# 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_spkb08768 # _entry.id spkb08768 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=O)N ? "L-PEPTIDE LINKING" "C4 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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 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 ASN 4 1 n LEU 5 1 n LEU 6 1 n VAL 7 1 n LEU 8 1 n LEU 9 1 n CYS 10 1 n ALA 11 1 n LEU 12 1 n ALA 13 1 n ALA 14 1 n ALA 15 1 n ASP 16 1 n ALA 17 # _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 @ 2025-07-07 16:01:51)" _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 92.37 _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 83.72 1 1 A LYS 2 2 85.35 1 2 A ALA 3 2 94.09 1 3 A ASN 4 2 92.34 1 4 A LEU 5 2 93.25 1 5 A LEU 6 2 93.45 1 6 A VAL 7 2 96.52 1 7 A LEU 8 2 94.35 1 8 A LEU 9 2 93.23 1 9 A CYS 10 2 95.12 1 10 A ALA 11 2 97.14 1 11 A LEU 12 2 93.92 1 12 A ALA 13 2 96.72 1 13 A ALA 14 2 97.18 1 14 A ALA 15 2 96.40 1 15 A ASP 16 2 88.19 1 16 A ALA 17 2 87.58 1 17 # _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 ASN . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n ASP . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? 5.748 1.849 12.903 1.00 88.97 1 A 1 ATOM 2 C CA . MET A 1 1 ? 5.928 1.262 11.559 1.00 89.78 1 A 1 ATOM 3 C C . MET A 1 1 ? 4.926 1.864 10.584 1.00 91.62 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.731 1.855 10.853 1.00 89.33 1 A 1 ATOM 5 C CB . MET A 1 1 ? 5.717 -0.248 11.629 1.00 86.04 1 A 1 ATOM 6 C CG . MET A 1 1 ? 6.850 -0.946 12.363 1.00 81.98 1 A 1 ATOM 7 S SD . MET A 1 1 ? 6.488 -2.691 12.629 1.00 76.28 1 A 1 ATOM 8 C CE . MET A 1 1 ? 6.227 -2.701 14.381 1.00 65.74 1 A 1 ATOM 9 N N . LYS A 1 2 ? 5.394 2.400 9.488 1.00 90.71 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 4.533 3.022 8.486 1.00 92.24 2 A 1 ATOM 11 C C . LYS A 1 2 ? 4.328 2.097 7.287 1.00 92.76 2 A 1 ATOM 12 O O . LYS A 1 2 ? 4.714 2.424 6.164 1.00 93.14 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 5.156 4.336 8.032 1.00 90.24 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 4.806 5.488 8.955 1.00 83.40 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 5.934 5.752 9.944 1.00 81.03 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 5.615 6.947 10.814 1.00 75.33 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 6.730 7.230 11.748 1.00 69.33 2 A 1 ATOM 18 N N . ALA A 1 3 ? 3.733 0.965 7.529 1.00 92.82 3 A 1 ATOM 19 C CA . ALA A 1 3 ? 3.483 -0.007 6.464 1.00 94.47 3 A 1 ATOM 20 C C . ALA A 1 3 ? 2.074 0.151 5.897 1.00 95.83 3 A 1 ATOM 21 O O . ALA A 1 3 ? 1.741 -0.427 4.868 1.00 94.66 3 A 1 ATOM 22 C CB . ALA A 1 3 ? 3.683 -1.412 7.015 1.00 92.66 3 A 1 ATOM 23 N N . ASN A 1 4 ? 1.264 0.947 6.587 1.00 93.89 4 A 1 ATOM 24 C CA . ASN A 1 4 ? -0.118 1.172 6.156 1.00 95.28 4 A 1 ATOM 25 C C . ASN A 1 4 ? -0.152 1.866 4.797 1.00 96.01 4 A 1 ATOM 26 O O . ASN A 1 4 ? -0.938 1.511 3.921 1.00 95.14 4 A 1 ATOM 27 C CB . ASN A 1 4 ? -0.837 2.028 7.198 1.00 94.25 4 A 1 ATOM 28 C CG . ASN A 1 4 ? -0.584 1.530 8.606 1.00 91.66 4 A 1 ATOM 29 O OD1 . ASN A 1 4 ? 