# 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_spkb32463 # _entry.id spkb32463 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "PEPTIDE LINKING" "C6 H13 N O2" 131.173 LEU y LEUCINE CC(C)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 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)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 LEU 2 1 n TRP 3 1 n PHE 4 1 n VAL 5 1 n VAL 6 1 n GLY 7 1 n ALA 8 1 n LEU 9 1 n PHE 10 1 n PRO 11 1 n ALA 12 1 n LEU 13 1 n LEU 14 1 n LEU 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 @ 2025-07-11 11:58:49)" _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 92.38 _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 84.91 1 1 A LEU 2 2 90.16 1 2 A TRP 3 2 91.67 1 3 A PHE 4 2 90.76 1 4 A VAL 5 2 94.96 1 5 A VAL 6 2 94.49 1 6 A GLY 7 2 96.15 1 7 A ALA 8 2 95.95 1 8 A LEU 9 2 94.46 1 9 A PHE 10 2 91.74 1 10 A PRO 11 2 95.58 1 11 A ALA 12 2 95.74 1 12 A LEU 13 2 93.98 1 13 A LEU 14 2 92.91 1 14 A LEU 15 2 92.25 1 15 A ALA 16 2 88.11 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 LEU . 2 A 2 A 3 1 n TRP . 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 GLY . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n PRO . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n LEU . 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 ? -5.652 8.455 5.869 1.00 89.61 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.476 8.293 6.741 1.00 90.19 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.311 7.675 5.957 1.00 91.52 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.490 7.200 4.841 1.00 89.37 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.841 7.398 7.922 1.00 86.20 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.882 8.050 8.822 1.00 81.31 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.418 6.950 10.133 1.00 79.14 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.541 8.037 11.003 1.00 71.90 1 A 1 ATOM 9 N N . LEU A 1 2 ? -2.122 7.682 6.551 1.00 91.03 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -0.922 7.149 5.895 1.00 93.05 2 A 1 ATOM 11 C C . LEU A 1 2 ? -1.040 5.650 5.626 1.00 94.92 2 A 1 ATOM 12 O O . LEU A 1 2 ? -0.576 5.164 4.594 1.00 93.68 2 A 1 ATOM 13 C CB . LEU A 1 2 ? 0.304 7.417 6.771 1.00 91.80 2 A 1 ATOM 14 C CG . LEU A 1 2 ? 0.664 8.897 6.893 1.00 87.87 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? 