# 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_spkb25013 # _entry.id spkb25013 # 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 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" "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 PHE 3 1 n LEU 4 1 n ALA 5 1 n VAL 6 1 n VAL 7 1 n SER 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n ALA 12 1 n THR 13 1 n ALA 14 1 n LEU 15 1 n ALA 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 @ 2025-07-10 11:54:49)" _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 94.04 _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 87.10 1 1 A LYS 2 2 91.38 1 2 A PHE 3 2 92.04 1 3 A LEU 4 2 94.87 1 4 A ALA 5 2 97.29 1 5 A VAL 6 2 96.88 1 6 A VAL 7 2 96.82 1 7 A SER 8 2 95.38 1 8 A LEU 9 2 95.64 1 9 A LEU 10 2 95.35 1 10 A ALA 11 2 97.06 1 11 A ALA 12 2 97.10 1 12 A THR 13 2 95.52 1 13 A ALA 14 2 96.88 1 14 A LEU 15 2 92.16 1 15 A ALA 16 2 88.70 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 PHE . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n SER . 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 ALA . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n ALA . 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 ? -1.795 11.876 -1.449 1.00 90.66 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.350 10.534 -1.172 1.00 92.75 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.310 9.626 -0.529 1.00 94.25 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.373 9.200 -1.190 1.00 91.81 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.815 9.899 -2.471 1.00 88.80 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.012 10.620 -3.033 1.00 84.90 1 A 1 ATOM 7 S SD . MET A 1 1 ? -4.602 9.843 -4.536 1.00 81.90 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.712 10.799 -5.747 1.00 71.74 1 A 1 ATOM 9 N N . LYS A 1 2 ? -1.469 9.362 0.744 1.00 94.55 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -0.527 8.512 1.477 1.00 95.97 2 A 1 ATOM 11 C C . LYS A 1 2 ? -1.168 7.166 1.815 1.00 96.70 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.486 6.150 1.899 1.00 96.32 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -0.092 9.229 2.760 1.00 94.66 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 0.520 10.589 2.475 1.00 91.03 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 2.005 10.607 2.781 1.00 88.88 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 2.664 11.767 2.074 1.00 84.53 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 3.792 12.325 2.859 1.00 79.77 2 A 1 ATOM 18 N N . PHE A 1 3 ? -2.459 7.169 2.003 1.00 92.37 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -3.195 5.948 2.330 1.00 94.78 3 A 1 ATOM 20 C C . PHE A 1 3 ? -3.115 4.945 1.188 1.00 96.64 3 A 1 ATOM 21 O O . PHE A 1 3 ? -2.979 3.743 1.407 1.00 95.59 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -4.651 6.296 2.621 1.00 94.06 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -4.953 6.280 4.095 1.00 92.48 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -4.360 