# 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_spkb20472 # _entry.id spkb20472 # 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 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" "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 LYS 3 1 n ILE 4 1 n VAL 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n ALA 9 1 n ILE 10 1 n VAL 11 1 n SER 12 1 n LEU 13 1 n VAL 14 1 n LYS 15 1 n SER 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 @ 2025-07-06 15:09:07)" _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 93.89 _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 92.22 1 1 A LYS 2 2 90.07 1 2 A LYS 3 2 91.81 1 3 A ILE 4 2 96.15 1 4 A VAL 5 2 96.99 1 5 A LEU 6 2 94.72 1 6 A LEU 7 2 94.69 1 7 A LEU 8 2 94.66 1 8 A ALA 9 2 97.78 1 9 A ILE 10 2 95.78 1 10 A VAL 11 2 96.67 1 11 A SER 12 2 96.54 1 12 A LEU 13 2 94.66 1 13 A VAL 14 2 96.22 1 14 A LYS 15 2 90.30 1 15 A SER 16 2 86.43 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 LYS . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n LYS . 15 A 15 A 16 1 n SER . 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 ? 8.474 2.952 5.590 1.00 96.34 1 A 1 ATOM 2 C CA . MET A 1 1 ? 8.909 1.751 4.866 1.00 97.70 1 A 1 ATOM 3 C C . MET A 1 1 ? 8.305 1.742 3.468 1.00 97.67 1 A 1 ATOM 4 O O . MET A 1 1 ? 7.106 1.943 3.306 1.00 96.57 1 A 1 ATOM 5 C CB . MET A 1 1 ? 8.478 0.492 5.617 1.00 96.20 1 A 1 ATOM 6 C CG . MET A 1 1 ? 9.146 0.384 6.976 1.00 89.29 1 A 1 ATOM 7 S SD . MET A 1 1 ? 8.602 -1.056 7.897 1.00 86.85 1 A 1 ATOM 8 C CE . MET A 1 1 ? 9.584 -0.865 9.375 1.00 77.18 1 A 1 ATOM 9 N N . LYS A 1 2 ? 9.124 1.502 2.466 1.00 96.97 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 8.707 1.592 1.066 1.00 97.50 2 A 1 ATOM 11 C C . LYS A 1 2 ? 7.655 0.543 0.701 1.00 97.70 2 A 1 ATOM 12 O O . LYS A 1 2 ? 6.688 0.841 0.008 1.00 96.64 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 9.932 1.455 0.160 1.00 96.17 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 10.924 2.585 0.358 1.00 88.11 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 12.163 2.395 -0.493 1.00 87.12 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 13.157 3.524 -0.260 1.00 78.72 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 14.415 3.312 -1.008 1.00 71.71 2 A 1 ATOM 18 N N . LYS A 1 3 ? 