# 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_spkb28663 # _entry.id spkb28663 # 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" # _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 ILE 3 1 n ILE 4 1 n LEU 5 1 n PHE 6 1 n LEU 7 1 n THR 8 1 n LEU 9 1 n ILE 10 1 n ALA 11 1 n LEU 12 1 n ALA 13 1 n SER 14 1 n SER 15 # _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 @ 2025-07-13 01:40:03)" _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 95.68 _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 91.79 1 1 A LYS 2 2 93.21 1 2 A ILE 3 2 97.40 1 3 A ILE 4 2 97.86 1 4 A LEU 5 2 96.15 1 5 A PHE 6 2 95.79 1 6 A LEU 7 2 96.18 1 7 A THR 8 2 97.02 1 8 A LEU 9 2 96.18 1 9 A ILE 10 2 97.50 1 10 A ALA 11 2 98.59 1 11 A LEU 12 2 96.00 1 12 A ALA 13 2 98.31 1 13 A SER 14 2 96.17 1 14 A SER 15 2 88.86 1 15 # _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 ILE . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n THR . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n SER . 15 A 15 # _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 ? -9.205 6.913 5.187 1.00 97.04 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.228 7.483 4.235 1.00 97.23 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.596 6.381 3.391 1.00 97.20 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.978 5.470 3.929 1.00 95.78 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.137 8.235 4.983 1.00 95.23 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.483 9.690 5.198 1.00 89.53 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.227 10.535 6.145 1.00 85.92 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.758 12.227 5.969 1.00 76.42 1 A 1 ATOM 9 N N . LYS A 1 2 ? -7.767 6.482 2.082 1.00 98.25 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -7.225 5.495 1.153 1.00 98.31 2 A 1 ATOM 11 C C . LYS A 1 2 ? -5.755 5.772 0.853 1.00 98.40 2 A 1 ATOM 12 O O . LYS A 1 2 ? -4.988 4.850 0.578 1.00 98.10 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -8.036 5.501 -0.140 1.00 97.76 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -9.532 5.357 0.070 1.00 93.95 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -9.911 3.954 0.507 1.00 90.34 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -11.411 3.759 0.493 1.00 85.19 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -11.781 2.359 0.795 1.00 78.55 2 A 1 ATOM 18 N N . ILE A 1 3 ? -5.381 7.031 0.899 1.00 98.41 3 A 1 ATOM 19 C CA . ILE A 1 3 ? -4.006 7.435 0.619 1.00 98.53 3 A 1 ATOM 20 C C . ILE A 1 3 ? -3.051 6.852 1.653 1.00 98.65 3 A 1 ATOM 21 O O . ILE A 1 3 ? -1.942 6.428 1.332 1.00 98.39 3 A 1 ATOM 22 C CB . ILE A 1 3 ? -3.884 8.965 0.589 1.00 98.28 3 A 1 ATOM 23 C CG1 . ILE A 1 3 ? -4.943 9.572 -0.342 1.00 96.72 3 A 1 ATOM 24 C CG2 . ILE A 1 3 ? -2.481 9.378 0.152 1.00 96.36 3 A 1 ATOM 25 C CD1 . ILE A 1 3 ? -4.823 9.092 -1.778 1.00 93.84 3 A 1 ATOM 26 N N . ILE A 1 4 ? -3.492 6.841 2.895 1.00 98.74 4 A 1 ATOM 27 C CA . ILE A 1 4 ? -2.683 6.309 3.989 1.00 98.70 4 A 1 ATOM 28 C C . ILE A 1 4 ? -2.432 4.822 3.786 1.00 98.70 4 A 1 ATOM 29 O O . ILE A 1 4 ? -1.330 4.323 4.026 1.00 98.54 4 A 1 ATOM 30 C CB . ILE A 1 4 ? -3.377 6.548 5.342 1.00 98.61 4 A 1 ATOM 31 C CG1 . ILE A 1 4 ? -3.752 8.026 5.507 1.00 97.69 4 A 1 ATOM 32 C CG2 . ILE A 1 4 ? -2.482 6.084 6.491 1.00 97.31 4 A 1 ATOM 33 C CD1 . ILE A 1 4 ? -2.558 8.961 5.450 1.00 94.58 4 A 1 ATOM 34 N N . LEU A 1 5 ? -3.461 4.126 3.349 1.00 98.51 5 A 1 ATOM 35 C CA . LEU A 1 5 ? -3.363 2.693 3.093 1.00 98.45 5 A 1 ATOM 36 C C . LEU A 1 5 ? -2.363 2.413 1.980 1.00 98.56 5 A 1 ATOM 37 O O . LEU A 1 5 ? -1.588 1.460 2.049 1.00 98.50 5 A 1 ATOM 38 C CB . LEU A 1 5 ? -4.742 2.149 2.715 1.00 98.28 5 A 1 ATOM 39 C CG . LEU A 1 5 ? -5.261 1.076 3.660 1.00 93.84 5 A 1 ATOM 40 C CD1 . LEU A 1 5 ? -6.773 1.137 3.764 1.00 90.80 5 A 1 ATOM 41 C CD2 . LEU A 1 5 ? -4.825 -0.299 3.178 1.00 92.23 5 A 1 ATOM 42 N N . PHE A 1 6 ? -2.386 3.247 0.976 1.00 98.41 6 A 1 ATOM 43 C CA . PHE A 1 6 ? -1.475 3.114 -0.157 1.00 98.47 6 A 1 ATOM 44 C C . PHE A 1 6 ? -0.039 3.372 0.283 1.00 98.57 6 A 1 ATOM 45 O O . PHE A 1 6 ? 0.887 2.689 -0.148 1.00 98.39 6 A 1 ATOM 46 C CB . PHE A 1 6 ? -1.873 4.099 -1.253 1.00 98.27 6 A 1 ATOM 47 C CG . PHE A 1 6 ? -2.037 3.436 -2.597 1.00 96.63 6 A 1 ATOM 48 C CD1 . PHE A 1 6 ? -3.186 2.725 -2.893 1.00 93.43 6 A 1 ATOM 49 C CD2 . PHE A 1 6 ? -1.037 3.532 -3.546 1.00 94.08 6 A 1 ATOM 50 C CE1 . PHE A 1 6 ? -3.342 2.111 -4.125 1.00 92.54 6 A 1 ATOM 51 C CE2 . PHE A 1 6 ? -1.184 2.918 -4.784 1.00 92.78 6 A 1 ATOM 52 C CZ . PHE A 1 6 ? -2.335 2.209 -5.075 1.00 92.16 6 A 1 ATOM 53 N N . LEU A 1 7 ? 0.122 4.352 1.143 1.00 98.64 7 A 1 ATOM 54 C CA . LEU A 1 7 ? 1.443 4.705 1.660 1.00 98.60 7 A 1 ATOM 55 C C . LEU A 1 7 ? 2.049 3.536 2.426 1.00 98.69 7 A 1 ATOM 56 O O . LEU A 1 7 ? 3.242 3.254 2.308 1.00 98.60 7 A 1 ATOM 57 C CB . LEU A 1 7 ? 1.325 5.922 2.574 1.00 98.38 7 A 1 ATOM 58 C CG . LEU A 1 7 ? 2.652 6.617 2.843 1.00 92.57 7 A 1 ATOM 59 C CD1 . LEU A 1 7 ? 2.670 7.997 2.208 1.00 91.34 7 A 1 ATOM 60 C CD2 . LEU A 1 7 ? 2.917 6.726 4.329 1.00 92.64 7 A 1 ATOM 61 N N . THR A 1 8 ? 1.224 2.860 3.199 1.00 98.46 8 A 1 ATOM 62 C CA . THR A 1 8 ? 1.665 1.712 3.984 1.00 98.44 8 A 1 ATOM 63 C C . THR A 1 8 ? 2.064 0.563 3.068 1.00 98.54 8 A 1 ATOM 64 O O . THR A 1 8 ? 3.047 -0.137 3.331 1.00 98.35 8 A 1 ATOM 65 C CB . THR A 1 8 ? 0.546 1.263 4.929 1.00 98.21 8 A 1 ATOM 66 O OG1 . THR A 1 8 ? 0.125 2.365 5.722 1.00 94.39 8 A 1 ATOM 67 C CG2 . THR A 1 8 ? 1.019 0.156 5.853 1.00 92.73 8 A 1 ATOM 68 N N . LEU A 1 9 ? 1.304 0.380 2.009 1.00 98.66 9 A 1 ATOM 69 C CA . LEU A 1 9 ? 1.568 -0.686 1.049 1.00 98.59 9 A 1 ATOM 70 C C . LEU A 1 9 ? 2.909 -0.470 0.357 1.00 98.64 9 A 1 ATOM 71 O O . LEU A 1 9 ? 