# 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_spkb34044 # _entry.id spkb34044 # 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 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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 MET 2 1 n VAL 3 1 n LYS 4 1 n LEU 5 1 n ILE 6 1 n CYS 7 1 n ALA 8 1 n ILE 9 1 n VAL 10 1 n ASP 11 1 n ILE 12 1 n ALA 13 1 n GLY 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 @ 2025-07-13 08:54:23)" _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 94.54 _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 86.85 1 1 A MET 2 2 91.83 1 2 A VAL 3 2 96.63 1 3 A LYS 4 2 93.55 1 4 A LEU 5 2 95.27 1 5 A ILE 6 2 96.45 1 6 A CYS 7 2 96.68 1 7 A ALA 8 2 97.28 1 8 A ILE 9 2 96.70 1 9 A VAL 10 2 97.36 1 10 A ASP 11 2 95.84 1 11 A ILE 12 2 96.17 1 12 A ALA 13 2 97.19 1 13 A GLY 14 2 94.92 1 14 A ALA 15 2 87.03 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 MET . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n CYS . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n ASP . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n GLY . 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 ? -7.350 -5.056 5.791 1.00 91.34 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.173 -3.779 5.070 1.00 92.85 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.857 -3.773 4.294 1.00 94.17 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.876 -3.159 4.709 1.00 91.46 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.178 -2.622 6.069 1.00 88.64 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.526 -2.451 6.738 1.00 83.34 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.466 -1.323 8.126 1.00 81.21 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.172 -1.338 8.641 1.00 71.78 1 A 1 ATOM 9 N N . MET A 1 2 ? -5.859 -4.466 3.167 1.00 96.60 2 A 1 ATOM 10 C CA . MET A 1 2 ? -4.662 -4.569 2.332 1.00 97.21 2 A 1 ATOM 11 C C . MET A 1 2 ? -4.343 -3.238 1.654 1.00 97.72 2 A 1 ATOM 12 O O . MET A 1 2 ? -3.187 -2.830 1.576 1.00 96.88 2 A 1 ATOM 13 C CB . MET A 1 2 ? -4.863 -5.650 1.272 1.00 95.87 2 A 1 ATOM 14 C CG . MET A 1 2 ? -4.321 -7.004 1.696 1.00 90.02 2 A 1 ATOM 15 S SD . MET A 1 2 ? -5.173 -7.647 3.132 1.00 85.13 2 A 1 ATOM 16 C CE . MET A 1 2 ? -4.340 -9.219 3.307 1.00 75.25 2 A 1 ATOM 17 N N . VAL A 1 3 ? -5.369 -2.566 1.170 1.00 97.44 3 A 1 ATOM 18 C CA . VAL A 1 3 ? -5.192 -1.284 0.490 1.00 97.95 3 A 1 ATOM 19 C C . VAL A 1 3 ? -4.483 -0.278 1.391 1.00 98.25 3 A 1 ATOM 20 O O . VAL A 1 3 ? -3.655 0.512 0.934 1.00 97.86 3 A 1 ATOM 21 C CB . VAL A 1 3 ? -6.548 -0.711 0.044 1.00 97.26 3 A 1 ATOM 22 C CG1 . VAL A 1 3 ? -6.364 0.607 -0.679 1.00 