# 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_spkb15406 # _entry.id spkb15406 # 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 H13 N O2" 131.173 LEU y LEUCINE CC(C)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" "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" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)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 ARG 2 1 n LEU 3 1 n ALA 4 1 n LEU 5 1 n LEU 6 1 n TRP 7 1 n ALA 8 1 n LEU 9 1 n GLY 10 1 n LEU 11 1 n LEU 12 1 n GLY 13 1 n ALA 14 1 n GLY 15 1 n SER 16 1 n PRO 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 @ 2025-07-02 17:28:43)" _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 92.95 _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 88.88 1 1 A ARG 2 2 89.52 1 2 A LEU 3 2 96.09 1 3 A ALA 4 2 97.87 1 4 A LEU 5 2 94.69 1 5 A LEU 6 2 95.41 1 6 A TRP 7 2 93.69 1 7 A ALA 8 2 96.90 1 8 A LEU 9 2 95.47 1 9 A GLY 10 2 97.02 1 10 A LEU 11 2 96.29 1 11 A LEU 12 2 94.74 1 12 A GLY 13 2 95.41 1 13 A ALA 14 2 93.45 1 14 A GLY 15 2 90.99 1 15 A SER 16 2 85.81 1 16 A PRO 17 2 82.62 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 ARG . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n TRP . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n GLY . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n GLY . 15 A 15 A 16 1 n SER . 16 A 16 A 17 1 n PRO . 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 ? -0.197 3.156 15.570 1.00 94.35 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.343 4.007 14.481 1.00 94.67 1 A 1 ATOM 3 C C . MET A 1 1 ? 0.887 3.121 13.365 1.00 95.27 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.150 2.347 12.766 1.00 92.86 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.453 4.925 15.011 1.00 91.39 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.923 5.874 16.097 1.00 86.76 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.565 5.025 17.641 1.00 83.94 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.035 6.405 18.645 1.00 71.82 1 A 1 ATOM 9 N N . ARG A 1 2 ? 2.189 3.227 13.097 1.00 96.18 2 A 1 ATOM 10 C CA . ARG A 1 2 ? 2.837 2.430 12.056 1.00 97.17 2 A 1 ATOM 11 C C . ARG A 1 2 ? 2.130 2.625 10.715 1.00 97.79 2 A 1 ATOM 12 O O . ARG A 1 2 ? 1.491 1.702 10.200 1.00 97.12 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 2.835 0.957 12.456 1.00 96.15 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 3.694 0.091 11.544 1.00 90.98 2 A 1 ATOM 15 C CD . ARG A 1 2 ? 