3.670 -1.415 0.148 1.00 98.45 9 A 1 ATOM 72 C CB . LEU A 1 9 ? 0.442 -0.740 0.017 1.00 98.30 9 A 1 ATOM 73 C CG . LEU A 1 9 ? 0.047 -2.157 -0.375 1.00 93.63 9 A 1 ATOM 74 C CD1 . LEU A 1 9 ? -1.445 -2.367 -0.195 1.00 91.12 9 A 1 ATOM 75 C CD2 . LEU A 1 9 ? 0.446 -2.451 -1.807 1.00 92.01 9 A 1 ATOM 76 N N . ILE A 1 10 ? 3.184 0.767 0.017 1.00 98.71 10 A 1 ATOM 77 C CA . ILE A 1 10 ? 4.437 1.116 -0.644 1.00 98.62 10 A 1 ATOM 78 C C . ILE A 1 10 ? 5.617 0.878 0.295 1.00 98.65 10 A 1 ATOM 79 O O . ILE A 1 10 ? 6.661 0.368 -0.113 1.00 98.48 10 A 1 ATOM 80 C CB . ILE A 1 10 ? 4.408 2.581 -1.107 1.00 98.39 10 A 1 ATOM 81 C CG1 . ILE A 1 10 ? 3.363 2.769 -2.206 1.00 96.94 10 A 1 ATOM 82 C CG2 . ILE A 1 10 ? 5.786 3.000 -1.624 1.00 96.65 10 A 1 ATOM 83 C CD1 . ILE A 1 10 ? 2.891 4.188 -2.346 1.00 93.54 10 A 1 ATOM 84 N N . ALA A 1 11 ? 5.436 1.247 1.549 1.00 98.70 11 A 1 ATOM 85 C CA . ALA A 1 11 ? 6.481 1.066 2.552 1.00 98.66 11 A 1 ATOM 86 C C . ALA A 1 11 ? 6.770 -0.415 2.774 1.00 98.69 11 A 1 ATOM 87 O O . ALA A 1 11 ? 7.917 -0.802 2.989 1.00 98.44 11 A 1 ATOM 88 C CB . ALA A 1 11 ? 6.056 1.725 3.855 1.00 98.45 11 A 1 ATOM 89 N N . LEU A 1 12 ? 5.738 -1.227 2.717 1.00 98.73 12 A 1 ATOM 90 C CA . LEU A 1 12 ? 5.874 -2.670 2.889 1.00 98.62 12 A 1 ATOM 91 C C . LEU A 1 12 ? 6.632 -3.285 1.724 1.00 98.62 12 A 1 ATOM 92 O O . LEU A 1 12 ? 7.473 -4.164 1.916 1.00 98.03 12 A 1 ATOM 93 C CB . LEU A 1 12 ? 4.490 -3.310 3.001 1.00 98.21 12 A 1 ATOM 94 C CG . LEU A 1 12 ? 4.518 -4.724 3.575 1.00 94.09 12 A 1 ATOM 95 C CD1 . LEU A 1 12 ? 4.341 -4.676 5.084 1.00 90.62 12 A 1 ATOM 96 C CD2 . LEU A 1 12 ? 3.447 -5.583 2.948 1.00 91.04 12 A 1 ATOM 97 N N . ALA A 1 13 ? 6.328 -2.830 0.533 1.00 98.59 13 A 1 ATOM 98 C CA . ALA A 1 13 ? 6.982 -3.328 -0.675 1.00 98.50 13 A 1 ATOM 99 C C . ALA A 1 13 ? 8.462 -2.963 -0.691 1.00 98.52 13 A 1 ATOM 100 O O . ALA A 1 13 ? 9.272 -3.646 -1.317 1.00 97.90 13 A 1 ATOM 101 C CB . ALA A 1 13 ? 6.288 -2.761 -1.907 1.00 98.02 13 A 1 ATOM 102 N N . SER A 1 14 ? 8.802 -1.898 -0.009 1.00 98.25 14 A 1 ATOM 103 C CA . SER A 1 14 ? 10.177 -1.422 0.071 1.00 98.06 14 A 1 ATOM 104 C C . SER A 1 14 ? 10.949 -2.125 1.185 1.00 97.57 14 A 1 ATOM 105 O O . SER A 1 14 ? 12.133 -1.853 1.395 1.00 94.69 14 A 1 ATOM 106 C CB . SER A 1 14 ? 10.194 0.088 0.308 1.00 97.25 14 A 1 ATOM 107 O OG . SER A 1 14 ? 11.482 0.617 0.114 1.00 91.17 14 A 1 ATOM 108 N N . SER A 1 15 ? 10.282 -3.028 1.880 1.00 95.45 15 A 1 ATOM 109 C CA . SER A 1 15 ? 10.884 -3.744 2.999 1.00 94.03 15 A 1 ATOM 110 C C . SER A 1 15 ? 11.758 -4.903 2.509 1.00 91.73 15 A 1 ATOM 111 O O . SER A 1 15 ? 12.948 -4.953 2.854 1.00 85.23 15 A 1 ATOM 112 C CB . SER A 1 15 ? 9.797 -4.250 3.945 1.00 90.24 15 A 1 ATOM 113 O OG . SER A 1 15 ? 10.343 -4.519 5.219 1.00 82.21 15 A 1 ATOM 114 O OXT . SER A 1 15 ? 11.243 -5.748 1.784 1.00 83.12 15 A 1 #