# 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_spkb18703 # _entry.id spkb18703 # 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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([C@@H](C(=O)O)N)O ? "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 LYS 4 1 n ILE 5 1 n LEU 6 1 n ALA 7 1 n ALA 8 1 n THR 9 1 n ALA 10 1 n ILE 11 1 n LEU 12 1 n LEU 13 1 n ALA 14 1 n ALA 15 1 n ILE 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 @ 2025-07-06 06:31:29)" _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 95.86 _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 91.62 1 1 A LYS 2 2 92.35 1 2 A LYS 3 2 93.17 1 3 A LYS 4 2 94.34 1 4 A ILE 5 2 96.96 1 5 A LEU 6 2 96.87 1 6 A ALA 7 2 98.57 1 7 A ALA 8 2 98.69 1 8 A THR 9 2 97.37 1 9 A ALA 10 2 98.66 1 10 A ILE 11 2 97.69 1 11 A LEU 12 2 97.04 1 12 A LEU 13 2 96.82 1 13 A ALA 14 2 98.64 1 14 A ALA 15 2 98.41 1 15 A ILE 16 2 95.13 1 16 A ALA 17 2 92.73 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 LYS . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n ILE . 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 ? 1.316 5.858 12.267 1.00 95.61 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.114 6.240 10.867 1.00 96.44 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.398 5.061 9.937 1.00 97.12 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.816 5.237 8.797 1.00 95.92 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.034 7.413 10.521 1.00 93.65 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.647 8.678 11.262 1.00 89.27 1 A 1 ATOM 7 S SD . MET A 1 1 ? 3.040 9.778 11.472 1.00 86.72 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.373 10.947 12.625 1.00 78.25 1 A 1 ATOM 9 N N . LYS A 1 2 ? 1.151 3.876 10.456 1.00 96.71 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 1.357 2.653 9.688 1.00 97.52 2 A 1 ATOM 11 C C . LYS A 1 2 ? 0.155 2.349 8.797 1.00 98.03 2 A 1 ATOM 12 O O . LYS A 1 2 ? 0.268 1.610 7.821 1.00 97.76 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 1.627 1.492 10.645 1.00 96.75 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 0.506 1.277 11.652 1.00 92.62 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 0.724 0.000 12.446 1.00 90.20 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 1.551 0.248 13.677 1.00 83.92 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.577 -0.948 14.551 1.00 77.60 2 A 1 ATOM 18 N N . LYS A 1 3 ? -0.982 2.928 9.138 1.00 97.77 3 A 1 ATOM 19 C CA . LYS A 1 3 ? -2.213 2.713 8.381 1.00 98.16 3 A 1 ATOM 20 C C . LYS A 1 3 ? -2.074 3.268 6.962 1.00 98.42 3 A 1 ATOM 21 O O . LYS A 1 3 ? -2.635 2.719 6.012 1.00 98.07 3 A 1 ATOM 22 C CB . LYS A 1 3 ? -3.389 3.374 9.106 1.00 97.68 3 A 1 ATOM 23 C CG . LYS A 1 3 ? -4.632 2.500 9.094 1.00 94.47 3 A 1 ATOM 24 C CD . LYS A 1 3 ? -5.793 3.184 9.783 1.00 91.10 3 A 1 ATOM 25 C CE . LYS A 1 3 ? -7.062 2.362 9.640 1.00 85.13 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? -8.207 3.005 10.343 1.00 77.77 3 A 1 ATOM 27 N N . LYS A 1 4 ? -1.316 4.347 6.837 1.00 98.20 4 A 1 ATOM 28 C CA . LYS A 