# 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_spkb07428 # _entry.id spkb07428 # 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" "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 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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 PHE 3 1 n ILE 4 1 n ILE 5 1 n ALA 6 1 n LEU 7 1 n ALA 8 1 n ALA 9 1 n LEU 10 1 n ILE 11 1 n ALA 12 1 n VAL 13 1 n ALA 14 1 n CYS 15 1 n ALA 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 @ 2025-07-03 08:57:11)" _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 94.77 _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 89.47 1 1 A LYS 2 2 92.77 1 2 A PHE 3 2 93.55 1 3 A ILE 4 2 96.02 1 4 A ILE 5 2 96.41 1 5 A ALA 6 2 97.74 1 6 A LEU 7 2 95.35 1 7 A ALA 8 2 97.61 1 8 A ALA 9 2 97.50 1 9 A LEU 10 2 95.69 1 10 A ILE 11 2 95.52 1 11 A ALA 12 2 97.87 1 12 A VAL 13 2 96.69 1 13 A ALA 14 2 96.88 1 14 A CYS 15 2 94.25 1 15 A ALA 16 2 87.08 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 PHE . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n ALA . 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 ? 3.145 10.014 4.939 1.00 94.15 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.406 8.574 5.129 1.00 94.71 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.299 7.837 3.797 1.00 95.26 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.204 7.543 3.325 1.00 93.33 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.405 7.983 6.115 1.00 91.93 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.596 8.538 7.515 1.00 87.68 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.324 7.979 8.645 1.00 84.10 1 A 1 ATOM 8 C CE . MET A 1 1 ? 1.847 8.797 10.142 1.00 74.60 1 A 1 ATOM 9 N N . LYS A 1 2 ? 4.443 7.561 3.192 1.00 96.78 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 4.489 6.895 1.894 1.00 97.10 2 A 1 ATOM 11 C C . LYS A 1 2 ? 4.374 5.380 2.046 1.00 97.40 2 A 1 ATOM 12 O O . LYS A 1 2 ? 3.913 4.690 1.141 1.00 96.87 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 5.796 7.256 1.193 1.00 96.43 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 5.753 7.014 -0.291 1.00 93.38 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 5.248 8.245 -1.031 1.00 90.68 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 5.305 8.025 -2.526 1.00 85.72 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 5.198 9.312 -3.266 1.00 80.56 2 A 1 ATOM 18 N N . PHE A 1 3 ? 4.799 4.877 3.191 1.00 96.63 3 A 1 ATOM 19 C CA . PHE A 1 3 ? 4.775 3.443 3.461 1.00 96.84 3 A 1 ATOM 20 C C . PHE A 1 3 ? 3.349 2.902 3.454 1.00 97.52 3 A 1 ATOM 21 O O . PHE A 1 3 ? 3.097 1.788 3.000 1.00 96.85 3 A 1 ATOM 22 C CB . PHE A 1 3 ? 5.441 3.163 4.812 1.00 96.22 3 A 1 ATOM 23 C CG . PHE A 1 3 ? 6.372 1.979 4.769 1.00 94.15 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? 7.661 2.117 4.281 1.00 90.83 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? 