1.737 9.089 7.949 1.00 85.49 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 1.157 9.438 5.553 1.00 83.46 2 A 1 ATOM 17 N N . TRP A 1 3 ? -1.648 4.922 6.556 1.00 94.12 3 A 1 ATOM 18 C CA . TRP A 1 3 ? -1.814 3.473 6.388 1.00 94.77 3 A 1 ATOM 19 C C . TRP A 1 3 ? -2.669 3.151 5.171 1.00 95.45 3 A 1 ATOM 20 O O . TRP A 1 3 ? -2.513 2.103 4.551 1.00 94.76 3 A 1 ATOM 21 C CB . TRP A 1 3 ? -2.446 2.869 7.647 1.00 93.95 3 A 1 ATOM 22 C CG . TRP A 1 3 ? -1.555 3.003 8.843 1.00 92.22 3 A 1 ATOM 23 C CD1 . TRP A 1 3 ? -1.915 3.448 10.075 1.00 90.82 3 A 1 ATOM 24 C CD2 . TRP A 1 3 ? -0.154 2.668 8.930 1.00 92.18 3 A 1 ATOM 25 N NE1 . TRP A 1 3 ? -0.832 3.416 10.922 1.00 89.51 3 A 1 ATOM 26 C CE2 . TRP A 1 3 ? 0.266 2.946 10.243 1.00 90.81 3 A 1 ATOM 27 C CE3 . TRP A 1 3 ? 0.776 2.163 8.019 1.00 90.48 3 A 1 ATOM 28 C CZ2 . TRP A 1 3 ? 1.584 2.734 10.660 1.00 89.69 3 A 1 ATOM 29 C CZ3 . TRP A 1 3 ? 2.087 1.955 8.437 1.00 87.28 3 A 1 ATOM 30 C CH2 . TRP A 1 3 ? 2.480 2.239 9.743 1.00 87.30 3 A 1 ATOM 31 N N . PHE A 1 4 ? -3.554 4.048 4.813 1.00 92.81 4 A 1 ATOM 32 C CA . PHE A 1 4 ? -4.415 3.858 3.650 1.00 93.49 4 A 1 ATOM 33 C C . PHE A 1 4 ? -3.581 3.889 2.375 1.00 95.17 4 A 1 ATOM 34 O O . PHE A 1 4 ? -3.850 3.151 1.426 1.00 94.21 4 A 1 ATOM 35 C CB . PHE A 1 4 ? -5.481 4.951 3.604 1.00 92.69 4 A 1 ATOM 36 C CG . PHE A 1 4 ? -6.697 4.603 4.425 1.00 90.93 4 A 1 ATOM 37 C CD1 . PHE A 1 4 ? -6.610 4.464 5.797 1.00 88.38 4 A 1 ATOM 38 C CD2 . PHE A 1 4 ? -7.926 4.409 3.809 1.00 88.06 4 A 1 ATOM 39 C CE1 . PHE A 1 4 ? -7.725 4.135 6.553 1.00 87.76 4 A 1 ATOM 40 C CE2 . PHE A 1 4 ? -9.048 4.085 4.556 1.00 87.09 4 A 1 ATOM 41 C CZ . PHE A 1 4 ? -8.950 3.946 5.934 1.00 87.73 4 A 1 ATOM 42 N N . VAL A 1 5 ? -2.580 4.730 2.338 1.00 95.37 5 A 1 ATOM 43 C CA . VAL A 1 5 ? -1.695 4.847 1.180 1.00 95.91 5 A 1 ATOM 44 C C . VAL A 1 5 ? -0.809 3.613 1.060 1.00 96.34 5 A 1 ATOM 45 O O . VAL A 1 5 ? -0.576 3.112 -0.042 1.00 96.01 5 A 1 ATOM 46 C CB . VAL A 1 5 ? -0.815 6.104 1.296 1.00 95.42 5 A 1 ATOM 47 C CG1 . VAL A 1 5 ? 0.078 6.245 0.073 1.00 92.70 5 A 1 ATOM 48 C CG2 . VAL A 1 5 ? -1.685 7.341 1.459 1.00 92.97 5 A 1 ATOM 49 N N . VAL A 1 6 ? -0.323 3.132 2.189 1.00 95.65 6 A 1 ATOM 50 C CA . VAL A 1 6 ? 0.538 1.946 2.211 1.00 95.65 6 A 1 ATOM 51 C C . VAL A 1 6 ? -0.222 0.728 1.698 1.00 95.91 6 A 1 ATOM 52 O O . VAL A 1 6 ? 0.326 -0.097 0.966 1.00 95.44 6 A 1 ATOM 53 C CB . VAL A 1 6 ? 