# 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_spkb28548 # _entry.id spkb28548 # 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" "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" # _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 ALA 3 1 n ALA 4 1 n ILE 5 1 n LEU 6 1 n ALA 7 1 n THR 8 1 n ALA 9 1 n ALA 10 1 n ALA 11 1 n LEU 12 1 n THR 13 1 n GLY 14 1 n SER 15 1 n ALA 16 1 n LEU 17 1 n ALA 18 # _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 04:45:09)" _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 93.56 _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 88.41 1 1 A LYS 2 2 90.72 1 2 A ALA 3 2 97.20 1 3 A ALA 4 2 97.64 1 4 A ILE 5 2 95.89 1 5 A LEU 6 2 95.14 1 6 A ALA 7 2 96.33 1 7 A THR 8 2 95.41 1 8 A ALA 9 2 96.51 1 9 A ALA 10 2 96.45 1 10 A ALA 11 2 97.28 1 11 A LEU 12 2 95.83 1 12 A THR 13 2 94.59 1 13 A GLY 14 2 95.36 1 14 A SER 15 2 92.56 1 15 A ALA 16 2 94.20 1 16 A LEU 17 2 89.06 1 17 A ALA 18 2 81.63 1 18 # _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 ALA . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n THR . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n THR . 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 A 17 1 n LEU . 17 A 17 A 18 1 n ALA . 18 A 18 # _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 ? -9.025 8.461 8.499 1.00 92.93 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.573 8.187 8.454 1.00 93.47 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.115 7.948 7.016 1.00 94.31 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.905 8.004 6.080 1.00 92.01 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.247 6.950 9.294 1.00 89.79 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.621 7.116 10.758 1.00 87.03 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.260 5.640 11.726 1.00 84.24 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.807 6.181 13.335 1.00 73.51 1 A 1 ATOM 9 N N . LYS A 1 2 ? -5.837 7.664 6.849 1.00 93.75 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -5.267 7.407 5.520 1.00 95.64 2 A 1 ATOM 11 C C . LYS A 1 2 ? -5.214 5.904 5.238 1.00 96.36 2 A 1 ATOM 12 O O . LYS A 1 2 ? -4.232 5.398 4.683 1.00 96.30 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -3.864 8.013 5.433 1.00 94.35 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -3.863 9.522 5.584 1.00 89.64 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.463 10.079 5.408 1.00 88.05 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.468 11.600 5.493 1.00 83.81 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -2.905 12.069 6.828 1.00 78.60 2 A 1 ATOM 18 N N . ALA A 1 3 ? -6.255 5.184 5.614 1.00 96.83 3 A 1 ATOM 19 C CA . ALA A 1 3 ? -6.316 3.732 5.430 1.00 97.53 3 A 1 ATOM 20 C C . ALA A 1 3 ? -6.190 3.341 3.958 1.00 97.79 3 A 1 ATOM 21 O O . ALA A 1 3 ? -5.503 2.377 3.616 1.00 96.92 3 A 1 ATOM 22 C CB . ALA A 1 3 ? -7.624 3.203 6.005 1.00 96.95 3 A 1 ATOM 23 N N . ALA A 1 4 ? -6.851 4.102 