# 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_spkb38350 # _entry.id spkb38350 # 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 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" "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 SER 3 1 n PHE 4 1 n VAL 5 1 n VAL 6 1 n VAL 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n VAL 11 1 n ALA 12 1 n VAL 13 1 n ALA 14 1 n ALA 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 @ 2025-07-05 20:22:10)" _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 96.33 _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 89.58 1 1 A LYS 2 2 92.15 1 2 A SER 3 2 96.79 1 3 A PHE 4 2 95.70 1 4 A VAL 5 2 98.02 1 5 A VAL 6 2 98.18 1 6 A VAL 7 2 98.02 1 7 A ALA 8 2 98.43 1 8 A LEU 9 2 97.29 1 9 A LEU 10 2 96.61 1 10 A VAL 11 2 97.93 1 11 A ALA 12 2 98.45 1 12 A VAL 13 2 97.80 1 13 A ALA 14 2 98.28 1 14 A ALA 15 2 98.08 1 15 A ALA 16 2 94.28 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 SER . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n VAL . 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 ALA . 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 ? -4.888 -10.618 6.054 1.00 93.72 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.421 -9.279 5.732 1.00 94.93 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.716 -8.723 4.496 1.00 95.43 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.777 -7.943 4.605 1.00 92.96 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.217 -8.336 6.914 1.00 91.97 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.032 -8.753 8.123 1.00 89.06 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.673 -7.732 9.559 1.00 84.57 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.834 -8.403 10.732 1.00 73.99 1 A 1 ATOM 9 N N . LYS A 1 2 ? -5.164 -9.149 3.335 1.00 96.37 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -4.549 -8.715 2.080 1.00 96.77 2 A 1 ATOM 11 C C . LYS A 1 2 ? -4.883 -7.254 1.789 1.00 96.96 2 A 1 ATOM 12 O O . LYS A 1 2 ? -4.121 -6.563 1.114 1.00 96.48 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -5.023 -9.628 0.948 1.00 95.73 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -4.031 -9.701 -0.191 1.00 92.24 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -3.908 -11.119 -0.718 1.00 89.45 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.743 -11.238 -1.676 1.00 85.23 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -2.488 -12.658 -2.029 1.00 80.11 2 A 1 ATOM 18 N N . SER A 1 3 ? -6.005 -6.792 2.311 1.00 97.42 3 A 1 ATOM 19 C CA . SER A 1 3 ? -6.448 -5.413 2.112 1.00 97.84 3 A 1 ATOM 20 C C . SER A 1 3 ? -5.444 -4.417 2.686 1.00 98.22 3 A 1 ATOM 21 O O . SER A 1 3 ? -5.286 -3.321 2.161 1.00 97.75 3 A 1 ATOM 22 C CB . SER A 1 3 ? -7.813 -5.209 2.759 1.00 96.91 3 A 1 ATOM 23 O OG . SER A 1 3 ? -8.722 -6.190 2.306 1.00 92.58 3 A 1 ATOM 24 N