# 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_spkb34476 # _entry.id spkb34476 # 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" "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 ILE 3 1 n VAL 4 1 n ALA 5 1 n LEU 6 1 n THR 7 1 n LEU 8 1 n VAL 9 1 n ALA 10 1 n PHE 11 1 n VAL 12 1 n ALA 13 1 n LEU 14 1 n ALA 15 1 n GLY 16 1 n ALA 17 # _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 @ 2025-07-11 12:22:09)" _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 95.87 _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 89.40 1 1 A LYS 2 2 91.05 1 2 A ILE 3 2 96.73 1 3 A VAL 4 2 97.89 1 4 A ALA 5 2 98.39 1 5 A LEU 6 2 96.96 1 6 A THR 7 2 97.53 1 7 A LEU 8 2 96.67 1 8 A VAL 9 2 98.05 1 9 A ALA 10 2 98.48 1 10 A PHE 11 2 96.29 1 11 A VAL 12 2 97.98 1 12 A ALA 13 2 98.50 1 13 A LEU 14 2 95.84 1 14 A ALA 15 2 97.48 1 15 A GLY 16 2 95.73 1 16 A ALA 17 2 90.32 1 17 # _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 VAL . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n THR . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n GLY . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? -4.248 11.024 4.443 1.00 94.64 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.331 9.578 4.182 1.00 95.25 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.942 8.981 3.924 1.00 95.72 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.474 8.947 2.792 1.00 92.58 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.229 9.306 2.980 1.00 91.70 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.945 10.224 1.801 1.00 87.95 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.191 10.077 0.525 1.00 84.35 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.068 11.686 -0.232 1.00 73.00 1 A 1 ATOM 9 N N . LYS A 1 2 ? -2.295 8.524 4.983 1.00 96.36 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -0.969 7.925 4.876 1.00 97.04 2 A 1 ATOM 11 C C . LYS A 1 2 ? -1.041 6.402 4.925 1.00 97.66 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.239 5.716 4.294 1.00 97.37 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -0.080 8.452 6.003 1.00 95.85 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -0.696 8.281 7.384 1.00 90.46 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -0.488 9.534 8.223 1.00 87.49 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -1.377 9.520 9.448 1.00 81.13 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -1.434 10.867 10.069 1.00 76.07 2 A 1 ATOM 18 N N . ILE A 1 3 ? -2.002 5.886 5.663 1.00 97.83 3 A 1 ATOM 19 C CA . ILE A 1 3 ? -2.190 4.444 5.808 1.00 98.13 3 A 1 ATOM 20 C C . ILE A 1 3 ? -2.737 3.831 4.526 1.00 98.43 3 A 1 ATOM 21 O O . ILE A 1 3 ? -2.331 2.743 4.117 1.00 98.24 3 A 1 ATOM 22 C CB . ILE A 1 3 ? -3.137 4.130 6.976 1.00 97.87 3 A 1 ATOM 23 C CG1 . ILE A 1 3 ? -2.662 4.799 8.262 1.00 96.06 3 A 1 ATOM 24 C CG2 . ILE A 1 3 ? -3.227 2.620 7.182 1.00 95.41 3 A 1 ATOM 25 C CD1 . ILE A 1 3 ? -3.729 4.810 9.337 1.00 91.87 3 A 1 ATOM 26 N N . VAL A 1 4 ? -3.662 4.528 3.894 