# 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_spkb37842 # _entry.id spkb37842 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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 LYS 3 1 n ARG 4 1 n GLY 5 1 n ARG 6 1 n PHE 7 1 n ALA 8 1 n LEU 9 1 n CYS 10 1 n LEU 11 1 n ALA 12 1 n VAL 13 1 n LEU 14 1 n LEU 15 1 n GLY 16 1 n ALA 17 # _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 03:45:17)" _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 86.40 _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 75.07 1 1 A VAL 2 2 85.22 1 2 A LYS 3 2 82.30 1 3 A ARG 4 2 76.29 1 4 A GLY 5 2 90.27 1 5 A ARG 6 2 82.01 1 6 A PHE 7 2 89.41 1 7 A ALA 8 2 93.07 1 8 A LEU 9 2 89.75 1 9 A CYS 10 2 91.80 1 10 A LEU 11 2 90.73 1 11 A ALA 12 2 94.40 1 12 A VAL 13 2 92.19 1 13 A LEU 14 2 90.86 1 14 A LEU 15 2 89.38 1 15 A GLY 16 2 91.50 1 16 A ALA 17 2 79.66 1 17 # _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 LYS . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n GLY . 5 A 5 A 6 1 n ARG . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n CYS . 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 LEU . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n GLY . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? -9.143 6.542 10.201 1.00 79.60 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.071 5.347 9.341 1.00 82.78 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.810 4.544 9.635 1.00 85.08 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.273 4.581 10.729 1.00 78.42 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.052 5.769 7.872 1.00 75.80 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.391 6.291 7.409 1.00 71.95 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.500 6.244 5.625 1.00 67.39 1 A 1 ATOM 8 C CE . MET A 1 1 ? -12.015 7.151 5.372 1.00 59.53 1 A 1 ATOM 9 N N . VAL A 1 2 ? -7.317 3.851 8.649 1.00 87.06 2 A 1 ATOM 10 C CA . VAL A 1 2 ? -6.105 3.053 8.810 1.00 88.57 2 A 1 ATOM 11 C C . VAL A 1 2 ? -4.890 3.971 8.857 1.00 91.03 2 A 1 ATOM 12 O O . VAL A 1 2 ? -4.876 5.022 8.220 1.00 88.48 2 A 1 ATOM 13 C CB . VAL A 1 2 ? -5.959 2.083 7.640 1.00 85.50 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? -4.846 1.094 7.925 1.00 76.21 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? -7.272 1.347 7.411 1.00 79.72 2 A 1 ATOM 16 N N . LYS A 1 3 ? -3.889 3.588 9.587 