# 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_spkb24664 # _entry.id spkb24664 # 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 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 TYR 3 1 n SER 4 1 n ALA 5 1 n VAL 6 1 n LEU 7 1 n VAL 8 1 n ALA 9 1 n ALA 10 1 n LEU 11 1 n ALA 12 1 n ALA 13 1 n ILE 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 @ 2025-07-08 06:34:03)" _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 94.97 _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 89.97 1 1 A LYS 2 2 91.44 1 2 A TYR 3 2 92.89 1 3 A SER 4 2 95.42 1 4 A ALA 5 2 97.55 1 5 A VAL 6 2 97.37 1 6 A LEU 7 2 96.19 1 7 A VAL 8 2 97.53 1 8 A ALA 9 2 97.60 1 9 A ALA 10 2 97.13 1 10 A LEU 11 2 96.00 1 11 A ALA 12 2 97.62 1 12 A ALA 13 2 97.96 1 13 A ILE 14 2 97.07 1 14 A ALA 15 2 97.55 1 15 A ASP 16 2 92.48 1 16 A ALA 17 2 89.33 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 TYR . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ILE . 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 ? -13.579 0.233 -0.356 1.00 92.94 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.122 0.295 -0.549 1.00 94.50 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.415 -0.810 0.233 1.00 95.22 1 A 1 ATOM 4 O O . MET A 1 1 ? -11.017 -0.620 1.377 1.00 93.06 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.589 1.651 -0.097 1.00 92.11 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.115 2.092 1.258 1.00 90.34 1 A 1 ATOM 7 S SD . MET A 1 1 ? -11.665 3.792 1.638 1.00 86.38 1 A 1 ATOM 8 C CE . MET A 1 1 ? -12.595 4.047 3.138 1.00 75.22 1 A 1 ATOM 9 N N . LYS A 1 2 ? -11.270 -1.969 -0.396 1.00 94.51 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -10.634 -3.118 0.248 1.00 96.28 2 A 1 ATOM 11 C C . LYS A 1 2 ? -9.161 -3.216 -0.125 1.00 96.92 2 A 1 ATOM 12 O O . LYS A 1 2 ? -8.282 -3.099 0.723 1.00 96.61 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -11.368 -4.405 -0.148 1.00 94.76 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -12.187 -4.997 0.986 1.00 90.82 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.308 -5.630 2.041 1.00 89.10 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -12.132 -6.197 3.178 1.00 84.31 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -11.273 -6.872 4.183 1.00 79.64 2 A 1 ATOM 18 N N . TYR A 1 3 ? -8.899 -3.422 -1.404 1.00 94.86 3 A 1 ATOM 19 C CA . TYR A 1 3 ? -7.532 -3.557 -1.889 1.00 95.86 3 A 1 ATOM 20 C C . TYR A 1 3 ? -6.968 -2.220 -2.352 1.00 96.97 3 A 1 ATOM 21 O O . TYR A 1 3 ? -5.767 -2.085 -2.558 1.00 96.56 3 A 1 ATOM 22 C CB . TYR A 1 3 ? -7.485 -4.567 -3.042 1.00 95.51 3 A 1 ATOM 23 C CG . TYR A 1 3 ? -7.652 -5.997 -2.569 1.00 93.42 3 A 1 ATOM 24 C CD1 . TYR A 1 3 ? -8.890 -6.485 -2.190 1.00 91.55 3 A 1 ATOM 25 C CD2 . TYR A 1 3 ? -6.559 -6.849 -2.504 1.00 91.25 3 A 1 ATOM 26 C CE1 . TYR A 1 3 ? -9.044 -7.787 -1.745 1.00 90.40 3 A 1 ATOM 27 C CE2 . TYR A 1 3 ? -6.699 -8.156 -2.064 1.00 89.90 3 A 1 ATOM 