N . PHE A 1 4 ? -4.763 -4.819 3.760 1.00 97.49 4 A 1 ATOM 25 C CA . PHE A 1 4 ? -3.760 -3.959 4.382 1.00 97.95 4 A 1 ATOM 26 C C . PHE A 1 4 ? -2.616 -3.673 3.419 1.00 98.30 4 A 1 ATOM 27 O O . PHE A 1 4 ? -2.110 -2.552 3.351 1.00 97.86 4 A 1 ATOM 28 C CB . PHE A 1 4 ? -3.219 -4.616 5.657 1.00 97.56 4 A 1 ATOM 29 C CG . PHE A 1 4 ? -3.766 -3.979 6.913 1.00 96.11 4 A 1 ATOM 30 C CD1 . PHE A 1 4 ? -3.366 -2.700 7.277 1.00 93.59 4 A 1 ATOM 31 C CD2 . PHE A 1 4 ? -4.670 -4.662 7.719 1.00 93.87 4 A 1 ATOM 32 C CE1 . PHE A 1 4 ? -3.864 -2.099 8.429 1.00 93.32 4 A 1 ATOM 33 C CE2 . PHE A 1 4 ? -5.172 -4.068 8.877 1.00 93.42 4 A 1 ATOM 34 C CZ . PHE A 1 4 ? -4.767 -2.786 9.232 1.00 93.27 4 A 1 ATOM 35 N N . VAL A 1 5 ? -2.219 -4.691 2.661 1.00 98.39 5 A 1 ATOM 36 C CA . VAL A 1 5 ? -1.143 -4.542 1.682 1.00 98.49 5 A 1 ATOM 37 C C . VAL A 1 5 ? -1.566 -3.565 0.589 1.00 98.61 5 A 1 ATOM 38 O O . VAL A 1 5 ? -0.779 -2.720 0.158 1.00 98.43 5 A 1 ATOM 39 C CB . VAL A 1 5 ? -0.766 -5.901 1.071 1.00 98.23 5 A 1 ATOM 40 C CG1 . VAL A 1 5 ? 0.368 -5.749 0.068 1.00 97.26 5 A 1 ATOM 41 C CG2 . VAL A 1 5 ? -0.360 -6.882 2.165 1.00 96.73 5 A 1 ATOM 42 N N . VAL A 1 6 ? -2.806 -3.672 0.167 1.00 98.51 6 A 1 ATOM 43 C CA . VAL A 1 6 ? -3.348 -2.784 -0.862 1.00 98.56 6 A 1 ATOM 44 C C . VAL A 1 6 ? -3.386 -1.345 -0.361 1.00 98.64 6 A 1 ATOM 45 O O . VAL A 1 6 ? -3.019 -0.418 -1.085 1.00 98.50 6 A 1 ATOM 46 C CB . VAL A 1 6 ? -4.756 -3.237 -1.282 1.00 98.34 6 A 1 ATOM 47 C CG1 . VAL A 1 6 ? -5.324 -2.310 -2.349 1.00 97.43 6 A 1 ATOM 48 C CG2 . VAL A 1 6 ? -4.721 -4.669 -1.802 1.00 97.25 6 A 1 ATOM 49 N N . VAL A 1 7 ? -3.819 -1.174 0.874 1.00 98.50 7 A 1 ATOM 50 C CA . VAL A 1 7 ? -3.882 0.159 1.480 1.00 98.51 7 A 1 ATOM 51 C C . VAL A 1 7 ? -2.484 0.751 1.599 1.00 98.61 7 A 1 ATOM 52 O O . VAL A 1 7 ? -2.272 1.928 1.302 1.00 98.48 7 A 1 ATOM 53 C CB . VAL A 1 7 ? -4.560 0.098 2.860 1.00 98.23 7 A 1 ATOM 54 C CG1 . VAL A 1 7 ? -4.505 1.452 3.554 1.00 96.96 7 A 1 ATOM 55 C CG2 . VAL A 1 7 ? -6.011 -0.341 2.717 1.00 96.85 7 A 1 ATOM 56 N N . ALA A 1 8 ? -1.538 -0.076 2.031 1.00 98.43 8 A 1 ATOM 57 C CA . ALA A 1 8 ? -0.154 0.366 2.170 1.00 98.46 8 A 1 ATOM 58 C C . ALA A 1 8 ? 0.409 0.805 0.818 1.00 98.60 8 A 1 ATOM 59 O O . ALA A 1 8 ? 1.113 1.812 0.728 1.00 98.41 8 A 1 ATOM 60 C CB . ALA A 1 8 ? 0.684 -0.762 2.758 1.00 98.24 8 A 1 ATOM 61 N N . LEU A 1 9 ? 0.082 0.060 -0.218 1.00 98.44 9 A 1 ATOM 62 C CA . LEU A 1 9 ? 0.517 0.389 -1.571 1.00 98.42 9 A 1 ATOM 63 C C . LEU A 1 9 ? -0.092 1.713 -2.021 1.00 98.59 9 A 1 ATOM 64 O O . LEU A 1 9 ? 0.594 2.556 -2.603 1.00 98.42 9 A 1 ATOM 65 C CB . LEU A 1 9 ? 0.108 -0.735 -2.529 1.00 98.22 9 A 1 ATOM 66 C CG . LEU A 1 9 ? 0.737 -0.602 -3.917 1.00 96.32 9 A 1 ATOM 67 C CD1 . LEU A 1 9 ? 