# 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_spkb12497 # _entry.id spkb12497 # 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" "C3 H7 N O3" 105.093 SER y SERINE C([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 ALA 3 1 n SER 4 1 n VAL 5 1 n SER 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n SER 11 1 n ALA 12 1 n ALA 13 1 n SER 14 1 n MET 15 1 n ALA 16 1 n SER 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 @ 2025-07-04 00:48:59)" _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 90.59 _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 82.38 1 1 A LYS 2 2 84.06 1 2 A ALA 3 2 93.01 1 3 A SER 4 2 93.18 1 4 A VAL 5 2 94.01 1 5 A SER 6 2 93.38 1 6 A LEU 7 2 93.21 1 7 A LEU 8 2 93.51 1 8 A LEU 9 2 92.80 1 9 A LEU 10 2 91.79 1 10 A SER 11 2 91.85 1 11 A ALA 12 2 95.19 1 12 A ALA 13 2 94.55 1 13 A SER 14 2 92.82 1 14 A MET 15 2 87.34 1 15 A ALA 16 2 92.82 1 16 A SER 17 2 87.36 1 17 A ALA 18 2 83.12 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 SER . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n MET . 15 A 15 A 16 1 n ALA . 16 A 16 A 17 1 n SER . 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 ? -12.090 -4.135 5.928 1.00 86.89 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.791 -3.693 5.397 1.00 88.90 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.636 -4.152 3.949 1.00 90.76 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.695 -5.345 3.654 1.00 87.45 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.642 -4.253 6.234 1.00 83.58 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.645 -5.775 6.337 1.00 80.65 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.433 -6.420 7.493 1.00 75.42 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.221 -6.025 9.036 1.00 65.37 1 A 1 ATOM 9 N N . LYS A 1 2 ? -10.460 -3.212 3.058 1.00 89.62 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -10.324 -3.525 1.639 1.00 92.23 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.866 -3.811 1.297 1.00 92.69 2 A 1 ATOM 12 O O . LYS A 1 2 ? -7.995 -2.971 1.533 1.00 92.05 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -10.841 -2.361 0.800 1.00 88.64 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -12.331 -2.131 0.958 1.00 81.36 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -12.776 -0.956 0.106 1.00 79.77 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -14.268 -0.713 0.264 1.00 73.47 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -15.055 -1.845 -0.275 1.00 66.70 2 A 1 ATOM 18 N N . ALA A 1 3 ? -8.609 -4.981 0.736 1.00 91.10 3 A 1 ATOM 19 C CA . ALA A 1 3 ? -7.257 -5.368 0.345 1.00 93.56 3 A 1 ATOM 20 C C . ALA A 1 3 ? -6.723 -4.457 -0.756 1.00 95.25 3 A 1 ATOM 21 O O . ALA A 1 3 ? -5.553 -4.068 -0.738 1.00 93.73 3 A 1 ATOM 22 C CB . ALA A 1 3 ? -7.251 -6.820 -0.115 1.00 91.41 3 A 1 ATOM 23 N N . SER A 1 4 ? -7.592 -4.102 -1.710 1.00 94.27 4 A 1 ATOM 24 C CA . SER A 1 4 ? -7.211 -3.236 -2.823 1.00 95.53 4 A 1 ATOM 25 C C . SER A 1 4 ? -6.768 -1.863 -2.330 1.00 96.14 4 A 1 ATOM 26 O O . SER A 1 4 ? -5.726 -1.350 -2.735 1.00 95.08 4 A 1 ATOM 27 C CB . SER A 1 4 ? -8.374 -3.087 -3.799 1.00 94.18 4 A 1 ATOM 28 O OG . SER A 1 4 ? -7.998 -2.260 -4.879 1.00 83.86 4 A 1 ATOM 29 N N . VAL A 1 5 ? -7.557 -1.269 -1.443 1.00 95.03 5 A 1 ATOM 30 C CA . VAL A 1 5 ? -7.239 0.048 -0.892 1.00 95.80 5 A 1 ATOM 31 C C . VAL A 1 5 ? -5.962 -0.019 -0.061 1.00 96.46 5 A 1 ATOM 32 O O . VAL A 1 5 ? -5.097 0.853 -0.155 1.00 95.48 5 A 1 ATOM 33 C CB . VAL A 1 5 ? -8.397 0.584 -0.043 1.00 94.88 5 A 1 ATOM 34 C CG1 . VAL A 1 5 ? -8.034 1.920 0.590 1.00 90.09 5 A 1 ATOM 35 C CG2 . VAL A 1 5 ? -9.643 0.733 -0.900 1.00 90.35 5 A 1 ATOM 36 N N . SER A 1 6 ? -5.843 -1.056 0.748 1.00 94.79 6 A 1 ATOM 37 C CA . SER A 1 6 ? -4.663 -1.235 1.588 1.00 95.09 6 A 1 ATOM 38 C C . SER A 1 6 ? -3.407 -1.366 0.733 1.00 95.77 6 A 1 ATOM 39 O O . SER A 1 6 ? -2.362 -0.800 1.056 1.00 95.29 6 A 1 ATOM 40 C CB . SER A 1 6 ? -4.819 -2.472 2.465 1.00 94.13 6 A 1 ATOM 41 O OG . SER A 1 6 ? -5.893 -2.305 3.372 1.00 85.21 6 A 1 ATOM 42 N N . LEU A 1 7 ? -3.519 -2.098 -0.364 1.00 95.73 7 A 1 ATOM 43 C CA . LEU A 1 7 ? -2.394 -2.290 -1.273 1.00 95.82 7 A 1 ATOM 44 C C . LEU A 1 7 ? -1.991 -0.974 -1.927 1.00 96.48 7 A 1 ATOM 45 O O . LEU A 1 7 ? -0.801 -0.712 -2.121 1.00 95.76 7 A 1 ATOM 46 C CB . LEU A 1 7 ? -2.756 -3.319 -2.345 1.00 95.61 7 A 1 ATOM 47 C CG . LEU A 1 7 ? -2.823 -4.753 -1.827 1.00 90.64 7 A 1 ATOM 48 C CD1 . LEU A 1 7 ? -3.433 -5.664 -2.882 1.00 87.72 7 A 1 ATOM 49 C CD2 . LEU A 1 7 ? -1.434 -5.250 -1.449 1.00 87.91 7 A 1 ATOM 50 N N . LEU A 1 8 ? -2.977 -0.142 -2.255 1.00 95.75 8 A 1 ATOM 51 C CA . LEU A 1 8 ? -2.706 1.155 -2.868 1.00 95.62 8 A 1 ATOM 52 C C . LEU A 1 8 ? -1.907 2.037 -1.917 1.00 96.20 8 A 1 ATOM 53 O O . LEU A 1 8 ? -0.944 2.691 -2.322 1.00 95.69 8 A 1 ATOM 54 C CB . LEU A 1 8 ? -4.020 1.844 -3.243 1.00 95.88 8 A 1 ATOM 55 C CG . LEU A 1 8 ? -4.705 1.234 -4.465 1.00 91.67 8 A 1 ATOM 56 C CD1 . LEU A 1 8 ? -6.119 1.781 -4.611 1.00 88.62 8 A 1 ATOM 57 C CD2 . LEU A 1 8 ? -3.908 1.534 -5.729 1.00 88.63 8 A 1 ATOM 58 N N . LEU A 1 9 ? -2.304 2.046 -0.655 1.00 95.29 9 A 1 ATOM 59 C CA . LEU A 1 9 ? -1.619 2.848 0.349 1.00 95.00 9 A 1 ATOM 60 C C . LEU A 1 9 ? -0.198 2.341 0.564 1.00 95.48 9 A 1 ATOM 61 O O . LEU A 1 9 ? 0.752 3.127 0.640 1.00 95.00 9 A 1 ATOM 62 C CB . LEU A 1 9 ? -2.395 2.813 1.666 1.00 94.92 9 A 1 ATOM 63 C CG . LEU A 1 9 ? -3.763 3.495 1.597 1.00 90.56 9 A 1 ATOM 64 C CD1 . LEU A 1 9 ? -4.536 3.251 2.887 1.00 88.27 9 A 1 ATOM 65 C CD2 . LEU A 1 9 ? -3.613 4.988 1.349 1.00 87.85 9 A 1 ATOM 66 N N . LEU A 1 10 ? -0.052 1.032 0.647 1.00 95.23 10 A 1 ATOM 67 C CA . LEU A 1 10 ? 1.261 0.424 0.834 1.00 94.71 10 A 1 ATOM 68 C C . LEU A 1 10 ? 2.136 0.648 -0.391 1.00 95.61 10 A 1 ATOM 69 O O . LEU A 1 10 ? 3.340 0.904 -0.267 1.00 94.48 10 A 1 ATOM 70 C CB . LEU A 1 10 ? 1.103 -1.072 1.104 1.00 94.24 10 A 1 ATOM 71 C CG . LEU A 1 10 ? 0.518 -1.389 2.483 1.00 88.94 10 A 1 ATOM 72 C CD1 . LEU A 1 10 ? 0.159 -2.868 2.570 1.00 85.47 10 A 1 ATOM 73 C CD2 . LEU A 1 10 ? 1.502 -1.026 3.581 1.00 85.67 10 A 1 ATOM 74 N N . SER A 1 11 ? 