6 A 1 ATOM 52 C CD1 . LEU A 1 6 ? 2.253 -3.547 4.904 1.00 92.10 6 A 1 ATOM 53 C CD2 . LEU A 1 6 ? 2.442 -5.461 3.314 1.00 92.55 6 A 1 ATOM 54 N N . VAL A 1 7 ? -0.375 -2.289 1.009 1.00 98.33 7 A 1 ATOM 55 C CA . VAL A 1 7 ? -0.016 -1.600 -0.230 1.00 98.27 7 A 1 ATOM 56 C C . VAL A 1 7 ? -0.449 -0.141 -0.169 1.00 98.30 7 A 1 ATOM 57 O O . VAL A 1 7 ? 0.298 0.762 -0.557 1.00 98.10 7 A 1 ATOM 58 C CB . VAL A 1 7 ? -0.664 -2.284 -1.445 1.00 97.99 7 A 1 ATOM 59 C CG1 . VAL A 1 7 ? -0.321 -1.540 -2.728 1.00 96.29 7 A 1 ATOM 60 C CG2 . VAL A 1 7 ? -0.212 -3.734 -1.541 1.00 96.49 7 A 1 ATOM 61 N N . LEU A 1 8 ? -1.652 0.084 0.327 1.00 98.19 8 A 1 ATOM 62 C CA . LEU A 1 8 ? -2.185 1.438 0.451 1.00 98.03 8 A 1 ATOM 63 C C . LEU A 1 8 ? -1.366 2.253 1.444 1.00 98.25 8 A 1 ATOM 64 O O . LEU A 1 8 ? -1.106 3.436 1.222 1.00 98.15 8 A 1 ATOM 65 C CB . LEU A 1 8 ? -3.644 1.377 0.895 1.00 97.68 8 A 1 ATOM 66 C CG . LEU A 1 8 ? -4.363 2.720 0.865 1.00 92.96 8 A 1 ATOM 67 C CD1 . LEU A 1 8 ? -4.497 3.223 -0.567 1.00 92.54 8 A 1 ATOM 68 C CD2 . LEU A 1 8 ? -5.736 2.600 1.507 1.00 93.15 8 A 1 ATOM 69 N N . CYS A 1 9 ? -0.957 1.623 2.511 1.00 98.22 9 A 1 ATOM 70 C CA . CYS A 1 9 ? -0.153 2.277 3.535 1.00 98.22 9 A 1 ATOM 71 C C . CYS A 1 9 ? 1.195 2.708 2.970 1.00 98.41 9 A 1 ATOM 72 O O . CYS A 1 9 ? 1.653 3.824 3.215 1.00 98.23 9 A 1 ATOM 73 C CB . CYS A 1 9 ? 0.047 1.331 4.718 1.00 97.95 9 A 1 ATOM 74 S SG . CYS A 1 9 ? 0.805 2.157 6.126 1.00 95.50 9 A 1 ATOM 75 N N . LEU A 1 10 ? 1.804 1.825 2.211 1.00 98.14 10 A 1 ATOM 76 C CA . LEU A 1 10 ? 3.091 2.123 1.592 1.00 98.09 10 A 1 ATOM 77 C C . LEU A 1 10 ? 2.947 3.252 0.581 1.00 98.33 10 A 1 ATOM 78 O O . LEU A 1 10 ? 3.805 4.135 0.490 1.00 98.20 10 A 1 ATOM 79 C CB . LEU A 1 10 ? 3.643 0.856 0.931 1.00 97.74 10 A 1 ATOM 80 C CG . LEU A 1 10 ? 5.136 0.918 0.621 1.00 94.34 10 A 1 ATOM 81 C CD1 . LEU A 1 10 ? 5.755 -0.466 0.719 1.00 92.48 10 A 1 ATOM 82 C CD2 . LEU A 1 10 ? 5.387 1.493 -0.757 1.00 92.59 10 A 1 ATOM 83 N N . ALA A 1 11 ? 1.861 3.225 -0.184 1.00 98.36 11 A 1 ATOM 84 C CA . ALA A 1 11 ? 1.589 4.269 -1.164 1.00 98.27 11 A 1 ATOM 85 C C . ALA A 1 11 ? 1.388 5.615 -0.474 1.00 98.40 11 A 1 ATOM 86 O O . ALA A 1 11 ? 