# 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_spkb13279 # _entry.id spkb13279 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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" "C3 H7 N O3" 105.093 SER y SERINE C([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 GLN 2 1 n ASN 3 1 n LEU 4 1 n PRO 5 1 n ALA 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n PHE 10 1 n CYS 11 1 n GLY 12 1 n VAL 13 1 n VAL 14 1 n CYS 15 1 n SER 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 @ 2025-07-04 01:32:05)" _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 92.20 _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 81.95 1 1 A GLN 2 2 83.77 1 2 A ASN 3 2 85.88 1 3 A LEU 4 2 90.79 1 4 A PRO 5 2 94.63 1 5 A ALA 6 2 95.44 1 6 A LEU 7 2 93.40 1 7 A LEU 8 2 94.26 1 8 A LEU 9 2 94.46 1 9 A PHE 10 2 94.29 1 10 A CYS 11 2 95.43 1 11 A GLY 12 2 97.12 1 12 A VAL 13 2 96.72 1 13 A VAL 14 2 96.60 1 14 A CYS 15 2 95.54 1 15 A SER 16 2 94.41 1 16 A ALA 17 2 89.71 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 GLN . 2 A 2 A 3 1 n ASN . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n PRO . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n SER . 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 ? -12.128 0.039 10.961 1.00 86.82 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.211 -0.780 10.148 1.00 87.86 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.944 -1.987 9.591 1.00 88.77 1 A 1 ATOM 4 O O . MET A 1 1 ? -12.640 -2.674 10.327 1.00 86.81 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.039 -1.276 10.991 1.00 84.15 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.356 -0.162 11.752 1.00 80.23 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.339 -0.790 13.091 1.00 74.56 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.053 0.709 14.008 1.00 66.38 1 A 1 ATOM 9 N N . GLN A 1 2 ? -11.798 -2.222 8.311 1.00 91.23 2 A 1 ATOM 10 C CA . GLN A 1 2 ? -12.458 -3.352 7.667 1.00 92.97 2 A 1 ATOM 11 C C . GLN A 1 2 ? -11.550 -4.010 6.633 1.00 93.53 2 A 1 ATOM 12 O O . GLN A 1 2 ? -11.234 -5.194 6.739 1.00 90.62 2 A 1 ATOM 13 C CB . GLN A 1 2 ? -13.750 -2.884 7.002 1.00 89.80 2 A 1 ATOM 14 C CG . GLN A 1 2 ? -13.563 -1.713 6.070 1.00 80.12 2 A 1 ATOM 15 C CD . GLN A 1 2 ? -14.767 -1.490 5.195 1.00 75.76 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? -15.066 -2.302 4.341 1.00 72.21 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? -15.470 -0.396 5.398 1.00 67.72 2 A 1 ATOM 18 N N . ASN A 1 3 ? -11.141 -3.244 5.624 1.00 88.37 3 A 1 ATOM 19 C CA . ASN A 1 3 ? -10.291 -3.771 4.560 1.00 91.34 3 A 1 ATOM 20 C C . ASN A 1 3 ? -8.907 -3.130 4.575 1.00 93.37 3 A 1 ATOM 21 O O . ASN A 1 3 ? -8.726 -2.032 5.093 1.00 92.53 3 A 1 ATOM 22 C CB . ASN A 1 3 ? -10.946 -3.533 3.199 1.00 88.89 3 A 1 ATOM 23 C CG . ASN A 1 3 ? -12.187 -4.384 3.018 1.00 81.61 3 A 1 ATOM 24 O OD1 . ASN A 1 3 ? -13.273 -3.869 2.825 1.00 76.75 3 A 1 ATOM 25 N ND2 . ASN A 1 3 ? -12.032 -5.700 3.076 1.00 74.15 3 A 1 ATOM 26 N N . LEU A 1 4 ? -7.942 -3.825 3.993 1.00 92.80 4 A 1 ATOM 27 C CA . LEU A 1 4 ? -6.576 -3.318 3.922 1.00 94.11 4 A 1 ATOM 28 C C . LEU A 1 4 ? -6.010 -3.567 2.532 1.00 95.42 4 A 1 ATOM 29 O O . LEU A 1 4 ? -5.420 -4.620 2.282 1.00 95.39 4 A 1 ATOM 30 C CB . LEU A 1 4 ? -5.713 -4.005 4.974 1.00 93.19 4 A 1 ATOM 31 C CG . LEU A 1 4 ? -6.260 -3.893 6.387 1.00 89.06 4 A 1 ATOM 32 C CD1 . LEU A 1 4 ? -6.308 -5.258 7.046 1.00 84.03 4 A 1 ATOM 33 C CD2 . LEU A 1 4 ? -5.402 -2.940 7.204 1.00 82.33 4 A 1 ATOM 34 N N . PRO A 1 5 ? -6.214 -2.618 1.615 1.00 94.96 5 A 1 ATOM 35 C CA . PRO A 1 5 ? -5.741 -2.752 0.239 1.00 95.32 5 A 1 ATOM 36 C C . PRO A 1 5 ? -4.220 -2.753 0.144 1.00 96.00 5 A 1 ATOM 37 O O . PRO A 1 5 ? -3.531 -2.351 1.079 1.00 95.74 5 A 1 ATOM 38 C CB . PRO A 1 5 ? -6.322 -1.521 -0.459 1.00 93.71 5 A 1 ATOM 39 C CG . PRO A 1 5 ? -6.506 -0.518 0.628 1.00 92.29 5 A 1 ATOM 40 C CD . PRO A 1 5 ? -6.867 -1.326 1.852 1.00 94.36 5 A 1 ATOM 41 N N . ALA A 1 6 ? -3.725 -3.205 -1.002 1.00 95.15 6 A 1 ATOM 42 C CA . ALA A 1 6 ? -2.283 -3.260 -1.231 1.00 95.40 6 A 1 ATOM 43 C C . ALA A 1 6 ? -1.677 -1.862 -1.221 1.00 96.23 6 A 1 ATOM 44 O O . ALA A 1 6 ? -0.469 -1.705 -1.053 1.00 95.77 6 A 1 ATOM 45 C CB . ALA A 1 6 ? -1.997 -3.939 -2.563 1.00 94.65 6 A 1 ATOM 46 N N . LEU A 1 7 ? -2.542 -0.862 -1.396 1.00 95.66 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -2.093 0.528 -1.392 1.00 95.78 7 A 1 ATOM 48 C C . LEU A 1 7 ? -1.368 0.845 -0.096 1.00 96.59 7 A 1 ATOM 49 O O . LEU A 1 7 ? -0.342 1.525 -0.087 1.00 96.54 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -3.285 1.469 -1.555 1.00 95.57 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -3.358 2.132 -2.927 1.00 90.64 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -3.755 1.118 -3.986 1.00 88.32 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -4.343 3.291 -2.898 1.00 88.07 7 A 1 ATOM 54 N N . LEU A 1 8 ? -1.930 0.353 0.989 1.00 95.81 8 A 1 ATOM 55 C CA . LEU A 1 8 ? -1.335 0.576 2.300 1.00 96.09 8 A 1 ATOM 56 C C . LEU A 1 8 ? 0.045 -0.066 2.352 1.00 96.82 8 A 1 ATOM 57 O O . LEU A 1 8 ? 1.016 0.528 2.825 1.00 96.89 8 A 1 ATOM 58 C CB . LEU A 1 8 ? -2.233 -0.018 3.394 1.00 96.11 8 A 1 ATOM 59 C CG . LEU A 1 8 ? -2.169 0.735 4.719 1.00 92.39 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? -0.755 0.747 5.276 1.00 89.70 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? -2.676 2.155 4.512 1.00 90.24 8 A 1 ATOM 62 N N . LEU A 1 9 ? 0.105 -1.299 1.860 1.00 95.87 9 A 1 ATOM 63 C CA . LEU A 1 9 ? 1.374 -2.028 1.835 1.00 96.13 9 A 1 ATOM 64 C C . LEU A 1 9 ? 2.343 -1.356 0.868 1.00 96.98 9 A 1 ATOM 65 O O . LEU A 1 9 ? 3.534 -1.228 1.143 1.00 97.12 9 A 1 ATOM 66 C CB . LEU A 1 9 ? 1.126 -3.479 1.412 1.00 95.91 9 A 1 ATOM 67 C CG . LEU A 1 9 ? 1.759 -4.491 2.350 1.00 91.85 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? 3.259 -4.250 2.457 1.00 90.50 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? 1.100 -4.405 3.715 1.00 91.33 9 A 1 ATOM 70 N N . PHE A 1 10 ? 1.800 -0.926 -0.280 1.00 95.85 10 A 1 ATOM 71 C CA . PHE A 1 10 ? 2.611 -0.259 -1.291 1.00 95.84 10 A 1 ATOM 72 C C . PHE A 1 10 ? 3.214 1.018 -0.721 1.00 96.60 10 A 1 ATOM 73 O O . PHE A 1 10 ? 4.366 1.353 -1.000 1.00 96.13 10 A 1 ATOM 74 C CB . PHE A 1 10 ? 