# 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_spkb29865 # _entry.id spkb29865 # 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" "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 THR 2 1 n LYS 3 1 n LEU 4 1 n SER 5 1 n LEU 6 1 n LEU 7 1 n PRO 8 1 n LEU 9 1 n LEU 10 1 n THR 11 1 n LEU 12 1 n ALA 13 1 n SER 14 1 n ALA 15 1 n VAL 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 @ 2025-07-12 01:33:17)" _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 88.19 _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 74.80 1 1 A THR 2 2 81.95 1 2 A LYS 3 2 76.42 1 3 A LEU 4 2 80.54 1 4 A SER 5 2 87.87 1 5 A LEU 6 2 87.87 1 6 A LEU 7 2 88.73 1 7 A PRO 8 2 93.20 1 8 A LEU 9 2 91.75 1 9 A LEU 10 2 92.16 1 10 A THR 11 2 92.15 1 11 A LEU 12 2 92.12 1 12 A ALA 13 2 95.24 1 13 A SER 14 2 93.47 1 14 A ALA 15 2 96.05 1 15 A VAL 16 2 93.87 1 16 A LEU 17 2 91.03 1 17 A ALA 18 2 87.33 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 THR . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PRO . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n VAL . 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 ? -5.099 8.769 14.638 1.00 79.51 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.893 7.478 13.955 1.00 82.18 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.225 7.677 12.596 1.00 83.11 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.762 8.360 11.732 1.00 79.49 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.234 6.774 13.769 1.00 75.49 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.239 7.627 13.012 1.00 72.80 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.861 6.863 12.928 1.00 67.97 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.478 7.290 14.546 1.00 57.88 1 A 1 ATOM 9 N N . THR A 1 2 ? -3.053 7.083 12.418 1.00 84.49 2 A 1 ATOM 10 C CA . THR A 1 2 ? -2.302 7.201 11.166 1.00 85.77 2 A 1 ATOM 11 C C . THR A 1 2 ? -2.085 5.844 10.492 1.00 86.21 2 A 1 ATOM 12 O O . THR A 1 2 ? -1.575 5.782 9.374 1.00 83.07 2 A 1 ATOM 13 C CB . THR A 1 2 ? -0.943 7.843 11.439 1.00 83.06 2 A 1 ATOM 14 O OG1 . THR A 1 2 ? -0.296 7.150 12.498 1.00 76.45 2 A 1 ATOM 15 C CG2 . THR A 1 2 ? -1.106 9.301 11.829 1.00 74.61 2 A 1 ATOM 16 N N . LYS A 1 3 ? -2.463 4.765 11.173 1.00 82.53 3 A 1 ATOM 17 C CA . LYS A 1 3 ? -2.295 3.412 10.630 1.00 83.53 3 A 1 ATOM 18 C C . LYS A 1 3 ? -3.125 3.218 9.368 1.00 84.61 3 A 1 ATOM 19 O O . LYS A 1 3 ? -2.726 2.487 8.462 1.00 85.12 3 A 1 ATOM 20 C CB . LYS A 1 3 ? -2.701 2.383 11.688 1.00 80.51 3 A 1 ATOM 21 C CG . LYS A 1 3 ? -1.620 2.172 12.734 1.00 74.50 3 A 1 ATOM 22 C CD . LYS A 1 3 ? -0.488 1.325 12.181 1.00 71.82 3 A 1 ATOM 23 C CE . LYS A 1 3 ? 