1.055 1.679 3.633 1.00 94.87 6 A 1 ATOM 54 C CG1 . VAL A 1 6 ? 1.941 0.443 3.659 1.00 91.66 6 A 1 ATOM 55 C CG2 . VAL A 1 6 ? 1.826 2.888 4.142 1.00 92.28 6 A 1 ATOM 56 N N . GLY A 1 7 ? -1.473 0.616 2.087 1.00 96.22 7 A 1 ATOM 57 C CA . GLY A 1 7 ? -2.305 -0.507 1.658 1.00 95.80 7 A 1 ATOM 58 C C . GLY A 1 7 ? -2.548 -0.497 0.162 1.00 96.55 7 A 1 ATOM 59 O O . GLY A 1 7 ? -2.792 -1.541 -0.445 1.00 96.04 7 A 1 ATOM 60 N N . ALA A 1 8 ? -2.489 0.670 -0.440 1.00 95.90 8 A 1 ATOM 61 C CA . ALA A 1 8 ? -2.696 0.815 -1.877 1.00 96.04 8 A 1 ATOM 62 C C . ALA A 1 8 ? -1.388 0.688 -2.652 1.00 96.72 8 A 1 ATOM 63 O O . ALA A 1 8 ? -1.394 0.344 -3.833 1.00 95.62 8 A 1 ATOM 64 C CB . ALA A 1 8 ? -3.343 2.164 -2.165 1.00 95.48 8 A 1 ATOM 65 N N . LEU A 1 9 ? -0.277 0.971 -1.991 1.00 95.97 9 A 1 ATOM 66 C CA . LEU A 1 9 ? 1.035 0.896 -2.635 1.00 95.88 9 A 1 ATOM 67 C C . LEU A 1 9 ? 1.435 -0.543 -2.933 1.00 96.46 9 A 1 ATOM 68 O O . LEU A 1 9 ? 2.006 -0.824 -3.987 1.00 96.10 9 A 1 ATOM 69 C CB . LEU A 1 9 ? 2.088 1.549 -1.740 1.00 95.78 9 A 1 ATOM 70 C CG . LEU A 1 9 ? 2.115 3.068 -1.841 1.00 93.05 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? 2.908 3.659 -0.690 1.00 91.47 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? 2.721 3.503 -3.171 1.00 90.98 9 A 1 ATOM 73 N N . PHE A 1 10 ? 1.141 -1.439 -2.002 1.00 94.96 10 A 1 ATOM 74 C CA . PHE A 1 10 ? 1.486 -2.850 -2.186 1.00 94.59 10 A 1 ATOM 75 C C . PHE A 1 10 ? 0.821 -3.449 -3.422 1.00 95.88 10 A 1 ATOM 76 O O . PHE A 1 10 ? 1.511 -3.942 -4.319 1.00 95.86 10 A 1 ATOM 77 C CB . PHE A 1 10 ? 1.095 -3.645 -0.939 1.00 93.50 10 A 1 ATOM 78 C CG . PHE A 1 10 ? 2.281 -3.938 -0.060 1.00 91.41 10 A 1 ATOM 79 C CD1 . PHE A 1 10 ? 2.930 -2.918 0.608 1.00 89.18 10 A 1 ATOM 80 C CD2 . PHE A 1 10 ? 2.740 -5.235 0.084 1.00 89.44 10 A 1 ATOM 81 C CE1 . PHE A 1 10 ? 4.026 -3.182 1.410 1.00 88.03 10 A 1 ATOM 82 C CE2 . PHE A 1 10 ? 3.832 -5.508 0.888 1.00 87.95 10 A 1 ATOM 83 C CZ . PHE A 1 10 ? 4.478 -4.480 1.555 1.00 88.36 10 A 1 ATOM 84 N N . PRO A 1 11 ? -0.505 -3.427 -3.498 1.00 96.28 11 A 1 ATOM 85 C CA . PRO A 1 11 ? -1.215 -3.981 -4.658 1.00 96.11 11 A 1 ATOM 86 C C . PRO A 1 11 ? -1.010 -3.146 -5.913 1.00 96.81 11 A 1 ATOM 87 O O . PRO A 1 11 ? -1.028 -3.680 -7.023 1.00 96.07 11 A 1 ATOM 88 C CB . PRO A 1 11 ? -2.682 -3.959 -4.223 1.00 94.86 11 A 1 ATOM 89 C CG . PRO A 1 11 ? -2.750 -2.879 -3.206 1.00 93.32 11 A 1 ATOM 90 C CD . PRO A 1 11 ? -1.418 -2.907 -2.495 1.00 95.62 11 A 1 ATOM 91 N N . ALA A 1 12 ? -0.816 -1.853 -5.752 1.00 95.77 12 A 1 ATOM 92 C CA . ALA A 1 12 ? -0.607 -0.955 -6.885 1.00 95.85 12 A 1 ATOM 93 C C . ALA A 1 12 ? 