# 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_spkb42345 # _entry.id spkb42345 # 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" "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 LYS 2 1 n SER 3 1 n ILE 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n PHE 8 1 n SER 9 1 n LEU 10 1 n ILE 11 1 n VAL 12 1 n LEU 13 1 n GLY 14 1 n SER 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 @ 2025-07-07 12:26:57)" _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 93.39 _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 83.11 1 1 A LYS 2 2 88.28 1 2 A SER 3 2 95.22 1 3 A ILE 4 2 95.05 1 4 A LEU 5 2 94.43 1 5 A LEU 6 2 94.60 1 6 A LEU 7 2 94.56 1 7 A PHE 8 2 94.27 1 8 A SER 9 2 96.24 1 9 A LEU 10 2 95.25 1 10 A ILE 11 2 95.88 1 11 A VAL 12 2 96.94 1 12 A LEU 13 2 94.87 1 13 A GLY 14 2 95.85 1 14 A SER 15 2 93.14 1 15 A ALA 16 2 88.33 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 SER . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n SER . 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 ? -2.389 4.384 11.374 1.00 88.64 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.419 3.330 11.287 1.00 91.10 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.936 2.170 10.410 1.00 91.80 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.215 2.380 9.437 1.00 87.82 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.703 3.886 10.692 1.00 85.20 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.198 5.149 11.386 1.00 79.99 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.666 4.889 13.072 1.00 74.32 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.321 6.477 13.506 1.00 66.02 1 A 1 ATOM 9 N N . LYS A 1 2 ? -3.349 0.953 10.755 1.00 95.69 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -2.968 -0.238 9.984 1.00 95.96 2 A 1 ATOM 11 C C . LYS A 1 2 ? -3.657 -0.267 8.620 1.00 96.19 2 A 1 ATOM 12 O O . LYS A 1 2 ? -3.092 -0.774 7.648 1.00 95.48 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -3.314 -1.496 10.772 1.00 94.42 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -2.474 -1.668 12.022 1.00 87.22 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.855 -2.932 12.770 1.00 83.50 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -1.951 -3.152 13.966 1.00 77.04 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -2.160 -2.114 15.005 1.00 68.98 2 A 1 ATOM 18 N N . SER A 1 3 ? -4.854 0.263 8.541 1.00 95.31 3 A 1 ATOM 19 C CA . SER A 1 3 ? -5.624 0.296 7.295 1.00 97.09 3 A 1 ATOM 20 C C . SER A 1 3 ? -4.913 1.113 6.218 1.00 97.70 3 A 1 ATOM 21 O O . SER A 1 3 ? -5.019 0.812 5.032 1.00 96.97 3 A 1 ATOM 22 C CB . SER A 1 3 ? -7.010 0.874 7.552 1.00 95.75 3 A 1 ATOM 23 O OG . SER A 1 3 ? -7.685 0.113 8.533 1.00 88.49 3 A 1 ATOM 24 N N . ILE A 1 4 ? -4.179 2.130 6.642 1.00 97.03 4 A 1 ATOM 25 C CA . ILE A 1 4 ? -3.438 2.985 5.716 1.00 97.12 4 A 1 ATOM 26 C C . ILE A 1 4 ? -2.309 2.204 5.049 1.00 97.47 4 A 1 ATOM 27 O O . ILE A 1 4 ? -2.029 2.389 3.863 1.00 96.89 4 A 1 ATOM 28 C CB . ILE A 1 4 ? -2.881 4.226 6.439 1.00 