# 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_spkb26681 # _entry.id spkb26681 # 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" "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 THR 3 1 n VAL 4 1 n VAL 5 1 n ILE 6 1 n LEU 7 1 n ALA 8 1 n GLY 9 1 n LEU 10 1 n VAL 11 1 n ALA 12 1 n LEU 13 1 n ALA 14 1 n LEU 15 1 n SER 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 @ 2025-07-11 10:32:08)" _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 95.33 _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 89.15 1 1 A LYS 2 2 90.74 1 2 A THR 3 2 96.47 1 3 A VAL 4 2 97.65 1 4 A VAL 5 2 97.79 1 5 A ILE 6 2 96.92 1 6 A LEU 7 2 95.48 1 7 A ALA 8 2 98.30 1 8 A GLY 9 2 98.16 1 9 A LEU 10 2 96.32 1 10 A VAL 11 2 97.59 1 11 A ALA 12 2 98.36 1 12 A LEU 13 2 95.43 1 13 A ALA 14 2 98.21 1 14 A LEU 15 2 94.72 1 15 A SER 16 2 89.55 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 THR . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n GLY . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n SER . 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 ? -13.630 0.404 3.991 1.00 94.24 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.322 -0.248 4.155 1.00 95.07 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.395 0.104 2.993 1.00 95.57 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.388 -0.559 2.764 1.00 93.20 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.497 -1.762 4.242 1.00 91.41 1 A 1 ATOM 6 C CG . MET A 1 1 ? -13.252 -2.157 5.495 1.00 86.70 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.544 -3.916 5.604 1.00 83.77 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.368 -4.001 7.176 1.00 73.27 1 A 1 ATOM 9 N N . LYS A 1 2 ? -11.777 1.138 2.285 1.00 96.53 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -10.967 1.604 1.162 1.00 97.29 2 A 1 ATOM 11 C C . LYS A 1 2 ? -9.620 2.107 1.651 1.00 97.77 2 A 1 ATOM 12 O O . LYS A 1 2 ? -8.610 1.980 0.960 1.00 97.25 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -11.707 2.716 0.415 1.00 96.05 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -12.628 2.174 -0.660 1.00 89.87 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.825 1.702 -1.858 1.00 87.13 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -12.705 1.097 -2.930 1.00 80.09 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -11.893 0.555 -4.052 1.00 74.66 2 A 1 ATOM 18 N N . THR A 1 3 ? -9.614 2.664 2.852 1.00 97.82 3 A 1 ATOM 19 C CA . THR A 1 3 ? -8.386 3.180 3.442 1.00 98.07 3 A 1 ATOM 20 C C . THR A 1 3 ? -7.358 2.065 3.595 1.00 98.30 3 A 1 ATOM 21 O O . THR A 1 3 ? -6.161 2.281 3.423 1.00 97.86 3 A 1 ATOM 22 C CB . THR A 1 3 ? -8.661 3.800 4.815 1.00 97.51 3 A 1 ATOM 23 O OG1 . THR A 1 3 ? -9.833 4.605 4.753 1.00 93.34 3 A 1 ATOM 24 C CG2 . THR A 1 3 ? -7.490 4.653 5.263 1.00 92.40 3 