0.533 1.003 13.252 1.00 65.90 3 A 1 ATOM 24 N NZ . LYS A 1 3 ? 1.645 0.197 12.701 1.00 59.30 3 A 1 ATOM 25 N N . LEU A 1 4 ? -4.265 3.876 9.293 1.00 84.16 4 A 1 ATOM 26 C CA . LEU A 1 4 ? -5.153 3.773 8.137 1.00 84.59 4 A 1 ATOM 27 C C . LEU A 1 4 ? -4.497 4.363 6.891 1.00 88.03 4 A 1 ATOM 28 O O . LEU A 1 4 ? -4.830 3.981 5.770 1.00 84.81 4 A 1 ATOM 29 C CB . LEU A 1 4 ? -6.466 4.498 8.434 1.00 81.95 4 A 1 ATOM 30 C CG . LEU A 1 4 ? -7.592 4.136 7.473 1.00 77.52 4 A 1 ATOM 31 C CD1 . LEU A 1 4 ? -8.102 2.727 7.781 1.00 72.99 4 A 1 ATOM 32 C CD2 . LEU A 1 4 ? -8.738 5.133 7.600 1.00 70.28 4 A 1 ATOM 33 N N . SER A 1 5 ? -3.565 5.275 7.074 1.00 88.73 5 A 1 ATOM 34 C CA . SER A 1 5 ? -2.867 5.920 5.964 1.00 89.58 5 A 1 ATOM 35 C C . SER A 1 5 ? -1.613 5.146 5.564 1.00 90.86 5 A 1 ATOM 36 O O . SER A 1 5 ? -1.148 5.249 4.433 1.00 90.16 5 A 1 ATOM 37 C CB . SER A 1 5 ? -2.492 7.350 6.346 1.00 88.31 5 A 1 ATOM 38 O OG . SER A 1 5 ? -3.649 8.114 6.621 1.00 79.56 5 A 1 ATOM 39 N N . LEU A 1 6 ? -1.071 4.362 6.488 1.00 90.72 6 A 1 ATOM 40 C CA . LEU A 1 6 ? 0.138 3.587 6.222 1.00 91.65 6 A 1 ATOM 41 C C . LEU A 1 6 ? -0.149 2.400 5.304 1.00 93.42 6 A 1 ATOM 42 O O . LEU A 1 6 ? 0.673 2.055 4.457 1.00 91.65 6 A 1 ATOM 43 C CB . LEU A 1 6 ? 0.732 3.091 7.541 1.00 90.55 6 A 1 ATOM 44 C CG . LEU A 1 6 ? 1.362 4.199 8.385 1.00 84.90 6 A 1 ATOM 45 C CD1 . LEU A 1 6 ? 1.650 3.691 9.789 1.00 80.69 6 A 1 ATOM 46 C CD2 . LEU A 1 6 ? 2.660 4.681 7.738 1.00 79.36 6 A 1 ATOM 47 N N . LEU A 1 7 ? -1.311 1.778 5.476 1.00 92.12 7 A 1 ATOM 48 C CA . LEU A 1 7 ? -1.695 0.626 4.662 1.00 92.29 7 A 1 ATOM 49 C C . LEU A 1 7 ? -1.749 0.969 3.171 1.00 93.85 7 A 1 ATOM 50 O O . LEU A 1 7 ? -1.133 0.277 2.357 1.00 92.68 7 A 1 ATOM 51 C CB . LEU A 1 7 ? -3.046 0.087 5.143 1.00 90.75 7 A 1 ATOM 52 C CG . LEU A 1 7 ? -2.952 -0.723 6.435 1.00 86.20 7 A 1 ATOM 53 C CD1 . LEU A 1 7 ? -4.321 -0.832 7.094 1.00 81.76 7 A 1 ATOM 54 C CD2 . LEU A 1 7 ? -2.406 -2.113 6.136 1.00 80.16 7 A 1 ATOM 55 N N . PRO A 1 8 ? -2.477 2.009 2.778 1.00 93.24 8 A 1 ATOM 56 C CA . PRO A 1 8 ? -2.576 2.388 1.362 1.00 93.83 8 A 1 ATOM 57 C C . PRO A 1 8 ? -1.248 