# 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_spkb35664 # _entry.id spkb35664 # 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 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" "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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 TYR 3 1 n LYS 4 1 n LEU 5 1 n LEU 6 1 n PRO 7 1 n CYS 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n ILE 12 1 n LEU 13 1 n LEU 14 1 n THR 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 @ 2025-07-08 12:37:07)" _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 90.62 _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 83.93 1 1 A LYS 2 2 82.53 1 2 A TYR 3 2 85.80 1 3 A LYS 4 2 86.09 1 4 A LEU 5 2 92.06 1 5 A LEU 6 2 91.96 1 6 A PRO 7 2 94.99 1 7 A CYS 8 2 94.31 1 8 A LEU 9 2 93.67 1 9 A LEU 10 2 94.19 1 10 A ALA 11 2 96.14 1 11 A ILE 12 2 95.06 1 12 A LEU 13 2 95.02 1 13 A LEU 14 2 95.07 1 14 A THR 15 2 91.15 1 15 A GLY 16 2 82.62 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 TYR . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n PRO . 7 A 7 A 8 1 n CYS . 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 ILE . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n THR . 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 . MET A 1 1 ? 2.531 11.505 -2.508 1.00 89.27 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.334 10.781 -2.971 1.00 90.80 1 A 1 ATOM 3 C C . MET A 1 1 ? 0.519 10.237 -1.800 1.00 91.14 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.687 10.065 -1.905 1.00 89.02 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.745 9.611 -3.866 1.00 87.19 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.449 10.095 -5.127 1.00 80.28 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.315 10.940 -6.219 1.00 75.94 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.467 11.621 -7.393 1.00 67.77 1 A 1 ATOM 9 N N . LYS A 1 2 ? 1.190 9.978 -0.705 1.00 89.09 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 0.510 9.491 0.506 1.00 90.16 2 A 1 ATOM 11 C C . LYS A 1 2 ? -0.203 8.160 0.232 1.00 90.16 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.313 7.926 0.704 1.00 89.33 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -0.485 10.560 0.966 1.00 88.20 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -0.812 10.443 2.437 1.00 80.55 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -1.656 11.629 2.873 1.00 78.74 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.112 11.459 4.308 1.00 72.16 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -2.807 12.692 4.768 1.00 64.40 2 A 1 ATOM 18 N N . TYR A 1 3 ? 