# 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_spkb24414 # _entry.id spkb24414 # 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" "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 VAL 3 1 n LEU 4 1 n ALA 5 1 n ALA 6 1 n LEU 7 1 n ALA 8 1 n LEU 9 1 n SER 10 1 n ALA 11 1 n LEU 12 1 n ALA 13 1 n LEU 14 1 n ALA 15 # _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 01:32:33)" _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 94.48 _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 88.64 1 1 A LYS 2 2 92.48 1 2 A VAL 3 2 96.01 1 3 A LEU 4 2 95.17 1 4 A ALA 5 2 97.54 1 5 A ALA 6 2 98.23 1 6 A LEU 7 2 96.48 1 7 A ALA 8 2 97.54 1 8 A LEU 9 2 96.51 1 9 A SER 10 2 96.68 1 10 A ALA 11 2 97.53 1 11 A LEU 12 2 94.65 1 12 A ALA 13 2 95.51 1 13 A LEU 14 2 90.22 1 14 A ALA 15 2 88.85 1 15 # _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 VAL . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 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 # _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 ? -10.572 6.571 3.744 1.00 92.28 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.523 6.260 2.768 1.00 93.54 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.252 5.751 3.456 1.00 94.88 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.173 6.305 3.270 1.00 92.92 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.202 7.506 1.945 1.00 90.17 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.882 8.715 2.796 1.00 87.04 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.596 10.192 1.810 1.00 84.20 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.266 10.594 1.361 1.00 74.09 1 A 1 ATOM 9 N N . LYS A 1 2 ? -8.416 4.716 4.259 1.00 94.24 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -7.281 4.144 4.982 1.00 96.26 2 A 1 ATOM 11 C C . LYS A 1 2 ? -6.876 2.804 4.377 1.00 97.10 2 A 1 ATOM 12 O O . LYS A 1 2 ? -5.772 2.322 4.613 1.00 96.72 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -7.625 3.969 6.467 1.00 95.53 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -7.549 5.276 7.256 1.00 92.13 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -8.759 6.158 7.022 1.00 90.24 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -8.665 7.450 7.810 1.00 87.11 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -9.849 8.310 7.553 1.00 83.03 2 A 1 ATOM 18 N N . VAL A 1 3 ? -7.775 2.211 3.607 1.00 96.28 3 A 1 ATOM 19 C CA . VAL A 1 3 ? -7.506 0.919 2.981 1.00 97.16 3 A 1 ATOM 20 C C . VAL A 1 3 ? -6.346 1.031 1.994 1.00 97.82 3 A 1 ATOM 21 O O . VAL A 1 3 ? -5.430 0.205 1.992 