7.835 -0.684 1.174 1.00 97.92 3 A 1 ATOM 19 C CA . LYS A 1 3 ? 6.907 -1.767 0.864 1.00 98.19 3 A 1 ATOM 20 C C . LYS A 1 3 ? 5.545 -1.536 1.513 1.00 98.18 3 A 1 ATOM 21 O O . LYS A 1 3 ? 4.508 -1.809 0.917 1.00 97.29 3 A 1 ATOM 22 C CB . LYS A 1 3 ? 7.492 -3.107 1.314 1.00 97.58 3 A 1 ATOM 23 C CG . LYS A 1 3 ? 8.752 -3.484 0.553 1.00 92.48 3 A 1 ATOM 24 C CD . LYS A 1 3 ? 9.310 -4.811 1.031 1.00 89.68 3 A 1 ATOM 25 C CE . LYS A 1 3 ? 10.573 -5.186 0.267 1.00 81.86 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? 11.167 -6.446 0.768 1.00 73.11 3 A 1 ATOM 27 N N . ILE A 1 4 ? 5.553 -1.026 2.725 1.00 97.81 4 A 1 ATOM 28 C CA . ILE A 1 4 ? 4.322 -0.749 3.454 1.00 97.79 4 A 1 ATOM 29 C C . ILE A 1 4 ? 3.541 0.363 2.775 1.00 97.90 4 A 1 ATOM 30 O O . ILE A 1 4 ? 2.326 0.278 2.596 1.00 97.10 4 A 1 ATOM 31 C CB . ILE A 1 4 ? 4.633 -0.370 4.914 1.00 97.50 4 A 1 ATOM 32 C CG1 . ILE A 1 4 ? 5.437 -1.484 5.606 1.00 95.40 4 A 1 ATOM 33 C CG2 . ILE A 1 4 ? 3.340 -0.086 5.671 1.00 94.36 4 A 1 ATOM 34 C CD1 . ILE A 1 4 ? 4.728 -2.831 5.607 1.00 91.30 4 A 1 ATOM 35 N N . VAL A 1 5 ? 4.238 1.406 2.387 1.00 98.07 5 A 1 ATOM 36 C CA . VAL A 1 5 ? 3.622 2.540 1.710 1.00 98.05 5 A 1 ATOM 37 C C . VAL A 1 5 ? 3.041 2.110 0.370 1.00 98.01 5 A 1 ATOM 38 O O . VAL A 1 5 ? 1.948 2.541 -0.012 1.00 97.37 5 A 1 ATOM 39 C CB . VAL A 1 5 ? 4.638 3.673 1.510 1.00 97.58 5 A 1 ATOM 40 C CG1 . VAL A 1 5 ? 4.029 4.812 0.710 1.00 94.81 5 A 1 ATOM 41 C CG2 . VAL A 1 5 ? 5.123 4.181 2.853 1.00 95.04 5 A 1 ATOM 42 N N . LEU A 1 6 ? 3.748 1.248 -0.325 1.00 98.02 6 A 1 ATOM 43 C CA . LEU A 1 6 ? 3.304 0.757 -1.625 1.00 97.85 6 A 1 ATOM 44 C C . LEU A 1 6 ? 1.997 -0.016 -1.501 1.00 97.96 6 A 1 ATOM 45 O O . LEU A 1 6 ? 1.055 0.222 -2.257 1.00 97.66 6 A 1 ATOM 46 C CB . LEU A 1 6 ? 4.385 -0.135 -2.241 1.00 97.60 6 A 1 ATOM 47 C CG . LEU A 1 6 ? 4.053 -0.644 -3.638 1.00 91.02 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? 3.943 0.512 -4.618 1.00 88.46 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? 5.106 -1.631 -4.107 1.00 89.22 6 A 1 ATOM 50 N N . LEU A 1 7 ? 1.933 -0.923 -0.541 1.00 97.91 7 A 1 ATOM 51 C CA . LEU A 1 7 ? 0.735 -1.719 -0.321 1.00 97.92 7 A 1 ATOM 52 C C . LEU A 1 7 ? -0.436 -0.840 0.094 1.00 98.08 7 A 1 ATOM 53 O O . LEU A 1 7 ? -1.553 -1.012 -0.390 1.00 97.73 7 A 1 ATOM 54 C CB . LEU A 1 7 ? 