1.744 0.076 -2.506 1.00 95.45 10 A 1 ATOM 75 C CG . PHE A 1 10 ? 2.566 0.364 -3.736 1.00 94.40 10 A 1 ATOM 76 C CD1 . PHE A 1 10 ? 3.274 -0.650 -4.360 1.00 92.84 10 A 1 ATOM 77 C CD2 . PHE A 1 10 ? 2.619 1.645 -4.261 1.00 93.00 10 A 1 ATOM 78 C CE1 . PHE A 1 10 ? 4.030 -0.389 -5.492 1.00 92.48 10 A 1 ATOM 79 C CE2 . PHE A 1 10 ? 3.378 1.909 -5.397 1.00 91.84 10 A 1 ATOM 80 C CZ . PHE A 1 10 ? 4.087 0.893 -6.010 1.00 92.77 10 A 1 ATOM 81 N N . CYS A 1 11 ? 2.410 1.707 0.060 1.00 96.24 11 A 1 ATOM 82 C CA . CYS A 1 11 ? 2.879 2.943 0.679 1.00 96.36 11 A 1 ATOM 83 C C . CYS A 1 11 ? 4.081 2.659 1.570 1.00 96.90 11 A 1 ATOM 84 O O . CYS A 1 11 ? 5.026 3.441 1.628 1.00 95.65 11 A 1 ATOM 85 C CB . CYS A 1 11 ? 1.763 3.581 1.509 1.00 95.16 11 A 1 ATOM 86 S SG . CYS A 1 11 ? 2.251 5.148 2.247 1.00 92.28 11 A 1 ATOM 87 N N . GLY A 1 12 ? 4.014 1.536 2.259 1.00 96.99 12 A 1 ATOM 88 C CA . GLY A 1 12 ? 5.115 1.149 3.132 1.00 97.03 12 A 1 ATOM 89 C C . GLY A 1 12 ? 6.405 0.967 2.354 1.00 97.53 12 A 1 ATOM 90 O O . GLY A 1 12 ? 7.473 1.391 2.790 1.00 96.93 12 A 1 ATOM 91 N N . VAL A 1 13 ? 6.293 0.328 1.190 1.00 97.40 13 A 1 ATOM 92 C CA . VAL A 1 13 ? 7.458 0.094 0.339 1.00 97.46 13 A 1 ATOM 93 C C . VAL A 1 13 ? 7.969 1.399 -0.263 1.00 97.79 13 A 1 ATOM 94 O O . VAL A 1 13 ? 9.169 1.690 -0.218 1.00 97.23 13 A 1 ATOM 95 C CB . VAL A 1 13 ? 7.119 -0.886 -0.793 1.00 96.89 13 A 1 ATOM 96 C CG1 . VAL A 1 13 ? 8.350 -1.145 -1.652 1.00 95.23 13 A 1 ATOM 97 C CG2 . VAL A 1 13 ? 6.596 -2.193 -0.211 1.00 95.04 13 A 1 ATOM 98 N N . VAL A 1 14 ? 7.044 2.167 -0.835 1.00 97.60 14 A 1 ATOM 99 C CA . VAL A 1 14 ? 7.404 3.444 -1.450 1.00 97.52 14 A 1 ATOM 100 C C . VAL A 1 14 ? 7.868 4.441 -0.400 1.00 97.70 14 A 1 ATOM 101 O O . VAL A 1 14 ? 8.855 5.154 -0.593 1.00 97.25 14 A 1 ATOM 102 C CB . VAL A 1 14 ? 6.214 4.029 -2.227 1.00 96.80 14 A 1 ATOM 103 C CG1 . VAL A 1 14 ? 6.578 5.381 -2.819 1.00 94.41 14 A 1 ATOM 104 C CG2 . VAL A 1 14 ? 5.789 3.071 -3.327 1.00 94.91 14 A 1 ATOM 105 N N . CYS A 1 15 ? 7.149 4.493 0.688 1.00 96.55 15 A 1 ATOM 106 C CA . CYS A 1 15 ? 7.496 5.413 1.768 1.00 96.60 15 A 1 ATOM 107 C C . CYS A 1 15 ? 8.842 5.038 2.390 1.00 97.02 15 A 1 ATOM 108 O O . CYS A 1 15 ? 9.567 5.896 2.883 1.00 95.93 15 A 1 ATOM 109 C CB . CYS A 1 15 ? 6.404 5.398 2.842 1.00 95.12 15 A 1 ATOM 110 S SG . CYS A 1 15 ? 4.877 6.194 2.291 1.00 92.03 15 A 1 ATOM 111 N N . SER A 1 16 ? 9.134 3.755 2.360 1.00 96.26 16 A 1 ATOM 112 C CA . SER A 1 16 ? 10.400 3.274 2.910 1.00 96.49 16 A 1 ATOM 113 C C . SER A 1 16 ? 11.575 3.730 2.055 1.00 96.41 16 A 1 ATOM 114 O O . SER A 1 16 ? 12.646 4.069 2.570 1.00 94.56 16 A 1 ATOM 115 C CB . SER A 1 16 ? 10.399 1.750 2.994 1.00 95.16 16 A 1 ATOM 116 O OG . SER A 1 16 ? 11.601 1.292 3.570 1.00 87.56 16 A 1 ATOM 117 N N . ALA A 1 17 ? 11.362 3.730 0.734 1.00 94.11 17 A 1 ATOM 118 C CA . ALA A 1 17 ? 12.405 4.136 -0.199 1.00 92.99 17 A 1 ATOM 119 C C . ALA A 1 17 ? 11.997 5.406 -0.947 1.00 91.88 17 A 1 ATOM 120 O O . ALA A 1 17 ? 10.834 5.506 -1.357 1.00 88.11 17 A 1 ATOM 121 C CB . ALA A 1 17 ? 12.701 3.016 -1.186 1.00 89.49 17 A 1 ATOM 122 O OXT . ALA A 1 17 ? 12.847 6.289 -1.138 1.00 81.68 17 A 1 #