# 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_spkb34134 # _entry.id spkb34134 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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" "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" "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" "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 GLY 2 1 n THR 3 1 n ALA 4 1 n ALA 5 1 n LEU 6 1 n LEU 7 1 n ILE 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n GLY 12 1 n VAL 13 1 n SER 14 1 n TRP 15 1 n ALA 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 @ 2025-07-13 15:22:36)" _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 93.17 _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 76.26 1 1 A GLY 2 2 92.60 1 2 A THR 3 2 94.32 1 3 A ALA 4 2 96.89 1 4 A ALA 5 2 97.36 1 5 A LEU 6 2 95.47 1 6 A LEU 7 2 95.83 1 7 A ILE 8 2 95.61 1 8 A LEU 9 2 95.50 1 9 A LEU 10 2 95.26 1 10 A ALA 11 2 96.91 1 11 A GLY 12 2 96.87 1 12 A VAL 13 2 95.29 1 13 A SER 14 2 95.68 1 14 A TRP 15 2 89.95 1 15 A ALA 16 2 89.30 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 GLY . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n TRP . 15 A 15 A 16 1 n ALA . 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 ? -7.521 12.145 -2.109 1.00 80.10 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.704 10.682 -2.296 1.00 82.03 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.626 9.902 -1.552 1.00 82.46 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.450 10.078 -1.816 1.00 79.11 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.604 10.356 -3.783 1.00 77.44 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.807 10.907 -4.532 1.00 74.51 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.818 10.344 -6.235 1.00 71.50 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.006 11.906 -7.070 1.00 62.91 1 A 1 ATOM 9 N N . GLY A 1 2 ? -7.036 9.063 -0.637 1.00 89.14 2 A 1 ATOM 10 C CA . GLY A 1 2 ? -6.080 8.256 0.127 1.00 92.63 2 A 1 ATOM 11 C C . GLY A 1 2 ? -6.272 6.767 -0.122 1.00 94.83 2 A 1 ATOM 12 O O . GLY A 1 2 ? -5.761 5.937 0.619 1.00 93.80 2 A 1 ATOM 13 N N . THR A 1 3 ? -7.022 6.442 -1.144 1.00 95.57 3 A 1 ATOM 14 C CA . THR A 1 3 ? -7.281 5.033 -1.480 1.00 96.52 3 A 1 ATOM 15 C C . THR A 1 3 ? -6.073 4.411 -2.168 1.00 97.21 3 A 1 ATOM 16 O O . THR A 1 3 ? -5.701 3.273 -1.892 1.00 96.27 3 A 1 ATOM 17 C CB . THR A 1 3 ? -8.494 4.933 -2.408 1.00 94.99 3 A 1 ATOM 18 O OG1 . THR A 1 3 ? -9.556 5.711 -1.869 1.00 90.53 3 A 1 ATOM 19 C CG2 . THR A 1 3 ? -8.944 3.488 -2.521 1.00 89.16 3 A 1 ATOM 20 N N . ALA A 1 4 ? -5.472 5.163 -3.064 1.00 96.35 4 A 1 ATOM 21 C CA . ALA A 1 4 ? -4.293 4.673 -3.786 1.00 97.13 4 A 1 ATOM 22 C C . ALA A 1 4 ? -3.200 4.279 -2.798 1.00 97.68 4 A 1 ATOM 23 O O . ALA A 1 4 ? -2.524 3.268 -2.968 1.00 97.13 4 A 1 ATOM 24 C CB . ALA A 1 4 ? -3.791 5.766 -4.718 1.00 96.18 4 A 1 ATOM 25 N N . ALA A 1 5 ? -3.042 5.087 -1.761 1.00 97.34 5 A 1 ATOM 26 C CA . ALA A 1 5 ? -2.031 4.813 -0.738 1.00 97.49 5 A 1 ATOM 27 C C . ALA A 1 5 ? -2.345 3.499 -0.026 1.00 97.74 5 A 1 ATOM 28 O O . ALA A 1 5 ? -1.443 2.755 0.348 1.00 97.16 5 A 1 ATOM 29 C CB . ALA A 1 5 ? -2.008 5.961 0.260 1.00 97.08 5 A 1 ATOM 30 N N . LEU A 1 6 ? -3.624 3.240 0.155 1.00 97.57 6 A 1 ATOM 31 C CA . LEU A 1 6 ? -4.057 2.007 0.821 1.00 97.28 6 A 1 ATOM 32 C C . LEU A 1 6 ? -3.644 0.791 -0.002 1.00 97.50 6 A 1 ATOM 33 O O . LEU A 1 6 ? -3.153 -0.199 0.536 1.00 97.09 6 A 1 ATOM 34 C CB . LEU A 1 6 ? -5.580 2.039 0.985 1.00 96.96 6 A 1 ATOM 35 C CG . LEU A 1 6 ? -5.996 2.351 2.422 1.00 94.32 6 A 1 ATOM 36 C CD1 . LEU A 1 6 ? -7.420 2.892 2.457 1.00 91.67 6 A 1 ATOM 37 C CD2 . LEU A 1 6 ? -5.904 1.081 3.268 1.00 91.34 6 A 1 ATOM 38 N N . LEU A 1 7 ? -3.852 0.880 -1.297 1.00 97.32 7 A 1 ATOM 39 C CA . LEU A 1 7 ? -3.496 -0.216 -2.204 1.00 97.21 7 A 1 ATOM 40 C C . LEU A 1 7 ? -1.996 -0.480 -2.139 1.00 97.52 7 A 1 ATOM 41 O O . LEU A 1 7 ? -1.550 -1.624 -2.084 1.00 97.47 7 A 1 ATOM 42 C CB . LEU A 1 7 ? -3.910 0.155 -3.634 1.00 96.98 7 A 1 ATOM 43 C CG . LEU A 1 7 ? -5.314 -0.334 -3.996 1.00 94.60 7 A 1 ATOM 44 C CD1 . LEU A 1 7 ? -5.324 -1.856 -4.079 1.00 92.80 7 A 1 ATOM 45 C CD2 . LEU A 1 7 ? -6.325 0.136 -2.968 1.00 92.75 7 A 1 ATOM 46 N N . ILE A 1 8 ? -1.242 0.592 -2.157 1.00 96.73 8 A 1 ATOM 47 C CA . ILE A 1 8 ? 0.216 0.478 -2.101 1.00 96.35 8 A 1 ATOM 48 C C . ILE A 1 8 ? 0.644 -0.053 -0.736 1.00 96.74 8 A 1 ATOM 49 O O . ILE A 1 8 ? 1.588 -0.836 -0.630 1.00 96.27 8 A 1 ATOM 50 C CB . ILE A 1 8 ? 0.852 1.854 -2.355 1.00 96.19 8 A 1 ATOM 51 C CG1 . ILE A 1 8 ? 0.540 2.318 -3.784 1.00 95.33 8 A 1 ATOM 52 C CG2 . ILE A 1 8 ? 2.375 1.766 -2.167 1.00 94.77 8 A 1 ATOM 53 C CD1 . ILE A 1 8 ? 0.760 3.812 -3.941 1.00 92.50 8 A 1 ATOM 54 N N . LEU A 1 9 ? -0.052 0.385 0.293 1.00 96.95 9 A 1 ATOM 55 C CA . LEU A 1 9 ? 0.264 -0.050 1.655 1.00 96.60 9 A 1 ATOM 56 C C . LEU A 1 9 ? 0.085 -1.562 1.774 1.00 97.02 9 A 1 ATOM 57 O O . LEU A 1 9 ? 0.936 -2.260 2.322 1.00 96.77 9 A 1 ATOM 58 C CB . LEU A 1 9 ? -0.661 0.667 2.639 1.00 96.33 9 A 1 ATOM 59 C CG . LEU A 1 9 ? 0.043 0.990 3.957 1.00 94.17 9 A 1 ATOM 60 C CD1 . LEU A 1 9 ? 0.854 2.275 3.813 1.00 93.02 9 A 1 ATOM 61 C CD2 . LEU A 1 9 ? -0.978 1.143 5.075 1.00 93.16 9 A 1 ATOM 62 N N . LEU A 1 10 ? -1.015 -2.041 1.255 1.00 96.85 10 A 1 ATOM 63 C CA . LEU A 1 10 ? -1.308 -3.477 1.296 1.00 96.49 10 A 1 ATOM 64 C C . LEU A 1 10 ? -0.222 -4.265 0.570 1.00 96.84 10 A 1 ATOM 65 O O . LEU A 1 10 ? 