A 1 ATOM 25 N N . VAL A 1 4 ? -7.845 0.877 3.913 1.00 98.38 4 A 1 ATOM 26 C CA . VAL A 1 4 ? -6.968 -0.279 4.078 1.00 98.51 4 A 1 ATOM 27 C C . VAL A 1 4 ? -6.281 -0.605 2.758 1.00 98.61 4 A 1 ATOM 28 O O . VAL A 1 4 ? -5.096 -0.936 2.718 1.00 98.33 4 A 1 ATOM 29 C CB . VAL A 1 4 ? -7.758 -1.501 4.567 1.00 98.21 4 A 1 ATOM 30 C CG1 . VAL A 1 4 ? -6.834 -2.690 4.769 1.00 95.97 4 A 1 ATOM 31 C CG2 . VAL A 1 4 ? -8.482 -1.168 5.865 1.00 95.56 4 A 1 ATOM 32 N N . VAL A 1 5 ? -7.036 -0.509 1.681 1.00 98.34 5 A 1 ATOM 33 C CA . VAL A 1 5 ? -6.502 -0.782 0.349 1.00 98.36 5 A 1 ATOM 34 C C . VAL A 1 5 ? -5.426 0.235 -0.008 1.00 98.45 5 A 1 ATOM 35 O O . VAL A 1 5 ? -4.397 -0.109 -0.596 1.00 98.21 5 A 1 ATOM 36 C CB . VAL A 1 5 ? -7.617 -0.746 -0.701 1.00 97.99 5 A 1 ATOM 37 C CG1 . VAL A 1 5 ? -7.063 -1.047 -2.083 1.00 96.70 5 A 1 ATOM 38 C CG2 . VAL A 1 5 ? -8.705 -1.743 -0.340 1.00 96.51 5 A 1 ATOM 39 N N . ILE A 1 6 ? -5.686 1.477 0.348 1.00 98.26 6 A 1 ATOM 40 C CA . ILE A 1 6 ? -4.734 2.549 0.077 1.00 98.22 6 A 1 ATOM 41 C C . ILE A 1 6 ? -3.451 2.318 0.857 1.00 98.34 6 A 1 ATOM 42 O O . ILE A 1 6 ? -2.347 2.440 0.321 1.00 98.30 6 A 1 ATOM 43 C CB . ILE A 1 6 ? -5.331 3.914 0.442 1.00 98.15 6 A 1 ATOM 44 C CG1 . ILE A 1 6 ? -6.623 4.153 -0.345 1.00 96.59 6 A 1 ATOM 45 C CG2 . ILE A 1 6 ? -4.321 5.021 0.150 1.00 96.02 6 A 1 ATOM 46 C CD1 . ILE A 1 6 ? -6.412 4.118 -1.850 1.00 91.52 6 A 1 ATOM 47 N N . LEU A 1 7 ? -3.617 1.983 2.123 1.00 98.28 7 A 1 ATOM 48 C CA . LEU A 1 7 ? -2.468 1.721 2.980 1.00 98.18 7 A 1 ATOM 49 C C . LEU A 1 7 ? -1.687 0.524 2.458 1.00 98.33 7 A 1 ATOM 50 O O . LEU A 1 7 ? -0.456 0.542 2.408 1.00 98.22 7 A 1 ATOM 51 C CB . LEU A 1 7 ? -2.938 1.461 4.408 1.00 97.76 7 A 1 ATOM 52 C CG . LEU A 1 7 ? -3.378 2.721 5.148 1.00 91.64 7 A 1 ATOM 53 C CD1 . LEU A 1 7 ? -4.163 2.363 6.396 1.00 90.47 7 A 1 ATOM 54 C CD2 . LEU A 1 7 ? -2.167 3.568 5.511 1.00 90.99 7 A 1 ATOM 55 N N . ALA A 1 8 ? -2.408 -0.511 2.072 1.00 98.36 8 A 1 ATOM 56 C CA . ALA A 1 8 ? -1.782 -1.711 1.532 1.00 98.38 8 A 1 ATOM 57 C C . ALA A 1 8 ? -1.037 -1.384 0.246 1.00 98.50 8 A 1 ATOM 58 O O . ALA A 1 8 ? 0.034 -1.928 -0.020 1.00 98.22 8 A 1 ATOM 59 C CB . ALA A 1 8 ? -2.840 -2.771 1.269 1.00 98.06 8 A 1 ATOM 60 N N . GLY A 1 9 ? -1.616 -0.491 -0.540 1.00 98.11 9 A 1 ATOM 61 C CA . GLY A 1 9 ? -0.982 -0.076 -1.784 1.00 98.06 9 A 1 ATOM 62 C C . GLY A 1 9 ? 0.324 0.642 -1.527 1.00 98.32 9 A 1 ATOM 63 O O . GLY A 1 9 ? 1.311 0.428 -2.234 1.00 98.15 9 A 1 ATOM 64 N N . LEU A 1 10 ? 0.322 1.484 -0.504 1.00 98.29 10 A 1 ATOM 65 C CA . LEU A 1 10 ? 1.526 2.222 -0.139 1.00 98.30 10 A 1 ATOM 66 C C . LEU A 1 10 ? 2.616 1.261 0.311 1.00 98.50 10 A 1 ATOM 67 O O . LEU A 1 10 ? 3.781 1.413 -0.055 1.00 98.21 10 A 1 ATOM 68 C CB . LEU A 1 10 ? 1.206 3.208 0.980 1.00 97.90 10 A 1 ATOM 69 C CG . LEU A 1 10 ? 