0.422 7.308 -0.524 1.00 89.01 3 A 1 ATOM 19 C CA . TYR A 1 3 ? -0.165 6.013 -0.889 1.00 90.26 3 A 1 ATOM 20 C C . TYR A 1 3 ? 0.461 4.863 -0.095 1.00 91.71 3 A 1 ATOM 21 O O . TYR A 1 3 ? -0.000 3.731 -0.178 1.00 90.21 3 A 1 ATOM 22 C CB . TYR A 1 3 ? 0.044 5.779 -2.390 1.00 89.20 3 A 1 ATOM 23 C CG . TYR A 1 3 ? 1.480 5.431 -2.734 1.00 84.22 3 A 1 ATOM 24 C CD1 . TYR A 1 3 ? 2.498 6.375 -2.626 1.00 83.72 3 A 1 ATOM 25 C CD2 . TYR A 1 3 ? 1.802 4.147 -3.156 1.00 83.01 3 A 1 ATOM 26 C CE1 . TYR A 1 3 ? 3.812 6.049 -2.935 1.00 80.95 3 A 1 ATOM 27 C CE2 . TYR A 1 3 ? 3.123 3.813 -3.473 1.00 83.15 3 A 1 ATOM 28 C CZ . TYR A 1 3 ? 4.119 4.770 -3.363 1.00 83.14 3 A 1 ATOM 29 O OH . TYR A 1 3 ? 5.418 4.438 -3.667 1.00 80.96 3 A 1 ATOM 30 N N . LYS A 1 4 ? 1.502 5.158 0.651 1.00 92.88 4 A 1 ATOM 31 C CA . LYS A 1 4 ? 2.201 4.144 1.441 1.00 93.94 4 A 1 ATOM 32 C C . LYS A 1 4 ? 1.473 3.895 2.766 1.00 94.92 4 A 1 ATOM 33 O O . LYS A 1 4 ? 2.066 3.978 3.841 1.00 93.94 4 A 1 ATOM 34 C CB . LYS A 1 4 ? 3.638 4.609 1.699 1.00 93.09 4 A 1 ATOM 35 C CG . LYS A 1 4 ? 4.456 4.710 0.421 1.00 85.15 4 A 1 ATOM 36 C CD . LYS A 1 4 ? 5.109 3.375 0.092 1.00 81.30 4 A 1 ATOM 37 C CE . LYS A 1 4 ? 6.055 3.512 -1.089 1.00 74.07 4 A 1 ATOM 38 N NZ . LYS A 1 4 ? 6.969 2.348 -1.188 1.00 65.55 4 A 1 ATOM 39 N N . LEU A 1 5 ? 0.206 3.597 2.666 1.00 94.66 5 A 1 ATOM 40 C CA . LEU A 1 5 ? -0.610 3.353 3.848 1.00 95.33 5 A 1 ATOM 41 C C . LEU A 1 5 ? -1.018 1.882 3.919 1.00 95.73 5 A 1 ATOM 42 O O . LEU A 1 5 ? -0.446 1.032 3.240 1.00 95.01 5 A 1 ATOM 43 C CB . LEU A 1 5 ? -1.843 4.264 3.786 1.00 95.16 5 A 1 ATOM 44 C CG . LEU A 1 5 ? -1.504 5.751 3.838 1.00 90.10 5 A 1 ATOM 45 C CD1 . LEU A 1 5 ? -2.611 6.561 3.179 1.00 85.27 5 A 1 ATOM 46 C CD2 . LEU A 1 5 ? -1.331 6.200 5.286 1.00 85.24 5 A 1 ATOM 47 N N . LEU A 1 6 ? -2.013 1.608 4.728 1.00 95.69 6 A 1 ATOM 48 C CA . LEU A 1 6 ? -2.507 0.237 4.880 1.00 95.56 6 A 1 ATOM 49 C C . LEU A 1 6 ? -2.953 -0.369 3.548 1.00 95.89 6 A 1 ATOM 50 O O . LEU A 1 6 ? -2.658 -1.534 3.279 1.00 95.62 6 A 1 ATOM 51 C CB . LEU A 1 6 ? -3.669 0.241 5.873 1.00 95.14 6 A 1 ATOM 52 C CG . LEU A 1 6 ? -3.208 