1.00 97.39 3 A 1 ATOM 22 C CB . VAL A 1 3 ? -8.760 0.390 2.268 1.00 96.54 3 A 1 ATOM 23 C CG1 . VAL A 1 3 ? -8.478 -0.961 1.636 1.00 93.71 3 A 1 ATOM 24 C CG2 . VAL A 1 3 ? -9.919 0.284 3.251 1.00 93.20 3 A 1 ATOM 25 N N . LEU A 1 4 ? -6.398 2.054 1.157 1.00 96.07 4 A 1 ATOM 26 C CA . LEU A 1 4 ? -5.348 2.261 0.163 1.00 96.88 4 A 1 ATOM 27 C C . LEU A 1 4 ? -4.014 2.534 0.846 1.00 97.54 4 A 1 ATOM 28 O O . LEU A 1 4 ? -2.967 2.067 0.396 1.00 97.56 4 A 1 ATOM 29 C CB . LEU A 1 4 ? -5.721 3.432 -0.746 1.00 96.65 4 A 1 ATOM 30 C CG . LEU A 1 4 ? -6.998 3.203 -1.550 1.00 93.85 4 A 1 ATOM 31 C CD1 . LEU A 1 4 ? -7.357 4.447 -2.340 1.00 91.58 4 A 1 ATOM 32 C CD2 . LEU A 1 4 ? -6.822 2.010 -2.483 1.00 91.21 4 A 1 ATOM 33 N N . ALA A 1 5 ? -4.065 3.287 1.934 1.00 97.40 5 A 1 ATOM 34 C CA . ALA A 1 5 ? -2.861 3.601 2.695 1.00 97.53 5 A 1 ATOM 35 C C . ALA A 1 5 ? -2.242 2.325 3.258 1.00 97.96 5 A 1 ATOM 36 O O . ALA A 1 5 ? -1.021 2.154 3.245 1.00 97.72 5 A 1 ATOM 37 C CB . ALA A 1 5 ? -3.196 4.568 3.822 1.00 97.08 5 A 1 ATOM 38 N N . ALA A 1 6 ? -3.094 1.435 3.744 1.00 98.23 6 A 1 ATOM 39 C CA . ALA A 1 6 ? -2.634 0.170 4.306 1.00 98.27 6 A 1 ATOM 40 C C . ALA A 1 6 ? -1.971 -0.683 3.228 1.00 98.48 6 A 1 ATOM 41 O O . ALA A 1 6 ? -0.928 -1.301 3.461 1.00 98.18 6 A 1 ATOM 42 C CB . ALA A 1 6 ? -3.808 -0.577 4.924 1.00 98.01 6 A 1 ATOM 43 N N . LEU A 1 7 ? -2.581 -0.706 2.055 1.00 98.10 7 A 1 ATOM 44 C CA . LEU A 1 7 ? -2.039 -1.476 0.938 1.00 97.98 7 A 1 ATOM 45 C C . LEU A 1 7 ? -0.695 -0.911 0.504 1.00 98.31 7 A 1 ATOM 46 O O . LEU A 1 7 ? 0.238 -1.664 0.214 1.00 98.24 7 A 1 ATOM 47 C CB . LEU A 1 7 ? -3.022 -1.449 -0.229 1.00 97.76 7 A 1 ATOM 48 C CG . LEU A 1 7 ? -4.280 -2.275 0.025 1.00 94.64 7 A 1 ATOM 49 C CD1 . LEU A 1 7 ? -5.321 -2.005 -1.048 1.00 93.26 7 A 1 ATOM 50 C CD2 . LEU A 1 7 ? -3.939 -3.758 0.066 1.00 93.53 7 A 1 ATOM 51 N N . ALA A 1 8 ? -0.617 0.410 0.457 1.00 97.47 8 A 1 ATOM 52 C CA . ALA A 1 8 ? 0.620 1.076 0.069 1.00 97.50 8 A 1 ATOM 53 C C . ALA A 1 8 ? 1.728 0.761 1.066 1.00 97.93 8 A 1 ATOM 54 O O . ALA A 1 8 ? 2.864 0.469 0.681 1.00 97.59 8 A 1 ATOM 55 C CB . ALA A 1 8 ? 0.397 2.578 -0.010 1.00 97.22 8 A 1 ATOM 56 N N . LEU A 1 9 ? 1.383 0.806 2.343 1.00 98.25 9 A 1 ATOM 57 C CA . LEU A 1 9 ? 2.349 0.516 3.399 1.00 98.10 9 A 1 ATOM 58 C C . LEU A 1 9 ? 2.792 -0.939 3.314 1.00 98.40 9 A 1 ATOM 59 O O . LEU A 1 9 ? 3.972 -1.258 3.470 1.00 98.18 9 A 1 ATOM 60 C CB . LEU A 1 9 ? 1.726 0.800 4.766 1.00 97.73 9 A 1 ATOM 61 C CG . LEU A 1 9 ? 2.749 1.312 5.779 1.00 94.65 9 A 1 ATOM 62 C CD1 . LEU A 1 9 ? 