0.436 4.437 0.500 1.00 94.80 10 A 1 ATOM 70 C CD1 . LEU A 1 10 ? -0.157 5.188 1.672 1.00 92.20 10 A 1 ATOM 71 C CD2 . LEU A 1 10 ? 1.350 5.346 -0.307 1.00 92.38 10 A 1 ATOM 72 N N . VAL A 1 11 ? 2.224 0.285 1.101 1.00 98.24 11 A 1 ATOM 73 C CA . VAL A 1 11 ? 3.168 -0.720 1.585 1.00 98.25 11 A 1 ATOM 74 C C . VAL A 1 11 ? 3.724 -1.514 0.415 1.00 98.45 11 A 1 ATOM 75 O O . VAL A 1 11 ? 4.921 -1.796 0.350 1.00 98.28 11 A 1 ATOM 76 C CB . VAL A 1 11 ? 2.496 -1.669 2.577 1.00 97.83 11 A 1 ATOM 77 C CG1 . VAL A 1 11 ? 3.472 -2.749 3.023 1.00 95.90 11 A 1 ATOM 78 C CG2 . VAL A 1 11 ? 1.980 -0.895 3.775 1.00 96.21 11 A 1 ATOM 79 N N . ALA A 1 12 ? 2.851 -1.875 -0.499 1.00 98.46 12 A 1 ATOM 80 C CA . ALA A 1 12 ? 3.261 -2.633 -1.674 1.00 98.44 12 A 1 ATOM 81 C C . ALA A 1 12 ? 4.227 -1.820 -2.524 1.00 98.58 12 A 1 ATOM 82 O O . ALA A 1 12 ? 5.188 -2.358 -3.071 1.00 98.26 12 A 1 ATOM 83 C CB . ALA A 1 12 ? 2.041 -3.017 -2.496 1.00 98.08 12 A 1 ATOM 84 N N . LEU A 1 13 ? 3.962 -0.530 -2.622 1.00 98.31 13 A 1 ATOM 85 C CA . LEU A 1 13 ? 4.825 0.363 -3.390 1.00 98.15 13 A 1 ATOM 86 C C . LEU A 1 13 ? 6.212 0.424 -2.771 1.00 98.34 13 A 1 ATOM 87 O O . LEU A 1 13 ? 7.219 0.417 -3.480 1.00 97.92 13 A 1 ATOM 88 C CB . LEU A 1 13 ? 4.220 1.762 -3.431 1.00 97.56 13 A 1 ATOM 89 C CG . LEU A 1 13 ? 4.967 2.717 -4.358 1.00 92.87 13 A 1 ATOM 90 C CD1 . LEU A 1 13 ? 4.725 2.343 -5.809 1.00 90.02 13 A 1 ATOM 91 C CD2 . LEU A 1 13 ? 4.530 4.149 -4.103 1.00 90.24 13 A 1 ATOM 92 N N . ALA A 1 14 ? 6.252 0.495 -1.449 1.00 98.35 14 A 1 ATOM 93 C CA . ALA A 1 14 ? 7.519 0.549 -0.727 1.00 98.34 14 A 1 ATOM 94 C C . ALA A 1 14 ? 8.262 -0.773 -0.842 1.00 98.42 14 A 1 ATOM 95 O O . ALA A 1 14 ? 9.491 -0.799 -0.916 1.00 97.95 14 A 1 ATOM 96 C CB . ALA A 1 14 ? 7.270 0.882 0.738 1.00 97.97 14 A 1 ATOM 97 N N . LEU A 1 15 ? 7.503 -1.855 -0.845 1.00 97.92 15 A 1 ATOM 98 C CA . LEU A 1 15 ? 8.090 -3.188 -0.945 1.00 97.63 15 A 1 ATOM 99 C C . LEU A 1 15 ? 8.542 -3.476 -2.368 1.00 97.65 15 A 1 ATOM 100 O O . LEU A 1 15 ? 9.539 -4.161 -2.593 1.00 96.64 15 A 1 ATOM 101 C CB . LEU A 1 15 ? 7.070 -4.236 -0.490 1.00 96.81 15 A 1 ATOM 102 C CG . LEU A 1 15 ? 7.675 -5.474 0.177 1.00 93.12 15 A 1 ATOM 103 C CD1 . LEU A 1 15 ? 6.584 -6.484 0.487 1.00 89.54 15 A 1 ATOM 104 C CD2 . LEU A 1 15 ? 8.750 -6.118 -0.677 1.00 88.43 15 A 1 ATOM 105 N N . SER A 1 16 ? 7.801 -2.940 -3.328 1.00 95.77 16 A 1 ATOM 106 C CA . SER A 1 16 ? 8.082 -3.146 -4.750 1.00 94.34 16 A 1 ATOM 107 C C . SER A 1 16 ? 9.569 -3.005 -5.059 1.00 92.56 16 A 1 ATOM 108 O O . SER A 1 16 ? 10.129 -3.937 -5.665 1.00 87.04 16 A 1 ATOM 109 C CB . SER A 1 16 ? 7.301 -2.161 -5.607 1.00 90.77 16 A 1 ATOM 110 O OG . SER A 1 16 ? 7.609 -2.361 -6.967 1.00 82.74 16 A 1 ATOM 111 O OXT . SER A 1 16 ? 10.139 -1.978 -4.726 1.00 83.63 16 A 1 #