# 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_spkb23434 # _entry.id spkb23434 # 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" "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" # _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 PHE 5 1 n ALA 6 1 n LEU 7 1 n ALA 8 1 n LEU 9 1 n ILE 10 1 n ALA 11 1 n PRO 12 1 n LEU 13 1 n LEU 14 1 n ILE 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 @ 2025-07-05 15:20:58)" _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 94.62 _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 91.77 1 1 A LYS 2 2 91.70 1 2 A LYS 3 2 92.58 1 3 A ILE 4 2 96.78 1 4 A PHE 5 2 94.73 1 5 A ALA 6 2 97.72 1 6 A LEU 7 2 95.69 1 7 A ALA 8 2 97.95 1 8 A LEU 9 2 96.04 1 9 A ILE 10 2 96.34 1 10 A ALA 11 2 97.71 1 11 A PRO 12 2 97.65 1 12 A LEU 13 2 94.43 1 13 A LEU 14 2 93.99 1 14 A ILE 15 2 95.38 1 15 A SER 16 2 87.07 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 PHE . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ILE . 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 ? 1.193 2.184 13.153 1.00 96.34 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.592 0.775 13.026 1.00 96.95 1 A 1 ATOM 3 C C . MET A 1 1 ? 2.419 0.560 11.759 1.00 97.00 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.564 1.457 10.938 1.00 96.11 1 A 1 ATOM 5 C CB . MET A 1 1 ? 0.348 -0.119 12.991 1.00 94.57 1 A 1 ATOM 6 C CG . MET A 1 1 ? -0.443 -0.052 14.283 1.00 88.82 1 A 1 ATOM 7 S SD . MET A 1 1 ? -1.924 -1.072 14.239 1.00 86.16 1 A 1 ATOM 8 C CE . MET A 1 1 ? -2.548 -0.789 15.884 1.00 78.23 1 A 1 ATOM 9 N N . LYS A 1 2 ? 2.966 -0.628 11.585 1.00 97.50 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 3.807 -0.941 10.427 1.00 97.87 2 A 1 ATOM 11 C C . LYS A 1 2 ? 2.987 -1.446 9.238 1.00 98.09 2 A 1 ATOM 12 O O . LYS A 1 2 ? 3.284 -1.122 8.093 1.00 97.47 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 4.849 -1.988 10.823 1.00 97.14 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 5.809 -1.482 11.885 1.00 91.40 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 6.769 -2.566 12.320 1.00 89.14 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 7.697 -2.056 13.409 1.00 81.72 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 8.573 -3.139 13.927 1.00 74.93 2 A 1 ATOM 18 N N . LYS A 1 3 ? 1.949 -2.234 9.513 1.00 98.08 3 A 1 ATOM 19 C CA . LYS A 1 3 ? 1.092 -2.772 8.459 1.00 98.21 3 A 1 ATOM 20 C C . LYS A 1 3 ? 0.298 -1.664 7.780 1.00 98.14 3 A 1 ATOM 21 O O . LYS A 1 3 ? 0.181 -1.636 6.554 1.00 97.38 3 A 1 ATOM 22 C CB . LYS A 1 3 ? 0.140 -3.818 9.040 1.00 97.93 3 A 1 ATOM 23 C CG . LYS A 1 3 ? 0.839 -5.115 9.431 1.00 93.93 3 A 1 ATOM 24 C CD . LYS A 1 3 ? 1.332 -5.866 8.211 1.00 89.98 3 A 1 ATOM 25 C CE . LYS A 1 3 ? 1.940 -7.206 8.576 1.00 84.00 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? 