93.66 3 A 1 ATOM 23 C CG2 . VAL A 1 3 ? -7.276 -1.707 -0.843 1.00 93.98 3 A 1 ATOM 24 N N . LYS A 1 4 ? -4.815 -0.330 2.683 1.00 97.88 4 A 1 ATOM 25 C CA . LYS A 1 4 ? -4.205 0.579 3.650 1.00 98.04 4 A 1 ATOM 26 C C . LYS A 1 4 ? -2.699 0.363 3.733 1.00 98.12 4 A 1 ATOM 27 O O . LYS A 1 4 ? -1.930 1.320 3.789 1.00 97.82 4 A 1 ATOM 28 C CB . LYS A 1 4 ? -4.836 0.387 5.024 1.00 97.78 4 A 1 ATOM 29 C CG . LYS A 1 4 ? -5.586 1.618 5.500 1.00 93.64 4 A 1 ATOM 30 C CD . LYS A 1 4 ? -4.654 2.784 5.722 1.00 90.50 4 A 1 ATOM 31 C CE . LYS A 1 4 ? -5.382 4.020 6.205 1.00 86.92 4 A 1 ATOM 32 N NZ . LYS A 1 4 ? -4.435 5.155 6.412 1.00 81.25 4 A 1 ATOM 33 N N . LEU A 1 5 ? -2.284 -0.893 3.721 1.00 97.54 5 A 1 ATOM 34 C CA . LEU A 1 5 ? -0.868 -1.242 3.776 1.00 97.67 5 A 1 ATOM 35 C C . LEU A 1 5 ? -0.126 -0.669 2.578 1.00 97.95 5 A 1 ATOM 36 O O . LEU A 1 5 ? 0.929 -0.055 2.721 1.00 97.69 5 A 1 ATOM 37 C CB . LEU A 1 5 ? -0.700 -2.759 3.812 1.00 97.25 5 A 1 ATOM 38 C CG . LEU A 1 5 ? -0.629 -3.343 5.217 1.00 92.61 5 A 1 ATOM 39 C CD1 . LEU A 1 5 ? -1.980 -3.197 5.921 1.00 90.84 5 A 1 ATOM 40 C CD2 . LEU A 1 5 ? -0.220 -4.801 5.170 1.00 90.61 5 A 1 ATOM 41 N N . ILE A 1 6 ? -0.687 -0.877 1.401 1.00 97.58 6 A 1 ATOM 42 C CA . ILE A 1 6 ? -0.082 -0.384 0.167 1.00 97.52 6 A 1 ATOM 43 C C . ILE A 1 6 ? -0.025 1.139 0.178 1.00 97.63 6 A 1 ATOM 44 O O . ILE A 1 6 ? 0.990 1.740 -0.186 1.00 97.48 6 A 1 ATOM 45 C CB . ILE A 1 6 ? -0.876 -0.870 -1.054 1.00 97.46 6 A 1 ATOM 46 C CG1 . ILE A 1 6 ? -0.884 -2.397 -1.106 1.00 96.04 6 A 1 ATOM 47 C CG2 . ILE A 1 6 ? -0.264 -0.304 -2.340 1.00 95.91 6 A 1 ATOM 48 C CD1 . ILE A 1 6 ? -1.942 -2.948 -2.040 1.00 91.97 6 A 1 ATOM 49 N N . CYS A 1 7 ? -1.111 1.751 0.602 1.00 97.34 7 A 1 ATOM 50 C CA . CYS A 1 7 ? -1.193 3.208 0.662 1.00 97.31 7 A 1 ATOM 51 C C . CYS A 1 7 ? -0.127 3.775 1.597 1.00 97.40 7 A 1 ATOM 52 O O . CYS A 1 7 ? 0.502 4.785 1.296 1.00 97.08 7 A 1 ATOM 53 C CB . CYS A 1 7 ? -2.582 3.630 1.141 1.00 96.94 7 A 1 ATOM 54 S SG . CYS A 1 7 ? -2.854 5.401 0.965 1.00 94.02 7 A 1 ATOM 55 N N . ALA A 1 8 ? 0.075 3.110 2.727 1.00 97.20 8 A 1 ATOM 56 C CA . ALA A 1 8 ? 1.070 3.545 3.703 1.00 97.27 8 A 1 ATOM 57 C C . ALA A 1 8 ? 2.479 3.458 3.127 1.00 97.62 8 A 1 ATOM 58 O O . ALA A 1 8 ? 3.284 4.373 3.289 1.00 97.31 8 A 1 ATOM 59 C CB . ALA A 1 8 ? 0.967 2.694 4.961 1.00 97.02 8 A 1 ATOM 60 N N . ILE A 1 9 ? 2.775 2.350 2.453 1.00 97.87 9 A 1 ATOM 61 C CA . ILE A 1 9 ? 4.087 2.144 1.847 1.00 97.86 9 A 1 ATOM 62 C C . ILE A 1 9 ? 4.360 3.202 0.790 1.00 97.96 9 A 1 ATOM 63 O O . ILE A 1 9 ? 5.448 3.781 0.740 1.00 97.67 9 A 1 ATOM 64 C CB . ILE A 1 9 ? 