2.062 -1.352 -3.983 1.00 94.85 9 A 1 ATOM 68 C CD2 . LEU A 1 9 ? -0.205 -1.123 -4.992 1.00 95.07 9 A 1 ATOM 69 N N . LEU A 1 10 ? -1.362 1.889 -1.732 1.00 98.40 10 A 1 ATOM 70 C CA . LEU A 1 10 ? -2.067 3.117 -2.094 1.00 98.39 10 A 1 ATOM 71 C C . LEU A 1 10 ? -1.430 4.329 -1.423 1.00 98.57 10 A 1 ATOM 72 O O . LEU A 1 10 ? -1.243 5.373 -2.053 1.00 98.40 10 A 1 ATOM 73 C CB . LEU A 1 10 ? -3.537 3.002 -1.680 1.00 98.08 10 A 1 ATOM 74 C CG . LEU A 1 10 ? -4.468 3.837 -2.560 1.00 94.64 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? -4.867 3.065 -3.806 1.00 93.03 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? -5.708 4.253 -1.785 1.00 93.39 10 A 1 ATOM 77 N N . VAL A 1 11 ? -1.105 4.172 -0.150 1.00 98.52 11 A 1 ATOM 78 C CA . VAL A 1 11 ? -0.466 5.246 0.614 1.00 98.48 11 A 1 ATOM 79 C C . VAL A 1 11 ? 0.909 5.559 0.036 1.00 98.60 11 A 1 ATOM 80 O O . VAL A 1 11 ? 1.287 6.726 -0.092 1.00 98.39 11 A 1 ATOM 81 C CB . VAL A 1 11 ? -0.354 4.864 2.100 1.00 98.12 11 A 1 ATOM 82 C CG1 . VAL A 1 11 ? 0.421 5.920 2.879 1.00 96.64 11 A 1 ATOM 83 C CG2 . VAL A 1 11 ? -1.740 4.700 2.715 1.00 96.79 11 A 1 ATOM 84 N N . ALA A 1 12 ? 1.647 4.516 -0.310 1.00 98.55 12 A 1 ATOM 85 C CA . ALA A 1 12 ? 2.977 4.688 -0.888 1.00 98.53 12 A 1 ATOM 86 C C . ALA A 1 12 ? 2.901 5.425 -2.226 1.00 98.61 12 A 1 ATOM 87 O O . ALA A 1 12 ? 3.714 6.306 -2.501 1.00 98.27 12 A 1 ATOM 88 C CB . ALA A 1 12 ? 3.639 3.325 -1.057 1.00 98.27 12 A 1 ATOM 89 N N . VAL A 1 13 ? 1.918 5.080 -3.038 1.00 98.58 13 A 1 ATOM 90 C CA . VAL A 1 13 ? 1.720 5.731 -4.335 1.00 98.50 13 A 1 ATOM 91 C C . VAL A 1 13 ? 1.314 7.188 -4.151 1.00 98.63 13 A 1 ATOM 92 O O . VAL A 1 13 ? 1.773 8.066 -4.886 1.00 98.31 13 A 1 ATOM 93 C CB . VAL A 1 13 ? 0.660 4.982 -5.163 1.00 98.00 13 A 1 ATOM 94 C CG1 . VAL A 1 13 ? 0.345 5.734 -6.453 1.00 96.11 13 A 1 ATOM 95 C CG2 . VAL A 1 13 ? 1.143 3.582 -5.502 1.00 96.46 13 A 1 ATOM 96 N N . ALA A 1 14 ? 0.462 7.435 -3.172 1.00 98.50 14 A 1 ATOM 97 C CA . ALA A 1 14 ? 0.011 8.794 -2.879 1.00 98.40 14 A 1 ATOM 98 C C . ALA A 1 14 ? 1.163 9.661 -2.375 1.00 98.51 14 A 1 ATOM 99 O O . ALA A 1 14 ? 1.207 10.862 -2.645 1.00 98.04 14 A 1 ATOM 100 C CB . ALA A 1 14 ? -1.114 8.747 -1.848 1.00 97.95 14 A 1 ATOM 101 N N . ALA A 1 15 ? 2.078 9.050 -1.629 1.00 98.45 15 A 1 ATOM 102 C CA . ALA A 1 15 ? 3.239 9.759 -1.096 1.00 98.30 15 A 1 ATOM 103 C C . ALA A 1 15 ? 4.270 10.045 -2.185 1.00 98.31 15 A 1 ATOM 104 O O . ALA A 1 15 ? 5.003 11.035 -2.112 1.00 97.60 15 A 1 ATOM 105 C CB . ALA A 1 15 ? 3.869 8.945 0.030 1.00 97.76 15 A 1 ATOM 106 N N . ALA A 1 16 ? 4.333 9.166 -3.187 1.00 97.73 16 A 1 ATOM 107 C CA . ALA A 1 16 ? 5.278 9.303 -4.283 1.00 96.89 16 A 1 ATOM 108 C C . ALA A 1 16 ? 4.795 10.316 -5.322 1.00 96.00 16 A 1 ATOM 109 O O . ALA A 1 16 ? 3.576 10.417 -5.547 1.00 92.63 16 A 1 ATOM 110 C CB . ALA A 1 16 ? 5.529 7.945 -4.931 1.00 95.04 16 A 1 ATOM 111 O OXT . ALA A 1 16 ? 5.634 11.005 -5.923 1.00 87.41 16 A 1 #