1.002 -2.768 0.760 1.00 97.67 7 A 1 ATOM 55 C CG . LEU A 1 7 ? 1.987 -3.857 0.349 1.00 90.61 7 A 1 ATOM 56 C CD1 . LEU A 1 7 ? 2.325 -4.737 1.542 1.00 88.49 7 A 1 ATOM 57 C CD2 . LEU A 1 7 ? 1.412 -4.706 -0.773 1.00 89.14 7 A 1 ATOM 58 N N . LEU A 1 8 ? -0.174 0.098 0.968 1.00 98.22 8 A 1 ATOM 59 C CA . LEU A 1 8 ? -1.202 1.010 1.443 1.00 98.02 8 A 1 ATOM 60 C C . LEU A 1 8 ? -1.755 1.856 0.305 1.00 98.11 8 A 1 ATOM 61 O O . LEU A 1 8 ? -2.965 2.060 0.202 1.00 97.66 8 A 1 ATOM 62 C CB . LEU A 1 8 ? -0.625 1.905 2.536 1.00 97.58 8 A 1 ATOM 63 C CG . LEU A 1 8 ? -1.646 2.842 3.170 1.00 90.80 8 A 1 ATOM 64 C CD1 . LEU A 1 8 ? -2.735 2.055 3.881 1.00 88.01 8 A 1 ATOM 65 C CD2 . LEU A 1 8 ? -0.964 3.787 4.144 1.00 88.88 8 A 1 ATOM 66 N N . ALA A 1 9 ? -0.876 2.343 -0.541 1.00 98.02 9 A 1 ATOM 67 C CA . ALA A 1 9 ? -1.268 3.176 -1.669 1.00 98.01 9 A 1 ATOM 68 C C . ALA A 1 9 ? -2.108 2.396 -2.676 1.00 98.10 9 A 1 ATOM 69 O O . ALA A 1 9 ? -3.141 2.882 -3.138 1.00 97.19 9 A 1 ATOM 70 C CB . ALA A 1 9 ? -0.025 3.745 -2.344 1.00 97.60 9 A 1 ATOM 71 N N . ILE A 1 10 ? -1.689 1.188 -2.999 1.00 97.88 10 A 1 ATOM 72 C CA . ILE A 1 10 ? -2.399 0.356 -3.964 1.00 97.74 10 A 1 ATOM 73 C C . ILE A 1 10 ? -3.766 -0.048 -3.427 1.00 97.73 10 A 1 ATOM 74 O O . ILE A 1 10 ? -4.772 0.051 -4.128 1.00 96.66 10 A 1 ATOM 75 C CB . ILE A 1 10 ? -1.573 -0.894 -4.316 1.00 97.36 10 A 1 ATOM 76 C CG1 . ILE A 1 10 ? -0.285 -0.484 -5.037 1.00 94.71 10 A 1 ATOM 77 C CG2 . ILE A 1 10 ? -2.394 -1.839 -5.191 1.00 94.04 10 A 1 ATOM 78 C CD1 . ILE A 1 10 ? 0.689 -1.631 -5.220 1.00 90.15 10 A 1 ATOM 79 N N . VAL A 1 11 ? -3.805 -0.493 -2.184 1.00 98.30 11 A 1 ATOM 80 C CA . VAL A 1 11 ? -5.058 -0.901 -1.557 1.00 98.14 11 A 1 ATOM 81 C C . VAL A 1 11 ? -6.022 0.272 -1.484 1.00 98.07 11 A 1 ATOM 82 O O . VAL A 1 11 ? -7.213 0.127 -1.761 1.00 96.97 11 A 1 ATOM 83 C CB . VAL A 1 11 ? -4.810 -1.474 -0.158 1.00 97.59 11 A 1 ATOM 84 C CG1 . VAL A 1 11 ? -6.123 -1.730 0.564 1.00 93.34 11 A 1 ATOM 85 C CG2 . VAL A 1 11 ? -4.018 -2.762 -0.258 1.00 94.27 11 A 1 ATOM 86 N N . SER A 1 12 ? -5.519 1.417 -1.118 1.00 98.32 12 A 1 ATOM 87 C CA . SER A 1 12 ? -6.334 2.623 -1.033 1.00 98.25 12 A 1 ATOM 88 C C . SER A 1 12 ? -6.887 3.014 -2.400 1.00 98.28 12 A 1 ATOM 89 O O . SER A 1 