2.399 -7.953 7.380 1.00 75.53 3 A 1 ATOM 27 N N . ILE A 1 4 ? -0.251 -0.746 8.559 1.00 97.93 4 A 1 ATOM 28 C CA . ILE A 1 4 ? -1.023 0.362 8.020 1.00 97.77 4 A 1 ATOM 29 C C . ILE A 1 4 ? -0.142 1.279 7.182 1.00 97.68 4 A 1 ATOM 30 O O . ILE A 1 4 ? -0.602 1.895 6.218 1.00 97.19 4 A 1 ATOM 31 C CB . ILE A 1 4 ? -1.694 1.164 9.149 1.00 97.81 4 A 1 ATOM 32 C CG1 . ILE A 1 4 ? -2.626 2.235 8.567 1.00 96.38 4 A 1 ATOM 33 C CG2 . ILE A 1 4 ? -0.655 1.816 10.044 1.00 96.04 4 A 1 ATOM 34 C CD1 . ILE A 1 4 ? -3.822 1.651 7.855 1.00 93.48 4 A 1 ATOM 35 N N . PHE A 1 5 ? 1.120 1.363 7.524 1.00 97.26 5 A 1 ATOM 36 C CA . PHE A 1 5 ? 2.064 2.201 6.798 1.00 97.07 5 A 1 ATOM 37 C C . PHE A 1 5 ? 2.291 1.656 5.394 1.00 97.29 5 A 1 ATOM 38 O O . PHE A 1 5 ? 2.399 2.417 4.435 1.00 96.72 5 A 1 ATOM 39 C CB . PHE A 1 5 ? 3.390 2.268 7.546 1.00 96.86 5 A 1 ATOM 40 C CG . PHE A 1 5 ? 4.349 3.246 6.926 1.00 95.09 5 A 1 ATOM 41 C CD1 . PHE A 1 5 ? 4.181 4.610 7.102 1.00 92.20 5 A 1 ATOM 42 C CD2 . PHE A 1 5 ? 5.410 2.796 6.161 1.00 92.90 5 A 1 ATOM 43 C CE1 . PHE A 1 5 ? 5.059 5.518 6.526 1.00 92.01 5 A 1 ATOM 44 C CE2 . PHE A 1 5 ? 6.296 3.699 5.573 1.00 92.30 5 A 1 ATOM 45 C CZ . PHE A 1 5 ? 6.117 5.061 5.759 1.00 92.37 5 A 1 ATOM 46 N N . ALA A 1 6 ? 2.356 0.349 5.274 1.00 97.89 6 A 1 ATOM 47 C CA . ALA A 1 6 ? 2.551 -0.294 3.980 1.00 97.82 6 A 1 ATOM 48 C C . ALA A 1 6 ? 1.306 -0.163 3.110 1.00 97.94 6 A 1 ATOM 49 O O . ALA A 1 6 ? 1.404 0.042 1.901 1.00 97.37 6 A 1 ATOM 50 C CB . ALA A 1 6 ? 2.886 -1.765 4.184 1.00 97.56 6 A 1 ATOM 51 N N . LEU A 1 7 ? 0.131 -0.273 3.731 1.00 98.05 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -1.135 -0.157 3.013 1.00 97.90 7 A 1 ATOM 53 C C . LEU A 1 7 ? -1.358 1.269 2.537 1.00 98.06 7 A 1 ATOM 54 O O . LEU A 1 7 ? -1.974 1.497 1.495 1.00 97.60 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -2.291 -0.584 3.920 1.00 97.48 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -2.308 -2.069 4.268 1.00 93.75 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -3.330 -2.341 5.360 1.00 90.98 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -2.619 -2.902 3.036 1.00 91.69 7 A 1 ATOM 59 N N . ALA A 1 8 ? -0.877 2.224 3.288 1.00 97.99 8 A 1 ATOM 60 C CA . ALA A 1 8 ? -1.036 3.634 2.947 1.00 98.05 8 A 1 ATOM 61 C C . ALA A 1 8 ? -0.165 4.028 1.755 1.00 98.19 8 A 1 ATOM 62 O O . ALA A 1 8 ? -0.382 5.073 1.144 1.00 97.63 8 A 1 ATOM 63 C CB . ALA A 1 8 ? -0.690 4.497 4.154 1.00 97.87 8 A 1 ATOM 64 N N . LEU A 1 9 ? 0.797 3.203 1.413 1.00 98.08 9 A 1 ATOM 65 C CA . LEU A 1 9 ? 1.698 3.484 0.301 1.00 98.03 9 A 1 ATOM 66 C C . LEU A 1 9 ? 1.274 2.767 -0.976 1.00 98.23 9 A 1 ATOM 67 O O . LEU A 1 9 ? 1.848 2.998 -2.040 1.00 97.80 9 A 1 ATOM 68 C CB . LEU A 1 9 ? 3.120 3.065 0.675 1.00 97.66 9 A 1 ATOM 69 C CG . LEU A 1 9 ? 3.748 3.894 1.794 1.00 94.52 9 A 1 ATOM 70 C CD1 . LEU A 1 9 ? 5.087 3.294 2.200 1.00 91.76 9 A 1 ATOM 71 C CD2 . LEU A 1 9 ? 3.942 5.336 1.349 1.00 92.23 9 A 1 ATOM 72 N N . ILE A 1 10 ? 