1.00 98.46 4 A 1 ATOM 27 C CA . VAL A 1 4 ? -4.289 4.059 2.658 1.00 98.51 4 A 1 ATOM 28 C C . VAL A 1 4 ? -3.255 3.854 1.557 1.00 98.62 4 A 1 ATOM 29 O O . VAL A 1 4 ? -3.223 2.808 0.903 1.00 98.50 4 A 1 ATOM 30 C CB . VAL A 1 4 ? -5.363 5.052 2.177 1.00 98.28 4 A 1 ATOM 31 C CG1 . VAL A 1 4 ? -6.010 4.560 0.892 1.00 96.49 4 A 1 ATOM 32 C CG2 . VAL A 1 4 ? -6.416 5.260 3.252 1.00 96.35 4 A 1 ATOM 33 N N . ALA A 1 5 ? -2.421 4.855 1.352 1.00 98.38 5 A 1 ATOM 34 C CA . ALA A 1 5 ? -1.396 4.796 0.313 1.00 98.44 5 A 1 ATOM 35 C C . ALA A 1 5 ? -0.369 3.702 0.597 1.00 98.55 5 A 1 ATOM 36 O O . ALA A 1 5 ? -0.017 2.922 -0.287 1.00 98.37 5 A 1 ATOM 37 C CB . ALA A 1 5 ? -0.706 6.150 0.203 1.00 98.23 5 A 1 ATOM 38 N N . LEU A 1 6 ? 0.106 3.652 1.823 1.00 98.47 6 A 1 ATOM 39 C CA . LEU A 1 6 ? 1.101 2.657 2.229 1.00 98.50 6 A 1 ATOM 40 C C . LEU A 1 6 ? 0.551 1.241 2.121 1.00 98.63 6 A 1 ATOM 41 O O . LEU A 1 6 ? 1.217 0.340 1.614 1.00 98.51 6 A 1 ATOM 42 C CB . LEU A 1 6 ? 1.541 2.941 3.664 1.00 98.32 6 A 1 ATOM 43 C CG . LEU A 1 6 ? 2.924 3.568 3.758 1.00 95.34 6 A 1 ATOM 44 C CD1 . LEU A 1 6 ? 2.944 4.700 4.768 1.00 93.89 6 A 1 ATOM 45 C CD2 . LEU A 1 6 ? 3.948 2.511 4.130 1.00 94.04 6 A 1 ATOM 46 N N . THR A 1 7 ? -0.662 1.055 2.589 1.00 98.37 7 A 1 ATOM 47 C CA . THR A 1 7 ? -1.309 -0.255 2.557 1.00 98.46 7 A 1 ATOM 48 C C . THR A 1 7 ? -1.529 -0.722 1.123 1.00 98.64 7 A 1 ATOM 49 O O . THR A 1 7 ? -1.284 -1.883 0.792 1.00 98.54 7 A 1 ATOM 50 C CB . THR A 1 7 ? -2.659 -0.210 3.285 1.00 98.31 7 A 1 ATOM 51 O OG1 . THR A 1 7 ? -2.476 0.284 4.604 1.00 95.91 7 A 1 ATOM 52 C CG2 . THR A 1 7 ? -3.277 -1.598 3.366 1.00 94.51 7 A 1 ATOM 53 N N . LEU A 1 8 ? -1.980 0.185 0.277 1.00 98.50 8 A 1 ATOM 54 C CA . LEU A 1 8 ? -2.241 -0.130 -1.126 1.00 98.50 8 A 1 ATOM 55 C C . LEU A 1 8 ? -0.958 -0.534 -1.838 1.00 98.64 8 A 1 ATOM 56 O O . LEU A 1 8 ? -0.912 -1.551 -2.531 1.00 98.59 8 A 1 ATOM 57 C CB . LEU A 1 8 ? -2.863 1.082 -1.825 1.00 98.33 8 A 1 ATOM 58 C CG . LEU A 1 8 ? -3.423 0.767 -3.207 1.00 94.43 8 A 1 ATOM 59 C CD1 . LEU A 1 8 ? -4.782 0.094 -3.088 1.00 92.52 8 A 1 ATOM 60 C CD2 . LEU A 1 8 ? -3.536 2.028 -4.047 1.00 93.82 8 A 1 ATOM 61 N N . VAL A 1 9 ? 0.085 0.260 -1.673 1.00 98.47 9 A 1 ATOM 62 C CA . VAL A 1 9 ? 1.377 -0.013 -2.304 1.00 98.48 9 A 1 ATOM 63 C C . VAL A 1 9 ? 1.943 -1.345 -1.825 1.00 98.61 9 A 1 ATOM 64 O O . VAL A 1 9 ? 2.477 -2.127 -2.615 1.00 98.52 9 A 1 ATOM 65 C CB . VAL A 1 9 ? 2.378 1.119 -2.004 1.00 98.18 9 A 1 ATOM 66 C CG1 . VAL A 1 9 ? 3.758 0.780 -2.546 1.00 97.07 9 A 1 ATOM 67 C CG2 . VAL A 1 9 ? 1.892 2.430 -2.605 1.00 97.01 9 A 1 ATOM 68 N N . ALA A 1 10 ? 1.833 -1.592 -0.536 1.00 98.50 10 A 1 ATOM 69 C CA . ALA A 1 10 ? 2.337 -2.830 0.053 1.00 98.51 10 A 1 ATOM 70 C C . ALA A 1 10 ? 1.618 -4.047 -0.522 1.00 98.62 10 A 1 ATOM 71 O O . ALA A 1 10 ? 2.247 -5.053 -0.850 1.00 98.46 10 A 1 ATOM 72 C CB . ALA A 1 10 ? 2.165 -2.787 1.565 1.00 98.32 10 A 1 ATOM 73 N N . PHE A 1 11 ? 