# 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_spkb17561 # _entry.id spkb17561 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=O)N ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 ILE y ISOLEUCINE CC[C@H](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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 ALA 3 1 n ILE 4 1 n ILE 5 1 n VAL 6 1 n LEU 7 1 n LEU 8 1 n MET 9 1 n VAL 10 1 n VAL 11 1 n THR 12 1 n SER 13 1 n ASN 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 @ 2025-07-08 04:52:09)" _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 96.32 _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 91.15 1 1 A LYS 2 2 93.13 1 2 A ALA 3 2 98.37 1 3 A ILE 4 2 97.59 1 4 A ILE 5 2 97.66 1 5 A VAL 6 2 98.34 1 6 A LEU 7 2 97.17 1 7 A LEU 8 2 97.12 1 8 A MET 9 2 94.76 1 9 A VAL 10 2 98.22 1 10 A VAL 11 2 98.27 1 11 A THR 12 2 97.31 1 12 A SER 13 2 97.30 1 13 A ASN 14 2 96.03 1 14 A ALA 15 2 94.14 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 LYS . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n MET . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n ASN . 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 ? 4.323 11.034 -0.532 1.00 95.91 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.209 10.074 -0.484 1.00 96.57 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.735 8.673 -0.182 1.00 96.95 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.859 7.833 -1.071 1.00 95.33 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.460 10.064 -1.815 1.00 94.21 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.857 11.409 -2.151 1.00 89.00 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.063 11.427 -3.762 1.00 85.34 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.552 13.127 -3.853 1.00 75.87 1 A 1 ATOM 9 N N . LYS A 1 2 ? 4.046 8.447 1.069 1.00 97.48 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 4.624 7.179 1.505 1.00 97.92 2 A 1 ATOM 11 C C . LYS A 1 2 ? 3.529 6.154 1.809 1.00 98.21 2 A 1 ATOM 12 O O . LYS A 1 2 ? 3.695 4.959 1.559 1.00 97.85 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 5.497 7.436 2.740 1.00 97.16 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 6.471 6.314 3.055 1.00 92.71 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 5.800 5.209 3.837 1.00 90.28 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 6.798 4.139 4.233 1.00 86.28 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 7.832 4.709 5.145 1.00 80.26 2 A 1 ATOM 18 N N . ALA A 1 3 ? 2.396 6.638 2.324 1.00 98.22 3 A 1 ATOM 19 C CA . ALA A 1 3 ? 1.276 5.774 2.684 1.00 98.50 3 A 1 ATOM 20 C C . ALA A 1 3 ? 0.665 5.093 1.465 1.00 98.63 3 A 1 ATOM 21 O O . ALA A 1 3 ? 0.065 4.025 1.577 1.00 98.31 3 A 1 ATOM 22 C CB . ALA A 1 3 ? 0.216 6.577 3.423 1.00 98.17 3 A 1 ATOM 23 N N . ILE A 1 4 ? 0.829 5.719 0.306 1.00 98.57 4 A 1 ATOM 24 C CA . ILE A 1 4 ? 