# 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_spkb23008 # _entry.id spkb23008 # 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 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" "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" "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 LYS 3 1 n ILE 4 1 n LEU 5 1 n ALA 6 1 n LEU 7 1 n LEU 8 1 n VAL 9 1 n ILE 10 1 n ALA 11 1 n PRO 12 1 n LEU 13 1 n LEU 14 1 n VAL 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 @ 2025-07-05 02:58:52)" _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 95.68 _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 92.12 1 1 A LYS 2 2 92.10 1 2 A LYS 3 2 94.06 1 3 A ILE 4 2 97.13 1 4 A LEU 5 2 95.80 1 5 A ALA 6 2 98.22 1 6 A LEU 7 2 96.93 1 7 A LEU 8 2 97.16 1 8 A VAL 9 2 97.96 1 9 A ILE 10 2 97.45 1 10 A ALA 11 2 98.21 1 11 A PRO 12 2 98.11 1 12 A LEU 13 2 96.53 1 13 A LEU 14 2 95.69 1 14 A VAL 15 2 96.61 1 15 A SER 16 2 89.21 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 LYS . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n VAL . 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 ? 10.441 11.084 3.154 1.00 96.64 1 A 1 ATOM 2 C CA . MET A 1 1 ? 9.504 10.757 2.055 1.00 97.25 1 A 1 ATOM 3 C C . MET A 1 1 ? 8.252 10.090 2.623 1.00 97.27 1 A 1 ATOM 4 O O . MET A 1 1 ? 8.312 8.970 3.111 1.00 96.32 1 A 1 ATOM 5 C CB . MET A 1 1 ? 10.177 9.813 1.063 1.00 95.42 1 A 1 ATOM 6 C CG . MET A 1 1 ? 11.368 10.473 0.393 1.00 89.78 1 A 1 ATOM 7 S SD . MET A 1 1 ? 12.262 9.341 -0.666 1.00 86.53 1 A 1 ATOM 8 C CE . MET A 1 1 ? 13.615 10.385 -1.169 1.00 77.73 1 A 1 ATOM 9 N N . LYS A 1 2 ? 7.119 10.790 2.562 1.00 97.15 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 5.854 10.288 3.103 1.00 97.76 2 A 1 ATOM 11 C C . LYS A 1 2 ? 5.057 9.501 2.064 1.00 97.98 2 A 1 ATOM 12 O O . LYS A 1 2 ? 4.202 8.696 2.423 1.00 97.23 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 5.023 11.467 3.609 1.00 96.92 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 5.667 12.184 4.784 1.00 91.81 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 5.265 11.551 6.099 1.00 89.93 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 5.780 12.353 7.275 1.00 83.47 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 5.392 11.727 8.553 1.00 76.68 2 A 1 ATOM 18 N N . LYS A 1 3 ? 5.320 9.739 0.796 1.00 98.12 3 A 1 ATOM 19 C CA . LYS A 1 3 ? 4.600 9.058 -0.282 1.00 98.33 3 A 1 ATOM 20 C C . LYS A 1 3 ? 4.826 7.549 -0.235 1.00 98.36 3 A 1 ATOM 21 O O . LYS A 1 3 ? 3.923 6.774 -0.537 1.00 97.80 3 A 1 ATOM 22 C CB . LYS A 1 3 ? 5.026 9.633 -1.636 1.00 98.05 3 A 1 ATOM 23 C CG . LYS A 1 3 ? 6.468 9.332 -1.994 1.00 95.17 3 A 1 ATOM 24 C CD . LYS A 1 3 ? 6.645 9.318 -3.501 1.00 92.13 3 A 1 ATOM 25 C CE . LYS A 1 3 ? 7.919 8.603 -3.897 1.00 87.71 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? 7.947 8.341 -5.354 1.00 80.91 3 A 1 ATOM 27 N N . ILE A 1 4 ? 6.014 7.137 0.149 1.00 98.05 4 A 1 ATOM 28 C CA . ILE A 1 4 ? 6.344 5.719 0.235 1.00 98.05 4 A 1 ATOM 29 C C . ILE A 1 4 ? 