# 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_spkb09215 # _entry.id spkb09215 # 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" "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" "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 TRP 2 1 n VAL 3 1 n LEU 4 1 n ALA 5 1 n LEU 6 1 n GLY 7 1 n GLY 8 1 n ALA 9 1 n PHE 10 1 n LEU 11 1 n ALA 12 1 n VAL 13 1 n ALA 14 1 n LYS 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 @ 2025-07-04 13:51:22)" _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 90.70 _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 85.38 1 1 A TRP 2 2 87.10 1 2 A VAL 3 2 90.79 1 3 A LEU 4 2 89.19 1 4 A ALA 5 2 95.72 1 5 A LEU 6 2 91.06 1 6 A GLY 7 2 95.61 1 7 A GLY 8 2 95.50 1 8 A ALA 9 2 95.50 1 9 A PHE 10 2 90.97 1 10 A LEU 11 2 91.73 1 11 A ALA 12 2 94.50 1 12 A VAL 13 2 92.77 1 13 A ALA 14 2 95.25 1 14 A LYS 15 2 87.19 1 15 A ALA 16 2 87.01 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 TRP . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n GLY . 7 A 7 A 8 1 n GLY . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n LEU . 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 LYS . 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 ? -3.434 3.971 12.899 1.00 90.58 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.286 3.391 11.567 1.00 90.73 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.476 4.453 10.485 1.00 90.95 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.533 4.558 9.876 1.00 88.16 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.309 2.287 11.351 1.00 86.69 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.080 1.088 12.255 1.00 83.33 1 A 1 ATOM 7 S SD . MET A 1 1 ? -2.591 0.205 11.806 1.00 80.21 1 A 1 ATOM 8 C CE . MET A 1 1 ? -2.582 -1.057 13.068 1.00 72.36 1 A 1 ATOM 9 N N . TRP A 1 2 ? -2.466 5.242 10.277 1.00 89.74 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -2.498 6.309 9.279 1.00 91.11 2 A 1 ATOM 11 C C . TRP A 1 2 ? -1.473 6.050 8.180 1.00 93.10 2 A 1 ATOM 12 O O . TRP A 1 2 ? -1.825 5.950 7.012 1.00 92.22 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -2.219 7.659 9.942 1.00 89.37 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -1.722 7.550 11.352 1.00 87.33 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -2.169 8.253 12.422 1.00 85.94 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? -0.684 6.695 11.854 1.00 87.48 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? -1.469 7.906 13.539 1.00 84.66 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? -0.554 6.937 13.224 1.00 86.69 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? 0.146 5.745 11.264 1.00 85.09 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? 0.377 6.261 14.014 1.00 85.10 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? 1.068 5.073 12.047 1.00 80.79 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? 