# 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_spkb24917 # _entry.id spkb24917 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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 ILE 5 1 n GLY 6 1 n VAL 7 1 n SER 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n THR 12 1 n LEU 13 1 n ALA 14 1 n GLY 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 @ 2025-07-06 04:58:02)" _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 92.18 _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 84.02 1 1 A LYS 2 2 86.20 1 2 A PHE 3 2 90.08 1 3 A SER 4 2 93.71 1 4 A ILE 5 2 93.56 1 5 A GLY 6 2 96.15 1 6 A VAL 7 2 96.15 1 7 A SER 8 2 94.32 1 8 A LEU 9 2 94.18 1 9 A LEU 10 2 94.23 1 10 A ALA 11 2 97.27 1 11 A THR 12 2 95.31 1 12 A LEU 13 2 94.08 1 13 A ALA 14 2 95.96 1 14 A GLY 15 2 93.34 1 15 A ALA 16 2 83.45 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 ILE . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n LEU . 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 GLY . 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 ? 0.032 -10.614 5.632 1.00 88.92 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.063 -9.751 5.146 1.00 89.88 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.586 -8.847 4.011 1.00 90.85 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.401 -7.646 4.195 1.00 87.62 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.595 -8.887 6.285 1.00 85.46 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.273 -9.708 7.358 1.00 83.39 1 A 1 ATOM 7 S SD . MET A 1 1 ? -2.983 -8.674 8.647 1.00 78.34 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.793 -9.915 9.636 1.00 67.71 1 A 1 ATOM 9 N N . LYS A 1 2 ? -0.393 -9.448 2.852 1.00 91.51 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 0.055 -8.688 1.688 1.00 92.85 2 A 1 ATOM 11 C C . LYS A 1 2 ? -1.038 -7.732 1.210 1.00 93.75 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.754 -6.675 0.653 1.00 93.22 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 0.459 -9.651 0.565 1.00 89.41 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 1.095 -8.966 -0.615 1.00 85.13 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 2.414 -8.299 -0.238 1.00 83.17 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 3.528 -9.308 -0.074 1.00 76.33 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 4.812 -8.642 0.264 1.00 70.46 2 A 1 ATOM 18 N N . PHE A 1 3 ? -2.294 -8.110 1.457 1.00 92.45 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -3.434 -7.275 1.071 1.00 93.93 3 A 1 ATOM 20 C C . PHE A 1 3 ? -3.400 -5.947 1.815 1.00 95.74 3 A 1 ATOM 21 O O . PHE A 1 3 ? -3.687 -4.892 1.248 1.00 94.68 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -4.738 -8.004 1.379 1.00 93.08 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -4.835 -9.339 0.691 1.00 90.81 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -4.506 -10.500 1.363 1.00 87.20 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -5.250 -9.413 -0.628 1.00 87.06 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -4.592 -11.731 0.731 1.00 86.05 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -5.337 -10.639 -1.271 1.00 85.51 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -5.007 -11.799 -0.590 1.00 84.33 3 A 1 ATOM 29 N N . SER A 1 4 ? -3.031 -5.999 3.087 1.00 95.04 4 A 1 ATOM 30 C CA . SER A 1 4 ? -2.944 -4.799 3.915 1.00 95.80 4 A 1 ATOM 31 C C . SER A 1 4 ? -1.875 -3.850 3.382 1.00 96.51 4 A 1 ATOM 32 O O . SER A 1 4 ? -2.053 -2.631 3.373 1.00 95.79 4 A 1 ATOM 33 C CB . SER A 1 4 ? -2.627 -5.175 5.360 1.00 94.41 4 A 1 ATOM 34 O OG . SER A 1 4 ? -2.740 -4.055 6.198 1.00 84.72 4 A 1 ATOM 35 N N . ILE A 1 5 ? -0.759 -4.431 2.922 1.00 95.29 5 A 1 ATOM 36 C CA . ILE A 1 5 ? 0.339 -3.650 2.357 1.00 95.64 5 A 1 ATOM 37 C C . ILE A 1 5 ? -0.118 -2.934 1.094 1.00 96.38 5 A 1 ATOM 38 O O . ILE A 1 5 ? 0.213 -1.770 0.861 1.00 96.03 5 A 1 ATOM 39 C CB . ILE A 1 5 ? 1.548 -4.551 2.050 1.00 95.31 5 A 1 ATOM 40 C CG1 . ILE A 1 5 ? 1.991 -5.308 3.311 1.00 92.54 5 A 1 ATOM 41 C CG2 . ILE A 1 5 ? 2.702 -3.722 1.488 1.00 91.10 5 A 1 ATOM 42 C CD1 . ILE A 1 5 ? 2.388 -4.387 4.450 1.00 86.15 5 A 1 ATOM 43 N N . GLY A 1 6 ? -0.872 -3.643 0.283 1.00 95.45 6 A 1 ATOM 44 C CA . GLY A 1 6 ? -1.385 -3.067 -0.953 1.00 95.83 6 A 1 ATOM 45 C C . GLY A 1 6 ? -2.322 -1.905 -0.687 1.00 96.76 6 A 1 ATOM 46 O O . GLY A 1 6 ? -2.259 -0.870 -1.350 1.00 96.56 6 A 1 ATOM 47 N N . VAL A 1 7 ? -3.190 -2.072 0.299 1.00 97.01 7 A 1 ATOM 48 C CA . VAL A 1 7 ? -4.137 -1.024 0.680 1.00 97.16 7 A 1 ATOM 49 C C . VAL A 1 7 ? -3.396 0.198 1.207 1.00 97.40 7 A 1 ATOM 50 O O . VAL A 1 7 ? -3.749 1.337 0.894 1.00 97.14 7 A 1 ATOM 51 C CB . VAL A 1 7 ? -5.120 -1.541 1.743 1.00 96.62 7 A 1 ATOM 52 C CG1 . VAL A 1 7 ? -6.046 -0.427 2.213 1.00 93.82 7 A 1 ATOM 53 C CG2 . VAL A 1 7 ? -5.935 -2.694 1.182 1.00 93.87 7 A 1 ATOM 54 N N . SER A 1 8 ? -2.361 -0.052 2.003 1.00 96.15 8 A 1 ATOM 55 C CA . SER A 1 8 ? -1.559 1.028 2.568 1.00 96.06 8 A 1 ATOM 56 C C . SER A 1 8 ? -0.860 1.819 1.465 1.00 96.75 8 A 1 ATOM 57 O O . SER A 1 8 ? -0.795 3.047 1.515 1.00 96.30 8 A 1 ATOM 58 C CB . SER A 1 8 ? -0.522 0.465 3.536 1.00 95.23 8 A 1 ATOM 59 O OG . SER A 1 8 ? -1.156 -0.133 4.647 1.00 85.45 8 A 1 ATOM 60 N N . LEU A 1 9 ? -0.352 1.099 0.468 1.00 96.12 9 A 1 ATOM 61 C CA . LEU A 1 9 ? 0.323 1.732 -0.663 1.00 96.37 9 A 1 ATOM 62 C C . LEU A 1 9 ? -0.650 2.609 -1.441 1.00 97.33 9 A 1 ATOM 63 O O . LEU A 1 9 ? -0.320 3.728 -1.843 1.00 97.26 9 A 1 ATOM 64 C CB . LEU A 1 9 ? 0.912 0.660 -1.579 1.00 96.04 9 A 1 ATOM 65 C CG . LEU A 1 9 ? 2.437 0.605 -1.542 1.00 91.31 9 A 1 ATOM 66 C CD1 . LEU A 1 9 ? 2.947 -0.663 -2.209 1.00 89.13 9 A 1 ATOM 67 C CD2 . LEU A 1 9 ? 