96.75 4 A 1 ATOM 29 C CG1 . ILE A 1 4 ? -4.034 5.066 7.007 1.00 94.26 4 A 1 ATOM 30 C CG2 . ILE A 1 4 ? -2.032 5.068 5.490 1.00 92.77 4 A 1 ATOM 31 C CD1 . ILE A 1 4 ? -3.581 6.142 7.968 1.00 88.09 4 A 1 ATOM 32 N N . LEU A 1 5 ? -1.662 1.327 5.813 1.00 97.74 5 A 1 ATOM 33 C CA . LEU A 1 5 ? -0.571 0.506 5.285 1.00 97.69 5 A 1 ATOM 34 C C . LEU A 1 5 ? -1.078 -0.440 4.201 1.00 97.73 5 A 1 ATOM 35 O O . LEU A 1 5 ? -0.420 -0.627 3.173 1.00 97.54 5 A 1 ATOM 36 C CB . LEU A 1 5 ? 0.083 -0.295 6.412 1.00 97.56 5 A 1 ATOM 37 C CG . LEU A 1 5 ? 0.856 0.550 7.419 1.00 91.16 5 A 1 ATOM 38 C CD1 . LEU A 1 5 ? 1.263 -0.291 8.618 1.00 86.70 5 A 1 ATOM 39 C CD2 . LEU A 1 5 ? 2.095 1.157 6.770 1.00 89.30 5 A 1 ATOM 40 N N . LEU A 1 6 ? -2.239 -1.024 4.431 1.00 97.69 6 A 1 ATOM 41 C CA . LEU A 1 6 ? -2.843 -1.934 3.459 1.00 97.59 6 A 1 ATOM 42 C C . LEU A 1 6 ? -3.268 -1.175 2.206 1.00 97.72 6 A 1 ATOM 43 O O . LEU A 1 6 ? -3.113 -1.669 1.088 1.00 97.68 6 A 1 ATOM 44 C CB . LEU A 1 6 ? -4.050 -2.639 4.082 1.00 97.57 6 A 1 ATOM 45 C CG . LEU A 1 6 ? -3.690 -3.671 5.149 1.00 91.57 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? -4.934 -4.091 5.917 1.00 87.25 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? -3.035 -4.892 4.515 1.00 89.73 6 A 1 ATOM 48 N N . LEU A 1 7 ? -3.784 0.015 2.405 1.00 97.20 7 A 1 ATOM 49 C CA . LEU A 1 7 ? -4.212 0.859 1.291 1.00 97.32 7 A 1 ATOM 50 C C . LEU A 1 7 ? -3.018 1.265 0.435 1.00 97.50 7 A 1 ATOM 51 O O . LEU A 1 7 ? -3.101 1.295 -0.795 1.00 97.56 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -4.930 2.099 1.828 1.00 97.30 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -5.921 2.697 0.835 1.00 91.61 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -7.314 2.770 1.453 1.00 88.06 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -5.477 4.085 0.403 1.00 89.89 7 A 1 ATOM 56 N N . PHE A 1 8 ? -1.897 1.570 1.096 1.00 97.20 8 A 1 ATOM 57 C CA . PHE A 1 8 ? -0.666 1.939 0.403 1.00 96.89 8 A 1 ATOM 58 C C . PHE A 1 8 ? -0.161 0.783 -0.454 1.00 97.11 8 A 1 ATOM 59 O O . PHE A 1 8 ? 0.261 0.985 -1.595 1.00 96.98 8 A 1 ATOM 60 C CB . PHE A 1 8 ? 0.399 2.346 1.421 1.00 96.70 8 A 1 ATOM 61 C CG . PHE A 1 8 ? 1.721 2.697 0.788 1.00 94.79 8 A 1 ATOM 62 C CD1 . PHE A 1 8 ? 1.892 3.914 0.141 1.00 91.08 8 A 1 ATOM 63 C CD2 . PHE A 1 8 ? 2.781 1.804 0.839 1.00 92.25 8 A 1 ATOM 64 C CE1 . PHE A 1 8 ? 3.106 4.241 -0.450 1.00 91.27 8 A 1 ATOM 65 C CE2 . PHE A 1 8 ? 4.003 2.122 0.245 1.00 90.97 8 A 1 ATOM 66 C CZ . PHE A 1 8 ? 4.164 3.339 -0.399 1.00 91.74 8 A 1 ATOM 67 N N . SER A 1 9 ? -0.206 -0.424 0.097 1.00 97.35 9 A 1 ATOM 68 C CA . SER A 1 9 ? 0.238 -1.618 -0.620 1.00 97.35 9 A 1 ATOM 69 C C . SER A 1 9 ? -0.615 -1.855 -1.864 1.00 97.66 9 A 1 ATOM 70 O O . SER A 1 9 ? -0.108 -2.290 -2.898 1.00 97.16 9 A 1 ATOM 71 C CB . SER A 1 9 ? 0.167 -2.842 0.292 1.00 96.94 9 A 1 ATOM 72 O OG . SER A 1 9 ? 