5.950 0.742 5.217 1.00 90.44 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? 8.525 1.032 4.236 1.00 89.94 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? 6.807 -0.353 5.176 1.00 90.08 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? 8.098 -0.207 4.688 1.00 89.53 3 A 1 ATOM 29 N N . ILE A 1 4 ? 2.418 3.701 3.945 1.00 97.28 4 A 1 ATOM 30 C CA . ILE A 1 4 ? 1.011 3.312 4.001 1.00 97.60 4 A 1 ATOM 31 C C . ILE A 1 4 ? 0.451 3.135 2.597 1.00 97.83 4 A 1 ATOM 32 O O . ILE A 1 4 ? -0.303 2.200 2.324 1.00 97.57 4 A 1 ATOM 33 C CB . ILE A 1 4 ? 0.186 4.352 4.773 1.00 97.55 4 A 1 ATOM 34 C CG1 . ILE A 1 4 ? 0.809 4.615 6.148 1.00 95.50 4 A 1 ATOM 35 C CG2 . ILE A 1 4 ? -1.253 3.867 4.927 1.00 94.91 4 A 1 ATOM 36 C CD1 . ILE A 1 4 ? 0.890 3.371 7.007 1.00 89.89 4 A 1 ATOM 37 N N . ILE A 1 5 ? 0.810 4.052 1.712 1.00 97.76 5 A 1 ATOM 38 C CA . ILE A 1 5 ? 0.345 4.017 0.331 1.00 97.57 5 A 1 ATOM 39 C C . ILE A 1 5 ? 0.884 2.782 -0.378 1.00 97.60 5 A 1 ATOM 40 O O . ILE A 1 5 ? 0.157 2.087 -1.095 1.00 97.51 5 A 1 ATOM 41 C CB . ILE A 1 5 ? 0.775 5.283 -0.423 1.00 97.52 5 A 1 ATOM 42 C CG1 . ILE A 1 5 ? 0.330 6.536 0.335 1.00 96.03 5 A 1 ATOM 43 C CG2 . ILE A 1 5 ? 0.193 5.274 -1.836 1.00 95.63 5 A 1 ATOM 44 C CD1 . ILE A 1 5 ? -1.171 6.622 0.520 1.00 91.63 5 A 1 ATOM 45 N N . ALA A 1 6 ? 2.163 2.526 -0.187 1.00 97.78 6 A 1 ATOM 46 C CA . ALA A 1 6 ? 2.807 1.376 -0.811 1.00 97.78 6 A 1 ATOM 47 C C . ALA A 1 6 ? 2.207 0.069 -0.299 1.00 98.00 6 A 1 ATOM 48 O O . ALA A 1 6 ? 1.983 -0.870 -1.064 1.00 97.65 6 A 1 ATOM 49 C CB . ALA A 1 6 ? 4.305 1.412 -0.529 1.00 97.51 6 A 1 ATOM 50 N N . LEU A 1 7 ? 1.933 0.031 0.989 1.00 97.20 7 A 1 ATOM 51 C CA . LEU A 1 7 ? 1.342 -1.148 1.614 1.00 97.26 7 A 1 ATOM 52 C C . LEU A 1 7 ? -0.060 -1.393 1.075 1.00 97.79 7 A 1 ATOM 53 O O . LEU A 1 7 ? -0.416 -2.520 0.722 1.00 97.78 7 A 1 ATOM 54 C CB . LEU A 1 7 ? 1.294 -0.958 3.129 1.00 96.99 7 A 1 ATOM 55 C CG . LEU A 1 7 ? 0.910 -2.216 3.896 1.00 93.58 7 A 1 ATOM 56 C CD1 . LEU A 1 7 ? 2.059 -3.209 3.908 1.00 90.89 7 A 1 ATOM 57 C CD2 . LEU A 1 7 ? 0.492 -1.868 5.317 1.00 91.34 7 A 1 ATOM 58 N N . ALA A 1 8 ? -0.857 -0.336 1.014 1.00 97.44 8 A 1 ATOM 59 C CA . ALA A 1 8 ? -2.226 -0.426 0.518 1.00 97.63 8 A 1 ATOM 60 C C . ALA A 1 8 ? -2.248 -0.883 -0.935 1.00 97.95 8 A 1 ATOM 61 O O . ALA A 1 8 ? -3.121 -1.657 -1.337 1.00 97.66 8 A 1 ATOM 62 C CB . ALA A 1 8 ? -2.911 0.929 0.653 1.00 97.37 8 A 1 ATOM 63 N N . ALA A 1 9 ? -1.294 -0.410 -1.714 1.00 97.49 9 A 1 ATOM 64 C CA . ALA A 1 9 ? -1.192 -0.779 -3.121 1.00 97.52 9 A 1 ATOM 65 C C . ALA A 1 9 ? -0.912 -2.268 -3.269 1.00 97.95 9 A 1 ATOM 66 O O . ALA A 1 9 ? -1.479 -2.933 -4.135 1.00 97.42 9 A 1 ATOM 67 C CB . ALA A 1 9 ? -0.088 0.033 -3.790 1.00 97.10 9 A 1 ATOM 68 N N . LEU A 1 10 ? -0.048 -2.784 -2.418 1.00 97.71 10 A 1 ATOM 69 C CA . LEU A 1 10 ? 