1.00 89.37 3 A 1 ATOM 17 C CA . LYS A 1 3 ? -2.681 4.409 9.711 1.00 89.78 3 A 1 ATOM 18 C C . LYS A 1 3 ? -1.748 4.140 8.535 1.00 90.47 3 A 1 ATOM 19 O O . LYS A 1 3 ? -2.004 4.596 7.426 1.00 87.79 3 A 1 ATOM 20 C CB . LYS A 1 3 ? -2.004 4.109 11.049 1.00 88.19 3 A 1 ATOM 21 C CG . LYS A 1 3 ? -2.305 2.710 11.549 1.00 80.83 3 A 1 ATOM 22 C CD . LYS A 1 3 ? -1.944 2.581 13.008 1.00 78.68 3 A 1 ATOM 23 C CE . LYS A 1 3 ? -2.384 1.236 13.541 1.00 71.01 3 A 1 ATOM 24 N NZ . LYS A 1 3 ? -1.995 1.073 14.966 1.00 64.58 3 A 1 ATOM 25 N N . ARG A 1 4 ? -0.671 3.416 8.779 1.00 85.71 4 A 1 ATOM 26 C CA . ARG A 1 4 ? 0.277 3.102 7.710 1.00 86.79 4 A 1 ATOM 27 C C . ARG A 1 4 ? 0.054 1.697 7.164 1.00 89.44 4 A 1 ATOM 28 O O . ARG A 1 4 ? 0.904 1.157 6.475 1.00 85.34 4 A 1 ATOM 29 C CB . ARG A 1 4 ? 1.690 3.229 8.255 1.00 83.52 4 A 1 ATOM 30 C CG . ARG A 1 4 ? 2.157 4.662 8.268 1.00 77.49 4 A 1 ATOM 31 C CD . ARG A 1 4 ? 3.486 4.767 8.978 1.00 75.49 4 A 1 ATOM 32 N NE . ARG A 1 4 ? 3.298 4.897 10.420 1.00 68.85 4 A 1 ATOM 33 C CZ . ARG A 1 4 ? 4.100 4.368 11.321 1.00 66.62 4 A 1 ATOM 34 N NH1 . ARG A 1 4 ? 5.166 3.689 10.971 1.00 59.92 4 A 1 ATOM 35 N NH2 . ARG A 1 4 ? 3.805 4.511 12.591 1.00 60.04 4 A 1 ATOM 36 N N . GLY A 1 5 ? -1.088 1.117 7.479 1.00 89.40 5 A 1 ATOM 37 C CA . GLY A 1 5 ? -1.386 -0.237 7.030 1.00 90.03 5 A 1 ATOM 38 C C . GLY A 1 5 ? -1.407 -0.333 5.517 1.00 92.01 5 A 1 ATOM 39 O O . GLY A 1 5 ? -0.450 -0.763 4.883 1.00 89.63 5 A 1 ATOM 40 N N . ARG A 1 6 ? -2.523 0.089 4.943 1.00 91.40 6 A 1 ATOM 41 C CA . ARG A 1 6 ? -2.661 0.052 3.483 1.00 92.46 6 A 1 ATOM 42 C C . ARG A 1 6 ? -1.891 1.190 2.823 1.00 94.16 6 A 1 ATOM 43 O O . ARG A 1 6 ? -1.478 1.080 1.674 1.00 92.02 6 A 1 ATOM 44 C CB . ARG A 1 6 ? -4.141 0.156 3.109 1.00 90.15 6 A 1 ATOM 45 C CG . ARG A 1 6 ? -4.896 -1.127 3.451 1.00 83.87 6 A 1 ATOM 46 C CD . ARG A 1 6 ? -4.431 -2.268 2.576 1.00 81.58 6 A 1 ATOM 47 N NE . ARG A 1 6 ? -5.197 -3.496 2.840 1.00 74.95 6 A 1 ATOM 48 C CZ . ARG A 1 6 ? -6.250 -3.859 2.140 1.00 71.64 6 A 1 ATOM 49 N NH1 . ARG A 1 6 ? -6.707 -3.111 1.160 1.00 64.69 6 A 1 ATOM 50 N NH2 . ARG A 1 6 ? -6.857 -4.998 2.427 1.00 65.20 6 A 1 ATOM 51 N N . PHE A 1 7 ? -1.722 2.286 3.542 1.00 91.41 7 A 1 ATOM 52 C CA . PHE A 1 7 ? -1.015 3.446 2.998 1.00 91.77 7 A 1 ATOM 53 C C . PHE A 1 7 ? 0.414 3.077 2.619 1.00 93.25 7 A 1 ATOM 54 O O . PHE A 1 7 ? 