5.143 0.546 11.577 1.00 89.08 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 6.012 -0.288 10.749 1.00 84.45 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 7.300 -0.042 10.542 1.00 82.94 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 7.874 1.013 11.092 1.00 75.79 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 8.014 -0.847 9.784 1.00 77.09 2 A 1 ATOM 20 N N . LEU A 1 3 ? 2.247 3.826 10.149 1.00 97.51 3 A 1 ATOM 21 C CA . LEU A 1 3 ? 1.630 4.146 8.865 1.00 97.60 3 A 1 ATOM 22 C C . LEU A 1 3 ? 2.241 3.323 7.733 1.00 97.81 3 A 1 ATOM 23 O O . LEU A 1 3 ? 1.714 3.311 6.618 1.00 97.44 3 A 1 ATOM 24 C CB . LEU A 1 3 ? 1.789 5.643 8.573 1.00 97.26 3 A 1 ATOM 25 C CG . LEU A 1 3 ? 3.236 6.100 8.409 1.00 95.28 3 A 1 ATOM 26 C CD1 . LEU A 1 3 ? 3.661 6.035 6.948 1.00 93.25 3 A 1 ATOM 27 C CD2 . LEU A 1 3 ? 3.386 7.520 8.926 1.00 92.60 3 A 1 ATOM 28 N N . ALA A 1 4 ? 3.352 2.634 8.014 1.00 98.15 4 A 1 ATOM 29 C CA . ALA A 1 4 ? 4.023 1.802 7.016 1.00 97.99 4 A 1 ATOM 30 C C . ALA A 1 4 ? 3.060 0.785 6.411 1.00 98.01 4 A 1 ATOM 31 O O . ALA A 1 4 ? 3.088 0.533 5.207 1.00 97.48 4 A 1 ATOM 32 C CB . ALA A 1 4 ? 5.208 1.087 7.654 1.00 97.71 4 A 1 ATOM 33 N N . LEU A 1 5 ? 2.196 0.190 7.235 1.00 97.16 5 A 1 ATOM 34 C CA . LEU A 1 5 ? 1.222 -0.789 6.756 1.00 96.97 5 A 1 ATOM 35 C C . LEU A 1 5 ? 0.249 -0.130 5.784 1.00 97.28 5 A 1 ATOM 36 O O . LEU A 1 5 ? -0.251 -0.766 4.853 1.00 97.13 5 A 1 ATOM 37 C CB . LEU A 1 5 ? 0.467 -1.403 7.945 1.00 96.68 5 A 1 ATOM 38 C CG . LEU A 1 5 ? -0.172 -0.383 8.893 1.00 92.01 5 A 1 ATOM 39 C CD1 . LEU A 1 5 ? -1.553 0.037 8.396 1.00 89.83 5 A 1 ATOM 40 C CD2 . LEU A 1 5 ? -0.291 -0.985 10.291 1.00 90.43 5 A 1 ATOM 41 N N . LEU A 1 6 ? -0.024 1.141 5.994 1.00 96.83 6 A 1 ATOM 42 C CA . LEU A 1 6 ? -0.925 1.898 5.132 1.00 96.68 6 A 1 ATOM 43 C C . LEU A 1 6 ? -0.294 2.044 3.747 1.00 97.11 6 A 1 ATOM 44 O O . LEU A 1 6 ? -0.978 1.969 2.722 1.00 97.26 6 A 1 ATOM 45 C CB . LEU A 1 6 ? -1.202 3.282 5.743 1.00 96.65 6 A 1 ATOM 46 C CG . LEU A 1 6 ? -2.569 3.881 5.426 1.00 94.35 6 A 1 ATOM 47 C CD1 . LEU A 1 6 ? -2.777 4.029 3.923 1.00 92.43 6 A 1 ATOM 48 C CD2 . LEU A 1 6 ? -3.661 3.013 6.031 1.00 91.98 6 A 1 ATOM 49 N N . TRP A 1 7 ? 1.021 2.227 3.741 1.00 95.45 7 A 1 ATOM 50 C CA . TRP A 1 7 ? 