0.306 -3.951 -0.648 1.00 98.26 11 A 1 ATOM 74 C CA . PHE A 1 11 ? -0.504 -5.040 -1.185 1.00 98.27 11 A 1 ATOM 75 C C . PHE A 1 11 ? -0.185 -5.287 -2.651 1.00 98.50 11 A 1 ATOM 76 O O . PHE A 1 11 ? -0.030 -6.432 -3.079 1.00 98.25 11 A 1 ATOM 77 C CB . PHE A 1 11 ? -1.986 -4.708 -1.027 1.00 97.95 11 A 1 ATOM 78 C CG . PHE A 1 11 ? -2.880 -5.873 -1.363 1.00 96.64 11 A 1 ATOM 79 C CD1 . PHE A 1 11 ? -3.054 -6.904 -0.455 1.00 94.79 11 A 1 ATOM 80 C CD2 . PHE A 1 11 ? -3.542 -5.928 -2.580 1.00 95.05 11 A 1 ATOM 81 C CE1 . PHE A 1 11 ? -3.874 -7.979 -0.756 1.00 93.89 11 A 1 ATOM 82 C CE2 . PHE A 1 11 ? -4.363 -7.003 -2.891 1.00 93.64 11 A 1 ATOM 83 C CZ . PHE A 1 11 ? -4.529 -8.030 -1.975 1.00 93.91 11 A 1 ATOM 84 N N . VAL A 1 12 ? -0.085 -4.211 -3.422 1.00 98.58 12 A 1 ATOM 85 C CA . VAL A 1 12 ? 0.222 -4.308 -4.849 1.00 98.52 12 A 1 ATOM 86 C C . VAL A 1 12 ? 1.587 -4.947 -5.065 1.00 98.62 12 A 1 ATOM 87 O O . VAL A 1 12 ? 1.762 -5.788 -5.948 1.00 98.42 12 A 1 ATOM 88 C CB . VAL A 1 12 ? 0.189 -2.922 -5.513 1.00 98.19 12 A 1 ATOM 89 C CG1 . VAL A 1 12 ? 0.658 -3.002 -6.959 1.00 96.63 12 A 1 ATOM 90 C CG2 . VAL A 1 12 ? -1.213 -2.342 -5.457 1.00 96.89 12 A 1 ATOM 91 N N . ALA A 1 13 ? 2.555 -4.544 -4.262 1.00 98.63 13 A 1 ATOM 92 C CA . ALA A 1 13 ? 3.910 -5.078 -4.363 1.00 98.58 13 A 1 ATOM 93 C C . ALA A 1 13 ? 3.934 -6.575 -4.068 1.00 98.66 13 A 1 ATOM 94 O O . ALA A 1 13 ? 4.628 -7.337 -4.740 1.00 98.31 13 A 1 ATOM 95 C CB . ALA A 1 13 ? 4.829 -4.341 -3.397 1.00 98.31 13 A 1 ATOM 96 N N . LEU A 1 14 ? 3.185 -6.988 -3.070 1.00 98.41 14 A 1 ATOM 97 C CA . LEU A 1 14 ? 3.108 -8.395 -2.683 1.00 98.19 14 A 1 ATOM 98 C C . LEU A 1 14 ? 2.431 -9.228 -3.757 1.00 98.29 14 A 1 ATOM 99 O O . LEU A 1 14 ? 2.915 -10.303 -4.121 1.00 97.76 14 A 1 ATOM 100 C CB . LEU A 1 14 ? 2.337 -8.534 -1.373 1.00 97.78 14 A 1 ATOM 101 C CG . LEU A 1 14 ? 2.412 -9.930 -0.771 1.00 93.51 14 A 1 ATOM 102 C CD1 . LEU A 1 14 ? 3.593 -10.029 0.175 1.00 91.17 14 A 1 ATOM 103 C CD2 . LEU A 1 14 ? 1.124 -10.281 -0.052 1.00 91.62 14 A 1 ATOM 104 N N . ALA A 1 15 ? 1.309 -8.740 -4.263 1.00 98.11 15 A 1 ATOM 105 C CA . ALA A 1 15 ? 0.549 -9.444 -5.291 1.00 97.84 15 A 1 ATOM 106 C C . ALA A 1 15 ? 1.290 -9.465 -6.622 1.00 97.90 15 A 1 ATOM 107 O O . ALA A 1 15 ? 1.250 -10.457 -7.350 1.00 96.57 15 A 1 ATOM 108 C CB . ALA A 1 15 ? -0.817 -8.787 -5.465 1.00 96.99 15 A 1 ATOM 109 N N . GLY A 1 16 ? 1.963 -8.377 -6.940 1.00 96.93 16 A 1 ATOM 110 C CA . GLY A 1 16 ? 2.712 -8.267 -8.188 1.00 95.88 16 A 1 ATOM 111 C C . GLY A 1 16 ? 4.000 -9.060 -8.174 1.00 96.03 16 A 1 ATOM 112 O O . GLY A 1 16 ? 4.534 -9.417 -9.222 1.00 94.06 16 A 1 ATOM 113 N N . ALA A 1 17 ? 4.516 -9.347 -6.989 1.00 95.90 17 A 1 ATOM 114 C CA . ALA A 1 17 ? 5.756 -10.103 -6.821 1.00 94.12 17 A 1 ATOM 115 C C . ALA A 1 17 ? 5.642 -11.470 -7.487 1.00 92.85 17 A 1 ATOM 116 O O . ALA A 1 17 ? 6.594 -11.883 -8.169 1.00 87.07 17 A 1 ATOM 117 C CB . ALA A 1 17 ? 6.087 -10.251 -5.336 1.00 90.32 17 A 1 ATOM 118 O OXT . ALA A 1 17 ? 4.607 -12.116 -7.341 1.00 81.67 17 A 1 #