5.600 5.063 1.389 1.00 98.07 4 A 1 ATOM 30 O O . ILE A 1 4 ? 5.083 3.955 1.265 1.00 97.54 4 A 1 ATOM 31 C CB . ILE A 1 4 ? 7.861 5.527 0.405 1.00 98.12 4 A 1 ATOM 32 C CG1 . ILE A 1 4 ? 8.617 6.101 -0.791 1.00 96.93 4 A 1 ATOM 33 C CG2 . ILE A 1 4 ? 8.188 4.039 0.538 1.00 96.32 4 A 1 ATOM 34 C CD1 . ILE A 1 4 ? 9.968 6.625 -0.405 1.00 93.93 4 A 1 ATOM 35 N N . LEU A 1 5 ? 5.538 5.741 2.503 1.00 98.02 5 A 1 ATOM 36 C CA . LEU A 1 5 ? 4.842 5.224 3.678 1.00 97.87 5 A 1 ATOM 37 C C . LEU A 1 5 ? 3.345 5.118 3.414 1.00 97.98 5 A 1 ATOM 38 O O . LEU A 1 5 ? 2.698 4.161 3.831 1.00 97.84 5 A 1 ATOM 39 C CB . LEU A 1 5 ? 5.098 6.141 4.872 1.00 97.65 5 A 1 ATOM 40 C CG . LEU A 1 5 ? 4.565 5.586 6.189 1.00 93.66 5 A 1 ATOM 41 C CD1 . LEU A 1 5 ? 5.365 4.365 6.620 1.00 91.55 5 A 1 ATOM 42 C CD2 . LEU A 1 5 ? 4.621 6.649 7.276 1.00 91.84 5 A 1 ATOM 43 N N . ALA A 1 6 ? 2.791 6.096 2.734 1.00 98.35 6 A 1 ATOM 44 C CA . ALA A 1 6 ? 1.368 6.117 2.410 1.00 98.28 6 A 1 ATOM 45 C C . ALA A 1 6 ? 1.005 4.959 1.484 1.00 98.39 6 A 1 ATOM 46 O O . ALA A 1 6 ? -0.010 4.296 1.670 1.00 98.04 6 A 1 ATOM 47 C CB . ALA A 1 6 ? 1.014 7.442 1.752 1.00 98.05 6 A 1 ATOM 48 N N . LEU A 1 7 ? 1.847 4.712 0.491 1.00 98.37 7 A 1 ATOM 49 C CA . LEU A 1 7 ? 1.610 3.629 -0.462 1.00 98.46 7 A 1 ATOM 50 C C . LEU A 1 7 ? 1.739 2.272 0.219 1.00 98.61 7 A 1 ATOM 51 O O . LEU A 1 7 ? 1.038 1.326 -0.133 1.00 98.41 7 A 1 ATOM 52 C CB . LEU A 1 7 ? 2.616 3.737 -1.608 1.00 98.29 7 A 1 ATOM 53 C CG . LEU A 1 7 ? 2.279 4.844 -2.603 1.00 95.86 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? 3.525 5.281 -3.359 1.00 93.39 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? 1.224 4.358 -3.588 1.00 94.06 7 A 1 ATOM 56 N N . LEU A 1 8 ? 2.619 2.180 1.179 1.00 98.54 8 A 1 ATOM 57 C CA . LEU A 1 8 ? 2.847 0.937 1.912 1.00 98.57 8 A 1 ATOM 58 C C . LEU A 1 8 ? 1.664 0.601 2.812 1.00 98.67 8 A 1 ATOM 59 O O . LEU A 1 8 ? 1.552 -0.512 3.311 1.00 98.49 8 A 1 ATOM 60 C CB . LEU A 1 8 ? 4.128 1.066 2.737 1.00 98.42 8 A 1 ATOM 61 C CG . LEU A 1 8 ? 4.961 -0.212 2.763 1.00 96.09 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? 6.440 0.122 2.884 1.00 93.78 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? 4.546 -1.108 3.916 1.00 94.69 8 A 1 ATOM 64 N N . VAL A 1 9 ? 0.784 1.552 3.022 1.00 98.57 9 A 1 ATOM 65 C CA . VAL A 1 9 ? -0.397 1.342 3.857 1.00 98.54 9 A 1 ATOM 66 C C . VAL A 1 9 ? -1.644 1.126 3.004 1.00 98.63 9 A 1 ATOM 67 O O . VAL A 1 9 ? -2.544 0.376 3.381 1.00 98.37 9 A 1 ATOM 68 C CB . VAL A 1 9 ? -0.610 2.541 4.793 1.00 98.19 9 A 1 ATOM 69 C CG1 . VAL A 1 9 ? -1.839 2.334 5.658 1.00 96.63 9 A 1 ATOM 70 C CG2 . VAL A 1 9 ? 