1.767 2.366 2.491 1.00 95.40 7 A 1 ATOM 51 C C . TRP A 1 7 ? 1.708 1.067 1.684 1.00 96.01 7 A 1 ATOM 52 O O . TRP A 1 7 ? 1.555 1.094 0.459 1.00 96.16 7 A 1 ATOM 53 C CB . TRP A 1 7 ? 3.223 2.732 2.813 1.00 95.37 7 A 1 ATOM 54 C CG . TRP A 1 7 ? 4.199 2.347 1.758 1.00 95.01 7 A 1 ATOM 55 C CD1 . TRP A 1 7 ? 4.636 3.134 0.733 1.00 91.60 7 A 1 ATOM 56 C CD2 . TRP A 1 7 ? 4.878 1.080 1.596 1.00 93.67 7 A 1 ATOM 57 N NE1 . TRP A 1 7 ? 5.540 2.438 -0.042 1.00 91.98 7 A 1 ATOM 58 C CE2 . TRP A 1 7 ? 5.702 1.171 0.461 1.00 93.31 7 A 1 ATOM 59 C CE3 . TRP A 1 7 ? 4.855 -0.120 2.311 1.00 93.22 7 A 1 ATOM 60 C CZ2 . TRP A 1 7 ? 6.499 0.099 0.030 1.00 92.58 7 A 1 ATOM 61 C CZ3 . TRP A 1 7 ? 5.646 -1.185 1.876 1.00 90.42 7 A 1 ATOM 62 C CH2 . TRP A 1 7 ? 6.458 -1.069 0.743 1.00 91.48 7 A 1 ATOM 63 N N . ALA A 1 8 ? 1.830 -0.063 2.363 1.00 97.10 8 A 1 ATOM 64 C CA . ALA A 1 8 ? 1.807 -1.370 1.711 1.00 96.93 8 A 1 ATOM 65 C C . ALA A 1 8 ? 0.427 -1.699 1.148 1.00 97.28 8 A 1 ATOM 66 O O . ALA A 1 8 ? 0.295 -2.046 -0.024 1.00 96.69 8 A 1 ATOM 67 C CB . ALA A 1 8 ? 2.244 -2.445 2.700 1.00 96.49 8 A 1 ATOM 68 N N . LEU A 1 9 ? -0.606 -1.614 1.977 1.00 96.38 9 A 1 ATOM 69 C CA . LEU A 1 9 ? -1.967 -1.931 1.545 1.00 96.40 9 A 1 ATOM 70 C C . LEU A 1 9 ? -2.438 -0.949 0.476 1.00 97.01 9 A 1 ATOM 71 O O . LEU A 1 9 ? -3.247 -1.297 -0.386 1.00 96.80 9 A 1 ATOM 72 C CB . LEU A 1 9 ? -2.915 -1.918 2.753 1.00 95.98 9 A 1 ATOM 73 C CG . LEU A 1 9 ? -3.139 -0.542 3.380 1.00 94.97 9 A 1 ATOM 74 C CD1 . LEU A 1 9 ? -4.305 0.178 2.705 1.00 93.16 9 A 1 ATOM 75 C CD2 . LEU A 1 9 ? -3.426 -0.702 4.869 1.00 93.05 9 A 1 ATOM 76 N N . GLY A 1 10 ? -1.939 0.267 0.545 1.00 96.87 10 A 1 ATOM 77 C CA . GLY A 1 10 ? -2.301 1.283 -0.437 1.00 96.80 10 A 1 ATOM 78 C C . GLY A 1 10 ? -1.833 0.919 -1.832 1.00 97.35 10 A 1 ATOM 79 O O . GLY A 1 10 ? -2.548 1.129 -2.814 1.00 97.07 10 A 1 ATOM 80 N N . LEU A 1 11 ? -0.637 0.355 -1.936 1.00 97.42 11 A 1 ATOM 81 C CA . LEU A 1 11 ? -0.069 -0.042 -3.223 1.00 97.44 11 A 1 ATOM 82 C C . LEU A 1 11 ? -0.885 -1.164 -3.853 1.00 97.75 11 A 1 ATOM 83 O O . LEU A 1 11 ? -1.181 -1.137 -5.050 1.00 97.22 11 A 1 ATOM 84 C CB . LEU A 1 11 ? 1.377 -0.510 -3.033 1.00 97.00 11 A 1 ATOM 85 C CG . LEU A 1 11 ? 2.299 0.515 -2.374 1.00 95.80 11 A 1 ATOM 86 C CD1 . LEU A 1 11 ? 3.706 -0.054 -2.257 1.00 94.43 11 A 1 ATOM 87 C CD2 . LEU A 1 11 ? 