28 C CZ . TYR A 1 3 ? -7.946 -8.616 -1.690 1.00 89.86 3 A 1 ATOM 29 O OH . TYR A 1 3 ? -8.091 -9.908 -1.255 1.00 88.55 3 A 1 ATOM 30 N N . SER A 1 4 ? -7.823 -1.230 -2.498 1.00 96.15 4 A 1 ATOM 31 C CA . SER A 1 4 ? -7.408 0.098 -2.945 1.00 96.78 4 A 1 ATOM 32 C C . SER A 1 4 ? -6.455 0.742 -1.945 1.00 97.61 4 A 1 ATOM 33 O O . SER A 1 4 ? -5.358 1.169 -2.291 1.00 97.29 4 A 1 ATOM 34 C CB . SER A 1 4 ? -8.624 0.994 -3.151 1.00 95.53 4 A 1 ATOM 35 O OG . SER A 1 4 ? -8.227 2.229 -3.696 1.00 89.15 4 A 1 ATOM 36 N N . ALA A 1 5 ? -6.871 0.808 -0.687 1.00 97.07 5 A 1 ATOM 37 C CA . ALA A 1 5 ? -6.055 1.405 0.364 1.00 97.70 5 A 1 ATOM 38 C C . ALA A 1 5 ? -4.799 0.582 0.630 1.00 98.17 5 A 1 ATOM 39 O O . ALA A 1 5 ? -3.727 1.127 0.881 1.00 97.80 5 A 1 ATOM 40 C CB . ALA A 1 5 ? -6.875 1.535 1.645 1.00 97.03 5 A 1 ATOM 41 N N . VAL A 1 6 ? -4.939 -0.733 0.579 1.00 97.66 6 A 1 ATOM 42 C CA . VAL A 1 6 ? -3.816 -1.641 0.816 1.00 98.01 6 A 1 ATOM 43 C C . VAL A 1 6 ? -2.730 -1.453 -0.238 1.00 98.26 6 A 1 ATOM 44 O O . VAL A 1 6 ? -1.546 -1.350 0.087 1.00 98.02 6 A 1 ATOM 45 C CB . VAL A 1 6 ? -4.283 -3.104 0.817 1.00 97.70 6 A 1 ATOM 46 C CG1 . VAL A 1 6 ? -3.097 -4.040 1.017 1.00 96.29 6 A 1 ATOM 47 C CG2 . VAL A 1 6 ? -5.315 -3.323 1.911 1.00 95.68 6 A 1 ATOM 48 N N . LEU A 1 7 ? -3.136 -1.403 -1.495 1.00 97.53 7 A 1 ATOM 49 C CA . LEU A 1 7 ? -2.190 -1.241 -2.596 1.00 97.73 7 A 1 ATOM 50 C C . LEU A 1 7 ? -1.497 0.114 -2.532 1.00 98.06 7 A 1 ATOM 51 O O . LEU A 1 7 ? -0.284 0.212 -2.718 1.00 98.13 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -2.919 -1.390 -3.930 1.00 97.62 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -3.311 -2.823 -4.263 1.00 94.32 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -4.324 -2.846 -5.397 1.00 92.92 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -2.075 -3.628 -4.643 1.00 93.23 7 A 1 ATOM 56 N N . VAL A 1 8 ? -2.255 1.146 -2.260 1.00 97.72 8 A 1 ATOM 57 C CA . VAL A 1 8 ? -1.712 2.498 -2.165 1.00 97.97 8 A 1 ATOM 58 C C . VAL A 1 8 ? -0.718 2.598 -1.014 1.00 98.20 8 A 1 ATOM 59 O O . VAL A 1 8 ? 0.367 3.162 -1.159 1.00 98.17 8 A 1 ATOM 60 C CB . VAL A 1 8 ? -2.836 3.526 -1.972 1.00 97.73 8 A 1 ATOM 61 C CG1 . VAL A 1 8 ? -2.257 4.918 -1.752 1.00 96.53 8 A 1 ATOM 62 C CG2 . VAL A 1 8 ? -3.755 3.530 -3.182 1.00 96.41 8 A 1 ATOM 63 N N . ALA A 1 9 ? -1.094 2.058 0.133 1.00 97.62 9 A 1 ATOM 64 C CA . ALA A 1 9 ? -0.233 2.094 1.310 1.00 97.50 9 A 1 ATOM 65 C C . ALA A 1 9 ? 1.052 1.309 1.076 1.00 97.94 9 A 1 ATOM 66 O O . ALA A 1 9 ? 2.134 1.737 1.479 1.00 97.73 9 A 1 ATOM 67 C CB . ALA A 1 9 ? -0.973 1.524 2.511 1.00 97.19 9 A 1 ATOM 68 N N . ALA A 1 10 ? 0.935 0.163 0.426 1.00 97.09 10 A 1 ATOM 69 C CA . ALA A 1 10 ? 2.091 -0.679 0.137 1.00 97.07 10 A 1 ATOM 70 C C . ALA A 1 10 ? 3.060 0.030 -0.799 1.00 97.65 10 A 1 ATOM 71 O O . ALA A 1 10 ? 4.269 0.039 -0.564 1.00 97.17 10 A 1 ATOM 72 C CB . ALA A 1 10 ? 