2.877 0.796 1.00 94.97 8 A 1 ATOM 58 O O . PRO A 1 8 ? -0.960 2.683 -0.383 1.00 93.84 8 A 1 ATOM 59 C CB . PRO A 1 8 ? -3.624 3.509 1.361 1.00 92.31 8 A 1 ATOM 60 C CG . PRO A 1 8 ? -3.612 4.044 2.753 1.00 91.34 8 A 1 ATOM 61 C CD . PRO A 1 8 ? -3.285 2.874 3.638 1.00 92.85 8 A 1 ATOM 62 N N . LEU A 1 9 ? -0.428 3.486 1.617 1.00 93.85 9 A 1 ATOM 63 C CA . LEU A 1 9 ? 0.873 3.991 1.181 1.00 94.19 9 A 1 ATOM 64 C C . LEU A 1 9 ? 1.803 2.837 0.818 1.00 95.10 9 A 1 ATOM 65 O O . LEU A 1 9 ? 2.577 2.930 -0.136 1.00 93.74 9 A 1 ATOM 66 C CB . LEU A 1 9 ? 1.495 4.835 2.297 1.00 93.81 9 A 1 ATOM 67 C CG . LEU A 1 9 ? 0.907 6.242 2.409 1.00 90.62 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? 1.360 6.901 3.707 1.00 86.62 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? 1.352 7.095 1.221 1.00 86.08 9 A 1 ATOM 70 N N . LEU A 1 10 ? 1.721 1.750 1.573 1.00 94.70 10 A 1 ATOM 71 C CA . LEU A 1 10 ? 2.550 0.574 1.321 1.00 94.69 10 A 1 ATOM 72 C C . LEU A 1 10 ? 2.188 -0.053 -0.019 1.00 95.65 10 A 1 ATOM 73 O O . LEU A 1 10 ? 3.061 -0.505 -0.760 1.00 94.86 10 A 1 ATOM 74 C CB . LEU A 1 10 ? 2.353 -0.444 2.444 1.00 94.20 10 A 1 ATOM 75 C CG . LEU A 1 10 ? 3.412 -1.544 2.455 1.00 90.65 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? 4.749 -0.989 2.946 1.00 85.79 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? 2.978 -2.693 3.353 1.00 86.72 10 A 1 ATOM 78 N N . THR A 1 11 ? 0.915 -0.084 -0.328 1.00 93.08 11 A 1 ATOM 79 C CA . THR A 1 11 ? 0.431 -0.654 -1.587 1.00 93.55 11 A 1 ATOM 80 C C . THR A 1 11 ? 0.920 0.181 -2.770 1.00 94.56 11 A 1 ATOM 81 O O . THR A 1 11 ? 1.275 -0.357 -3.821 1.00 93.78 11 A 1 ATOM 82 C CB . THR A 1 11 ? -1.099 -0.703 -1.590 1.00 92.73 11 A 1 ATOM 83 O OG1 . THR A 1 11 ? -1.555 -1.384 -0.426 1.00 89.70 11 A 1 ATOM 84 C CG2 . THR A 1 11 ? -1.611 -1.445 -2.819 1.00 87.62 11 A 1 ATOM 85 N N . LEU A 1 12 ? 0.950 1.472 -2.603 1.00 95.52 12 A 1 ATOM 86 C CA . LEU A 1 12 ? 1.397 2.381 -3.656 1.00 95.29 12 A 1 ATOM 87 C C . LEU A 1 12 ? 2.874 2.146 -3.964 1.00 96.07 12 A 1 ATOM 88 O O . LEU A 1 12 ? 3.288 2.151 -5.125 1.00 95.34 12 A 1 ATOM 89 C CB . LEU A 1 12 ? 1.160 3.828 -3.219 1.00 94.50 12 A 1 ATOM 90 C CG . LEU A 1 12 ? 1.048 4.809 -4.388 1.00 88.29 12 A 1 ATOM 91 C CD1 . LEU A 1 12 ? 0.216 6.016 -3.974 1.00 85.15 12 A 1 ATOM 92 C CD2 . LEU A 1 12 ? 2.416 5.270 -4.848 1.00 86.81 12 A 1 ATOM 93 N N . ALA A 1 13 ? 