3.075 1.00 97.69 4 A 1 ATOM 24 C CA . ALA A 1 4 ? -6.795 3.839 1.638 1.00 97.84 4 A 1 ATOM 25 C C . ALA A 1 4 ? -5.381 4.024 1.091 1.00 97.93 4 A 1 ATOM 26 O O . ALA A 1 4 ? -4.906 3.232 0.278 1.00 97.22 4 A 1 ATOM 27 C CB . ALA A 1 4 ? -7.765 4.763 0.912 1.00 97.52 4 A 1 ATOM 28 N N . ILE A 1 5 ? -4.712 5.075 1.545 1.00 97.46 5 A 1 ATOM 29 C CA . ILE A 1 5 ? -3.348 5.369 1.105 1.00 97.09 5 A 1 ATOM 30 C C . ILE A 1 5 ? -2.387 4.293 1.603 1.00 96.79 5 A 1 ATOM 31 O O . ILE A 1 5 ? -1.504 3.835 0.876 1.00 95.94 5 A 1 ATOM 32 C CB . ILE A 1 5 ? -2.896 6.755 1.603 1.00 97.18 5 A 1 ATOM 33 C CG1 . ILE A 1 5 ? -3.811 7.843 1.025 1.00 95.79 5 A 1 ATOM 34 C CG2 . ILE A 1 5 ? -1.442 7.018 1.197 1.00 94.51 5 A 1 ATOM 35 C CD1 . ILE A 1 5 ? -3.535 9.222 1.588 1.00 92.32 5 A 1 ATOM 36 N N . LEU A 1 6 ? -2.570 3.873 2.850 1.00 97.42 6 A 1 ATOM 37 C CA . LEU A 1 6 ? -1.714 2.848 3.441 1.00 96.86 6 A 1 ATOM 38 C C . LEU A 1 6 ? -1.855 1.527 2.688 1.00 96.65 6 A 1 ATOM 39 O O . LEU A 1 6 ? -0.871 0.840 2.427 1.00 96.50 6 A 1 ATOM 40 C CB . LEU A 1 6 ? -2.082 2.652 4.911 1.00 96.56 6 A 1 ATOM 41 C CG . LEU A 1 6 ? -1.715 3.837 5.804 1.00 92.97 6 A 1 ATOM 42 C CD1 . LEU A 1 6 ? -2.317 3.650 7.196 1.00 91.91 6 A 1 ATOM 43 C CD2 . LEU A 1 6 ? -0.207 3.979 5.903 1.00 92.24 6 A 1 ATOM 44 N N . ALA A 1 7 ? -3.082 1.181 2.335 1.00 96.78 7 A 1 ATOM 45 C CA . ALA A 1 7 ? -3.354 -0.046 1.596 1.00 96.24 7 A 1 ATOM 46 C C . ALA A 1 7 ? -2.728 0.001 0.207 1.00 96.73 7 A 1 ATOM 47 O O . ALA A 1 7 ? -2.163 -0.988 -0.265 1.00 96.14 7 A 1 ATOM 48 C CB . ALA A 1 7 ? -4.859 -0.256 1.489 1.00 95.76 7 A 1 ATOM 49 N N . THR A 1 8 ? -2.815 1.154 -0.444 1.00 96.16 8 A 1 ATOM 50 C CA . THR A 1 8 ? -2.251 1.333 -1.783 1.00 95.94 8 A 1 ATOM 51 C C . THR A 1 8 ? -0.731 1.197 -1.750 1.00 96.78 8 A 1 ATOM 52 O O . THR A 1 8 ? -0.138 0.504 -2.576 1.00 96.53 8 A 1 ATOM 53 C CB . THR A 1 8 ? -2.620 2.710 -2.350 1.00 95.58 8 A 1 ATOM 54 O OG1 . THR A 1 8 ? -4.038 2.849 -2.385 1.00 94.12 8 A 1 ATOM 55 C CG2 . THR A 1 8 ? -2.072 2.872 -3.767 1.00 92.77 8 A 1 ATOM 56 N N . ALA A 1 9 ? -0.094 1.853 -0.784 1.00 96.43 9 A 1 ATOM 57 C CA . ALA A 1 9 ? 1.358 1.798 -0.646 1.00 96.37 9 A 1 ATOM 58 C C . ALA A 1 9 ? 1.819 0.377 -0.345 1.00 97.11 9 A 1 ATOM 59 O O . ALA A 1 9 ? 2.821 -0.091 -0.884 1.00 96.72 9 A 1 ATOM 60 C CB . ALA A 1 9 ? 1.808 2.741 0.466 1.00 95.94 9 A 1 ATOM 61 N N . ALA A 1 10 ? 1.086 -0.322 0.509 1.00 96.82 10 A 1 ATOM 62 C CA . ALA A 1 10 ? 1.420 -1.696 0.873 1.00 96.47 10 A 1 ATOM 63 C C . ALA A 1 10 ? 1.301 -2.621 -0.329 1.00 97.07 10 A 1 ATOM 64 O O . ALA A 1 10 ? 2.116 -3.526 -0.505 1.00 96.31 10 A 1 ATOM 65 C CB . ALA A 1 10 ? 0.500 -2.170 1.990 1.00 95.59 10 A 1 ATOM 66 N N . ALA A 1 11 ? 0.294 -2.400 -1.168 1.00 97.59 11 A 1 ATOM 67 C CA . ALA A 1 11 ? 0.083 -3.217 -2.360 1.00 97.47 11 A 1 ATOM 68 C C . ALA A 1 11 ? 1.220 -3.037 -3.359 1.00 97.78 11 A 1 ATOM 69 O O . ALA A 1 11 ? 