0.275 2.041 9.299 1.00 87.24 4 A 1 ATOM 30 N ND2 . ASN A 1 4 ? -1.323 0.526 9.033 1.00 85.25 4 A 1 ATOM 31 N N . LEU A 1 5 ? 0.704 2.850 4.632 1.00 95.76 5 A 1 ATOM 32 C CA . LEU A 1 5 ? 0.777 3.586 3.370 1.00 96.22 5 A 1 ATOM 33 C C . LEU A 1 5 ? 1.221 2.673 2.233 1.00 96.76 5 A 1 ATOM 34 O O . LEU A 1 5 ? 0.685 2.733 1.128 1.00 96.29 5 A 1 ATOM 35 C CB . LEU A 1 5 ? 1.760 4.749 3.522 1.00 95.91 5 A 1 ATOM 36 C CG . LEU A 1 5 ? 1.067 6.088 3.736 1.00 89.78 5 A 1 ATOM 37 C CD1 . LEU A 1 5 ? 2.037 7.098 4.323 1.00 87.62 5 A 1 ATOM 38 C CD2 . LEU A 1 5 ? 0.516 6.605 2.413 1.00 87.65 5 A 1 ATOM 39 N N . LEU A 1 6 ? 2.192 1.838 2.524 1.00 96.31 6 A 1 ATOM 40 C CA . LEU A 1 6 ? 2.705 0.904 1.518 1.00 96.24 6 A 1 ATOM 41 C C . LEU A 1 6 ? 1.616 -0.074 1.091 1.00 96.61 6 A 1 ATOM 42 O O . LEU A 1 6 ? 1.458 -0.359 -0.093 1.00 96.36 6 A 1 ATOM 43 C CB . LEU A 1 6 ? 3.901 0.146 2.095 1.00 95.94 6 A 1 ATOM 44 C CG . LEU A 1 6 ? 5.193 0.967 2.074 1.00 89.97 6 A 1 ATOM 45 C CD1 . LEU A 1 6 ? 6.199 0.398 3.062 1.00 88.45 6 A 1 ATOM 46 C CD2 . LEU A 1 6 ? 5.791 0.955 0.668 1.00 87.76 6 A 1 ATOM 47 N N . VAL A 1 7 ? 0.884 -0.571 2.065 1.00 96.84 7 A 1 ATOM 48 C CA . VAL A 1 7 ? -0.197 -1.520 1.785 1.00 97.10 7 A 1 ATOM 49 C C . VAL A 1 7 ? -1.284 -0.841 0.958 1.00 97.38 7 A 1 ATOM 50 O O . VAL A 1 7 ? -1.794 -1.415 -0.007 1.00 97.10 7 A 1 ATOM 51 C CB . VAL A 1 7 ? -0.784 -2.067 3.099 1.00 96.82 7 A 1 ATOM 52 C CG1 . VAL A 1 7 ? -1.979 -2.970 2.824 1.00 95.27 7 A 1 ATOM 53 C CG2 . VAL A 1 7 ? 0.275 -2.847 3.870 1.00 95.16 7 A 1 ATOM 54 N N . LEU A 1 8 ? -1.623 0.375 1.338 1.00 96.98 8 A 1 ATOM 55 C CA . LEU A 1 8 ? -2.650 1.133 0.626 1.00 96.78 8 A 1 ATOM 56 C C . LEU A 1 8 ? -2.205 1.429 -0.801 1.00 96.98 8 A 1 ATOM 57 O O . LEU A 1 8 ? -2.986 1.297 -1.747 1.00 96.73 8 A 1 ATOM 58 C CB . LEU A 1 8 ? -2.924 2.439 1.379 1.00 96.58 8 A 1 ATOM 59 C CG . LEU A 1 8 ? -4.036 2.304 2.420 1.00 91.25 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? -3.858 3.330 3.530 1.00 89.70 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? -5.394 2.495 1.752 1.00 89.79 8 A 1 ATOM 62 N N . LEU A 1 9 ? -0.964 1.820 -0.937 1.00 96.11 9 A 1 ATOM 63 C CA . LEU A 1 9 ? -0.409 2.127 -2.256 1.00 96.00 9 A 1 ATOM 64 C C . LEU A 1 9 ? -0.370 0.877 -3.126 1.00 96.50 9 A 1 ATOM 65 O O . LEU A 1 9 ? -0.692 0.921 -4.313 1.00 96.20 9 A 1 ATOM 66 C CB . LEU A 1 9 ? 0.997 2.708 -2.083 1.00 95.54 9 A 1 ATOM 67 C CG . LEU A 1 9 ? 1.155 4.079 -2.740 1.00 89.74 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? 2.196 4.910 -2.002 1.00 88.03 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? 1.552 3.922 -4.196 1.00 87.69 9 A 1 ATOM 70 N N . CYS A 1 10 ? 0.015 -0.226 -2.527 1.00 96.07 10 A 1 ATOM 71 C CA . CYS A 1 10 ? 0.080 -1.497 -3.249 1.00 96.27 10 A 1 ATOM 72 C C . CYS A 1 10 ? -1.312 -1.922 -3.704 1.00 96.66 10 A 1 ATOM 73 O O . CYS A 1 10 ? -1.500 -2.372 -4.829 1.00 95.75 10 A 1 ATOM 74 C CB . CYS A 1 10 ? 