3.661 1.924 -2.927 1.00 95.38 13 A 1 ATOM 94 C CA . ALA A 1 13 ? 5.093 1.674 -3.090 1.00 95.18 13 A 1 ATOM 95 C C . ALA A 1 13 ? 5.333 0.383 -3.867 1.00 96.16 13 A 1 ATOM 96 O O . ALA A 1 13 ? 6.268 0.293 -4.663 1.00 95.23 13 A 1 ATOM 97 C CB . ALA A 1 13 ? 5.755 1.598 -1.719 1.00 94.25 13 A 1 ATOM 98 N N . SER A 1 14 ? 4.489 -0.616 -3.640 1.00 95.62 14 A 1 ATOM 99 C CA . SER A 1 14 ? 4.600 -1.902 -4.326 1.00 95.49 14 A 1 ATOM 100 C C . SER A 1 14 ? 4.333 -1.746 -5.818 1.00 95.95 14 A 1 ATOM 101 O O . SER A 1 14 ? 4.985 -2.381 -6.647 1.00 94.55 14 A 1 ATOM 102 C CB . SER A 1 14 ? 3.608 -2.894 -3.725 1.00 94.01 14 A 1 ATOM 103 O OG . SER A 1 14 ? 3.813 -4.169 -4.268 1.00 85.19 14 A 1 ATOM 104 N N . ALA A 1 15 ? 3.380 -0.910 -6.166 1.00 96.35 15 A 1 ATOM 105 C CA . ALA A 1 15 ? 3.025 -0.659 -7.564 1.00 96.32 15 A 1 ATOM 106 C C . ALA A 1 15 ? 4.150 0.079 -8.290 1.00 97.02 15 A 1 ATOM 107 O O . ALA A 1 15 ? 4.382 -0.137 -9.479 1.00 95.41 15 A 1 ATOM 108 C CB . ALA A 1 15 ? 1.735 0.154 -7.623 1.00 95.17 15 A 1 ATOM 109 N N . VAL A 1 16 ? 4.842 0.941 -7.590 1.00 96.05 16 A 1 ATOM 110 C CA . VAL A 1 16 ? 5.945 1.714 -8.170 1.00 95.79 16 A 1 ATOM 111 C C . VAL A 1 16 ? 7.145 0.818 -8.468 1.00 96.15 16 A 1 ATOM 112 O O . VAL A 1 16 ? 7.907 1.070 -9.406 1.00 94.98 16 A 1 ATOM 113 C CB . VAL A 1 16 ? 6.364 2.852 -7.221 1.00 94.15 16 A 1 ATOM 114 C CG1 . VAL A 1 16 ? 7.571 3.606 -7.767 1.00 89.88 16 A 1 ATOM 115 C CG2 . VAL A 1 16 ? 5.209 3.817 -7.016 1.00 90.06 16 A 1 ATOM 116 N N . LEU A 1 17 ? 7.308 -0.237 -7.677 1.00 95.50 17 A 1 ATOM 117 C CA . LEU A 1 17 ? 8.422 -1.170 -7.855 1.00 94.99 17 A 1 ATOM 118 C C . LEU A 1 17 ? 8.341 -1.875 -9.206 1.00 95.28 17 A 1 ATOM 119 O O . LEU A 1 17 ? 9.363 -2.141 -9.842 1.00 94.02 17 A 1 ATOM 120 C CB . LEU A 1 17 ? 8.412 -2.196 -6.721 1.00 93.41 17 A 1 ATOM 121 C CG . LEU A 1 17 ? 8.963 -1.652 -5.399 1.00 88.30 17 A 1 ATOM 122 C CD1 . LEU A 1 17 ? 8.638 -2.603 -4.257 1.00 83.71 17 A 1 ATOM 123 C CD2 . LEU A 1 17 ? 10.475 -1.468 -5.500 1.00 83.07 17 A 1 ATOM 124 N N . ALA A 1 18 ? 7.131 -2.194 -9.639 1.00 92.99 18 A 1 ATOM 125 C CA . ALA A 1 18 ? 6.917 -2.876 -10.909 1.00 90.64 18 A 1 ATOM 126 C C . ALA A 1 18 ? 6.424 -1.911 -11.987 1.00 88.99 18 A 1 ATOM 127 O O . ALA A 1 18 ? 5.902 -0.840 -11.651 1.00 85.91 18 A 1 ATOM 128 C CB . ALA A 1 18 ? 5.931 -4.027 -10.719 1.00 86.68 18 A 1 ATOM 129 O OXT . ALA A 1 18 ? 6.543 -2.236 -13.185 1.00 78.80 18 A 1 #