1.021 -2.685 1.404 1.00 90.97 9 A 1 ATOM 73 N N . LEU A 1 10 ? -1.896 -1.560 -1.755 1.00 97.81 10 A 1 ATOM 74 C CA . LEU A 1 10 ? -2.826 -1.727 -2.874 1.00 97.68 10 A 1 ATOM 75 C C . LEU A 1 10 ? -2.463 -0.798 -4.028 1.00 97.89 10 A 1 ATOM 76 O O . LEU A 1 10 ? -2.577 -1.175 -5.197 1.00 97.39 10 A 1 ATOM 77 C CB . LEU A 1 10 ? -4.259 -1.458 -2.407 1.00 97.16 10 A 1 ATOM 78 C CG . LEU A 1 10 ? -5.318 -2.010 -3.362 1.00 93.00 10 A 1 ATOM 79 C CD1 . LEU A 1 10 ? -6.232 -2.997 -2.636 1.00 89.74 10 A 1 ATOM 80 C CD2 . LEU A 1 10 ? -6.149 -0.885 -3.954 1.00 91.31 10 A 1 ATOM 81 N N . ILE A 1 11 ? -2.019 0.404 -3.698 1.00 97.35 11 A 1 ATOM 82 C CA . ILE A 1 11 ? -1.628 1.388 -4.708 1.00 97.28 11 A 1 ATOM 83 C C . ILE A 1 11 ? -0.393 0.909 -5.469 1.00 97.52 11 A 1 ATOM 84 O O . ILE A 1 11 ? -0.322 1.030 -6.694 1.00 97.04 11 A 1 ATOM 85 C CB . ILE A 1 11 ? -1.360 2.759 -4.061 1.00 96.83 11 A 1 ATOM 86 C CG1 . ILE A 1 11 ? -2.645 3.315 -3.429 1.00 95.09 11 A 1 ATOM 87 C CG2 . ILE A 1 11 ? -0.826 3.748 -5.101 1.00 94.71 11 A 1 ATOM 88 C CD1 . ILE A 1 11 ? -2.393 4.442 -2.448 1.00 91.25 11 A 1 ATOM 89 N N . VAL A 1 12 ? 0.570 0.357 -4.737 1.00 98.02 12 A 1 ATOM 90 C CA . VAL A 1 12 ? 1.804 -0.150 -5.343 1.00 97.93 12 A 1 ATOM 91 C C . VAL A 1 12 ? 1.503 -1.321 -6.274 1.00 97.95 12 A 1 ATOM 92 O O . VAL A 1 12 ? 2.026 -1.388 -7.390 1.00 97.33 12 A 1 ATOM 93 C CB . VAL A 1 12 ? 2.818 -0.574 -4.265 1.00 97.30 12 A 1 ATOM 94 C CG1 . VAL A 1 12 ? 4.091 -1.121 -4.898 1.00 95.01 12 A 1 ATOM 95 C CG2 . VAL A 1 12 ? 3.161 0.599 -3.366 1.00 95.03 12 A 1 ATOM 96 N N . LEU A 1 13 ? 0.664 -2.235 -5.826 1.00 97.75 13 A 1 ATOM 97 C CA . LEU A 1 13 ? 0.293 -3.400 -6.627 1.00 97.56 13 A 1 ATOM 98 C C . LEU A 1 13 ? -0.557 -2.994 -7.827 1.00 97.57 13 A 1 ATOM 99 O O . LEU A 1 13 ? -0.430 -3.572 -8.909 1.00 96.42 13 A 1 ATOM 100 C CB . LEU A 1 13 ? -0.467 -4.406 -5.760 1.00 96.91 13 A 1 ATOM 101 C CG . LEU A 1 13 ? 0.395 -5.078 -4.691 1.00 93.99 13 A 1 ATOM 102 C CD1 . LEU A 1 13 ? -0.489 -5.814 -3.693 1.00 89.60 13 A 1 ATOM 103 C CD2 . LEU A 1 13 ? 1.380 -6.046 -5.333 1.00 89.12 13 A 1 ATOM 104 N N . GLY A 1 14 ? -1.412 -2.019 -7.636 1.00 96.41 14 A 1 ATOM 105 C CA . GLY A 1 14 ? -2.269 -1.526 -8.708 1.00 95.87 14 A 1 ATOM 106 C C . GLY A 1 14 ? -1.490 -0.833 -9.809 1.00 96.10 14 A 1 ATOM 107 O O . GLY A 1 14 ? -1.902 -0.845 -10.971 1.00 95.02 14 A 1 ATOM 108 N N . SER A 1 15 ? -0.361 -0.233 -9.459 1.00 96.41 15 A 1 ATOM 109 C CA . SER A 1 15 ? 0.492 0.459 -10.429 1.00 96.17 15 A 1 ATOM 110 C C . SER A 1 15 ? 1.275 -0.517 -11.302 1.00 95.59 15 A 1 ATOM 111 O O . SER A 1 15 ? 1.709 -0.164 -12.400 1.00 91.63 15 A 1 ATOM 112 C CB . SER A 1 15 ? 1.471 1.385 -9.705 1.00 94.19 15 A 1 ATOM 113 O OG . SER A 1 15 ? 2.386 0.644 -8.928 1.00 84.83 15 A 1 ATOM 114 N N . ALA A 1 16 ? 1.470 -1.748 -10.817 1.00 94.31 16 A 1 ATOM 115 C CA . ALA A 1 16 ? 2.212 -2.773 -11.537 1.00 92.69 16 A 1 ATOM 116 C C . ALA A 1 16 ? 1.397 -3.352 -12.689 1.00 90.89 16 A 1 ATOM 117 O O . ALA A 1 16 ? 0.164 -3.443 -12.574 1.00 86.18 16 A 1 ATOM 118 C CB . ALA A 1 16 ? 2.663 -3.881 -10.585 1.00 88.16 16 A 1 ATOM 119 O OXT . ALA A 1 16 ? 1.995 -3.730 -13.708 1.00 77.76 16 A 1 #