# 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_spkb22979 # _entry.id spkb22979 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[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 ILE 2 1 n ARG 3 1 n ARG 4 1 n LEU 5 1 n ALA 6 1 n ALA 7 1 n LEU 8 1 n SER 9 1 n ALA 10 1 n LEU 11 1 n SER 12 1 n GLY 13 1 n LEU 14 1 n ALA 15 1 n THR 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 @ 2025-07-10 04:17:43)" _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 90.08 _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 85.88 1 1 A ILE 2 2 89.04 1 2 A ARG 3 2 87.54 1 3 A ARG 4 2 86.78 1 4 A LEU 5 2 92.51 1 5 A ALA 6 2 96.20 1 6 A ALA 7 2 95.35 1 7 A LEU 8 2 93.08 1 8 A SER 9 2 93.02 1 9 A ALA 10 2 96.02 1 10 A LEU 11 2 93.31 1 11 A SER 12 2 93.10 1 12 A GLY 13 2 94.43 1 13 A LEU 14 2 90.39 1 14 A ALA 15 2 91.09 1 15 A THR 16 2 82.12 1 16 A ALA 17 2 80.97 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 ILE . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n THR . 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 ? 5.596 2.174 12.786 1.00 89.35 1 A 1 ATOM 2 C CA . MET A 1 1 ? 4.692 2.984 11.945 1.00 91.60 1 A 1 ATOM 3 C C . MET A 1 1 ? 4.859 2.586 10.477 1.00 92.95 1 A 1 ATOM 4 O O . MET A 1 1 ? 5.748 3.080 9.788 1.00 90.70 1 A 1 ATOM 5 C CB . MET A 1 1 ? 5.018 4.467 12.119 1.00 86.74 1 A 1 ATOM 6 C CG . MET A 1 1 ? 4.811 4.932 13.556 1.00 82.06 1 A 1 ATOM 7 S SD . MET A 1 1 ? 5.284 6.645 13.797 1.00 81.80 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.933 6.829 15.532 1.00 71.80 1 A 1 ATOM 9 N N . ILE A 1 2 ? 4.000 1.673 10.009 1.00 90.63 2 A 1 ATOM 10 C CA . ILE A 1 2 ? 4.079 1.177 8.636 1.00 92.46 2 A 1 ATOM 11 C C . ILE A 1 2 ? 2.774 1.463 7.891 1.00 94.33 2 A 1 ATOM 12 O O . ILE A 1 2 ? 2.160 0.568 7.299 1.00 91.75 2 A 1 ATOM 13 C CB . ILE A 1 2 ? 4.381 -0.329 8.617 1.00 90.92 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? 5.492 -0.683 9.610 1.00 87.07 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? 4.798 -0.750 7.202 1.00 85.53 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? 5.655 -2.182 9.802 1.00 79.65 2 A 1 ATOM 17 N N . ARG A 1 3 ? 2.321 2.709 7.938 1.00 95.65 3 A 1 ATOM 18 C CA . ARG A 1 3 ? 