0.676 -1.302 -7.630 1.00 96.67 12 A 1 ATOM 94 O O . ALA A 1 12 ? 0.735 -1.203 -8.856 1.00 95.29 12 A 1 ATOM 95 C CB . ALA A 1 12 ? -0.551 0.489 -6.404 1.00 95.14 12 A 1 ATOM 96 N N . LEU A 1 13 ? 1.705 -1.710 -6.883 1.00 95.92 13 A 1 ATOM 97 C CA . LEU A 1 13 ? 2.985 -2.072 -7.483 1.00 95.70 13 A 1 ATOM 98 C C . LEU A 1 13 ? 2.865 -3.349 -8.304 1.00 96.26 13 A 1 ATOM 99 O O . LEU A 1 13 ? 3.466 -3.471 -9.371 1.00 95.06 13 A 1 ATOM 100 C CB . LEU A 1 13 ? 4.041 -2.257 -6.391 1.00 95.48 13 A 1 ATOM 101 C CG . LEU A 1 13 ? 5.469 -2.167 -6.908 1.00 93.47 13 A 1 ATOM 102 C CD1 . LEU A 1 13 ? 5.839 -0.710 -7.178 1.00 90.56 13 A 1 ATOM 103 C CD2 . LEU A 1 13 ? 6.439 -2.775 -5.911 1.00 89.42 13 A 1 ATOM 104 N N . LEU A 1 14 ? 2.086 -4.306 -7.803 1.00 95.01 14 A 1 ATOM 105 C CA . LEU A 1 14 ? 1.891 -5.575 -8.498 1.00 94.48 14 A 1 ATOM 106 C C . LEU A 1 14 ? 0.940 -5.416 -9.674 1.00 94.61 14 A 1 ATOM 107 O O . LEU A 1 14 ? 1.134 -6.025 -10.727 1.00 92.98 14 A 1 ATOM 108 C CB . LEU A 1 14 ? 1.339 -6.614 -7.521 1.00 94.13 14 A 1 ATOM 109 C CG . LEU A 1 14 ? 2.376 -7.104 -6.511 1.00 92.85 14 A 1 ATOM 110 C CD1 . LEU A 1 14 ? 1.698 -7.785 -5.341 1.00 90.46 14 A 1 ATOM 111 C CD2 . LEU A 1 14 ? 3.342 -8.074 -7.191 1.00 88.76 14 A 1 ATOM 112 N N . LEU A 1 15 ? -0.086 -4.610 -9.494 1.00 95.22 15 A 1 ATOM 113 C CA . LEU A 1 15 ? -1.074 -4.370 -10.540 1.00 95.12 15 A 1 ATOM 114 C C . LEU A 1 15 ? -0.531 -3.443 -11.616 1.00 95.43 15 A 1 ATOM 115 O O . LEU A 1 15 ? -0.956 -3.512 -12.773 1.00 93.95 15 A 1 ATOM 116 C CB . LEU A 1 15 ? -2.338 -3.774 -9.923 1.00 93.77 15 A 1 ATOM 117 C CG . LEU A 1 15 ? -3.205 -4.791 -9.187 1.00 90.98 15 A 1 ATOM 118 C CD1 . LEU A 1 15 ? -4.180 -4.093 -8.258 1.00 87.80 15 A 1 ATOM 119 C CD2 . LEU A 1 15 ? -3.962 -5.649 -10.195 1.00 85.73 15 A 1 ATOM 120 N N . ALA A 1 16 ? 0.399 -2.595 -11.241 1.00 93.16 16 A 1 ATOM 121 C CA . ALA A 1 16 ? 1.003 -1.639 -12.171 1.00 91.47 16 A 1 ATOM 122 C C . ALA A 1 16 ? 1.667 -2.374 -13.334 1.00 89.92 16 A 1 ATOM 123 O O . ALA A 1 16 ? 1.398 -2.020 -14.493 1.00 86.37 16 A 1 ATOM 124 C CB . ALA A 1 16 ? 2.009 -0.762 -11.434 1.00 87.69 16 A 1 ATOM 125 O OXT . ALA A 1 16 ? 2.441 -3.286 -13.085 1.00 80.06 16 A 1 #