3.144 2.745 5.449 1.00 93.32 9 A 1 ATOM 63 C CD2 . LEU A 1 9 ? 2.192 1.236 7.193 1.00 93.43 9 A 1 ATOM 64 N N . SER A 1 10 ? 1.837 -1.815 3.060 1.00 97.98 10 A 1 ATOM 65 C CA . SER A 1 10 ? 2.117 -3.241 2.938 1.00 97.96 10 A 1 ATOM 66 C C . SER A 1 10 ? 3.030 -3.501 1.750 1.00 98.25 10 A 1 ATOM 67 O O . SER A 1 10 ? 3.927 -4.343 1.813 1.00 97.85 10 A 1 ATOM 68 C CB . SER A 1 10 ? 0.819 -4.026 2.768 1.00 97.44 10 A 1 ATOM 69 O OG . SER A 1 10 ? 1.087 -5.408 2.754 1.00 90.62 10 A 1 ATOM 70 N N . ALA A 1 11 ? 2.789 -2.773 0.670 1.00 97.58 11 A 1 ATOM 71 C CA . ALA A 1 11 ? 3.604 -2.914 -0.534 1.00 97.58 11 A 1 ATOM 72 C C . ALA A 1 11 ? 5.057 -2.573 -0.235 1.00 98.04 11 A 1 ATOM 73 O O . ALA A 1 11 ? 5.973 -3.252 -0.703 1.00 97.44 11 A 1 ATOM 74 C CB . ALA A 1 11 ? 3.065 -2.009 -1.633 1.00 97.02 11 A 1 ATOM 75 N N . LEU A 1 12 ? 5.263 -1.530 0.548 1.00 97.46 12 A 1 ATOM 76 C CA . LEU A 1 12 ? 6.611 -1.114 0.919 1.00 97.15 12 A 1 ATOM 77 C C . LEU A 1 12 ? 7.269 -2.173 1.789 1.00 97.58 12 A 1 ATOM 78 O O . LEU A 1 12 ? 8.469 -2.427 1.671 1.00 96.71 12 A 1 ATOM 79 C CB . LEU A 1 12 ? 6.555 0.214 1.671 1.00 96.47 12 A 1 ATOM 80 C CG . LEU A 1 12 ? 6.149 1.393 0.791 1.00 92.83 12 A 1 ATOM 81 C CD1 . LEU A 1 12 ? 5.878 2.622 1.645 1.00 90.04 12 A 1 ATOM 82 C CD2 . LEU A 1 12 ? 7.232 1.689 -0.233 1.00 88.97 12 A 1 ATOM 83 N N . ALA A 1 13 ? 6.484 -2.778 2.655 1.00 95.75 13 A 1 ATOM 84 C CA . ALA A 1 13 ? 6.990 -3.821 3.542 1.00 95.71 13 A 1 ATOM 85 C C . ALA A 1 13 ? 7.401 -5.056 2.745 1.00 96.69 13 A 1 ATOM 86 O O . ALA A 1 13 ? 8.398 -5.708 3.061 1.00 95.26 13 A 1 ATOM 87 C CB . ALA A 1 13 ? 5.928 -4.188 4.574 1.00 94.13 13 A 1 ATOM 88 N N . LEU A 1 14 ? 6.621 -5.369 1.722 1.00 94.60 14 A 1 ATOM 89 C CA . LEU A 1 14 ? 6.905 -6.528 0.877 1.00 94.20 14 A 1 ATOM 90 C C . LEU A 1 14 ? 8.129 -6.280 0.012 1.00 95.24 14 A 1 ATOM 91 O O . LEU A 1 14 ? 8.974 -7.161 -0.162 1.00 93.69 14 A 1 ATOM 92 C CB . LEU A 1 14 ? 5.691 -6.831 0.003 1.00 92.43 14 A 1 ATOM 93 C CG . LEU A 1 14 ? 4.473 -7.296 0.797 1.00 87.54 14 A 1 ATOM 94 C CD1 . LEU A 1 14 ? 3.252 -7.376 -0.108 1.00 83.88 14 A 1 ATOM 95 C CD2 . LEU A 1 14 ? 4.746 -8.657 1.432 1.00 80.14 14 A 1 ATOM 96 N N . ALA A 1 15 ? 8.203 -5.090 -0.556 1.00 94.19 15 A 1 ATOM 97 C CA . ALA A 1 15 ? 9.310 -4.733 -1.428 1.00 91.87 15 A 1 ATOM 98 C C . ALA A 1 15 ? 9.749 -3.297 -1.174 1.00 90.54 15 A 1 ATOM 99 O O . ALA A 1 15 ? 8.880 -2.422 -1.067 1.00 87.81 15 A 1 ATOM 100 C CB . ALA A 1 15 ? 8.915 -4.901 -2.884 1.00 87.83 15 A 1 ATOM 101 O OXT . ALA A 1 15 ? 10.955 -3.049 -1.092 1.00 80.83 15 A 1 #