1.068 3.098 7.278 1.00 96.05 3 A 1 ATOM 19 C C . ARG A 1 3 ? 1.248 3.179 5.764 1.00 96.68 3 A 1 ATOM 20 O O . ARG A 1 3 ? 0.290 3.021 5.011 1.00 95.04 3 A 1 ATOM 21 C CB . ARG A 1 3 ? 0.584 4.445 7.824 1.00 94.74 3 A 1 ATOM 22 C CG . ARG A 1 3 ? 0.273 4.395 9.310 1.00 90.08 3 A 1 ATOM 23 C CD . ARG A 1 3 ? -0.959 3.546 9.597 1.00 87.44 3 A 1 ATOM 24 N NE . ARG A 1 3 ? -2.205 4.254 9.289 1.00 82.32 3 A 1 ATOM 25 C CZ . ARG A 1 3 ? -2.752 5.170 10.079 1.00 79.90 3 A 1 ATOM 26 N NH1 . ARG A 1 3 ? -2.183 5.532 11.205 1.00 72.49 3 A 1 ATOM 27 N NH2 . ARG A 1 3 ? -3.897 5.752 9.727 1.00 72.51 3 A 1 ATOM 28 N N . ARG A 1 4 ? 2.486 3.431 5.306 1.00 95.26 4 A 1 ATOM 29 C CA . ARG A 1 4 ? 2.776 3.516 3.872 1.00 95.74 4 A 1 ATOM 30 C C . ARG A 1 4 ? 2.467 2.194 3.174 1.00 96.58 4 A 1 ATOM 31 O O . ARG A 1 4 ? 1.805 2.166 2.139 1.00 95.47 4 A 1 ATOM 32 C CB . ARG A 1 4 ? 4.244 3.875 3.644 1.00 94.80 4 A 1 ATOM 33 C CG . ARG A 1 4 ? 4.686 5.156 4.341 1.00 89.47 4 A 1 ATOM 34 C CD . ARG A 1 4 ? 3.827 6.342 3.945 1.00 86.85 4 A 1 ATOM 35 N NE . ARG A 1 4 ? 4.485 7.611 4.229 1.00 80.98 4 A 1 ATOM 36 C CZ . ARG A 1 4 ? 3.861 8.763 4.409 1.00 78.54 4 A 1 ATOM 37 N NH1 . ARG A 1 4 ? 2.556 8.824 4.389 1.00 70.90 4 A 1 ATOM 38 N NH2 . ARG A 1 4 ? 4.560 9.869 4.611 1.00 69.96 4 A 1 ATOM 39 N N . LEU A 1 5 ? 2.948 1.089 3.734 1.00 95.24 5 A 1 ATOM 40 C CA . LEU A 1 5 ? 2.721 -0.236 3.156 1.00 95.34 5 A 1 ATOM 41 C C . LEU A 1 5 ? 1.235 -0.581 3.158 1.00 95.85 5 A 1 ATOM 42 O O . LEU A 1 5 ? 0.720 -1.158 2.200 1.00 94.65 5 A 1 ATOM 43 C CB . LEU A 1 5 ? 3.509 -1.288 3.940 1.00 94.84 5 A 1 ATOM 44 C CG . LEU A 1 5 ? 5.013 -1.226 3.701 1.00 90.59 5 A 1 ATOM 45 C CD1 . LEU A 1 5 ? 5.743 -2.139 4.677 1.00 87.04 5 A 1 ATOM 46 C CD2 . LEU A 1 5 ? 5.337 -1.638 2.269 1.00 86.52 5 A 1 ATOM 47 N N . ALA A 1 6 ? 0.545 -0.222 4.230 1.00 96.61 6 A 1 ATOM 48 C CA . ALA A 1 6 ? -0.888 -0.482 4.340 1.00 96.37 6 A 1 ATOM 49 C C . ALA A 1 6 ? -1.655 0.278 3.259 1.00 96.55 6 A 1 ATOM 50 O O . ALA A 1 6 ? -2.583 -0.255 2.648 1.00 95.75 6 A 1 ATOM 51 C CB . ALA A 1 6 ? -1.381 -0.077 5.726 1.00 95.73 6 A 1 ATOM 52 N N . ALA A 1 7 ? -1.267 1.515 3.028 1.00 95.75 7 A 1 ATOM 53 C CA . ALA A 1 7 ? -1.913 2.342 2.011 1.00 95.42 