0.611 2.746 5.672 1.00 96.79 9 A 1 ATOM 71 N N . ILE A 1 10 ? -1.701 1.788 1.865 1.00 98.54 10 A 1 ATOM 72 C CA . ILE A 1 10 ? -2.850 1.684 0.969 1.00 98.49 10 A 1 ATOM 73 C C . ILE A 1 10 ? -2.882 0.335 0.264 1.00 98.58 10 A 1 ATOM 74 O O . ILE A 1 10 ? -3.935 -0.283 0.134 1.00 98.35 10 A 1 ATOM 75 C CB . ILE A 1 10 ? -2.828 2.820 -0.065 1.00 98.20 10 A 1 ATOM 76 C CG1 . ILE A 1 10 ? -2.890 4.182 0.645 1.00 96.43 10 A 1 ATOM 77 C CG2 . ILE A 1 10 ? -3.998 2.680 -1.035 1.00 96.16 10 A 1 ATOM 78 C CD1 . ILE A 1 10 ? -4.150 4.365 1.467 1.00 94.83 10 A 1 ATOM 79 N N . ALA A 1 11 ? -1.730 -0.118 -0.206 1.00 98.41 11 A 1 ATOM 80 C CA . ALA A 1 11 ? -1.641 -1.392 -0.918 1.00 98.36 11 A 1 ATOM 81 C C . ALA A 1 11 ? -2.064 -2.570 -0.036 1.00 98.44 11 A 1 ATOM 82 O O . ALA A 1 11 ? -2.963 -3.326 -0.400 1.00 97.88 11 A 1 ATOM 83 C CB . ALA A 1 11 ? -0.231 -1.588 -1.462 1.00 97.97 11 A 1 ATOM 84 N N . PRO A 1 12 ? -1.433 -2.750 1.117 1.00 98.56 12 A 1 ATOM 85 C CA . PRO A 1 12 ? -1.779 -3.858 2.020 1.00 98.42 12 A 1 ATOM 86 C C . PRO A 1 12 ? -3.174 -3.719 2.611 1.00 98.50 12 A 1 ATOM 87 O O . PRO A 1 12 ? -3.796 -4.711 2.977 1.00 97.99 12 A 1 ATOM 88 C CB . PRO A 1 12 ? -0.715 -3.767 3.116 1.00 97.92 12 A 1 ATOM 89 C CG . PRO A 1 12 ? -0.213 -2.375 3.058 1.00 97.08 12 A 1 ATOM 90 C CD . PRO A 1 12 ? -0.313 -1.962 1.617 1.00 98.31 12 A 1 ATOM 91 N N . LEU A 1 13 ? -3.668 -2.519 2.706 1.00 98.23 13 A 1 ATOM 92 C CA . LEU A 1 13 ? -5.002 -2.267 3.250 1.00 98.26 13 A 1 ATOM 93 C C . LEU A 1 13 ? -6.068 -2.874 2.351 1.00 98.38 13 A 1 ATOM 94 O O . LEU A 1 13 ? -7.081 -3.379 2.831 1.00 97.55 13 A 1 ATOM 95 C CB . LEU A 1 13 ? -5.234 -0.761 3.378 1.00 97.93 13 A 1 ATOM 96 C CG . LEU A 1 13 ? -6.448 -0.422 4.236 1.00 95.67 13 A 1 ATOM 97 C CD1 . LEU A 1 13 ? -6.008 0.263 5.523 1.00 93.40 13 A 1 ATOM 98 C CD2 . LEU A 1 13 ? -7.408 0.476 3.475 1.00 92.81 13 A 1 ATOM 99 N N . LEU A 1 14 ? -5.843 -2.835 1.046 1.00 97.77 14 A 1 ATOM 100 C CA . LEU A 1 14 ? -6.791 -3.385 0.079 1.00 97.76 14 A 1 ATOM 101 C C . LEU A 1 14 ? -6.816 -4.906 0.157 1.00 97.85 14 A 1 ATOM 102 O O . LEU A 1 14 ? -7.865 -5.527 -0.013 1.00 97.00 14 A 1 ATOM 103 C CB . LEU A 1 14 ? -6.407 -2.944 -1.332 1.00 97.40 14 A 1 ATOM 104 C CG . LEU A 1 14 ? -7.457 -3.286 -2.381 1.00 95.08 14 A 1 ATOM 105 C CD1 . LEU A 1 14 ? -8.635 -2.325 -2.277 1.00 91.72 14 A 1 ATOM 106 C CD2 . LEU A 1 14 ? -6.859 -3.218 -3.777 1.00 90.98 14 A 1 ATOM 107 N N . VAL A 1 15 ? -5.683 -5.511 0.395 1.00 98.08 15 A 1 ATOM 108 C CA . VAL A 1 15 ? -5.568 -6.966 0.496 1.00 97.95 15 A 1 ATOM 109 C C . VAL A 1 15 ? -6.295 -7.486 1.733 1.00 98.01 15 A 1 ATOM 110 O O . VAL A 1 15 ? -6.884 -8.569 1.711 1.00 97.25 15 A 1 ATOM 111 C CB . VAL A 1 15 ? -4.094 -7.384 0.543 1.00 97.19 15 A 1 ATOM 112 C CG1 . VAL A 1 15 ? -3.972 -8.895 0.613 1.00 93.47 15 A 1 ATOM 113 C CG2 . VAL A 1 15 ? -3.351 -6.854 -0.667 1.00 94.29 15 A 1 ATOM 114 N N . SER A 1 16 ? -6.252 -6.719 2.785 1.00 95.80 16 A 1 ATOM 115 C CA . SER A 1 16 ? -6.893 -7.110 4.046 1.00 94.27 16 A 1 ATOM 116 C C . SER A 1 16 ? -8.257 -6.456 4.198 1.00 91.41 16 A 1 ATOM 117 O O . SER A 1 16 ? -8.397 -5.517 5.000 1.00 85.59 16 A 1 ATOM 118 C CB . SER A 1 16 ? -6.006 -6.732 5.223 1.00 91.19 16 A 1 ATOM 119 O OG . SER A 1 16 ? -4.750 -7.356 5.135 1.00 82.58 16 A 1 ATOM 120 O OXT . SER A 1 16 ? -9.201 -6.889 3.515 1.00 83.63 16 A 1 #