4.184 0.748 1.217 1.00 97.66 9 A 1 ATOM 65 C CG1 . ILE A 1 9 ? 4.061 -0.326 2.296 1.00 96.22 9 A 1 ATOM 66 C CG2 . ILE A 1 9 ? 5.515 0.591 0.473 1.00 95.95 9 A 1 ATOM 67 C CD1 . ILE A 1 9 ? 3.727 -1.692 1.732 1.00 92.45 9 A 1 ATOM 68 N N . VAL A 1 10 ? 3.376 3.443 -0.056 1.00 98.11 10 A 1 ATOM 69 C CA . VAL A 1 10 ? 3.507 4.438 -1.116 1.00 98.03 10 A 1 ATOM 70 C C . VAL A 1 10 ? 3.707 5.828 -0.526 1.00 98.02 10 A 1 ATOM 71 O O . VAL A 1 10 ? 4.516 6.613 -1.022 1.00 97.58 10 A 1 ATOM 72 C CB . VAL A 1 10 ? 2.270 4.434 -2.022 1.00 97.59 10 A 1 ATOM 73 C CG1 . VAL A 1 10 ? 2.332 5.566 -3.036 1.00 95.97 10 A 1 ATOM 74 C CG2 . VAL A 1 10 ? 2.148 3.102 -2.736 1.00 96.24 10 A 1 ATOM 75 N N . ASP A 1 11 ? 2.972 6.120 0.529 1.00 97.62 11 A 1 ATOM 76 C CA . ASP A 1 11 ? 3.064 7.419 1.190 1.00 97.63 11 A 1 ATOM 77 C C . ASP A 1 11 ? 4.444 7.628 1.799 1.00 97.88 11 A 1 ATOM 78 O O . ASP A 1 11 ? 5.029 8.708 1.685 1.00 97.41 11 A 1 ATOM 79 C CB . ASP A 1 11 ? 2.002 7.537 2.282 1.00 97.07 11 A 1 ATOM 80 C CG . ASP A 1 11 ? 1.841 8.967 2.753 1.00 94.99 11 A 1 ATOM 81 O OD1 . ASP A 1 11 ? 1.871 9.875 1.907 1.00 92.46 11 A 1 ATOM 82 O OD2 . ASP A 1 11 ? 1.678 9.178 3.966 1.00 91.68 11 A 1 ATOM 83 N N . ILE A 1 12 ? 4.968 6.589 2.444 1.00 97.78 12 A 1 ATOM 84 C CA . ILE A 1 12 ? 6.289 6.653 3.062 1.00 97.73 12 A 1 ATOM 85 C C . ILE A 1 12 ? 7.369 6.780 2.004 1.00 97.84 12 A 1 ATOM 86 O O . ILE A 1 12 ? 8.294 7.585 2.138 1.00 97.24 12 A 1 ATOM 87 C CB . ILE A 1 12 ? 6.547 5.403 3.918 1.00 97.19 12 A 1 ATOM 88 C CG1 . ILE A 1 12 ? 5.578 5.370 5.099 1.00 94.80 12 A 1 ATOM 89 C CG2 . ILE A 1 12 ? 7.991 5.392 4.425 1.00 94.82 12 A 1 ATOM 90 C CD1 . ILE A 1 12 ? 5.500 4.014 5.765 1.00 92.00 12 A 1 ATOM 91 N N . ALA A 1 13 ? 7.262 5.980 0.955 1.00 97.60 13 A 1 ATOM 92 C CA . ALA A 1 13 ? 8.225 6.010 -0.137 1.00 97.52 13 A 1 ATOM 93 C C . ALA A 1 13 ? 8.220 7.366 -0.817 1.00 97.62 13 A 1 ATOM 94 O O . ALA A 1 13 ? 9.260 8.018 -0.926 1.00 96.44 13 A 1 ATOM 95 C CB . ALA A 1 13 ? 7.902 4.919 -1.147 1.00 96.77 13 A 1 ATOM 96 N N . GLY A 1 14 ? 7.044 7.787 -1.267 1.00 95.99 14 A 1 ATOM 97 C CA . GLY A 1 14 ? 6.880 9.084 -1.914 1.00 95.31 14 A 1 ATOM 98 C C . GLY A 1 14 ? 7.964 9.385 -2.930 1.00 95.39 14 A 1 ATOM 99 O O . GLY A 1 14 ? 8.216 10.545 -3.264 1.00 93.01 14 A 1 ATOM 100 N N . ALA A 1 15 ? 8.606 8.315 -3.402 1.00 93.26 15 A 1 ATOM 101 C CA . ALA A 1 15 ? 9.709 8.469 -4.348 1.00 91.37 15 A 1 ATOM 102 C C . ALA A 1 15 ? 10.028 7.133 -4.976 1.00 89.79 15 A 1 ATOM 103 O O . ALA A 1 15 ? 10.123 7.073 -6.218 1.00 83.19 15 A 1 ATOM 104 C CB . ALA A 1 15 ? 10.941 9.031 -3.643 1.00 87.51 15 A 1 ATOM 105 O OXT . ALA A 1 15 ? 10.181 6.159 -4.243 1.00 77.04 15 A 1 #