1 4 ? -1.089 4.966 5.532 1.00 98.46 4 A 1 ATOM 29 C C . LYS A 1 4 ? -0.294 4.026 4.628 1.00 98.62 4 A 1 ATOM 30 O O . LYS A 1 4 ? -0.513 3.982 3.417 1.00 98.44 4 A 1 ATOM 31 C CB . LYS A 1 4 ? -0.344 6.288 5.708 1.00 98.30 4 A 1 ATOM 32 C CG . LYS A 1 4 ? -1.219 7.378 6.313 1.00 96.32 4 A 1 ATOM 33 C CD . LYS A 1 4 ? -2.035 8.094 5.245 1.00 92.53 4 A 1 ATOM 34 C CE . LYS A 1 4 ? -2.578 9.418 5.755 1.00 87.98 4 A 1 ATOM 35 N NZ . LYS A 1 4 ? -2.374 10.512 4.771 1.00 80.17 4 A 1 ATOM 36 N N . ILE A 1 5 ? 0.619 3.284 5.225 1.00 97.51 5 A 1 ATOM 37 C CA . ILE A 1 5 ? 1.447 2.340 4.485 1.00 97.70 5 A 1 ATOM 38 C C . ILE A 1 5 ? 0.592 1.207 3.933 1.00 98.10 5 A 1 ATOM 39 O O . ILE A 1 5 ? 0.747 0.795 2.781 1.00 98.00 5 A 1 ATOM 40 C CB . ILE A 1 5 ? 2.564 1.783 5.382 1.00 97.99 5 A 1 ATOM 41 C CG1 . ILE A 1 5 ? 3.349 2.928 6.048 1.00 96.72 5 A 1 ATOM 42 C CG2 . ILE A 1 5 ? 3.505 0.891 4.572 1.00 96.54 5 A 1 ATOM 43 C CD1 . ILE A 1 5 ? 3.969 3.890 5.054 1.00 93.09 5 A 1 ATOM 44 N N . LEU A 1 6 ? -0.293 0.705 4.764 1.00 98.62 6 A 1 ATOM 45 C CA . LEU A 1 6 ? -1.176 -0.388 4.371 1.00 98.57 6 A 1 ATOM 46 C C . LEU A 1 6 ? -2.127 0.063 3.273 1.00 98.64 6 A 1 ATOM 47 O O . LEU A 1 6 ? -2.406 -0.683 2.331 1.00 98.61 6 A 1 ATOM 48 C CB . LEU A 1 6 ? -1.955 -0.879 5.591 1.00 98.54 6 A 1 ATOM 49 C CG . LEU A 1 6 ? -1.821 -2.372 5.845 1.00 95.82 6 A 1 ATOM 50 C CD1 . LEU A 1 6 ? -2.155 -2.703 7.284 1.00 92.84 6 A 1 ATOM 51 C CD2 . LEU A 1 6 ? -2.709 -3.160 4.900 1.00 93.35 6 A 1 ATOM 52 N N . ALA A 1 7 ? -2.618 1.285 3.396 1.00 98.61 7 A 1 ATOM 53 C CA . ALA A 1 7 ? -3.533 1.847 2.407 1.00 98.61 7 A 1 ATOM 54 C C . ALA A 1 7 ? -2.846 1.988 1.053 1.00 98.63 7 A 1 ATOM 55 O O . ALA A 1 7 ? -3.430 1.674 0.014 1.00 98.51 7 A 1 ATOM 56 C CB . ALA A 1 7 ? -4.039 3.202 2.884 1.00 98.48 7 A 1 ATOM 57 N N . ALA A 1 8 ? -1.606 2.448 1.080 1.00 98.70 8 A 1 ATOM 58 C CA . ALA A 1 8 ? -0.838 2.622 -0.148 1.00 98.72 8 A 1 ATOM 59 C C . ALA A 1 8 ? -0.547 1.276 -0.801 1.00 98.77 8 A 1 ATOM 60 O O . ALA A 1 8 ? -0.597 1.146 -2.025 1.00 98.64 8 A 1 ATOM 61 C CB . ALA A 1 8 ? 0.461 3.352 0.161 1.00 98.62 8 A 1 ATOM 62 N N . THR A 1 9 ? -0.259 0.279 0.018 1.00 98.64 9 A 1 ATOM 63 C CA . THR A 1 9 ? 0.036 -1.063 -0.474 1.00 98.60 9 A 1 ATOM 64 C C . THR A 1 9 ? -1.205 -1.681 -1.113 1.00 98.70 9 A 1 ATOM 65 O O . THR A 1 9 ? -1.106 -2.379 -2.122 1.00 98.58 9 A 1 ATOM 66 C CB . THR A 1 9 ? 0.525 -1.955 0.672 1.00 98.35 9 A 1 ATOM 67 O OG1 . THR A 1 9 ? 1.550 -1.284 1.394 1.00 95.00 9 A 1 ATOM 68 C CG2 . THR A 1 9 ? 1.084 -3.259 0.137 1.00 93.69 9 A 1 ATOM 69 N N . ALA A 1 10 ? -2.354 -1.419 -0.524 1.00 98.73 10 A 1 ATOM 70 C CA . ALA A 1 10 ? -3.618 -1.941 -1.037 1.00 98.71 10 A 1 ATOM 71 C C . ALA A 1 10 ? -3.906 -1.398 -2.435 1.00 98.77 10 A 1 ATOM 72 O O . ALA A 1 10 ? -4.392 -2.123 -3.302 1.00 98.56 10 A 1 ATOM 73 C CB . ALA A 1 10 ? -4.751 -1.571 -0.086 1.00 98.52 10 A 1 ATOM 74 N N . ILE A 1 11 ? -3.604 -0.130 -2.631 1.00 98.66 11 A 1 ATOM 75 C CA . ILE A 1 11 ? -3.819 0.513 -3.927 1.00 98.64 11 A 1 ATOM 76 C C . ILE A 1 11 ? -2.883 -0.079 -4.973 1.00 98.73 11 A 1 ATOM 77 O O . ILE A 1 11 ? -3.281 -0.328 -6.116 1.00 98.56 11 A 1 ATOM 78 C CB . ILE A 1 11 ? -3.608 2.036 -3.817 1.00 98.51 11 A 1 ATOM 79 C CG1 . ILE A 1 11 ? -4.629 2.658 -2.860 1.00 97.37 11 A 1 ATOM 80 C CG2 . ILE A 1 11 ? -3.732 2.688 -5.201 1.00 97.10 11 A 1 ATOM 81 C CD1 . ILE A 1 11 ? -4.179 3.981 -2.291 1.00 93.98 11 A 1 ATOM 82 N N . LEU A 1 12 ? -1.641 -0.299 -4.564 1.00 98.55 12 A 1 ATOM 83 C CA . LEU A 1 12 ? -0.642 -0.872 -5.461 1.00 98.57 12 A 1 ATOM 84 C C . LEU A 1 12 ? -1.033 -2.289 -5.860 1.00 98.71 12 A 1 ATOM 85 O O . LEU A 1 12 ? -0.873 -2.683 -7.016 1.00 98.62 12 A 1 ATOM 86 C CB . LEU A 1 12 ? 0.726 -0.877 -4.778 1.00 98.46 12 A 1 ATOM 87 C CG . LEU A 1 12 ? 1.902 -0.887 -5.755 1.00 96.39 12 A 1 ATOM 88 C CD1 . LEU A 1 12 ? 2.215 0.528 -6.214 1.00 93.32 12 A 1 ATOM 89 C CD2 . LEU A 1 12 ? 3.126 -1.514 -5.116 1.00 93.73 12 A 1 ATOM 90 N N . LEU A 1 13 ? -1.537 -3.041 -4.903 1.00 98.67 13 A 1 ATOM 91 C CA . LEU A 1 13 ? -1.963 -4.416 -5.144 1.00 98.61 13 A 1 ATOM 92 C C . LEU A 1 13 ? -3.145 -4.450 -6.104 1.00 98.71 13 A 1 ATOM 93 O O . LEU A 1 13 ? -3.216 -5.310 -6.985 1.00 98.53 13 A 1 ATOM 94 C CB . LEU A 1 13 ? -2.344 -5.077 -3.819 1.00 98.37 13 A 1 ATOM 95 C CG . LEU A 1 13 ? -2.296 -6.601 -3.868 1.00 95.83 13 A 1 ATOM 96 C CD1 . LEU A 1 13 ? -0.883 -7.095 -3.594 1.00 92.84 13 A 1 ATOM 97 C CD2 . LEU A 1 13 ? -3.265 -7.201 -2.870 1.00 93.04 13 A 1 ATOM 98 N N . ALA A 1 14 ? -4.060 -3.527 -5.931 1.00 98.75 14 A 1 ATOM 99 C CA . ALA A 1 14 ? -5.245 -3.440 -6.785 1.00 98.73 14 A 1 ATOM 100 C C . ALA A 1 14 ? -4.864 -3.084 -8.219 1.00 98.78 14 A 1 ATOM 101 O O . ALA A 1 14 ? -5.540 -3.484 -9.168 1.00 98.47 14 A 1 ATOM 102 C CB . ALA A 1 14 ? -6.208 -2.402 -6.226 1.00 98.48 14 A 1 ATOM 103 N N . ALA A 1 15 ? -3.791 -2.327 -8.364 1.00 98.54 15 A 1 ATOM 104 C CA . ALA A 1 15 ? -3.325 -1.908 -9.685 1.00 98.52 15 A 1 ATOM 105 C C . ALA A 1 15 ? -2.792 -3.092 -10.488 1.00 98.64 15 A 1 ATOM 106 O O . ALA A 1 15 ? -2.998 -3.171 -11.699 1.00 98.17 15 A 1 ATOM 107 C CB . ALA A 1 15 ? -2.246 -0.836 -9.541 1.00 98.18 15 A 1 ATOM 108 N N . ILE A 1 16 ? -2.102 -4.005 -9.811 1.00 97.42 16 A 1 ATOM 109 C CA . ILE A 1 16 ? -1.537 -5.185 -10.464 1.00 97.57 16 A 1 ATOM 110 C C . ILE A 1 16 ? -2.539 -6.327 -10.557 1.00 98.04 16 A 1 ATOM 111 O O . ILE A 1 16 ? -2.360 -7.266 -11.333 1.00 97.45 16 A 1 ATOM 112 C CB . ILE A 1 16 ? -0.273 -5.663 -9.725 1.00 96.78 16 A 1 ATOM 113 C CG1 . ILE A 1 16 ? -0.564 -5.891 -8.241 1.00 93.32 16 A 1 ATOM 114 C CG2 . ILE A 1 16 ? 0.859 -4.660 -9.913 1.00 92.01 16 A 1 ATOM 115 C CD1 . ILE A 1 16 ? 0.402 -6.843 -7.583 1.00 88.42 16 A 1 ATOM 116 N N . ALA A 1 17 ? -3.570 -6.249 -9.764 1.00 96.76 17 A 1 ATOM 117 C CA . ALA A 1 17 ? -4.596 -7.279 -9.722 1.00 95.53 17 A 1 ATOM 118 C C . ALA A 1 17 ? -5.843 -6.845 -10.488 1.00 94.78 17 A 1 ATOM 119 O O . ALA A 1 17 ? -6.053 -5.630 -10.664 1.00 91.72 17 A 1 ATOM 120 C CB . ALA A 1 17 ? -4.933 -7.621 -8.276 1.00 92.76 17 A 1 ATOM 121 O OXT . ALA A 1 17 ? -6.629 -7.715 -10.892 1.00 84.81 17 A 1 #