# 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_spkb38507 # _entry.id spkb38507 # 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" "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" "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 ILE 2 1 n THR 3 1 n GLY 4 1 n LYS 5 1 n THR 6 1 n ILE 7 1 n SER 8 1 n LEU 9 1 n PRO 10 1 n LEU 11 1 n SER 12 1 n VAL 13 1 n ILE 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 @ 2025-07-04 10:11:37)" _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 86.42 _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 73.90 1 1 A ILE 2 2 83.43 1 2 A THR 3 2 85.63 1 3 A GLY 4 2 89.22 1 4 A LYS 5 2 80.60 1 5 A THR 6 2 87.48 1 6 A ILE 7 2 85.84 1 7 A SER 8 2 88.28 1 8 A LEU 9 2 87.56 1 9 A PRO 10 2 90.32 1 10 A LEU 11 2 90.93 1 11 A SER 12 2 91.19 1 12 A VAL 13 2 90.58 1 13 A ILE 14 2 88.74 1 14 A ALA 15 2 87.78 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 ILE . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n GLY . 4 A 4 A 5 1 n LYS . 5 A 5 A 6 1 n THR . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PRO . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n ILE . 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 ? 1.450 7.571 -0.779 1.00 76.61 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.738 6.154 -0.518 1.00 80.13 1 A 1 ATOM 3 C C . MET A 1 1 ? 2.061 5.936 0.954 1.00 82.35 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.163 6.226 1.394 1.00 78.42 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.921 5.666 -1.359 1.00 73.96 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.667 5.744 -2.841 1.00 70.87 1 A 1 ATOM 7 S SD . MET A 1 1 ? 4.090 5.193 -3.803 1.00 68.17 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.457 5.409 -5.460 1.00 60.69 1 A 1 ATOM 9 N N . ILE A 1 2 ? 1.081 5.441 1.694 1.00 84.03 2 A 1 ATOM 10 C CA . ILE A 1 2 ? 1.290 5.132 3.099 1.00 86.41 2 A 1 ATOM 11 C C . ILE A 1 2 ? 0.748 3.737 3.395 1.00 89.48 2 A 1 ATOM 12 O O . ILE A 1 2 ? -0.461 3.489 3.377 1.00 89.33 2 A 1 ATOM 13 C CB . ILE A 1 2 ? 0.625 6.170 4.022 1.00 84.55 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -0.847 6.377 3.674 1.00 81.71 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? 1.375 7.490 3.949 1.00 79.62 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -1.576 7.286 4.650 1.00 72.33 2 A 1 ATOM 17 N N . THR A 1 3 ? 1.639 2.815 3.658 1.00 84.81 3 A 1 ATOM 18 C CA . THR A 1 3 ? 1.268 1.440 3.939 1.00 87.23 3 A 1 ATOM 19 C C . THR A 1 3 ? 0.846 1.272 5.392 1.00 88.82 3 A 1 ATOM 20 O O . THR A 1 3 ? 1.555 1.689 6.304 1.00 87.30 3 A 1 ATOM 21 C CB . THR A 1 3 ? 2.433 0.485 3.647 1.00 86.49 3 A 1 ATOM 22 O OG1 . THR A 1 3 ? 3.600 0.904 4.347 1.00 82.40 3 A 1 ATOM 23 C CG2 . THR A 1 3 ? 