0.337 7.322 1.00 89.25 6 A 1 ATOM 53 C CD1 . LEU A 1 6 ? -4.172 1.173 8.134 1.00 84.06 6 A 1 ATOM 54 C CD2 . LEU A 1 6 ? -3.095 -1.061 7.916 1.00 84.44 6 A 1 ATOM 55 N N . PRO A 1 7 ? -3.665 0.397 2.732 1.00 95.43 7 A 1 ATOM 56 C CA . PRO A 1 7 ? -4.129 -0.126 1.435 1.00 95.63 7 A 1 ATOM 57 C C . PRO A 1 7 ? -2.979 -0.605 0.560 1.00 95.94 7 A 1 ATOM 58 O O . PRO A 1 7 ? -3.132 -1.528 -0.235 1.00 95.26 7 A 1 ATOM 59 C CB . PRO A 1 7 ? -4.846 1.072 0.800 1.00 94.52 7 A 1 ATOM 60 C CG . PRO A 1 7 ? -4.389 2.256 1.569 1.00 93.27 7 A 1 ATOM 61 C CD . PRO A 1 7 ? -4.108 1.765 2.952 1.00 94.85 7 A 1 ATOM 62 N N . CYS A 1 8 ? -1.833 0.018 0.708 1.00 95.21 8 A 1 ATOM 63 C CA . CYS A 1 8 ? -0.656 -0.360 -0.077 1.00 95.36 8 A 1 ATOM 64 C C . CYS A 1 8 ? -0.184 -1.756 0.331 1.00 95.91 8 A 1 ATOM 65 O O . CYS A 1 8 ? 0.237 -2.550 -0.503 1.00 95.28 8 A 1 ATOM 66 C CB . CYS A 1 8 ? 0.457 0.660 0.154 1.00 94.62 8 A 1 ATOM 67 S SG . CYS A 1 8 ? 1.752 0.534 -1.082 1.00 89.47 8 A 1 ATOM 68 N N . LEU A 1 9 ? -0.262 -2.040 1.612 1.00 94.90 9 A 1 ATOM 69 C CA . LEU A 1 9 ? 0.141 -3.345 2.126 1.00 95.38 9 A 1 ATOM 70 C C . LEU A 1 9 ? -0.743 -4.448 1.550 1.00 96.18 9 A 1 ATOM 71 O O . LEU A 1 9 ? -0.253 -5.520 1.197 1.00 96.28 9 A 1 ATOM 72 C CB . LEU A 1 9 ? 0.035 -3.337 3.650 1.00 95.40 9 A 1 ATOM 73 C CG . LEU A 1 9 ? 0.972 -4.342 4.310 1.00 92.46 9 A 1 ATOM 74 C CD1 . LEU A 1 9 ? 2.373 -3.744 4.431 1.00 88.64 9 A 1 ATOM 75 C CD2 . LEU A 1 9 ? 0.455 -4.717 5.690 1.00 90.08 9 A 1 ATOM 76 N N . LEU A 1 10 ? -2.020 -4.181 1.464 1.00 96.06 10 A 1 ATOM 77 C CA . LEU A 1 10 ? -2.969 -5.151 0.913 1.00 95.91 10 A 1 ATOM 78 C C . LEU A 1 10 ? -2.665 -5.422 -0.554 1.00 96.34 10 A 1 ATOM 79 O O . LEU A 1 10 ? -2.757 -6.561 -1.015 1.00 96.39 10 A 1 ATOM 80 C CB . LEU A 1 10 ? -4.389 -4.602 1.065 1.00 95.68 10 A 1 ATOM 81 C CG . LEU A 1 10 ? -5.102 -5.156 2.294 1.00 92.78 10 A 1 ATOM 82 C CD1 . LEU A 1 10 ? -6.194 -4.208 2.752 1.00 89.15 10 A 1 ATOM 83 C CD2 . LEU A 1 10 ? -5.699 -6.522 1.966 1.00 91.18 10 A 1 ATOM 84 N N . ALA A 1 11 ? -2.311 -4.385 -1.269 1.00 96.46 11 A 1 ATOM 85 C CA . ALA A 1 11 ? -1.994 -4.507 -2.692 1.00 96.33 11 A 1 ATOM 86 C C . ALA A 1 11 ? -0.745 -5.366 -2.888 1.00 96.73 11 A 1 ATOM 87 O O . ALA A 1 11 ? -0.663 -6.155 -3.823 1.00 95.67 11 A 1 ATOM 88 C CB . ALA A 1 11 ? -1.778 -3.120 -3.282 1.00 95.52 11 A 1 ATOM 89 N N . ILE A 1 12 ? 