0.293 5.183 -0.940 1.00 98.55 4 A 1 ATOM 25 C C . ILE A 1 4 ? 0.931 3.842 -1.269 1.00 98.57 4 A 1 ATOM 26 O O . ILE A 1 4 ? 0.256 2.888 -1.660 1.00 98.30 4 A 1 ATOM 27 C CB . ILE A 1 4 ? 0.513 6.162 -2.104 1.00 98.37 4 A 1 ATOM 28 C CG1 . ILE A 1 4 ? -0.047 7.541 -1.754 1.00 97.23 4 A 1 ATOM 29 C CG2 . ILE A 1 4 ? -0.125 5.627 -3.378 1.00 96.81 4 A 1 ATOM 30 C CD1 . ILE A 1 4 ? -1.531 7.517 -1.455 1.00 94.28 4 A 1 ATOM 31 N N . ILE A 1 5 ? 2.235 3.779 -1.113 1.00 98.57 5 A 1 ATOM 32 C CA . ILE A 1 5 ? 2.984 2.563 -1.397 1.00 98.50 5 A 1 ATOM 33 C C . ILE A 1 5 ? 2.602 1.454 -0.428 1.00 98.52 5 A 1 ATOM 34 O O . ILE A 1 5 ? 2.429 0.297 -0.810 1.00 98.34 5 A 1 ATOM 35 C CB . ILE A 1 5 ? 4.495 2.823 -1.313 1.00 98.34 5 A 1 ATOM 36 C CG1 . ILE A 1 5 ? 4.872 4.016 -2.193 1.00 97.26 5 A 1 ATOM 37 C CG2 . ILE A 1 5 ? 5.265 1.577 -1.730 1.00 97.06 5 A 1 ATOM 38 C CD1 . ILE A 1 5 ? 4.488 3.831 -3.646 1.00 94.72 5 A 1 ATOM 39 N N . VAL A 1 6 ? 2.478 1.822 0.821 1.00 98.74 6 A 1 ATOM 40 C CA . VAL A 1 6 ? 2.107 0.875 1.868 1.00 98.72 6 A 1 ATOM 41 C C . VAL A 1 6 ? 0.721 0.302 1.605 1.00 98.74 6 A 1 ATOM 42 O O . VAL A 1 6 ? 0.496 -0.904 1.729 1.00 98.59 6 A 1 ATOM 43 C CB . VAL A 1 6 ? 2.128 1.540 3.253 1.00 98.56 6 A 1 ATOM 44 C CG1 . VAL A 1 6 ? 1.719 0.545 4.331 1.00 97.64 6 A 1 ATOM 45 C CG2 . VAL A 1 6 ? 3.505 2.108 3.546 1.00 97.36 6 A 1 ATOM 46 N N . LEU A 1 7 ? -0.197 1.177 1.236 1.00 98.54 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -1.572 0.772 0.952 1.00 98.51 7 A 1 ATOM 48 C C . LEU A 1 7 ? -1.622 -0.216 -0.204 1.00 98.59 7 A 1 ATOM 49 O O . LEU A 1 7 ? -2.337 -1.217 -0.144 1.00 98.49 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -2.426 2.001 0.628 1.00 98.38 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -3.901 1.712 0.358 1.00 95.72 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -4.569 1.106 1.581 1.00 94.17 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -4.623 2.983 -0.063 1.00 95.00 7 A 1 ATOM 54 N N . LEU A 1 8 ? -0.858 0.060 -1.232 1.00 98.54 8 A 1 ATOM 55 C CA . LEU A 1 8 ? -0.804 -0.806 -2.404 1.00 98.48 8 A 1 ATOM 56 C C . LEU A 1 8 ? -0.286 -2.191 -2.043 1.00 98.59 8 A 1 ATOM 57 O O . LEU A 1 8 ? -0.804 -3.203 -2.514 1.00 98.48 8 A 1 ATOM 58 C CB . LEU A 1 8 ? 0.091 -0.177 -3.468 1.00 98.27 8 A 1 ATOM 59 C CG . LEU A 1 8 ? 0.193 -0.971 -4.765 1.00 95.76 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? -1.162 -1.052 -5.451 1.00 94.07 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? 1.219 -0.343 -5.696 1.00 94.78 8 A 1 ATOM 62 N N . MET A 1 9 ? 0.727 -2.229 -1.205 1.00 98.47 9 A 1 ATOM 63 C CA . MET A 1 9 ? 1.327 -3.484 -0.785 1.00 98.38 9 A 1 ATOM 64 C C . MET A 1 9 ? 0.347 -4.303 0.057 1.00 98.51 9 A 1 ATOM 65 O O . MET A 1 9 ? 0.294 -5.523 -0.050 1.00 98.21 9 A 1 ATOM 66 C CB . MET A 1 9 ? 2.607 -3.214 0.007 1.00 98.09 9 A 1 ATOM 67 C CG . MET A 1 9 ? 