7.196 4.943 1.00 90.02 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -5.823 5.339 4.616 1.00 90.17 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -4.623 7.179 6.305 1.00 89.05 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -6.096 5.313 5.974 1.00 88.74 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -5.496 6.235 6.822 1.00 88.51 3 A 1 ATOM 29 N N . LEU A 1 4 ? -3.195 5.438 -0.022 1.00 96.69 4 A 1 ATOM 30 C CA . LEU A 1 4 ? -3.116 4.573 -1.197 1.00 97.10 4 A 1 ATOM 31 C C . LEU A 1 4 ? -1.787 3.831 -1.239 1.00 97.54 4 A 1 ATOM 32 O O . LEU A 1 4 ? -1.712 2.680 -1.666 1.00 97.05 4 A 1 ATOM 33 C CB . LEU A 1 4 ? -3.283 5.422 -2.455 1.00 96.83 4 A 1 ATOM 34 C CG . LEU A 1 4 ? -4.739 5.557 -2.880 1.00 93.23 4 A 1 ATOM 35 C CD1 . LEU A 1 4 ? -4.932 6.774 -3.765 1.00 90.38 4 A 1 ATOM 36 C CD2 . LEU A 1 4 ? -5.153 4.294 -3.633 1.00 90.14 4 A 1 ATOM 37 N N . ALA A 1 5 ? -0.747 4.502 -0.798 1.00 97.35 5 A 1 ATOM 38 C CA . ALA A 1 5 ? 0.583 3.903 -0.774 1.00 97.40 5 A 1 ATOM 39 C C . ALA A 1 5 ? 0.618 2.710 0.179 1.00 97.76 5 A 1 ATOM 40 O O . ALA A 1 5 ? 1.242 1.691 -0.109 1.00 97.05 5 A 1 ATOM 41 C CB . ALA A 1 5 ? 1.601 4.948 -0.347 1.00 96.87 5 A 1 ATOM 42 N N . VAL A 1 6 ? -0.060 2.842 1.294 1.00 97.64 6 A 1 ATOM 43 C CA . VAL A 1 6 ? -0.119 1.774 2.293 1.00 97.70 6 A 1 ATOM 44 C C . VAL A 1 6 ? -0.851 0.565 1.724 1.00 97.97 6 A 1 ATOM 45 O O . VAL A 1 6 ? -0.437 -0.579 1.916 1.00 97.68 6 A 1 ATOM 46 C CB . VAL A 1 6 ? -0.826 2.261 3.564 1.00 97.19 6 A 1 ATOM 47 C CG1 . VAL A 1 6 ? -0.862 1.157 4.608 1.00 94.97 6 A 1 ATOM 48 C CG2 . VAL A 1 6 ? -0.118 3.487 4.120 1.00 95.01 6 A 1 ATOM 49 N N . VAL A 1 7 ? -1.927 0.830 1.033 1.00 97.74 7 A 1 ATOM 50 C CA . VAL A 1 7 ? -2.727 -0.235 0.428 1.00 97.68 7 A 1 ATOM 51 C C . VAL A 1 7 ? -1.898 -0.991 -0.604 1.00 97.84 7 A 1 ATOM 52 O O . VAL A 1 7 ? -1.947 -2.221 -0.686 1.00 97.60 7 A 1 ATOM 53 C CB . VAL A 1 7 ? -3.983 0.345 -0.239 1.00 97.27 7 A 1 ATOM 54 C CG1 . VAL A 1 7 ? -4.808 -0.763 -0.879 1.00 94.81 7 A 1 ATOM 55 C CG2 . VAL A 1 7 ? -4.818 1.094 0.788 1.00 94.83 7 A 1 ATOM 56 N N . SER A 1 8 ? -1.148 -0.246 -1.374 1.00 96.97 8 A 1 ATOM 57 C CA . SER A 1 8 ? -0.301 -0.833 -2.409 1.00 96.80 8 A 1 ATOM 58 C C . SER A 1 8 ? 0.772 -1.715 -1.784 1.00 97.27 8 A 1 ATOM 59 O O . SER A 1 8 ? 1.100 -2.779 -2.308 1.00 97.07 8 A 1 ATOM 60 C CB . SER A 1 8 ? 0.351 0.272 -3.235 1.00 96.19 8 A 1 ATOM 61 O OG . SER A 1 8 ? 1.024 -0.270 -4.344 1.00 87.96 8 A 1 ATOM 62 N N . LEU A 1 9 ? 1.301 -1.272 -0.669 1.00 97.54 9 A 1 ATOM 63 C CA . LEU A 1 9 ? 2.334 -2.022 0.042 1.00 97.53 9 A 1 ATOM 64 C C . LEU A 1 9 ? 1.790 -3.366 0.511 1.00 97.97 9 A 1 ATOM 65 O O . LEU A 1 9 ? 2.435 -4.404 0.348 1.00 97.58 9 A 1 ATOM 66 C CB . LEU A 1 9 ? 2.815 -1.214 1.247 1.00 97.27 9 A 1 ATOM 67 C CG . LEU A 1 9 ? 4.144 -1.726 1.795 1.00 93.19 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? 5.303 -1.006 1.122 1.00 91.86 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? 