2.726 0.452 2.159 1.00 82.38 3 A 1 ATOM 24 N N . GLY A 1 4 ? -0.327 0.673 5.584 1.00 88.23 4 A 1 ATOM 25 C CA . GLY A 1 4 ? -0.819 0.464 6.935 1.00 88.69 4 A 1 ATOM 26 C C . GLY A 1 4 ? -2.126 1.181 7.180 1.00 90.83 4 A 1 ATOM 27 O O . GLY A 1 4 ? -3.037 0.646 7.807 1.00 89.15 4 A 1 ATOM 28 N N . LYS A 1 5 ? -2.235 2.410 6.663 1.00 87.41 5 A 1 ATOM 29 C CA . LYS A 1 5 ? -3.426 3.223 6.856 1.00 88.21 5 A 1 ATOM 30 C C . LYS A 1 5 ? -4.366 3.129 5.664 1.00 89.56 5 A 1 ATOM 31 O O . LYS A 1 5 ? -5.518 2.720 5.792 1.00 87.78 5 A 1 ATOM 32 C CB . LYS A 1 5 ? -3.038 4.676 7.098 1.00 85.27 5 A 1 ATOM 33 C CG . LYS A 1 5 ? -2.204 4.896 8.354 1.00 77.79 5 A 1 ATOM 34 C CD . LYS A 1 5 ? -2.993 4.587 9.609 1.00 76.48 5 A 1 ATOM 35 C CE . LYS A 1 5 ? -2.182 4.884 10.862 1.00 70.10 5 A 1 ATOM 36 N NZ . LYS A 1 5 ? -2.963 4.629 12.104 1.00 62.79 5 A 1 ATOM 37 N N . THR A 1 6 ? -3.875 3.524 4.480 1.00 88.66 6 A 1 ATOM 38 C CA . THR A 1 6 ? -4.683 3.536 3.264 1.00 89.59 6 A 1 ATOM 39 C C . THR A 1 6 ? -4.636 2.197 2.541 1.00 90.63 6 A 1 ATOM 40 O O . THR A 1 6 ? -5.669 1.641 2.175 1.00 89.32 6 A 1 ATOM 41 C CB . THR A 1 6 ? -4.216 4.627 2.301 1.00 88.13 6 A 1 ATOM 42 O OG1 . THR A 1 6 ? -4.187 5.882 2.983 1.00 83.50 6 A 1 ATOM 43 C CG2 . THR A 1 6 ? -5.138 4.724 1.104 1.00 82.51 6 A 1 ATOM 44 N N . ILE A 1 7 ? -3.448 1.675 2.323 1.00 88.95 7 A 1 ATOM 45 C CA . ILE A 1 7 ? -3.273 0.431 1.594 1.00 87.97 7 A 1 ATOM 46 C C . ILE A 1 7 ? -2.657 -0.641 2.482 1.00 89.82 7 A 1 ATOM 47 O O . ILE A 1 7 ? -1.516 -0.517 2.929 1.00 88.50 7 A 1 ATOM 48 C CB . ILE A 1 7 ? -2.401 0.627 0.345 1.00 87.89 7 A 1 ATOM 49 C CG1 . ILE A 1 7 ? -2.989 1.715 -0.557 1.00 83.99 7 A 1 ATOM 50 C CG2 . ILE A 1 7 ? -2.269 -0.687 -0.420 1.00 82.48 7 A 1 ATOM 51 C CD1 . ILE A 1 7 ? -2.116 2.058 -1.744 1.00 77.13 7 A 1 ATOM 52 N N . SER A 1 8 ? -3.424 -1.694 2.719 1.00 90.58 8 A 1 ATOM 53 C CA . SER A 1 8 ? -2.950 -2.812 3.526 1.00 90.01 8 A 1 ATOM 54 C C . SER A 1 8 ? -2.266 -3.862 2.656 1.00 90.98 8 A 1 ATOM 55 O O . SER A 1 8 ? -1.551 -4.729 3.144 1.00 89.23 8 A 1 ATOM 56 C CB . SER A 1 8 ? -4.112 -3.452 4.280 1.00 88.46 8 A 1 ATOM 57 O OG . SER A 1 8 ? -3.652 -4.492 5.120 1.00 80.41 8 A 1 ATOM 58 N N . LEU A 1 9 ? -2.505 -3.781 1.346 1.00 90.58 9 A 1 ATOM 59 C CA . LEU A 1 9 ? -1.918 -4.702 0.384 1.00 90.46 9 A 1 ATOM 60 C C . LEU A 1 9 ? -0.587 -4.167 -0.135 1.00 92.18 9 A 1 ATOM 61 O O . LEU A 1 9 ? -0.461 -2.967 -0.382 1.00 91.09 9 A 1 ATOM 62 C CB . LEU A 1 9 ? -2.873 -4.926 -0.787 1.00 88.81 9 A 1 ATOM 63 C CG . LEU A 1 9 ? -4.243 -5.497 -0.416 1.00 83.53 9 A 1 ATOM 64 C CD1 . LEU A 1 9 ? -5.136 -5.566 -1.641 1.00 81.78 9 A 1 ATOM 65 C CD2 . LEU A 1 9 ? -4.107 -6.866 0.225 1.00 82.03 9 A 1 ATOM 66 N N . PRO A 1 10 ? 