# 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_spkb38491 # _entry.id spkb38491 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N ? "L-PEPTIDE LINKING" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "PEPTIDE LINKING" "C6 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "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 VAL 2 1 n ALA 3 1 n LEU 4 1 n LYS 5 1 n SER 6 1 n PHE 7 1 n ARG 8 1 n HIS 9 1 n SER 10 1 n GLY 11 1 n PRO 12 1 n SER 13 1 n PHE 14 1 n ALA 15 # _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 @ 2025-07-07 03:11:55)" _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 77.33 _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 68.35 1 1 A VAL 2 2 75.72 1 2 A ALA 3 2 82.60 1 3 A LEU 4 2 80.66 1 4 A LYS 5 2 80.15 1 5 A SER 6 2 83.84 1 6 A PHE 7 2 81.22 1 7 A ARG 8 2 75.31 1 8 A HIS 9 2 76.56 1 9 A SER 10 2 80.73 1 10 A GLY 11 2 82.87 1 11 A PRO 12 2 79.34 1 12 A SER 13 2 76.88 1 13 A PHE 14 2 70.54 1 14 A ALA 15 2 72.95 1 15 # _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 VAL . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LYS . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n ARG . 8 A 8 A 9 1 n HIS . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n PHE . 14 A 14 A 15 1 n ALA . 15 A 15 # _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 ? -6.610 -4.782 4.486 1.00 72.32 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.318 -5.255 5.022 1.00 75.60 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.249 -5.239 3.931 1.00 76.46 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.144 -4.753 4.143 1.00 70.60 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.469 -6.675 5.578 1.00 68.47 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.351 -6.704 6.820 1.00 66.19 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.659 -8.364 7.395 1.00 61.89 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.651 -8.004 8.852 1.00 55.26 1 A 1 ATOM 9 N N . VAL A 1 2 ? -4.611 -5.758 2.769 1.00 72.66 2 A 1 ATOM 10 C CA . VAL A 1 2 ? -3.670 -5.773 1.644 1.00 78.86 2 A 1 ATOM 11 C C . VAL A 1 2 ? -3.355 -4.356 1.187 1.00 82.37 2 A 1 ATOM 12 O O . VAL A 1 2 ? -2.258 -4.065 0.714 1.00 79.91 2 A 1 ATOM 13 C CB . VAL A 1 2 ? -4.245 -6.576 0.466 1.00 74.44 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? -4.325 -8.052 0.813 1.00 68.55 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? -5.620 -6.046 0.077 1.00 73.26 2 A 1 ATOM 16 N N . ALA A 1 3 ? -4.329 -3.464 1.333 1.00 78.42 3 A 1 ATOM 17 C CA . ALA A 1 3 ? -4.149 -2.066 0.948 1.00 83.16 3 A 1 ATOM 18 C C . ALA A 1 3 ? -3.027 -1.419 1.750 1.00 85.46 3 A 1 ATOM 19 O O . ALA A 1 3 ? -2.321 -0.543 1.251 1.00 84.43 3 A 1 ATOM 20 C CB . ALA A 1 3 ? -5.449 -1.304 1.154 1.00 81.54 3 A 1 ATOM 21 N N . LEU A 1 4 ? -2.876 -1.860 2.976 1.00 83.81 4 A 1 ATOM 22 C CA . LEU A 1 4 ? -1.831 -1.343 3.857 1.00 83.83 4 A 1 ATOM 23 C C . LEU A 1 4 ? -0.458 -1.558 3.227 1.00 85.10 4 A 1 ATOM 24 O O . LEU A 1 4 ? 