1.180 5.338 13.408 1.00 80.79 2 A 1 ATOM 23 N N . VAL A 1 3 ? -0.214 5.933 8.549 1.00 91.70 3 A 1 ATOM 24 C CA . VAL A 1 3 ? 0.854 5.682 7.593 1.00 92.96 3 A 1 ATOM 25 C C . VAL A 1 3 ? 0.664 4.340 6.903 1.00 94.55 3 A 1 ATOM 26 O O . VAL A 1 3 ? 1.046 4.161 5.746 1.00 93.59 3 A 1 ATOM 27 C CB . VAL A 1 3 ? 2.228 5.713 8.280 1.00 90.45 3 A 1 ATOM 28 C CG1 . VAL A 1 3 ? 3.327 5.536 7.255 1.00 85.86 3 A 1 ATOM 29 C CG2 . VAL A 1 3 ? 2.408 7.009 9.040 1.00 86.44 3 A 1 ATOM 30 N N . LEU A 1 4 ? 0.065 3.388 7.619 1.00 90.95 4 A 1 ATOM 31 C CA . LEU A 1 4 ? -0.180 2.064 7.065 1.00 92.00 4 A 1 ATOM 32 C C . LEU A 1 4 ? -1.229 2.130 5.968 1.00 93.85 4 A 1 ATOM 33 O O . LEU A 1 4 ? -1.176 1.374 4.999 1.00 92.85 4 A 1 ATOM 34 C CB . LEU A 1 4 ? -0.630 1.097 8.164 1.00 90.23 4 A 1 ATOM 35 C CG . LEU A 1 4 ? 0.522 0.406 8.889 1.00 87.56 4 A 1 ATOM 36 C CD1 . LEU A 1 4 ? 1.308 -0.438 7.907 1.00 84.15 4 A 1 ATOM 37 C CD2 . LEU A 1 4 ? 1.410 1.428 9.554 1.00 81.93 4 A 1 ATOM 38 N N . ALA A 1 5 ? -2.193 3.038 6.132 1.00 95.54 5 A 1 ATOM 39 C CA . ALA A 1 5 ? -3.260 3.206 5.156 1.00 95.93 5 A 1 ATOM 40 C C . ALA A 1 5 ? -2.739 3.835 3.870 1.00 96.58 5 A 1 ATOM 41 O O . ALA A 1 5 ? -2.842 3.250 2.794 1.00 95.65 5 A 1 ATOM 42 C CB . ALA A 1 5 ? -4.373 4.059 5.744 1.00 94.92 5 A 1 ATOM 43 N N . LEU A 1 6 ? -2.182 5.040 3.972 1.00 93.86 6 A 1 ATOM 44 C CA . LEU A 1 6 ? -1.640 5.743 2.815 1.00 94.10 6 A 1 ATOM 45 C C . LEU A 1 6 ? -0.348 5.100 2.333 1.00 95.10 6 A 1 ATOM 46 O O . LEU A 1 6 ? -0.146 4.911 1.134 1.00 94.08 6 A 1 ATOM 47 C CB . LEU A 1 6 ? -1.389 7.212 3.158 1.00 92.91 6 A 1 ATOM 48 C CG . LEU A 1 6 ? -1.042 7.452 4.623 1.00 88.52 6 A 1 ATOM 49 C CD1 . LEU A 1 6 ? 0.093 8.459 4.728 1.00 85.94 6 A 1 ATOM 50 C CD2 . LEU A 1 6 ? -2.271 7.966 5.348 1.00 83.93 6 A 1 ATOM 51 N N . GLY A 1 7 ? 0.518 4.756 3.282 1.00 95.18 7 A 1 ATOM 52 C CA . GLY A 1 7 ? 1.778 4.125 2.932 1.00 95.21 7 A 1 ATOM 53 C C . GLY A 1 7 ? 1.586 2.752 2.332 1.00 96.17 7 A 1 ATOM 54 O O . GLY A 1 7 ? 2.233 2.393 1.350 1.00 95.87 7 A 1 ATOM 55 N N . GLY A 1 8 ? 0.678 1.973 2.928 1.00 95.18 8 A 1 ATOM 56 C CA . GLY A 1 8 ? 0.391 0.638 2.422 1.00 95.12 8 A 1 ATOM 57 C C . GLY A 1 8 ? -0.222 0.670 1.043 1.00 96.04 8 A 1 ATOM 58 O O . GLY A 1 8 ? 0.178 -0.085 0.159 1.00 95.66 8 A 1 ATOM 59 N N . ALA A 1 9 ? -1.207 1.544 0.857 1.00 95.54 9 A 1 ATOM 60 C CA . ALA A 1 9 ? -1.871 1.678 -0.434 1.00 95.68 9 A 1 ATOM 61 C C . ALA A 1 9 ? -0.875 2.097 -1.508 1.00 96.50 9 A 1 ATOM 62 O O . ALA A 1 9 ? -0.875 1.561 -2.614 1.00 95.11 9 A 1 ATOM 63 C CB . ALA A 1 9 ? -2.995 2.698 -0.341 1.00 94.66 9 A 1 ATOM 64 N N . PHE A 1 10 ? -0.025 3.059 -1.177 1.00 93.89 10 A 1 ATOM 65 C CA . PHE A 1 10 ? 0.990 3.538 -2.106 1.00 93.61 10 A 1 ATOM 66 C C . PHE A 1 10 ? 1.961 2.423 -2.471 1.00 95.08 10 A 1 ATOM 67 O O . PHE A 1 10 ? 2.374 2.294 -3.624 1.00 94.34 10 A 1 ATOM 68 C CB . PHE A 1 10 ? 1.759 4.695 -1.481 1.00 92.96 10 A 1 ATOM 69 C CG . PHE A 1 10 ? 2.994 5.049 -2.257 1.00 90.92 10 A 1 ATOM 70 C CD1 . PHE A 1 10 ? 