1.850 6.646 -0.961 1.00 98.03 11 A 1 ATOM 87 C CB . ALA A 1 11 ? 0.356 3.906 -1.983 1.00 98.00 11 A 1 ATOM 88 N N . THR A 1 12 ? 0.708 5.597 0.661 1.00 98.38 12 A 1 ATOM 89 C CA . THR A 1 12 ? 0.467 6.813 1.434 1.00 98.28 12 A 1 ATOM 90 C C . THR A 1 12 ? 1.779 7.366 1.980 1.00 98.38 12 A 1 ATOM 91 O O . THR A 1 12 ? 2.000 8.579 1.971 1.00 97.86 12 A 1 ATOM 92 C CB . THR A 1 12 ? -0.489 6.532 2.597 1.00 97.86 12 A 1 ATOM 93 O OG1 . THR A 1 12 ? -1.685 5.938 2.109 1.00 95.07 12 A 1 ATOM 94 C CG2 . THR A 1 12 ? -0.849 7.822 3.322 1.00 94.34 12 A 1 ATOM 95 N N . LEU A 1 13 ? 2.645 6.478 2.436 1.00 98.50 13 A 1 ATOM 96 C CA . LEU A 1 13 ? 3.943 6.878 2.961 1.00 98.38 13 A 1 ATOM 97 C C . LEU A 1 13 ? 4.798 7.503 1.868 1.00 98.48 13 A 1 ATOM 98 O O . LEU A 1 13 ? 5.510 8.482 2.106 1.00 98.19 13 A 1 ATOM 99 C CB . LEU A 1 13 ? 4.655 5.665 3.554 1.00 98.09 13 A 1 ATOM 100 C CG . LEU A 1 13 ? 5.973 5.990 4.245 1.00 95.97 13 A 1 ATOM 101 C CD1 . LEU A 1 13 ? 5.734 6.842 5.481 1.00 92.63 13 A 1 ATOM 102 C CD2 . LEU A 1 13 ? 6.703 4.712 4.614 1.00 92.58 13 A 1 ATOM 103 N N . ALA A 1 14 ? 4.732 6.942 0.679 1.00 98.49 14 A 1 ATOM 104 C CA . ALA A 1 14 ? 5.478 7.461 -0.461 1.00 98.42 14 A 1 ATOM 105 C C . ALA A 1 14 ? 4.939 8.815 -0.898 1.00 98.48 14 A 1 ATOM 106 O O . ALA A 1 14 ? 5.692 9.677 -1.352 1.00 98.09 14 A 1 ATOM 107 C CB . ALA A 1 14 ? 5.406 6.476 -1.621 1.00 98.08 14 A 1 ATOM 108 N N . LEU A 1 15 ? 3.633 8.994 -0.776 1.00 98.23 15 A 1 ATOM 109 C CA . LEU A 1 15 ? 2.991 10.251 -1.138 1.00 97.94 15 A 1 ATOM 110 C C . LEU A 1 15 ? 3.286 11.325 -0.102 1.00 97.92 15 A 1 ATOM 111 O O . LEU A 1 15 ? 3.415 12.507 -0.437 1.00 97.03 15 A 1 ATOM 112 C CB . LEU A 1 15 ? 1.481 10.042 -1.270 1.00 97.32 15 A 1 ATOM 113 C CG . LEU A 1 15 ? 0.705 11.262 -1.750 1.00 94.70 15 A 1 ATOM 114 C CD1 . LEU A 1 15 ? 1.048 11.579 -3.200 1.00 90.61 15 A 1 ATOM 115 C CD2 . LEU A 1 15 ? -0.793 11.034 -1.603 1.00 88.76 15 A 1 ATOM 116 N N . GLY A 1 16 ? 3.374 10.910 1.142 1.00 95.83 16 A 1 ATOM 117 C CA . GLY A 1 16 ? 3.660 11.827 2.243 1.00 92.60 16 A 1 ATOM 118 C C . GLY A 1 16 ? 5.105 12.262 2.254 1.00 89.69 16 A 1 ATOM 119 O O . GLY A 1 16 ? 5.365 13.472 2.280 1.00 85.43 16 A 1 ATOM 120 O OXT . GLY A 1 16 ? 5.983 11.387 2.259 1.00 89.32 16 A 1 #