1.635 -1.995 -0.482 1.00 96.65 10 A 1 ATOM 73 N N . LEU A 1 11 ? 2.537 0.626 -1.850 1.00 97.49 11 A 1 ATOM 74 C CA . LEU A 1 11 ? 3.362 1.339 -2.819 1.00 97.63 11 A 1 ATOM 75 C C . LEU A 1 11 ? 4.054 2.528 -2.168 1.00 98.09 11 A 1 ATOM 76 O O . LEU A 1 11 ? 5.235 2.783 -2.405 1.00 97.79 11 A 1 ATOM 77 C CB . LEU A 1 11 ? 2.501 1.822 -3.987 1.00 97.03 11 A 1 ATOM 78 C CG . LEU A 1 11 ? 3.310 2.367 -5.163 1.00 94.25 11 A 1 ATOM 79 C CD1 . LEU A 1 11 ? 4.028 1.240 -5.880 1.00 92.96 11 A 1 ATOM 80 C CD2 . LEU A 1 11 ? 2.411 3.124 -6.128 1.00 92.72 11 A 1 ATOM 81 N N . ALA A 1 12 ? 3.325 3.252 -1.340 1.00 97.80 12 A 1 ATOM 82 C CA . ALA A 1 12 ? 3.866 4.415 -0.646 1.00 97.62 12 A 1 ATOM 83 C C . ALA A 1 12 ? 4.981 4.011 0.309 1.00 97.96 12 A 1 ATOM 84 O O . ALA A 1 12 ? 6.000 4.694 0.413 1.00 97.63 12 A 1 ATOM 85 C CB . ALA A 1 12 ? 2.757 5.124 0.118 1.00 97.07 12 A 1 ATOM 86 N N . ALA A 1 13 ? 4.795 2.898 1.004 1.00 97.96 13 A 1 ATOM 87 C CA . ALA A 1 13 ? 5.795 2.403 1.948 1.00 98.00 13 A 1 ATOM 88 C C . ALA A 1 13 ? 7.077 2.000 1.231 1.00 98.29 13 A 1 ATOM 89 O O . ALA A 1 13 ? 8.179 2.276 1.704 1.00 97.93 13 A 1 ATOM 90 C CB . ALA A 1 13 ? 5.235 1.221 2.723 1.00 97.63 13 A 1 ATOM 91 N N . ILE A 1 14 ? 6.942 1.336 0.088 1.00 98.05 14 A 1 ATOM 92 C CA . ILE A 1 14 ? 8.093 0.899 -0.696 1.00 97.98 14 A 1 ATOM 93 C C . ILE A 1 14 ? 8.858 2.093 -1.250 1.00 98.12 14 A 1 ATOM 94 O O . ILE A 1 14 ? 10.093 2.116 -1.243 1.00 97.85 14 A 1 ATOM 95 C CB . ILE A 1 14 ? 7.649 -0.019 -1.850 1.00 97.59 14 A 1 ATOM 96 C CG1 . ILE A 1 14 ? 7.033 -1.303 -1.297 1.00 96.32 14 A 1 ATOM 97 C CG2 . ILE A 1 14 ? 8.840 -0.360 -2.747 1.00 96.11 14 A 1 ATOM 98 C CD1 . ILE A 1 14 ? 6.257 -2.084 -2.338 1.00 94.56 14 A 1 ATOM 99 N N . ALA A 1 15 ? 8.134 3.075 -1.727 1.00 97.75 15 A 1 ATOM 100 C CA . ALA A 1 15 ? 8.733 4.279 -2.295 1.00 97.64 15 A 1 ATOM 101 C C . ALA A 1 15 ? 8.968 5.353 -1.241 1.00 97.83 15 A 1 ATOM 102 O O . ALA A 1 15 ? 9.234 6.511 -1.568 1.00 97.43 15 A 1 ATOM 103 C CB . ALA A 1 15 ? 7.840 4.823 -3.406 1.00 97.09 15 A 1 ATOM 104 N N . ASP A 1 16 ? 8.864 4.962 0.004 1.00 95.11 16 A 1 ATOM 105 C CA . ASP A 1 16 ? 9.043 5.900 1.111 1.00 95.48 16 A 1 ATOM 106 C C . ASP A 1 16 ? 10.520 6.120 1.400 1.00 95.60 16 A 1 ATOM 107 O O . ASP A 1 16 ? 11.036 5.722 2.446 1.00 94.04 16 A 1 ATOM 108 C CB . ASP A 1 16 ? 8.345 5.384 2.366 1.00 93.91 16 A 1 ATOM 109 C CG . ASP A 1 16 ? 8.402 6.383 3.504 1.00 89.78 16 A 1 ATOM 110 O OD1 . ASP A 1 16 ? 8.384 7.591 3.231 1.00 87.97 16 A 1 ATOM 111 O OD2 . ASP A 1 16 ? 8.457 5.953 4.671 1.00 87.93 16 A 1 ATOM 112 N N . ALA A 1 17 ? 11.206 6.770 0.470 1.00 93.89 17 A 1 ATOM 113 C CA . ALA A 1 17 ? 12.632 7.020 0.622 1.00 92.39 17 A 1 ATOM 114 C C . ALA A 1 17 ? 12.897 8.519 0.678 1.00 90.86 17 A 1 ATOM 115 O O . ALA A 1 17 ? 13.185 9.044 1.769 1.00 87.92 17 A 1 ATOM 116 C CB . ALA A 1 17 ? 13.408 6.375 -0.522 1.00 89.26 17 A 1 ATOM 117 O OXT . ALA A 1 17 ? 12.799 9.163 -0.346 1.00 81.65 17 A 1 #