0.881 3.418 1.536 1.00 92.39 7 A 1 ATOM 55 C CB . PHE A 1 7 ? -1.002 4.563 4.031 1.00 91.65 7 A 1 ATOM 56 C CG . PHE A 1 7 ? -0.961 5.912 3.366 1.00 90.47 7 A 1 ATOM 57 C CD1 . PHE A 1 7 ? 0.230 6.432 2.897 1.00 87.17 7 A 1 ATOM 58 C CD2 . PHE A 1 7 ? -2.129 6.645 3.202 1.00 87.27 7 A 1 ATOM 59 C CE1 . PHE A 1 7 ? 0.265 7.666 2.271 1.00 86.46 7 A 1 ATOM 60 C CE2 . PHE A 1 7 ? -2.102 7.884 2.578 1.00 86.07 7 A 1 ATOM 61 C CZ . PHE A 1 7 ? -0.902 8.393 2.114 1.00 85.62 7 A 1 ATOM 62 N N . ALA A 1 8 ? 1.087 2.386 3.499 1.00 92.75 8 A 1 ATOM 63 C CA . ALA A 1 8 ? 2.466 1.973 3.232 1.00 93.07 8 A 1 ATOM 64 C C . ALA A 1 8 ? 2.521 0.991 2.069 1.00 94.32 8 A 1 ATOM 65 O O . ALA A 1 8 ? 3.393 1.079 1.210 1.00 93.05 8 A 1 ATOM 66 C CB . ALA A 1 8 ? 3.055 1.334 4.477 1.00 92.17 8 A 1 ATOM 67 N N . LEU A 1 9 ? 1.575 0.069 2.051 1.00 92.77 9 A 1 ATOM 68 C CA . LEU A 1 9 ? 1.508 -0.927 0.983 1.00 92.86 9 A 1 ATOM 69 C C . LEU A 1 9 ? 1.229 -0.251 -0.354 1.00 94.30 9 A 1 ATOM 70 O O . LEU A 1 9 ? 1.882 -0.533 -1.357 1.00 93.28 9 A 1 ATOM 71 C CB . LEU A 1 9 ? 0.403 -1.930 1.298 1.00 92.57 9 A 1 ATOM 72 C CG . LEU A 1 9 ? 0.318 -3.066 0.286 1.00 86.48 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? 1.475 -4.028 0.478 1.00 82.82 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? -1.006 -3.801 0.442 1.00 82.95 9 A 1 ATOM 75 N N . CYS A 1 10 ? 0.256 0.635 -0.356 1.00 92.72 10 A 1 ATOM 76 C CA . CYS A 1 10 ? -0.118 1.342 -1.579 1.00 92.86 10 A 1 ATOM 77 C C . CYS A 1 10 ? 1.027 2.236 -2.049 1.00 94.07 10 A 1 ATOM 78 O O . CYS A 1 10 ? 1.319 2.312 -3.239 1.00 92.66 10 A 1 ATOM 79 C CB . CYS A 1 10 ? -1.370 2.178 -1.312 1.00 91.65 10 A 1 ATOM 80 S SG . CYS A 1 10 ? -2.323 2.436 -2.821 1.00 86.81 10 A 1 ATOM 81 N N . LEU A 1 11 ? 1.652 2.900 -1.114 1.00 93.27 11 A 1 ATOM 82 C CA . LEU A 1 11 ? 2.770 3.791 -1.438 1.00 93.35 11 A 1 ATOM 83 C C . LEU A 1 11 ? 3.931 3.005 -2.031 1.00 94.62 11 A 1 ATOM 84 O O . LEU A 1 11 ? 4.552 3.440 -3.000 1.00 94.13 11 A 1 ATOM 85 C CB . LEU A 1 11 ? 3.222 4.508 -0.171 1.00 92.52 11 A 1 ATOM 86 C CG . LEU A 1 11 ? 4.252 5.587 -0.447 1.00 87.88 11 A 1 ATOM 87 C CD1 . LEU A 1 11 ? 3.624 6.740 -1.223 1.00 85.27 11 A 1 ATOM 88 C CD2 . LEU A 1 11 ? 4.826 6.097 0.869 1.00 84.80 11 A 1 ATOM 89 N N . ALA A 1 12 ? 4.215 1.858 -1.451 1.00 94.73 12 A 1 ATOM 90 C CA . ALA A 1 12 ? 5.309 1.014 -1.936 1.00 94.52 12 A 1 ATOM 91 C C . ALA A 1 12 ? 