3.020 1.833 -2.221 1.00 89.84 9 A 1 ATOM 68 N N . LEU A 1 10 ? -1.847 2.099 -1.640 1.00 96.82 10 A 1 ATOM 69 C CA . LEU A 1 10 ? -2.882 2.840 -2.358 1.00 96.69 10 A 1 ATOM 70 C C . LEU A 1 10 ? -3.252 4.104 -1.594 1.00 97.40 10 A 1 ATOM 71 O O . LEU A 1 10 ? -3.448 5.171 -2.184 1.00 97.32 10 A 1 ATOM 72 C CB . LEU A 1 10 ? -4.109 1.953 -2.552 1.00 96.02 10 A 1 ATOM 73 C CG . LEU A 1 10 ? -4.967 2.343 -3.749 1.00 90.76 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? -5.746 1.129 -4.250 1.00 89.25 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? -5.926 3.459 -3.402 1.00 89.54 10 A 1 ATOM 76 N N . ALA A 1 11 ? -3.349 3.978 -0.279 1.00 97.39 11 A 1 ATOM 77 C CA . ALA A 1 11 ? -3.671 5.115 0.577 1.00 97.35 11 A 1 ATOM 78 C C . ALA A 1 11 ? -2.569 6.164 0.520 1.00 97.71 11 A 1 ATOM 79 O O . ALA A 1 11 ? -2.842 7.365 0.551 1.00 97.10 11 A 1 ATOM 80 C CB . ALA A 1 11 ? -3.875 4.641 2.010 1.00 96.81 11 A 1 ATOM 81 N N . THR A 1 12 ? -1.327 5.702 0.430 1.00 97.10 12 A 1 ATOM 82 C CA . THR A 1 12 ? -0.177 6.605 0.351 1.00 96.84 12 A 1 ATOM 83 C C . THR A 1 12 ? -0.243 7.439 -0.923 1.00 97.36 12 A 1 ATOM 84 O O . THR A 1 12 ? -0.007 8.649 -0.898 1.00 96.54 12 A 1 ATOM 85 C CB . THR A 1 12 ? 1.136 5.814 0.372 1.00 96.05 12 A 1 ATOM 86 O OG1 . THR A 1 12 ? 1.195 5.027 1.558 1.00 92.24 12 A 1 ATOM 87 C CG2 . THR A 1 12 ? 2.337 6.748 0.352 1.00 91.02 12 A 1 ATOM 88 N N . LEU A 1 13 ? -0.569 6.792 -2.028 1.00 96.72 13 A 1 ATOM 89 C CA . LEU A 1 13 ? -0.677 7.481 -3.311 1.00 96.59 13 A 1 ATOM 90 C C . LEU A 1 13 ? -1.853 8.447 -3.312 1.00 97.04 13 A 1 ATOM 91 O O . LEU A 1 13 ? -1.783 9.528 -3.902 1.00 95.99 13 A 1 ATOM 92 C CB . LEU A 1 13 ? -0.842 6.455 -4.431 1.00 95.82 13 A 1 ATOM 93 C CG . LEU A 1 13 ? 0.451 5.720 -4.781 1.00 92.20 13 A 1 ATOM 94 C CD1 . LEU A 1 13 ? 0.152 4.460 -5.580 1.00 89.32 13 A 1 ATOM 95 C CD2 . LEU A 1 13 ? 1.377 6.634 -5.569 1.00 88.92 13 A 1 ATOM 96 N N . ALA A 1 14 ? -2.935 8.050 -2.660 1.00 96.69 14 A 1 ATOM 97 C CA . ALA A 1 14 ? -4.126 8.888 -2.580 1.00 96.37 14 A 1 ATOM 98 C C . ALA A 1 14 ? -3.909 10.078 -1.655 1.00 96.68 14 A 1 ATOM 99 O O . ALA A 1 14 ? -4.414 11.174 -1.908 1.00 95.22 14 A 1 ATOM 100 C CB . ALA A 1 14 ? -5.311 8.059 -2.098 1.00 94.86 14 A 1 ATOM 101 N N . GLY A 1 15 ? -3.157 9.856 -0.582 1.00 94.82 15 A 1 ATOM 102 C CA . GLY A 1 15 ? -2.876 10.918 0.382 1.00 93.57 15 A 1 ATOM 103 C C . GLY A 1 15 ? -1.773 11.853 -0.072 1.00 93.56 15 A 1 ATOM 104 O O . GLY A 1 15 ? -1.886 13.073 0.038 1.00 91.41 15 A 1 ATOM 105 N N . ALA A 1 16 ? -0.680 11.253 -0.588 1.00 91.11 16 A 1 ATOM 106 C CA . ALA A 1 16 ? 0.470 12.025 -1.032 1.00 88.56 16 A 1 ATOM 107 C C . ALA A 1 16 ? 0.806 11.721 -2.489 1.00 85.88 16 A 1 ATOM 108 O O . ALA A 1 16 ? 0.401 10.667 -3.000 1.00 79.40 16 A 1 ATOM 109 C CB . ALA A 1 16 ? 1.672 11.739 -0.141 1.00 82.46 16 A 1 ATOM 110 O OXT . ALA A 1 16 ? 1.509 12.524 -3.120 1.00 73.28 16 A 1 #