1.700 -4.005 -3.948 1.00 96.69 11 A 1 ATOM 70 C CB . ALA A 1 11 ? -1.246 -2.851 -3.011 1.00 96.87 11 A 1 ATOM 71 N N . LEU A 1 12 ? 1.659 -1.796 -3.552 1.00 97.60 12 A 1 ATOM 72 C CA . LEU A 1 12 ? 2.732 -1.492 -4.495 1.00 97.39 12 A 1 ATOM 73 C C . LEU A 1 12 ? 4.061 -2.070 -4.028 1.00 97.50 12 A 1 ATOM 74 O O . LEU A 1 12 ? 4.801 -2.665 -4.813 1.00 96.64 12 A 1 ATOM 75 C CB . LEU A 1 12 ? 2.863 0.023 -4.659 1.00 96.95 12 A 1 ATOM 76 C CG . LEU A 1 12 ? 1.677 0.668 -5.372 1.00 95.04 12 A 1 ATOM 77 C CD1 . LEU A 1 12 ? 1.755 2.181 -5.276 1.00 92.73 12 A 1 ATOM 78 C CD2 . LEU A 1 12 ? 1.641 0.239 -6.831 1.00 92.76 12 A 1 ATOM 79 N N . THR A 1 13 ? 4.363 -1.895 -2.749 1.00 96.81 13 A 1 ATOM 80 C CA . THR A 1 13 ? 5.626 -2.378 -2.187 1.00 96.37 13 A 1 ATOM 81 C C . THR A 1 13 ? 5.580 -3.874 -1.884 1.00 96.50 13 A 1 ATOM 82 O O . THR A 1 13 ? 6.557 -4.591 -2.101 1.00 95.14 13 A 1 ATOM 83 C CB . THR A 1 13 ? 5.967 -1.615 -0.900 1.00 95.09 13 A 1 ATOM 84 O OG1 . THR A 1 13 ? 5.969 -0.209 -1.162 1.00 91.21 13 A 1 ATOM 85 C CG2 . THR A 1 13 ? 7.338 -2.009 -0.382 1.00 90.99 13 A 1 ATOM 86 N N . GLY A 1 14 ? 4.452 -4.348 -1.378 1.00 95.61 14 A 1 ATOM 87 C CA . GLY A 1 14 ? 4.309 -5.753 -1.016 1.00 94.75 14 A 1 ATOM 88 C C . GLY A 1 14 ? 4.015 -6.662 -2.190 1.00 95.89 14 A 1 ATOM 89 O O . GLY A 1 14 ? 4.781 -7.576 -2.491 1.00 95.20 14 A 1 ATOM 90 N N . SER A 1 15 ? 2.900 -6.428 -2.882 1.00 95.57 15 A 1 ATOM 91 C CA . SER A 1 15 ? 2.495 -7.258 -4.017 1.00 95.13 15 A 1 ATOM 92 C C . SER A 1 15 ? 3.210 -6.865 -5.308 1.00 95.81 15 A 1 ATOM 93 O O . SER A 1 15 ? 3.116 -7.569 -6.313 1.00 94.01 15 A 1 ATOM 94 C CB . SER A 1 15 ? 0.984 -7.172 -4.226 1.00 92.80 15 A 1 ATOM 95 O OG . SER A 1 15 ? 0.300 -7.624 -3.071 1.00 82.07 15 A 1 ATOM 96 N N . ALA A 1 16 ? 3.941 -5.752 -5.277 1.00 94.08 16 A 1 ATOM 97 C CA . ALA A 1 16 ? 4.675 -5.264 -6.452 1.00 94.35 16 A 1 ATOM 98 C C . ALA A 1 16 ? 3.749 -5.067 -7.651 1.00 95.54 16 A 1 ATOM 99 O O . ALA A 1 16 ? 3.962 -5.635 -8.724 1.00 93.98 16 A 1 ATOM 100 C CB . ALA A 1 16 ? 5.803 -6.236 -6.799 1.00 93.04 16 A 1 ATOM 101 N N . LEU A 1 17 ? 2.711 -4.246 -7.460 1.00 93.15 17 A 1 ATOM 102 C CA . LEU A 1 17 ? 1.749 -3.956 -8.520 1.00 93.21 17 A 1 ATOM 103 C C . LEU A 1 17 ? 2.185 -2.726 -9.311 1.00 94.26 17 A 1 ATOM 104 O O . LEU A 1 17 ? 1.522 -1.687 -9.303 1.00 92.17 17 A 1 ATOM 105 C CB . LEU A 1 17 ? 0.354 -3.742 -7.927 1.00 91.08 17 A 1 ATOM 106 C CG . LEU A 1 17 ? -0.511 -4.997 -7.836 1.00 85.77 17 A 1 ATOM 107 C CD1 . LEU A 1 17 ? -0.832 -5.512 -9.219 1.00 82.61 17 A 1 ATOM 108 C CD2 . LEU A 1 17 ? 0.192 -6.070 -7.019 1.00 80.21 17 A 1 ATOM 109 N N . ALA A 1 18 ? 3.320 -2.852 -10.020 1.00 87.76 18 A 1 ATOM 110 C CA . ALA A 1 18 ? 3.882 -1.751 -10.808 1.00 85.33 18 A 1 ATOM 111 C C . ALA A 1 18 ? 3.860 -2.093 -12.295 1.00 83.71 18 A 1 ATOM 112 O O . ALA A 1 18 ? 4.806 -2.708 -12.791 1.00 79.29 18 A 1 ATOM 113 C CB . ALA A 1 18 ? 5.298 -1.454 -10.353 1.00 79.16 18 A 1 ATOM 114 O OXT . ALA A 1 18 ? 2.892 -1.711 -12.984 1.00 74.55 18 A 1 #