2.891 5.699 -3.471 1.00 88.69 10 A 1 ATOM 71 C CD2 . PHE A 1 10 ? 4.248 4.714 -1.778 1.00 88.66 10 A 1 ATOM 72 C CE1 . PHE A 1 10 ? 4.026 6.017 -4.198 1.00 87.63 10 A 1 ATOM 73 C CE2 . PHE A 1 10 ? 5.386 5.027 -2.503 1.00 87.49 10 A 1 ATOM 74 C CZ . PHE A 1 10 ? 5.275 5.680 -3.715 1.00 87.42 10 A 1 ATOM 75 N N . LEU A 1 11 ? 2.325 1.620 -1.480 1.00 94.67 11 A 1 ATOM 76 C CA . LEU A 1 11 ? 3.246 0.510 -1.695 1.00 94.42 11 A 1 ATOM 77 C C . LEU A 1 11 ? 2.639 -0.514 -2.638 1.00 95.56 11 A 1 ATOM 78 O O . LEU A 1 11 ? 3.323 -1.084 -3.484 1.00 95.60 11 A 1 ATOM 79 C CB . LEU A 1 11 ? 3.593 -0.161 -0.365 1.00 94.07 11 A 1 ATOM 80 C CG . LEU A 1 11 ? 5.091 -0.299 -0.119 1.00 87.74 11 A 1 ATOM 81 C CD1 . LEU A 1 11 ? 5.777 -0.943 -1.303 1.00 85.89 11 A 1 ATOM 82 C CD2 . LEU A 1 11 ? 5.672 1.061 0.189 1.00 85.90 11 A 1 ATOM 83 N N . ALA A 1 12 ? 1.338 -0.762 -2.473 1.00 94.52 12 A 1 ATOM 84 C CA . ALA A 1 12 ? 0.630 -1.711 -3.323 1.00 94.15 12 A 1 ATOM 85 C C . ALA A 1 12 ? 0.704 -1.283 -4.783 1.00 95.56 12 A 1 ATOM 86 O O . ALA A 1 12 ? 0.906 -2.107 -5.673 1.00 94.93 12 A 1 ATOM 87 C CB . ALA A 1 12 ? -0.824 -1.825 -2.887 1.00 93.33 12 A 1 ATOM 88 N N . VAL A 1 13 ? 0.536 0.009 -5.032 1.00 94.42 13 A 1 ATOM 89 C CA . VAL A 1 13 ? 0.593 0.545 -6.387 1.00 94.13 13 A 1 ATOM 90 C C . VAL A 1 13 ? 2.015 0.475 -6.930 1.00 94.95 13 A 1 ATOM 91 O O . VAL A 1 13 ? 2.232 0.232 -8.117 1.00 94.29 13 A 1 ATOM 92 C CB . VAL A 1 13 ? 0.111 2.002 -6.425 1.00 93.16 13 A 1 ATOM 93 C CG1 . VAL A 1 13 ? 0.136 2.527 -7.851 1.00 89.04 13 A 1 ATOM 94 C CG2 . VAL A 1 13 ? -1.281 2.109 -5.838 1.00 89.42 13 A 1 ATOM 95 N N . ALA A 1 14 ? 2.980 0.682 -6.052 1.00 95.23 14 A 1 ATOM 96 C CA . ALA A 1 14 ? 4.383 0.639 -6.444 1.00 95.36 14 A 1 ATOM 97 C C . ALA A 1 14 ? 4.788 -0.762 -6.890 1.00 96.02 14 A 1 ATOM 98 O O . ALA A 1 14 ? 5.609 -0.924 -7.791 1.00 95.18 14 A 1 ATOM 99 C CB . ALA A 1 14 ? 5.264 1.088 -5.289 1.00 94.48 14 A 1 ATOM 100 N N . LYS A 1 15 ? 4.204 -1.776 -6.255 1.00 95.05 15 A 1 ATOM 101 C CA . LYS A 1 15 ? 4.504 -3.163 -6.605 1.00 93.75 15 A 1 ATOM 102 C C . LYS A 1 15 ? 3.935 -3.525 -7.968 1.00 92.87 15 A 1 ATOM 103 O O . LYS A 1 15 ? 4.594 -4.173 -8.777 1.00 91.48 15 A 1 ATOM 104 C CB . LYS A 1 15 ? 3.928 -4.106 -5.551 1.00 92.41 15 A 1 ATOM 105 C CG . LYS A 1 15 ? 4.619 -3.977 -4.209 1.00 86.02 15 A 1 ATOM 106 C CD . LYS A 1 15 ? 3.997 -4.923 -3.203 1.00 83.53 15 A 1 ATOM 107 C CE . LYS A 1 15 ? 4.666 -4.806 -1.847 1.00 78.34 15 A 1 ATOM 108 N NZ . LYS A 1 15 ? 4.011 -5.689 -0.856 1.00 71.26 15 A 1 ATOM 109 N N . ALA A 1 16 ? 2.702 -3.132 -8.199 1.00 91.69 16 A 1 ATOM 110 C CA . ALA A 1 16 ? 2.032 -3.419 -9.457 1.00 90.49 16 A 1 ATOM 111 C C . ALA A 1 16 ? 1.891 -2.151 -10.305 1.00 89.22 16 A 1 ATOM 112 O O . ALA A 1 16 ? 2.441 -1.102 -9.916 1.00 85.45 16 A 1 ATOM 113 C CB . ALA A 1 16 ? 0.670 -4.047 -9.182 1.00 86.10 16 A 1 ATOM 114 O OXT . ALA A 1 16 ? 1.218 -2.184 -11.346 1.00 79.10 16 A 1 #