1.537 0.578 -1.574 1.00 93.75 11 A 1 ATOM 75 C CA . SER A 1 11 ? 2.259 0.794 -2.821 1.00 93.36 11 A 1 ATOM 76 C C . SER A 1 11 ? 2.802 2.215 -2.881 1.00 94.29 11 A 1 ATOM 77 O O . SER A 1 11 ? 3.956 2.432 -3.255 1.00 93.35 11 A 1 ATOM 78 C CB . SER A 1 11 ? 1.348 0.541 -4.017 1.00 92.40 11 A 1 ATOM 79 O OG . SER A 1 11 ? 2.063 0.738 -5.219 1.00 83.94 11 A 1 ATOM 80 N N . ALA A 1 12 ? 1.971 3.183 -2.499 1.00 95.36 12 A 1 ATOM 81 C CA . ALA A 1 12 ? 2.379 4.585 -2.491 1.00 95.39 12 A 1 ATOM 82 C C . ALA A 1 12 ? 3.526 4.804 -1.511 1.00 96.16 12 A 1 ATOM 83 O O . ALA A 1 12 ? 4.485 5.520 -1.810 1.00 94.56 12 A 1 ATOM 84 C CB . ALA A 1 12 ? 1.194 5.469 -2.120 1.00 94.47 12 A 1 ATOM 85 N N . ALA A 1 13 ? 3.426 4.187 -0.342 1.00 95.46 13 A 1 ATOM 86 C CA . ALA A 1 13 ? 4.475 4.298 0.667 1.00 94.80 13 A 1 ATOM 87 C C . ALA A 1 13 ? 5.775 3.687 0.160 1.00 95.61 13 A 1 ATOM 88 O O . ALA A 1 13 ? 6.861 4.216 0.411 1.00 93.31 13 A 1 ATOM 89 C CB . ALA A 1 13 ? 4.032 3.614 1.954 1.00 93.57 13 A 1 ATOM 90 N N . SER A 1 14 ? 5.666 2.580 -0.558 1.00 95.49 14 A 1 ATOM 91 C CA . SER A 1 14 ? 6.829 1.904 -1.122 1.00 95.12 14 A 1 ATOM 92 C C . SER A 1 14 ? 7.539 2.799 -2.131 1.00 95.32 14 A 1 ATOM 93 O O . SER A 1 14 ? 8.769 2.866 -2.162 1.00 93.10 14 A 1 ATOM 94 C CB . SER A 1 14 ? 6.419 0.600 -1.795 1.00 93.24 14 A 1 ATOM 95 O OG . SER A 1 14 ? 7.558 -0.067 -2.291 1.00 84.65 14 A 1 ATOM 96 N N . MET A 1 15 ? 6.765 3.501 -2.953 1.00 94.68 15 A 1 ATOM 97 C CA . MET A 1 15 ? 7.321 4.415 -3.949 1.00 93.78 15 A 1 ATOM 98 C C . MET A 1 15 ? 8.072 5.558 -3.283 1.00 94.25 15 A 1 ATOM 99 O O . MET A 1 15 ? 9.134 5.965 -3.741 1.00 92.14 15 A 1 ATOM 100 C CB . MET A 1 15 ? 6.210 4.984 -4.830 1.00 91.33 15 A 1 ATOM 101 C CG . MET A 1 15 ? 5.628 3.947 -5.764 1.00 84.71 15 A 1 ATOM 102 S SD . MET A 1 15 ? 4.316 4.629 -6.782 1.00 78.53 15 A 1 ATOM 103 C CE . MET A 1 15 ? 4.002 3.217 -7.830 1.00 69.32 15 A 1 ATOM 104 N N . ALA A 1 16 ? 7.510 6.076 -2.201 1.00 93.21 16 A 1 ATOM 105 C CA . ALA A 1 16 ? 8.140 7.160 -1.460 1.00 92.93 16 A 1 ATOM 106 C C . ALA A 1 16 ? 9.416 6.687 -0.776 1.00 94.41 16 A 1 ATOM 107 O O . ALA A 1 16 ? 10.393 7.431 -0.678 1.00 92.42 16 A 1 ATOM 108 C CB . ALA A 1 16 ? 7.165 7.722 -0.428 1.00 91.12 16 A 1 ATOM 109 N N . SER A 1 17 ? 9.396 5.454 -0.302 1.00 90.99 17 A 1 ATOM 110 C CA . SER A 1 17 ? 10.545 4.870 0.388 1.00 90.98 17 A 1 ATOM 111 C C . SER A 1 17 ? 11.666 4.524 -0.589 1.00 91.33 17 A 1 ATOM 112 O O . SER A 1 17 ? 12.848 4.729 -0.292 1.00 86.93 17 A 1 ATOM 113 C CB . SER A 1 17 ? 10.127 3.619 1.153 1.00 87.09 17 A 1 ATOM 114 O OG . SER A 1 17 ? 11.223 3.086 1.859 1.00 76.81 17 A 1 ATOM 115 N N . ALA A 1 18 ? 11.300 3.999 -1.754 1.00 89.36 18 A 1 ATOM 116 C CA . ALA A 1 18 ? 12.271 3.583 -2.762 1.00 86.89 18 A 1 ATOM 117 C C . ALA A 1 18 ? 12.068 4.364 -4.047 1.00 85.38 18 A 1 ATOM 118 O O . ALA A 1 18 ? 13.028 5.007 -4.512 1.00 81.06 18 A 1 ATOM 119 C CB . ALA A 1 18 ? 12.152 2.082 -3.014 1.00 81.45 18 A 1 ATOM 120 O OXT . ALA A 1 18 ? 10.966 4.304 -4.598 1.00 74.57 18 A 1 #