2.319 1.811 -3.165 1.00 93.24 11 A 1 ATOM 88 N N . LEU A 1 12 ? -1.256 -2.160 -3.053 1.00 96.73 12 A 1 ATOM 89 C CA . LEU A 1 12 ? -2.034 -3.299 -3.526 1.00 96.28 12 A 1 ATOM 90 C C . LEU A 1 12 ? -3.412 -2.855 -4.001 1.00 96.69 12 A 1 ATOM 91 O O . LEU A 1 12 ? -3.902 -3.323 -5.029 1.00 95.55 12 A 1 ATOM 92 C CB . LEU A 1 12 ? -2.179 -4.332 -2.406 1.00 95.63 12 A 1 ATOM 93 C CG . LEU A 1 12 ? -0.853 -4.808 -1.810 1.00 94.24 12 A 1 ATOM 94 C CD1 . LEU A 1 12 ? -1.111 -5.802 -0.689 1.00 91.76 12 A 1 ATOM 95 C CD2 . LEU A 1 12 ? 0.022 -5.426 -2.885 1.00 91.02 12 A 1 ATOM 96 N N . GLY A 1 13 ? -4.038 -1.968 -3.258 1.00 96.10 13 A 1 ATOM 97 C CA . GLY A 1 13 ? -5.360 -1.466 -3.613 1.00 95.56 13 A 1 ATOM 98 C C . GLY A 1 13 ? -5.376 -0.756 -4.949 1.00 95.62 13 A 1 ATOM 99 O O . GLY A 1 13 ? -6.398 -0.739 -5.637 1.00 94.38 13 A 1 ATOM 100 N N . ALA A 1 14 ? -4.246 -0.179 -5.339 1.00 94.77 14 A 1 ATOM 101 C CA . ALA A 1 14 ? -4.146 0.544 -6.605 1.00 93.88 14 A 1 ATOM 102 C C . ALA A 1 14 ? -3.780 -0.375 -7.770 1.00 94.31 14 A 1 ATOM 103 O O . ALA A 1 14 ? -3.847 0.035 -8.930 1.00 91.73 14 A 1 ATOM 104 C CB . ALA A 1 14 ? -3.111 1.659 -6.477 1.00 92.54 14 A 1 ATOM 105 N N . GLY A 1 15 ? -3.409 -1.619 -7.467 1.00 93.39 15 A 1 ATOM 106 C CA . GLY A 1 15 ? -3.012 -2.567 -8.502 1.00 91.24 15 A 1 ATOM 107 C C . GLY A 1 15 ? -3.971 -3.723 -8.678 1.00 91.36 15 A 1 ATOM 108 O O . GLY A 1 15 ? -4.345 -4.067 -9.798 1.00 87.97 15 A 1 ATOM 109 N N . SER A 1 16 ? -4.384 -4.353 -7.570 1.00 90.04 16 A 1 ATOM 110 C CA . SER A 1 16 ? -5.301 -5.494 -7.604 1.00 89.12 16 A 1 ATOM 111 C C . SER A 1 16 ? -6.596 -5.194 -8.367 1.00 88.41 16 A 1 ATOM 112 O O . SER A 1 16 ? -6.909 -5.873 -9.344 1.00 83.86 16 A 1 ATOM 113 C CB . SER A 1 16 ? -5.626 -5.947 -6.183 1.00 86.39 16 A 1 ATOM 114 O OG . SER A 1 16 ? -4.485 -6.497 -5.562 1.00 77.01 16 A 1 ATOM 115 N N . PRO A 1 17 ? -7.377 -4.204 -7.923 1.00 89.79 17 A 1 ATOM 116 C CA . PRO A 1 17 ? -8.650 -3.863 -8.576 1.00 86.60 17 A 1 ATOM 117 C C . PRO A 1 17 ? -8.442 -3.257 -9.968 1.00 84.69 17 A 1 ATOM 118 O O . PRO A 1 17 ? -9.239 -3.570 -10.867 1.00 76.61 17 A 1 ATOM 119 C CB . PRO A 1 17 ? -9.284 -2.857 -7.604 1.00 79.45 17 A 1 ATOM 120 C CG . PRO A 1 17 ? -8.124 -2.226 -6.919 1.00 79.87 17 A 1 ATOM 121 C CD . PRO A 1 17 ? -7.101 -3.327 -6.776 1.00 86.29 17 A 1 ATOM 122 O OXT . PRO A 1 17 ? -7.539 -2.467 -10.167 1.00 77.62 17 A 1 #