3.422 -4.462 0.239 1.00 95.15 9 A 1 ATOM 68 S SD . MET A 1 9 ? 4.994 -4.144 1.043 1.00 89.67 9 A 1 ATOM 69 C CE . MET A 1 9 ? 4.444 -3.652 2.665 1.00 81.59 9 A 1 ATOM 70 N N . VAL A 1 10 ? -0.423 -3.623 0.884 1.00 98.70 10 A 1 ATOM 71 C CA . VAL A 1 10 ? -1.419 -4.283 1.724 1.00 98.67 10 A 1 ATOM 72 C C . VAL A 1 10 ? -2.531 -4.884 0.875 1.00 98.72 10 A 1 ATOM 73 O O . VAL A 1 10 ? -2.975 -6.009 1.115 1.00 98.50 10 A 1 ATOM 74 C CB . VAL A 1 10 ? -2.021 -3.305 2.747 1.00 98.45 10 A 1 ATOM 75 C CG1 . VAL A 1 10 ? -3.144 -3.971 3.530 1.00 97.19 10 A 1 ATOM 76 C CG2 . VAL A 1 10 ? -0.948 -2.806 3.699 1.00 97.32 10 A 1 ATOM 77 N N . VAL A 1 11 ? -2.971 -4.134 -0.117 1.00 98.75 11 A 1 ATOM 78 C CA . VAL A 1 11 ? -4.040 -4.586 -1.002 1.00 98.71 11 A 1 ATOM 79 C C . VAL A 1 11 ? -3.607 -5.794 -1.817 1.00 98.75 11 A 1 ATOM 80 O O . VAL A 1 11 ? -4.330 -6.787 -1.905 1.00 98.53 11 A 1 ATOM 81 C CB . VAL A 1 11 ? -4.488 -3.460 -1.944 1.00 98.49 11 A 1 ATOM 82 C CG1 . VAL A 1 11 ? -5.518 -3.976 -2.939 1.00 97.18 11 A 1 ATOM 83 C CG2 . VAL A 1 11 ? -5.070 -2.309 -1.145 1.00 97.47 11 A 1 ATOM 84 N N . THR A 1 12 ? -2.436 -5.721 -2.405 1.00 98.60 12 A 1 ATOM 85 C CA . THR A 1 12 ? -1.926 -6.812 -3.230 1.00 98.51 12 A 1 ATOM 86 C C . THR A 1 12 ? -1.643 -8.054 -2.393 1.00 98.51 12 A 1 ATOM 87 O O . THR A 1 12 ? -1.720 -9.176 -2.890 1.00 98.11 12 A 1 ATOM 88 C CB . THR A 1 12 ? -0.651 -6.394 -3.979 1.00 98.10 12 A 1 ATOM 89 O OG1 . THR A 1 12 ? -0.279 -7.427 -4.895 1.00 94.61 12 A 1 ATOM 90 C CG2 . THR A 1 12 ? 0.499 -6.153 -3.026 1.00 94.71 12 A 1 ATOM 91 N N . SER A 1 13 ? -1.326 -7.857 -1.130 1.00 98.63 13 A 1 ATOM 92 C CA . SER A 1 13 ? -1.063 -8.963 -0.218 1.00 98.50 13 A 1 ATOM 93 C C . SER A 1 13 ? -2.363 -9.611 0.242 1.00 98.53 13 A 1 ATOM 94 O O . SER A 1 13 ? -2.416 -10.817 0.494 1.00 97.86 13 A 1 ATOM 95 C CB . SER A 1 13 ? -0.274 -8.478 0.995 1.00 97.96 13 A 1 ATOM 96 O OG . SER A 1 13 ? -0.011 -9.550 1.872 1.00 92.29 13 A 1 ATOM 97 N N . ASN A 1 14 ? -3.398 -8.806 0.358 1.00 98.24 14 A 1 ATOM 98 C CA . ASN A 1 14 ? -4.706 -9.284 0.793 1.00 98.18 14 A 1 ATOM 99 C C . ASN A 1 14 ? -5.502 -9.873 -0.361 1.00 98.15 14 A 1 ATOM 100 O O . ASN A 1 14 ? -6.075 -10.962 -0.247 1.00 97.33 14 A 1 ATOM 101 C CB . ASN A 1 14 ? -5.501 -8.147 1.435 1.00 97.56 14 A 1 ATOM 102 C CG . ASN A 1 14 ? -6.888 -8.582 1.843 1.00 95.07 14 A 1 ATOM 103 O OD1 . ASN A 1 14 ? -7.877 -8.213 1.219 1.00 92.55 14 A 1 ATOM 104 N ND2 . ASN A 1 14 ? -6.971 -9.369 2.899 1.00 91.15 14 A 1 ATOM 105 N N . ALA A 1 15 ? -5.549 -9.151 -1.459 1.00 97.22 15 A 1 ATOM 106 C CA . ALA A 1 15 ? -6.295 -9.580 -2.634 1.00 96.46 15 A 1 ATOM 107 C C . ALA A 1 15 ? -5.395 -10.343 -3.599 1.00 95.56 15 A 1 ATOM 108 O O . ALA A 1 15 ? -5.003 -11.489 -3.280 1.00 92.91 15 A 1 ATOM 109 C CB . ALA A 1 15 ? -6.921 -8.374 -3.323 1.00 94.83 15 A 1 ATOM 110 O OXT . ALA A 1 15 ? -5.086 -9.819 -4.673 1.00 87.84 15 A 1 #