0.300 -4.203 -2.443 1.00 97.75 10 A 1 ATOM 70 C C . LEU A 1 10 ? -0.914 -5.062 -2.113 1.00 98.10 10 A 1 ATOM 71 O O . LEU A 1 10 ? -1.160 -6.087 -2.752 1.00 97.69 10 A 1 ATOM 72 C CB . LEU A 1 10 ? 1.418 -4.483 -1.438 1.00 97.36 10 A 1 ATOM 73 C CG . LEU A 1 10 ? 2.127 -5.815 -1.665 1.00 94.08 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? 3.102 -5.712 -2.826 1.00 91.20 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? 2.848 -6.265 -0.405 1.00 91.66 10 A 1 ATOM 76 N N . ILE A 1 11 ? -1.665 -4.643 -1.118 1.00 97.31 11 A 1 ATOM 77 C CA . ILE A 1 11 ? -2.867 -5.358 -0.699 1.00 97.19 11 A 1 ATOM 78 C C . ILE A 1 11 ? -3.906 -5.351 -1.808 1.00 97.56 11 A 1 ATOM 79 O O . ILE A 1 11 ? -4.566 -6.359 -2.066 1.00 97.29 11 A 1 ATOM 80 C CB . ILE A 1 11 ? -3.458 -4.729 0.571 1.00 96.83 11 A 1 ATOM 81 C CG1 . ILE A 1 11 ? -2.422 -4.717 1.702 1.00 94.60 11 A 1 ATOM 82 C CG2 . ILE A 1 11 ? -4.711 -5.489 1.003 1.00 94.12 11 A 1 ATOM 83 C CD1 . ILE A 1 11 ? -1.967 -6.101 2.100 1.00 89.27 11 A 1 ATOM 84 N N . ALA A 1 12 ? -4.058 -4.207 -2.454 1.00 98.11 12 A 1 ATOM 85 C CA . ALA A 1 12 ? -5.021 -4.057 -3.539 1.00 98.02 12 A 1 ATOM 86 C C . ALA A 1 12 ? -4.679 -4.981 -4.704 1.00 98.19 12 A 1 ATOM 87 O O . ALA A 1 12 ? -5.564 -5.587 -5.307 1.00 97.58 12 A 1 ATOM 88 C CB . ALA A 1 12 ? -5.055 -2.609 -4.006 1.00 97.46 12 A 1 ATOM 89 N N . VAL A 1 13 ? -3.396 -5.095 -5.015 1.00 97.96 13 A 1 ATOM 90 C CA . VAL A 1 13 ? -2.932 -5.961 -6.097 1.00 97.82 13 A 1 ATOM 91 C C . VAL A 1 13 ? -3.217 -7.420 -5.774 1.00 97.98 13 A 1 ATOM 92 O O . VAL A 1 13 ? -3.652 -8.190 -6.636 1.00 97.09 13 A 1 ATOM 93 C CB . VAL A 1 13 ? -1.427 -5.769 -6.348 1.00 97.02 13 A 1 ATOM 94 C CG1 . VAL A 1 13 ? -0.915 -6.793 -7.350 1.00 94.31 13 A 1 ATOM 95 C CG2 . VAL A 1 13 ? -1.151 -4.365 -6.846 1.00 94.67 13 A 1 ATOM 96 N N . ALA A 1 14 ? -2.967 -7.798 -4.539 1.00 97.28 14 A 1 ATOM 97 C CA . ALA A 1 14 ? -3.196 -9.169 -4.096 1.00 97.12 14 A 1 ATOM 98 C C . ALA A 1 14 ? -4.682 -9.491 -4.012 1.00 97.41 14 A 1 ATOM 99 O O . ALA A 1 14 ? -5.085 -10.644 -4.176 1.00 96.31 14 A 1 ATOM 100 C CB . ALA A 1 14 ? -2.537 -9.389 -2.736 1.00 96.29 14 A 1 ATOM 101 N N . CYS A 1 15 ? -5.484 -8.485 -3.765 1.00 95.57 15 A 1 ATOM 102 C CA . CYS A 1 15 ? -6.932 -8.646 -3.639 1.00 95.97 15 A 1 ATOM 103 C C . CYS A 1 15 ? -7.557 -9.111 -4.953 1.00 96.35 15 A 1 ATOM 104 O O . CYS A 1 15 ? -8.133 -10.196 -5.033 1.00 94.78 15 A 1 ATOM 105 C CB . CYS A 1 15 ? -7.572 -7.334 -3.179 1.00 94.31 15 A 1 ATOM 106 S SG . CYS A 1 15 ? -9.323 -7.517 -2.806 1.00 88.54 15 A 1 ATOM 107 N N . ALA A 1 16 ? -7.437 -8.253 -5.975 1.00 92.62 16 A 1 ATOM 108 C CA . ALA A 1 16 ? -8.012 -8.571 -7.279 1.00 90.75 16 A 1 ATOM 109 C C . ALA A 1 16 ? -7.501 -7.610 -8.335 1.00 89.62 16 A 1 ATOM 110 O O . ALA A 1 16 ? -7.061 -8.082 -9.401 1.00 83.83 16 A 1 ATOM 111 C CB . ALA A 1 16 ? -9.535 -8.512 -7.210 1.00 86.40 16 A 1 ATOM 112 O OXT . ALA A 1 16 ? -7.548 -6.404 -8.109 1.00 79.28 16 A 1 #