0.437 -0.720 3.339 1.00 82.41 4 A 1 ATOM 25 C CB . LEU A 1 4 ? -1.897 -2.040 5.228 1.00 81.96 4 A 1 ATOM 26 C CG . LEU A 1 4 ? -1.215 -1.282 6.372 1.00 77.92 4 A 1 ATOM 27 C CD1 . LEU A 1 4 ? 0.292 -1.235 6.180 1.00 76.26 4 A 1 ATOM 28 C CD2 . LEU A 1 4 ? -1.778 0.130 6.470 1.00 74.00 4 A 1 ATOM 29 N N . LYS A 1 5 ? -0.320 -2.679 2.544 1.00 86.19 5 A 1 ATOM 30 C CA . LYS A 1 5 ? 0.945 -3.015 1.885 1.00 85.68 5 A 1 ATOM 31 C C . LYS A 1 5 ? 1.270 -1.973 0.815 1.00 85.73 5 A 1 ATOM 32 O O . LYS A 1 5 ? 2.404 -1.513 0.704 1.00 84.09 5 A 1 ATOM 33 C CB . LYS A 1 5 ? 0.846 -4.412 1.260 1.00 84.50 5 A 1 ATOM 34 C CG . LYS A 1 5 ? 2.208 -5.059 1.074 1.00 78.92 5 A 1 ATOM 35 C CD . LYS A 1 5 ? 2.069 -6.466 0.512 1.00 78.16 5 A 1 ATOM 36 C CE . LYS A 1 5 ? 3.428 -7.149 0.404 1.00 72.01 5 A 1 ATOM 37 N NZ . LYS A 1 5 ? 3.302 -8.494 -0.222 1.00 66.11 5 A 1 ATOM 38 N N . SER A 1 6 ? 0.268 -1.595 0.049 1.00 85.93 6 A 1 ATOM 39 C CA . SER A 1 6 ? 0.434 -0.590 -0.998 1.00 85.86 6 A 1 ATOM 40 C C . SER A 1 6 ? 0.665 0.789 -0.390 1.00 86.07 6 A 1 ATOM 41 O O . SER A 1 6 ? 1.422 1.596 -0.924 1.00 84.43 6 A 1 ATOM 42 C CB . SER A 1 6 ? -0.799 -0.563 -1.897 1.00 84.71 6 A 1 ATOM 43 O OG . SER A 1 6 ? -0.973 -1.806 -2.539 1.00 76.03 6 A 1 ATOM 44 N N . PHE A 1 7 ? -0.004 1.041 0.721 1.00 85.27 7 A 1 ATOM 45 C CA . PHE A 1 7 ? 0.126 2.313 1.428 1.00 85.16 7 A 1 ATOM 46 C C . PHE A 1 7 ? 1.580 2.586 1.792 1.00 86.68 7 A 1 ATOM 47 O O . PHE A 1 7 ? 2.092 3.684 1.576 1.00 84.01 7 A 1 ATOM 48 C CB . PHE A 1 7 ? -0.723 2.267 2.697 1.00 83.87 7 A 1 ATOM 49 C CG . PHE A 1 7 ? -1.608 3.475 2.837 1.00 80.65 7 A 1 ATOM 50 C CD1 . PHE A 1 7 ? -1.130 4.632 3.430 1.00 79.83 7 A 1 ATOM 51 C CD2 . PHE A 1 7 ? -2.918 3.440 2.383 1.00 78.76 7 A 1 ATOM 52 C CE1 . PHE A 1 7 ? -1.950 5.744 3.564 1.00 76.59 7 A 1 ATOM 53 C CE2 . PHE A 1 7 ? -3.744 4.550 2.518 1.00 76.63 7 A 1 ATOM 54 C CZ . PHE A 1 7 ? -3.261 5.703 3.113 1.00 75.94 7 A 1 ATOM 55 N N . ARG A 1 8 ? 2.230 1.575 2.308 1.00 82.62 8 A 1 ATOM 56 C CA . ARG A 1 8 ? 3.635 1.701 2.721 1.00 83.16 8 A 1 ATOM 57 C C . ARG A 1 8 ? 4.545 1.855 1.512 1.00 83.45 8 A 1 ATOM 58 O O . ARG A 1 8 ? 5.458 2.676 1.507 1.00 80.18 8 A 1 ATOM 59 C CB . ARG A 1 8 ? 4.045 0.467 3.529 1.00 81.58 8 A 1 ATOM 60 C CG . ARG A 1 8 ? 3.305 0.380 4.846 1.00 75.42 8 A 1 ATOM 61 C CD . ARG A 1 8 ? 4.149 0.944 5.975 1.00 76.48 8 A 1 ATOM 62 N NE . ARG A 1 8 ? 4.770 -0.144 6.742 1.00 69.79 8 A 1 ATOM 63 C CZ . ARG A 1 8 ? 5.564 0.045 7.779 1.00 68.63 8 A 1 ATOM 64 N NH1 . ARG A 1 8 ? 5.868 1.256 8.188 1.00 63.54 8 A 1 ATOM 65 N NH2 . ARG A 1 8 ? 6.067 -0.991 8.424 1.00 63.54 8 A 1 ATOM 66 N N . HIS A 1 9 ? 4.291 1.062 0.482 1.00 86.35 9 A 1 ATOM 67 C CA . HIS A 1 9 ? 5.103 1.102 -0.731 1.00 84.62 9 A 1 ATOM 68 C C . HIS A 1 9 ? 4.857 2.382 -1.528 1.00 85.72 9 A 1 ATOM 69 O O . HIS A 1 9 ? 5.786 2.970 -2.072 1.00 80.82 9 A 1 ATOM 70 C CB . HIS A 1 9 ? 