12 ? -8.036 3.439 -2.514 1.00 97.51 12 A 1 ATOM 90 C CB . SER A 1 12 ? -5.508 3.774 -0.462 1.00 97.80 12 A 1 ATOM 91 O OG . SER A 1 12 ? -6.304 4.924 -0.313 1.00 89.08 12 A 1 ATOM 92 N N . LEU A 1 13 ? -6.082 2.851 -3.426 1.00 97.98 13 A 1 ATOM 93 C CA . LEU A 1 13 ? -6.477 3.195 -4.786 1.00 97.86 13 A 1 ATOM 94 C C . LEU A 1 13 ? -7.583 2.285 -5.299 1.00 98.01 13 A 1 ATOM 95 O O . LEU A 1 13 ? -8.588 2.756 -5.832 1.00 96.73 13 A 1 ATOM 96 C CB . LEU A 1 13 ? -5.262 3.117 -5.709 1.00 97.16 13 A 1 ATOM 97 C CG . LEU A 1 13 ? -5.550 3.526 -7.151 1.00 92.72 13 A 1 ATOM 98 C CD1 . LEU A 1 13 ? -5.968 4.987 -7.223 1.00 88.16 13 A 1 ATOM 99 C CD2 . LEU A 1 13 ? -4.322 3.289 -8.015 1.00 88.65 13 A 1 ATOM 100 N N . VAL A 1 14 ? -7.404 0.976 -5.148 1.00 98.03 14 A 1 ATOM 101 C CA . VAL A 1 14 ? -8.384 0.008 -5.644 1.00 98.06 14 A 1 ATOM 102 C C . VAL A 1 14 ? -9.625 -0.041 -4.762 1.00 98.07 14 A 1 ATOM 103 O O . VAL A 1 14 ? -10.722 -0.304 -5.244 1.00 96.46 14 A 1 ATOM 104 C CB . VAL A 1 14 ? -7.769 -1.393 -5.760 1.00 97.30 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? -6.584 -1.369 -6.715 1.00 92.25 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? -7.343 -1.921 -4.404 1.00 93.37 14 A 1 ATOM 107 N N . LYS A 1 15 ? -9.445 0.192 -3.489 1.00 97.73 15 A 1 ATOM 108 C CA . LYS A 1 15 ? -10.555 0.167 -2.542 1.00 97.50 15 A 1 ATOM 109 C C . LYS A 1 15 ? -11.463 1.373 -2.729 1.00 97.25 15 A 1 ATOM 110 O O . LYS A 1 15 ? -12.680 1.277 -2.582 1.00 95.02 15 A 1 ATOM 111 C CB . LYS A 1 15 ? -10.020 0.126 -1.110 1.00 96.46 15 A 1 ATOM 112 C CG . LYS A 1 15 ? -11.118 -0.007 -0.076 1.00 88.10 15 A 1 ATOM 113 C CD . LYS A 1 15 ? -10.534 -0.093 1.322 1.00 86.79 15 A 1 ATOM 114 C CE . LYS A 1 15 ? -11.645 -0.226 2.358 1.00 81.76 15 A 1 ATOM 115 N NZ . LYS A 1 15 ? -11.099 -0.301 3.729 1.00 72.09 15 A 1 ATOM 116 N N . SER A 1 16 ? -10.875 2.483 -3.044 1.00 94.30 16 A 1 ATOM 117 C CA . SER A 1 16 ? -11.611 3.722 -3.249 1.00 92.44 16 A 1 ATOM 118 C C . SER A 1 16 ? -12.382 3.675 -4.568 1.00 90.22 16 A 1 ATOM 119 O O . SER A 1 16 ? -13.470 4.268 -4.646 1.00 83.65 16 A 1 ATOM 120 C CB . SER A 1 16 ? -10.657 4.919 -3.231 1.00 87.44 16 A 1 ATOM 121 O OG . SER A 1 16 ? -11.380 6.124 -3.425 1.00 77.92 16 A 1 ATOM 122 O OXT . SER A 1 16 ? -11.899 3.042 -5.506 1.00 79.01 16 A 1 #