5.029 0.515 -3.351 1.00 95.48 12 A 1 ATOM 92 O O . ALA A 1 12 ? 5.916 0.499 -4.199 1.00 93.84 12 A 1 ATOM 93 C CB . ALA A 1 12 ? 5.496 -0.171 -0.997 1.00 93.41 12 A 1 ATOM 94 N N . VAL A 1 13 ? 3.790 0.117 -3.590 1.00 94.20 13 A 1 ATOM 95 C CA . VAL A 1 13 ? 3.394 -0.378 -4.910 1.00 93.80 13 A 1 ATOM 96 C C . VAL A 1 13 ? 3.474 0.743 -5.942 1.00 94.77 13 A 1 ATOM 97 O O . VAL A 1 13 ? 4.008 0.559 -7.038 1.00 93.40 13 A 1 ATOM 98 C CB . VAL A 1 13 ? 1.964 -0.940 -4.867 1.00 92.69 13 A 1 ATOM 99 C CG1 . VAL A 1 13 ? 1.504 -1.347 -6.262 1.00 87.97 13 A 1 ATOM 100 C CG2 . VAL A 1 13 ? 1.911 -2.144 -3.941 1.00 88.51 13 A 1 ATOM 101 N N . LEU A 1 14 ? 2.936 1.885 -5.586 1.00 93.18 14 A 1 ATOM 102 C CA . LEU A 1 14 ? 2.946 3.035 -6.491 1.00 93.14 14 A 1 ATOM 103 C C . LEU A 1 14 ? 4.365 3.548 -6.691 1.00 94.33 14 A 1 ATOM 104 O O . LEU A 1 14 ? 4.729 3.965 -7.790 1.00 92.65 14 A 1 ATOM 105 C CB . LEU A 1 14 ? 2.066 4.143 -5.906 1.00 92.25 14 A 1 ATOM 106 C CG . LEU A 1 14 ? 0.583 3.780 -5.858 1.00 89.82 14 A 1 ATOM 107 C CD1 . LEU A 1 14 ? -0.183 4.833 -5.069 1.00 86.07 14 A 1 ATOM 108 C CD2 . LEU A 1 14 ? 0.014 3.673 -7.268 1.00 85.43 14 A 1 ATOM 109 N N . LEU A 1 15 ? 5.145 3.522 -5.636 1.00 92.69 15 A 1 ATOM 110 C CA . LEU A 1 15 ? 6.531 3.987 -5.686 1.00 92.58 15 A 1 ATOM 111 C C . LEU A 1 15 ? 7.349 3.096 -6.604 1.00 93.67 15 A 1 ATOM 112 O O . LEU A 1 15 ? 8.259 3.559 -7.292 1.00 90.30 15 A 1 ATOM 113 C CB . LEU A 1 15 ? 7.131 3.977 -4.270 1.00 90.66 15 A 1 ATOM 114 C CG . LEU A 1 15 ? 8.240 5.002 -4.040 1.00 88.72 15 A 1 ATOM 115 C CD1 . LEU A 1 15 ? 9.352 4.837 -5.062 1.00 83.60 15 A 1 ATOM 116 C CD2 . LEU A 1 15 ? 7.664 6.404 -4.112 1.00 82.84 15 A 1 ATOM 117 N N . GLY A 1 16 ? 7.020 1.833 -6.641 1.00 92.58 16 A 1 ATOM 118 C CA . GLY A 1 16 ? 7.765 0.886 -7.464 1.00 91.75 16 A 1 ATOM 119 C C . GLY A 1 16 ? 9.049 0.495 -6.761 1.00 92.26 16 A 1 ATOM 120 O O . GLY A 1 16 ? 10.129 0.862 -7.206 1.00 89.43 16 A 1 ATOM 121 N N . ALA A 1 17 ? 8.885 -0.245 -5.671 1.00 88.23 17 A 1 ATOM 122 C CA . ALA A 1 17 ? 10.026 -0.650 -4.852 1.00 85.01 17 A 1 ATOM 123 C C . ALA A 1 17 ? 11.163 -1.212 -5.700 1.00 81.79 17 A 1 ATOM 124 O O . ALA A 1 17 ? 10.916 -1.704 -6.817 1.00 75.58 17 A 1 ATOM 125 C CB . ALA A 1 17 ? 9.580 -1.676 -3.816 1.00 78.48 17 A 1 ATOM 126 O OXT . ALA A 1 17 ? 12.324 -1.177 -5.259 1.00 68.87 17 A 1 #