0.684 -2.569 -2.344 1.00 95.57 10 A 1 ATOM 75 S SG . CYS A 1 10 ? 2.461 -2.744 -2.612 1.00 90.38 10 A 1 ATOM 76 N N . ALA A 1 11 ? -2.273 -1.770 -2.813 1.00 96.96 11 A 1 ATOM 77 C CA . ALA A 1 11 ? -3.652 -2.136 -3.127 1.00 97.29 11 A 1 ATOM 78 C C . ALA A 1 11 ? -4.189 -1.253 -4.251 1.00 97.66 11 A 1 ATOM 79 O O . ALA A 1 11 ? -4.877 -1.733 -5.151 1.00 96.84 11 A 1 ATOM 80 C CB . ALA A 1 11 ? -4.509 -1.990 -1.879 1.00 96.93 11 A 1 ATOM 81 N N . LEU A 1 12 ? -3.864 0.016 -4.194 1.00 96.84 12 A 1 ATOM 82 C CA . LEU A 1 12 ? -4.304 0.964 -5.215 1.00 96.78 12 A 1 ATOM 83 C C . LEU A 1 12 ? -3.655 0.642 -6.555 1.00 97.15 12 A 1 ATOM 84 O O . LEU A 1 12 ? -4.308 0.681 -7.599 1.00 96.28 12 A 1 ATOM 85 C CB . LEU A 1 12 ? -3.941 2.387 -4.792 1.00 95.98 12 A 1 ATOM 86 C CG . LEU A 1 12 ? -4.864 3.435 -5.410 1.00 90.82 12 A 1 ATOM 87 C CD1 . LEU A 1 12 ? -5.835 3.968 -4.364 1.00 88.89 12 A 1 ATOM 88 C CD2 . LEU A 1 12 ? -4.062 4.573 -6.008 1.00 88.64 12 A 1 ATOM 89 N N . ALA A 1 13 ? -2.381 0.335 -6.512 1.00 96.84 13 A 1 ATOM 90 C CA . ALA A 1 13 ? -1.645 -0.005 -7.730 1.00 96.93 13 A 1 ATOM 91 C C . ALA A 1 13 ? -2.201 -1.277 -8.357 1.00 97.30 13 A 1 ATOM 92 O O . ALA A 1 13 ? -2.299 -1.392 -9.577 1.00 96.47 13 A 1 ATOM 93 C CB . ALA A 1 13 ? -0.172 -0.183 -7.393 1.00 96.07 13 A 1 ATOM 94 N N . ALA A 1 14 ? -2.562 -2.230 -7.517 1.00 97.58 14 A 1 ATOM 95 C CA . ALA A 1 14 ? -3.120 -3.496 -7.994 1.00 97.45 14 A 1 ATOM 96 C C . ALA A 1 14 ? -4.493 -3.273 -8.609 1.00 97.58 14 A 1 ATOM 97 O O . ALA A 1 14 ? -4.849 -3.900 -9.606 1.00 96.65 14 A 1 ATOM 98 C CB . ALA A 1 14 ? -3.213 -4.478 -6.835 1.00 96.64 14 A 1 ATOM 99 N N . ALA A 1 15 ? -5.259 -2.391 -8.006 1.00 96.98 15 A 1 ATOM 100 C CA . ALA A 1 15 ? -6.598 -2.079 -8.501 1.00 96.81 15 A 1 ATOM 101 C C . ALA A 1 15 ? -6.533 -1.142 -9.700 1.00 96.83 15 A 1 ATOM 102 O O . ALA A 1 15 ? -7.480 -1.059 -10.482 1.00 95.37 15 A 1 ATOM 103 C CB . ALA A 1 15 ? -7.418 -1.447 -7.383 1.00 96.00 15 A 1 ATOM 104 N N . ASP A 1 16 ? -5.433 -0.449 -9.830 1.00 91.96 16 A 1 ATOM 105 C CA . ASP A 1 16 ? -5.237 0.500 -10.935 1.00 92.79 16 A 1 ATOM 106 C C . ASP A 1 16 ? -5.211 -0.215 -12.279 1.00 93.14 16 A 1 ATOM 107 O O . ASP A 1 16 ? -5.524 0.374 -13.316 1.00 91.10 16 A 1 ATOM 108 C CB . ASP A 1 16 ? -3.923 1.256 -10.739 1.00 89.95 16 A 1 ATOM 109 C CG . ASP A 1 16 ? -3.766 2.364 -11.756 1.00 83.65 16 A 1 ATOM 110 O OD1 . ASP A 1 16 ? -3.485 2.060 -12.917 1.00 81.60 16 A 1 ATOM 111 O OD2 . ASP A 1 16 ? -3.908 3.541 -11.389 1.00 81.32 16 A 1 ATOM 112 N N . ALA A 1 17 ? -4.850 -1.478 -12.271 1.00 93.24 17 A 1 ATOM 113 C CA . ALA A 1 17 ? -4.757 -2.261 -13.501 1.00 91.67 17 A 1 ATOM 114 C C . ALA A 1 17 ? -6.052 -2.213 -14.315 1.00 89.77 17 A 1 ATOM 115 O O . ALA A 1 17 ? -7.112 -1.897 -13.748 1.00 84.63 17 A 1 ATOM 116 C CB . ALA A 1 17 ? -4.403 -3.700 -13.155 1.00 88.16 17 A 1 ATOM 117 O OXT . ALA A 1 17 ? -5.998 -2.489 -15.537 1.00 78.04 17 A 1 #