7 A 1 ATOM 54 C C . ALA A 1 7 ? -1.716 1.748 0.619 1.00 96.07 7 A 1 ATOM 55 O O . ALA A 1 7 ? -2.647 1.694 -0.184 1.00 94.96 7 A 1 ATOM 56 C CB . ALA A 1 7 ? -1.349 3.756 2.062 1.00 94.55 7 A 1 ATOM 57 N N . LEU A 1 8 ? -0.510 1.292 0.339 1.00 95.13 8 A 1 ATOM 58 C CA . LEU A 1 8 ? -0.201 0.683 -0.955 1.00 95.02 8 A 1 ATOM 59 C C . LEU A 1 8 ? -1.026 -0.582 -1.161 1.00 95.73 8 A 1 ATOM 60 O O . LEU A 1 8 ? -1.525 -0.836 -2.261 1.00 95.20 8 A 1 ATOM 61 C CB . LEU A 1 8 ? 1.291 0.354 -1.027 1.00 94.70 8 A 1 ATOM 62 C CG . LEU A 1 8 ? 2.173 1.586 -1.204 1.00 91.88 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? 3.633 1.242 -0.916 1.00 88.93 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? 2.049 2.130 -2.623 1.00 88.08 8 A 1 ATOM 65 N N . SER A 1 9 ? -1.177 -1.373 -0.108 1.00 95.41 9 A 1 ATOM 66 C CA . SER A 1 9 ? -1.958 -2.606 -0.172 1.00 94.97 9 A 1 ATOM 67 C C . SER A 1 9 ? -3.418 -2.296 -0.480 1.00 95.37 9 A 1 ATOM 68 O O . SER A 1 9 ? -4.064 -3.011 -1.246 1.00 94.77 9 A 1 ATOM 69 C CB . SER A 1 9 ? -1.853 -3.363 1.150 1.00 93.88 9 A 1 ATOM 70 O OG . SER A 1 9 ? -0.521 -3.795 1.359 1.00 83.71 9 A 1 ATOM 71 N N . ALA A 1 10 ? -3.936 -1.222 0.105 1.00 96.43 10 A 1 ATOM 72 C CA . ALA A 1 10 ? -5.320 -0.814 -0.123 1.00 96.20 10 A 1 ATOM 73 C C . ALA A 1 10 ? -5.535 -0.445 -1.589 1.00 96.75 10 A 1 ATOM 74 O O . ALA A 1 10 ? -6.551 -0.800 -2.188 1.00 95.36 10 A 1 ATOM 75 C CB . ALA A 1 10 ? -5.667 0.366 0.778 1.00 95.36 10 A 1 ATOM 76 N N . LEU A 1 11 ? -4.569 0.257 -2.168 1.00 95.65 11 A 1 ATOM 77 C CA . LEU A 1 11 ? -4.647 0.663 -3.570 1.00 95.29 11 A 1 ATOM 78 C C . LEU A 1 11 ? -4.687 -0.564 -4.478 1.00 95.72 11 A 1 ATOM 79 O O . LEU A 1 11 ? -5.475 -0.633 -5.420 1.00 94.45 11 A 1 ATOM 80 C CB . LEU A 1 11 ? -3.451 1.554 -3.936 1.00 94.87 11 A 1 ATOM 81 C CG . LEU A 1 11 ? -3.739 3.056 -3.875 1.00 92.70 11 A 1 ATOM 82 C CD1 . LEU A 1 11 ? -4.736 3.443 -4.955 1.00 89.40 11 A 1 ATOM 83 C CD2 . LEU A 1 11 ? -4.267 3.446 -2.508 1.00 88.39 11 A 1 ATOM 84 N N . SER A 1 12 ? -3.835 -1.539 -4.193 1.00 95.87 12 A 1 ATOM 85 C CA . SER A 1 12 ? -3.783 -2.773 -4.978 1.00 95.49 12 A 1 ATOM 86 C C . SER A 1 12 ? -5.076 -3.566 -4.837 1.00 95.83 12 A 1 ATOM 87 O O . SER A 