0.265 1.920 -0.881 1.00 97.86 10 A 1 ATOM 73 C CA . ILE A 1 10 ? -0.212 1.170 -2.038 1.00 97.74 10 A 1 ATOM 74 C C . ILE A 1 10 ? -0.971 2.073 -3.005 1.00 98.08 10 A 1 ATOM 75 O O . ILE A 1 10 ? -0.721 2.060 -4.210 1.00 97.73 10 A 1 ATOM 76 C CB . ILE A 1 10 ? -1.120 0.001 -1.610 1.00 97.26 10 A 1 ATOM 77 C CG1 . ILE A 1 10 ? -0.352 -0.971 -0.716 1.00 94.94 10 A 1 ATOM 78 C CG2 . ILE A 1 10 ? -1.649 -0.724 -2.842 1.00 94.53 10 A 1 ATOM 79 C CD1 . ILE A 1 10 ? -1.216 -2.082 -0.143 1.00 92.60 10 A 1 ATOM 80 N N . ALA A 1 11 ? -1.919 2.846 -2.481 1.00 97.83 11 A 1 ATOM 81 C CA . ALA A 1 11 ? -2.722 3.745 -3.308 1.00 97.89 11 A 1 ATOM 82 C C . ALA A 1 11 ? -1.871 4.820 -3.991 1.00 98.15 11 A 1 ATOM 83 O O . ALA A 1 11 ? -1.954 4.992 -5.207 1.00 97.40 11 A 1 ATOM 84 C CB . ALA A 1 11 ? -3.832 4.374 -2.471 1.00 97.29 11 A 1 ATOM 85 N N . PRO A 1 12 ? -1.076 5.566 -3.241 1.00 98.29 12 A 1 ATOM 86 C CA . PRO A 1 12 ? -0.239 6.623 -3.825 1.00 98.10 12 A 1 ATOM 87 C C . PRO A 1 12 ? 0.833 6.077 -4.761 1.00 98.24 12 A 1 ATOM 88 O O . PRO A 1 12 ? 1.340 6.810 -5.610 1.00 97.43 12 A 1 ATOM 89 C CB . PRO A 1 12 ? 0.388 7.298 -2.602 1.00 97.38 12 A 1 ATOM 90 C CG . PRO A 1 12 ? 0.335 6.266 -1.533 1.00 96.31 12 A 1 ATOM 91 C CD . PRO A 1 12 ? -0.940 5.512 -1.788 1.00 97.79 12 A 1 ATOM 92 N N . LEU A 1 13 ? 1.165 4.818 -4.636 1.00 97.13 13 A 1 ATOM 93 C CA . LEU A 1 13 ? 2.169 4.192 -5.490 1.00 97.12 13 A 1 ATOM 94 C C . LEU A 1 13 ? 1.633 3.995 -6.904 1.00 97.50 13 A 1 ATOM 95 O O . LEU A 1 13 ? 2.386 4.079 -7.876 1.00 96.19 13 A 1 ATOM 96 C CB . LEU A 1 13 ? 2.580 2.839 -4.904 1.00 96.62 13 A 1 ATOM 97 C CG . LEU A 1 13 ? 3.676 2.126 -5.684 1.00 93.11 13 A 1 ATOM 98 C CD1 . LEU A 1 13 ? 4.989 2.886 -5.563 1.00 88.81 13 A 1 ATOM 99 C CD2 . LEU A 1 13 ? 3.845 0.706 -5.167 1.00 88.99 13 A 1 ATOM 100 N N . LEU A 1 14 ? 0.322 3.744 -7.027 1.00 96.28 14 A 1 ATOM 101 C CA . LEU A 1 14 ? -0.317 3.514 -8.318 1.00 96.32 14 A 1 ATOM 102 C C . LEU A 1 14 ? -0.803 4.807 -8.957 1.00 96.47 14 A 1 ATOM 103 O O . LEU A 1 14 ? -0.564 5.052 -10.142 1.00 94.95 14 A 1 ATOM 104 C CB . LEU A 1 14 ? -1.497 2.554 -8.143 1.00 95.89 14 A 1 ATOM 105 C CG . LEU A 1 14 ? -1.104 1.159 -7.661 1.00 93.61 14 A 1 ATOM 106 C CD1 . LEU A 1 14 ? -2.348 0.355 -7.323 1.00 89.54 14 A 1 ATOM 107 C CD2 . LEU A 1 14 ? -0.295 0.441 -8.730 1.00 88.86 14 A 1 ATOM 108 N N . ILE A 1 15 ? -1.508 5.625 -8.196 1.00 97.62 15 A 1 ATOM 109 C CA . ILE A 1 15 ? -2.049 6.887 -8.693 1.00 97.38 15 A 1 ATOM 110 C C . ILE A 1 15 ? -1.018 8.010 -8.687 1.00 97.44 15 A 1 ATOM 111 O O . ILE A 1 15 ? -1.048 8.900 -9.535 1.00 96.56 15 A 1 ATOM 112 C CB . ILE A 1 15 ? -3.273 7.314 -7.866 1.00 96.82 15 A 1 ATOM 113 C CG1 . ILE A 1 15 ? -2.915 7.450 -6.386 1.00 94.33 15 A 1 ATOM 114 C CG2 . ILE A 1 15 ? -4.395 6.304 -8.051 1.00 93.36 15 A 1 ATOM 115 C CD1 . ILE A 1 15 ? -4.012 8.082 -5.555 1.00 89.55 15 A 1 ATOM 116 N N . SER A 1 16 ? -0.143 7.972 -7.727 1.00 94.58 16 A 1 ATOM 117 C CA . SER A 1 16 ? 0.873 9.012 -7.576 1.00 92.41 16 A 1 ATOM 118 C C . SER A 1 16 ? 2.189 8.423 -7.104 1.00 88.76 16 A 1 ATOM 119 O O . SER A 1 16 ? 2.816 8.986 -6.190 1.00 82.66 16 A 1 ATOM 120 C CB . SER A 1 16 ? 0.398 10.072 -6.585 1.00 88.80 16 A 1 ATOM 121 O OG . SER A 1 16 ? -0.790 10.688 -7.020 1.00 80.38 16 A 1 ATOM 122 O OXT . SER A 1 16 ? 2.617 7.372 -7.646 1.00 81.88 16 A 1 #