4.218 -1.532 3.298 1.00 92.15 9 A 1 ATOM 70 N N . LEU A 1 10 ? 0.620 -3.333 1.084 1.00 97.84 10 A 1 ATOM 71 C CA . LEU A 1 10 ? -0.019 -4.545 1.587 1.00 97.47 10 A 1 ATOM 72 C C . LEU A 1 10 ? -0.316 -5.502 0.447 1.00 97.73 10 A 1 ATOM 73 O O . LEU A 1 10 ? -0.127 -6.715 0.565 1.00 97.34 10 A 1 ATOM 74 C CB . LEU A 1 10 ? -1.305 -4.174 2.318 1.00 97.08 10 A 1 ATOM 75 C CG . LEU A 1 10 ? -1.615 -5.123 3.471 1.00 92.72 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? -2.271 -4.369 4.613 1.00 91.14 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? -2.504 -6.260 3.014 1.00 91.48 10 A 1 ATOM 78 N N . ALA A 1 11 ? -0.787 -4.954 -0.649 1.00 97.46 11 A 1 ATOM 79 C CA . ALA A 1 11 ? -1.108 -5.757 -1.824 1.00 97.16 11 A 1 ATOM 80 C C . ALA A 1 11 ? 0.148 -6.393 -2.396 1.00 97.48 11 A 1 ATOM 81 O O . ALA A 1 11 ? 0.123 -7.536 -2.852 1.00 96.65 11 A 1 ATOM 82 C CB . ALA A 1 11 ? -1.775 -4.881 -2.871 1.00 96.54 11 A 1 ATOM 83 N N . ALA A 1 12 ? 1.236 -5.662 -2.371 1.00 97.57 12 A 1 ATOM 84 C CA . ALA A 1 12 ? 2.504 -6.161 -2.892 1.00 97.25 12 A 1 ATOM 85 C C . ALA A 1 12 ? 2.983 -7.363 -2.094 1.00 97.71 12 A 1 ATOM 86 O O . ALA A 1 12 ? 3.481 -8.335 -2.658 1.00 96.55 12 A 1 ATOM 87 C CB . ALA A 1 12 ? 3.545 -5.051 -2.849 1.00 96.41 12 A 1 ATOM 88 N N . THR A 1 13 ? 2.828 -7.299 -0.791 1.00 97.59 13 A 1 ATOM 89 C CA . THR A 1 13 ? 3.246 -8.389 0.089 1.00 97.37 13 A 1 ATOM 90 C C . THR A 1 13 ? 2.379 -9.618 -0.122 1.00 97.71 13 A 1 ATOM 91 O O . THR A 1 13 ? 2.878 -10.743 -0.168 1.00 96.68 13 A 1 ATOM 92 C CB . THR A 1 13 ? 3.159 -7.958 1.551 1.00 96.39 13 A 1 ATOM 93 O OG1 . THR A 1 13 ? 3.927 -6.773 1.739 1.00 91.64 13 A 1 ATOM 94 C CG2 . THR A 1 13 ? 3.710 -9.041 2.461 1.00 91.28 13 A 1 ATOM 95 N N . ALA A 1 14 ? 1.092 -9.410 -0.241 1.00 97.12 14 A 1 ATOM 96 C CA . ALA A 1 14 ? 0.149 -10.504 -0.445 1.00 97.07 14 A 1 ATOM 97 C C . ALA A 1 14 ? 0.243 -11.057 -1.858 1.00 97.44 14 A 1 ATOM 98 O O . ALA A 1 14 ? 0.069 -12.255 -2.080 1.00 96.48 14 A 1 ATOM 99 C CB . ALA A 1 14 ? -1.266 -10.022 -0.166 1.00 96.29 14 A 1 ATOM 100 N N . LEU A 1 15 ? 0.490 -10.180 -2.791 1.00 96.34 15 A 1 ATOM 101 C CA . LEU A 1 15 ? 0.600 -10.565 -4.196 1.00 95.97 15 A 1 ATOM 102 C C . LEU A 1 15 ? 1.798 -11.467 -4.417 1.00 96.29 15 A 1 ATOM 103 O O . LEU A 1 15 ? 1.700 -12.506 -5.080 1.00 94.66 15 A 1 ATOM 104 C CB . LEU A 1 15 ? 0.716 -9.315 -5.066 1.00 94.50 15 A 1 ATOM 105 C CG . LEU A 1 15 ? 0.821 -9.615 -6.556 1.00 90.06 15 A 1 ATOM 106 C CD1 . LEU A 1 15 ? -0.084 -8.691 -7.350 1.00 85.87 15 A 1 ATOM 107 C CD2 . LEU A 1 15 ? 2.255 -9.478 -7.034 1.00 83.57 15 A 1 ATOM 108 N N . ALA A 1 16 ? 2.923 -11.075 -3.889 1.00 94.37 16 A 1 ATOM 109 C CA . ALA A 1 16 ? 4.151 -11.845 -4.042 1.00 92.07 16 A 1 ATOM 110 C C . ALA A 1 16 ? 4.145 -13.041 -3.110 1.00 90.66 16 A 1 ATOM 111 O O . ALA A 1 16 ? 4.127 -14.189 -3.601 1.00 86.51 16 A 1 ATOM 112 C CB . ALA A 1 16 ? 5.358 -10.956 -3.767 1.00 87.97 16 A 1 ATOM 113 O OXT . ALA A 1 16 ? 4.183 -12.823 -1.902 1.00 80.62 16 A 1 #