1 12 ? -5.504 -4.236 -5.776 1.00 93.62 12 A 1 ATOM 88 C CB . SER A 1 12 ? -2.602 -3.625 -4.527 1.00 93.85 12 A 1 ATOM 89 O OG . SER A 1 12 ? -1.385 -2.949 -4.796 1.00 83.92 12 A 1 ATOM 90 N N . GLY A 1 13 ? -5.702 -3.481 -3.664 1.00 94.47 13 A 1 ATOM 91 C CA . GLY A 1 13 ? -6.950 -4.194 -3.419 1.00 94.05 13 A 1 ATOM 92 C C . GLY A 1 13 ? -8.095 -3.659 -4.255 1.00 95.30 13 A 1 ATOM 93 O O . GLY A 1 13 ? -8.804 -4.418 -4.916 1.00 93.91 13 A 1 ATOM 94 N N . LEU A 1 14 ? -8.298 -2.334 -4.227 1.00 94.73 14 A 1 ATOM 95 C CA . LEU A 1 14 ? -9.374 -1.711 -4.997 1.00 94.00 14 A 1 ATOM 96 C C . LEU A 1 14 ? -9.078 -1.769 -6.491 1.00 94.65 14 A 1 ATOM 97 O O . LEU A 1 14 ? -9.994 -1.765 -7.320 1.00 92.14 14 A 1 ATOM 98 C CB . LEU A 1 14 ? -9.567 -0.262 -4.544 1.00 92.55 14 A 1 ATOM 99 C CG . LEU A 1 14 ? -8.357 0.639 -4.799 1.00 88.35 14 A 1 ATOM 100 C CD1 . LEU A 1 14 ? -8.489 1.362 -6.128 1.00 84.55 14 A 1 ATOM 101 C CD2 . LEU A 1 14 ? -8.214 1.645 -3.666 1.00 82.12 14 A 1 ATOM 102 N N . ALA A 1 15 ? -7.806 -1.815 -6.858 1.00 93.10 15 A 1 ATOM 103 C CA . ALA A 1 15 ? -7.390 -1.884 -8.258 1.00 91.43 15 A 1 ATOM 104 C C . ALA A 1 15 ? -6.950 -3.299 -8.605 1.00 92.24 15 A 1 ATOM 105 O O . ALA A 1 15 ? -5.930 -3.773 -8.110 1.00 89.59 15 A 1 ATOM 106 C CB . ALA A 1 15 ? -6.256 -0.897 -8.515 1.00 89.09 15 A 1 ATOM 107 N N . THR A 1 16 ? -7.723 -3.968 -9.461 1.00 87.52 16 A 1 ATOM 108 C CA . THR A 1 16 ? -7.405 -5.339 -9.876 1.00 85.41 16 A 1 ATOM 109 C C . THR A 1 16 ? -5.960 -5.434 -10.362 1.00 86.40 16 A 1 ATOM 110 O O . THR A 1 16 ? -5.488 -4.574 -11.112 1.00 81.46 16 A 1 ATOM 111 C CB . THR A 1 16 ? -8.357 -5.803 -10.986 1.00 82.42 16 A 1 ATOM 112 O OG1 . THR A 1 16 ? -8.053 -7.157 -11.334 1.00 76.94 16 A 1 ATOM 113 C CG2 . THR A 1 16 ? -8.230 -4.941 -12.230 1.00 74.71 16 A 1 ATOM 114 N N . ALA A 1 17 ? -5.271 -6.474 -9.911 1.00 88.03 17 A 1 ATOM 115 C CA . ALA A 1 17 ? -3.867 -6.662 -10.284 1.00 84.61 17 A 1 ATOM 116 C C . ALA A 1 17 ? -3.704 -7.897 -11.165 1.00 82.37 17 A 1 ATOM 117 O O . ALA A 1 17 ? -2.748 -7.947 -11.955 1.00 78.24 17 A 1 ATOM 118 C CB . ALA A 1 17 ? -3.006 -6.781 -9.026 1.00 79.50 17 A 1 ATOM 119 O OXT . ALA A 1 17 ? -4.513 -8.828 -11.048 1.00 73.06 17 A 1 #