0.217 -5.207 -2.006 1.00 96.51 12 A 1 ATOM 90 C CA . ILE A 1 12 ? 1.459 -5.973 -2.087 1.00 96.35 12 A 1 ATOM 91 C C . ILE A 1 12 ? 1.181 -7.457 -1.855 1.00 96.87 12 A 1 ATOM 92 O O . ILE A 1 12 ? 1.734 -8.320 -2.543 1.00 96.17 12 A 1 ATOM 93 C CB . ILE A 1 12 ? 2.472 -5.447 -1.046 1.00 95.88 12 A 1 ATOM 94 C CG1 . ILE A 1 12 ? 2.903 -4.015 -1.380 1.00 94.25 12 A 1 ATOM 95 C CG2 . ILE A 1 12 ? 3.709 -6.352 -1.018 1.00 93.75 12 A 1 ATOM 96 C CD1 . ILE A 1 12 ? 3.420 -3.267 -0.159 1.00 90.67 12 A 1 ATOM 97 N N . LEU A 1 13 ? 0.330 -7.746 -0.897 1.00 96.79 13 A 1 ATOM 98 C CA . LEU A 1 13 ? -0.024 -9.127 -0.576 1.00 96.74 13 A 1 ATOM 99 C C . LEU A 1 13 ? -0.784 -9.776 -1.727 1.00 97.11 13 A 1 ATOM 100 O O . LEU A 1 13 ? -0.630 -10.968 -1.993 1.00 96.65 13 A 1 ATOM 101 C CB . LEU A 1 13 ? -0.869 -9.151 0.708 1.00 96.43 13 A 1 ATOM 102 C CG . LEU A 1 13 ? -0.073 -9.441 1.986 1.00 94.46 13 A 1 ATOM 103 C CD1 . LEU A 1 13 ? 0.439 -10.874 1.961 1.00 90.16 13 A 1 ATOM 104 C CD2 . LEU A 1 13 ? 1.083 -8.483 2.143 1.00 91.81 13 A 1 ATOM 105 N N . LEU A 1 14 ? -1.608 -8.989 -2.384 1.00 97.18 14 A 1 ATOM 106 C CA . LEU A 1 14 ? -2.408 -9.487 -3.503 1.00 97.00 14 A 1 ATOM 107 C C . LEU A 1 14 ? -1.543 -9.686 -4.743 1.00 96.92 14 A 1 ATOM 108 O O . LEU A 1 14 ? -1.666 -10.687 -5.449 1.00 95.93 14 A 1 ATOM 109 C CB . LEU A 1 14 ? -3.538 -8.490 -3.792 1.00 96.67 14 A 1 ATOM 110 C CG . LEU A 1 14 ? -4.896 -9.158 -3.979 1.00 95.32 14 A 1 ATOM 111 C CD1 . LEU A 1 14 ? -6.012 -8.158 -3.714 1.00 90.32 14 A 1 ATOM 112 C CD2 . LEU A 1 14 ? -5.032 -9.733 -5.374 1.00 91.21 14 A 1 ATOM 113 N N . THR A 1 15 ? -0.683 -8.747 -5.018 1.00 96.24 15 A 1 ATOM 114 C CA . THR A 1 15 ? 0.196 -8.826 -6.188 1.00 95.40 15 A 1 ATOM 115 C C . THR A 1 15 ? 1.304 -9.851 -5.978 1.00 94.52 15 A 1 ATOM 116 O O . THR A 1 15 ? 1.833 -10.404 -6.944 1.00 88.52 15 A 1 ATOM 117 C CB . THR A 1 15 ? 0.824 -7.453 -6.472 1.00 93.17 15 A 1 ATOM 118 O OG1 . THR A 1 15 ? 1.330 -6.893 -5.275 1.00 85.48 15 A 1 ATOM 119 C CG2 . THR A 1 15 ? -0.185 -6.500 -7.085 1.00 84.72 15 A 1 ATOM 120 N N . GLY A 1 16 ? 1.656 -10.082 -4.736 1.00 89.71 16 A 1 ATOM 121 C CA . GLY A 1 16 ? 2.693 -11.062 -4.412 1.00 86.28 16 A 1 ATOM 122 C C . GLY A 1 16 ? 2.250 -12.478 -4.703 1.00 81.80 16 A 1 ATOM 123 O O . GLY A 1 16 ? 2.822 -13.114 -5.601 1.00 74.57 16 A 1 ATOM 124 O OXT . GLY A 1 16 ? 1.366 -12.955 -4.018 1.00 80.76 16 A 1 #