4.795 -0.116 -1.601 1.00 81.06 9 A 1 ATOM 71 C CG . HIS A 1 9 ? 5.819 -0.307 -2.682 1.00 73.95 9 A 1 ATOM 72 N ND1 . HIS A 1 9 ? 5.650 0.114 -3.969 1.00 67.66 9 A 1 ATOM 73 C CD2 . HIS A 1 9 ? 7.043 -0.878 -2.636 1.00 67.68 9 A 1 ATOM 74 C CE1 . HIS A 1 9 ? 6.739 -0.198 -4.666 1.00 68.68 9 A 1 ATOM 75 N NE2 . HIS A 1 9 ? 7.604 -0.801 -3.887 1.00 69.11 9 A 1 ATOM 76 N N . SER A 1 10 ? 3.602 2.801 -1.591 1.00 85.54 10 A 1 ATOM 77 C CA . SER A 1 10 ? 3.231 4.012 -2.321 1.00 84.06 10 A 1 ATOM 78 C C . SER A 1 10 ? 3.869 5.250 -1.701 1.00 84.37 10 A 1 ATOM 79 O O . SER A 1 10 ? 4.316 6.151 -2.405 1.00 78.13 10 A 1 ATOM 80 C CB . SER A 1 10 ? 1.716 4.177 -2.348 1.00 80.86 10 A 1 ATOM 81 O OG . SER A 1 10 ? 1.367 5.364 -3.011 1.00 71.42 10 A 1 ATOM 82 N N . GLY A 1 11 ? 3.905 5.288 -0.392 1.00 84.05 11 A 1 ATOM 83 C CA . GLY A 1 11 ? 4.473 6.435 0.309 1.00 82.77 11 A 1 ATOM 84 C C . GLY A 1 11 ? 3.525 6.977 1.357 1.00 84.05 11 A 1 ATOM 85 O O . GLY A 1 11 ? 2.531 7.605 1.013 1.00 80.60 11 A 1 ATOM 86 N N . PRO A 1 12 ? 3.807 6.774 2.627 1.00 81.37 12 A 1 ATOM 87 C CA . PRO A 1 12 ? 2.959 7.242 3.727 1.00 81.32 12 A 1 ATOM 88 C C . PRO A 1 12 ? 2.823 8.758 3.751 1.00 82.61 12 A 1 ATOM 89 O O . PRO A 1 12 ? 1.822 9.288 4.221 1.00 76.06 12 A 1 ATOM 90 C CB . PRO A 1 12 ? 3.675 6.736 4.980 1.00 77.31 12 A 1 ATOM 91 C CG . PRO A 1 12 ? 5.092 6.564 4.556 1.00 76.54 12 A 1 ATOM 92 C CD . PRO A 1 12 ? 5.034 6.141 3.110 1.00 80.15 12 A 1 ATOM 93 N N . SER A 1 13 ? 3.812 9.463 3.240 1.00 80.76 13 A 1 ATOM 94 C CA . SER A 1 13 ? 3.793 10.925 3.211 1.00 80.39 13 A 1 ATOM 95 C C . SER A 1 13 ? 2.697 11.448 2.292 1.00 80.47 13 A 1 ATOM 96 O O . SER A 1 13 ? 2.111 12.498 2.540 1.00 75.75 13 A 1 ATOM 97 C CB . SER A 1 13 ? 5.141 11.457 2.738 1.00 75.45 13 A 1 ATOM 98 O OG . SER A 1 13 ? 5.433 10.986 1.448 1.00 68.44 13 A 1 ATOM 99 N N . PHE A 1 14 ? 2.433 10.709 1.214 1.00 76.55 14 A 1 ATOM 100 C CA . PHE A 1 14 ? 1.407 11.101 0.254 1.00 77.22 14 A 1 ATOM 101 C C . PHE A 1 14 ? 0.010 10.932 0.841 1.00 78.49 14 A 1 ATOM 102 O O . PHE A 1 14 ? -0.882 11.740 0.575 1.00 72.59 14 A 1 ATOM 103 C CB . PHE A 1 14 ? 1.534 10.258 -1.016 1.00 72.46 14 A 1 ATOM 104 C CG . PHE A 1 14 ? 0.619 10.709 -2.113 1.00 69.50 14 A 1 ATOM 105 C CD1 . PHE A 1 14 ? 0.931 11.831 -2.863 1.00 68.02 14 A 1 ATOM 106 C CD2 . PHE A 1 14 ? -0.547 10.017 -2.397 1.00 66.55 14 A 1 ATOM 107 C CE1 . PHE A 1 14 ? 0.084 12.256 -3.873 1.00 64.26 14 A 1 ATOM 108 C CE2 . PHE A 1 14 ? -1.404 10.445 -3.410 1.00 64.86 14 A 1 ATOM 109 C CZ . PHE A 1 14 ? -1.080 11.566 -4.148 1.00 65.49 14 A 1 ATOM 110 N N . ALA A 1 15 ? -0.163 9.882 1.612 1.00 78.01 15 A 1 ATOM 111 C CA . ALA A 1 15 ? -1.463 9.597 2.216 1.00 76.95 15 A 1 ATOM 112 C C . ALA A 1 15 ? -1.550 10.221 3.604 1.00 74.94 15 A 1 ATOM 113 O O . ALA A 1 15 ? -2.352 11.158 3.790 1.00 70.24 15 A 1 ATOM 114 C CB . ALA A 1 15 ? -1.688 8.092 2.286 1.00 71.07 15 A 1 ATOM 115 O OXT . ALA A 1 15 ? -0.806 9.770 4.492 1.00 66.50 15 A 1 #