0.400 -5.046 -0.327 1.00 90.98 10 A 1 ATOM 67 C CA . PRO A 1 10 ? 1.700 -4.649 -0.877 1.00 90.96 10 A 1 ATOM 68 C C . PRO A 1 10 ? 1.550 -4.108 -2.293 1.00 92.37 10 A 1 ATOM 69 O O . PRO A 1 10 ? 0.911 -4.738 -3.132 1.00 90.91 10 A 1 ATOM 70 C CB . PRO A 1 10 ? 2.515 -5.947 -0.877 1.00 88.37 10 A 1 ATOM 71 C CG . PRO A 1 10 ? 1.843 -6.810 0.144 1.00 87.99 10 A 1 ATOM 72 C CD . PRO A 1 10 ? 0.382 -6.442 0.074 1.00 90.67 10 A 1 ATOM 73 N N . LEU A 1 11 ? 2.139 -2.960 -2.566 1.00 93.44 11 A 1 ATOM 74 C CA . LEU A 1 11 ? 2.041 -2.313 -3.869 1.00 93.58 11 A 1 ATOM 75 C C . LEU A 1 11 ? 2.682 -3.147 -4.969 1.00 94.55 11 A 1 ATOM 76 O O . LEU A 1 11 ? 2.232 -3.131 -6.112 1.00 93.34 11 A 1 ATOM 77 C CB . LEU A 1 11 ? 2.698 -0.935 -3.816 1.00 92.59 11 A 1 ATOM 78 C CG . LEU A 1 11 ? 2.033 0.050 -2.855 1.00 88.37 11 A 1 ATOM 79 C CD1 . LEU A 1 11 ? 2.821 1.344 -2.793 1.00 85.87 11 A 1 ATOM 80 C CD2 . LEU A 1 11 ? 0.599 0.312 -3.274 1.00 85.70 11 A 1 ATOM 81 N N . SER A 1 12 ? 3.720 -3.886 -4.630 1.00 92.62 12 A 1 ATOM 82 C CA . SER A 1 12 ? 4.443 -4.711 -5.595 1.00 92.66 12 A 1 ATOM 83 C C . SER A 1 12 ? 3.636 -5.929 -6.029 1.00 93.48 12 A 1 ATOM 84 O O . SER A 1 12 ? 3.898 -6.517 -7.072 1.00 91.65 12 A 1 ATOM 85 C CB . SER A 1 12 ? 5.777 -5.169 -5.011 1.00 91.54 12 A 1 ATOM 86 O OG . SER A 1 12 ? 6.581 -4.061 -4.645 1.00 85.22 12 A 1 ATOM 87 N N . VAL A 1 13 ? 2.637 -6.308 -5.233 1.00 92.45 13 A 1 ATOM 88 C CA . VAL A 1 13 ? 1.813 -7.476 -5.522 1.00 92.43 13 A 1 ATOM 89 C C . VAL A 1 13 ? 0.604 -7.112 -6.379 1.00 93.51 13 A 1 ATOM 90 O O . VAL A 1 13 ? 0.032 -7.953 -7.068 1.00 92.43 13 A 1 ATOM 91 C CB . VAL A 1 13 ? 1.347 -8.154 -4.219 1.00 90.55 13 A 1 ATOM 92 C CG1 . VAL A 1 13 ? 0.510 -9.397 -4.500 1.00 86.06 13 A 1 ATOM 93 C CG2 . VAL A 1 13 ? 2.540 -8.524 -3.359 1.00 86.65 13 A 1 ATOM 94 N N . ILE A 1 14 ? 0.209 -5.850 -6.332 1.00 91.52 14 A 1 ATOM 95 C CA . ILE A 1 14 ? -0.952 -5.380 -7.074 1.00 91.11 14 A 1 ATOM 96 C C . ILE A 1 14 ? -0.712 -5.424 -8.579 1.00 91.54 14 A 1 ATOM 97 O O . ILE A 1 14 ? -1.542 -5.918 -9.342 1.00 90.44 14 A 1 ATOM 98 C CB . ILE A 1 14 ? -1.337 -3.955 -6.645 1.00 89.69 14 A 1 ATOM 99 C CG1 . ILE A 1 14 ? -1.708 -3.939 -5.157 1.00 87.27 14 A 1 ATOM 100 C CG2 . ILE A 1 14 ? -2.505 -3.448 -7.485 1.00 85.90 14 A 1 ATOM 101 C CD1 . ILE A 1 14 ? -1.991 -2.553 -4.617 1.00 82.45 14 A 1 ATOM 102 N N . ALA A 1 15 ? 0.412 -4.896 -9.009 1.00 92.50 15 A 1 ATOM 103 C CA . ALA A 1 15 ? 0.739 -4.862 -10.434 1.00 91.10 15 A 1 ATOM 104 C C . ALA A 1 15 ? 2.154 -5.365 -10.661 1.00 89.19 15 A 1 ATOM 105 O O . ALA A 1 15 ? 2.337 -6.582 -10.886 1.00 86.35 15 A 1 ATOM 106 C CB . ALA A 1 15 ? 0.573 -3.451 -10.983 1.00 87.19 15 A 1 ATOM 107 O OXT . ALA A 1 15 ? 3.084 -4.566 -10.603 1.00 80.36 15 A 1 #