0.303 -5.245 1.095 1.00 96.36 10 A 1 ATOM 66 C CB . LEU A 1 10 ? -2.661 -3.741 0.635 1.00 96.18 10 A 1 ATOM 67 C CG . LEU A 1 10 ? -3.434 -4.848 1.348 1.00 94.17 10 A 1 ATOM 68 C CD1 . LEU A 1 10 ? -4.462 -4.239 2.294 1.00 92.65 10 A 1 ATOM 69 C CD2 . LEU A 1 10 ? -4.132 -5.746 0.344 1.00 92.55 10 A 1 ATOM 70 N N . ALA A 1 11 ? 0.095 -3.827 -0.627 1.00 97.31 11 A 1 ATOM 71 C CA . ALA A 1 11 ? 1.121 -4.497 -1.422 1.00 97.14 11 A 1 ATOM 72 C C . ALA A 1 11 ? 2.484 -4.364 -0.750 1.00 97.38 11 A 1 ATOM 73 O O . ALA A 1 11 ? 3.294 -5.289 -0.783 1.00 96.19 11 A 1 ATOM 74 C CB . ALA A 1 11 ? 1.152 -3.881 -2.812 1.00 96.51 11 A 1 ATOM 75 N N . GLY A 1 12 ? 2.717 -3.215 -0.146 1.00 97.15 12 A 1 ATOM 76 C CA . GLY A 1 12 ? 3.988 -2.974 0.537 1.00 96.83 12 A 1 ATOM 77 C C . GLY A 1 12 ? 4.201 -3.957 1.668 1.00 97.21 12 A 1 ATOM 78 O O . GLY A 1 12 ? 5.271 -4.542 1.811 1.00 96.29 12 A 1 ATOM 79 N N . VAL A 1 13 ? 3.178 -4.140 2.475 1.00 97.11 13 A 1 ATOM 80 C CA . VAL A 1 13 ? 3.265 -5.074 3.607 1.00 96.96 13 A 1 ATOM 81 C C . VAL A 1 13 ? 3.450 -6.499 3.093 1.00 97.16 13 A 1 ATOM 82 O O . VAL A 1 13 ? 4.197 -7.286 3.672 1.00 95.74 13 A 1 ATOM 83 C CB . VAL A 1 13 ? 1.992 -4.994 4.454 1.00 95.92 13 A 1 ATOM 84 C CG1 . VAL A 1 13 ? 2.066 -5.983 5.606 1.00 92.18 13 A 1 ATOM 85 C CG2 . VAL A 1 13 ? 1.815 -3.583 4.994 1.00 91.94 13 A 1 ATOM 86 N N . SER A 1 14 ? 2.766 -6.819 2.035 1.00 97.11 14 A 1 ATOM 87 C CA . SER A 1 14 ? 2.860 -8.157 1.443 1.00 97.07 14 A 1 ATOM 88 C C . SER A 1 14 ? 4.274 -8.409 0.931 1.00 97.30 14 A 1 ATOM 89 O O . SER A 1 14 ? 4.793 -9.518 1.024 1.00 95.98 14 A 1 ATOM 90 C CB . SER A 1 14 ? 1.868 -8.273 0.295 1.00 95.82 14 A 1 ATOM 91 O OG . SER A 1 14 ? 1.896 -9.578 -0.214 1.00 90.81 14 A 1 ATOM 92 N N . TRP A 1 15 ? 4.889 -7.368 0.397 1.00 94.38 15 A 1 ATOM 93 C CA . TRP A 1 15 ? 6.248 -7.463 -0.135 1.00 93.99 15 A 1 ATOM 94 C C . TRP A 1 15 ? 7.231 -7.790 0.988 1.00 94.71 15 A 1 ATOM 95 O O . TRP A 1 15 ? 8.217 -8.475 0.781 1.00 93.54 15 A 1 ATOM 96 C CB . TRP A 1 15 ? 6.639 -6.136 -0.783 1.00 92.39 15 A 1 ATOM 97 C CG . TRP A 1 15 ? 7.369 -6.344 -2.073 1.00 90.13 15 A 1 ATOM 98 C CD1 . TRP A 1 15 ? 6.936 -5.986 -3.311 1.00 88.78 15 A 1 ATOM 99 C CD2 . TRP A 1 15 ? 8.666 -6.949 -2.271 1.00 90.54 15 A 1 ATOM 100 N NE1 . TRP A 1 15 ? 7.869 -6.326 -4.259 1.00 87.27 15 A 1 ATOM 101 C CE2 . TRP A 1 15 ? 8.939 -6.923 -3.658 1.00 88.64 15 A 1 ATOM 102 C CE3 . TRP A 1 15 ? 9.617 -7.510 -1.416 1.00 87.78 15 A 1 ATOM 103 C CZ2 . TRP A 1 15 ? 10.132 -7.440 -4.189 1.00 87.78 15 A 1 ATOM 104 C CZ3 . TRP A 1 15 ? 10.807 -8.029 -1.949 1.00 84.67 15 A 1 ATOM 105 C CH2 . TRP A 1 15 ? 11.049 -7.989 -3.312 1.00 84.66 15 A 1 ATOM 106 N N . ALA A 1 16 ? 6.926 -7.300 2.167 1.00 94.30 16 A 1 ATOM 107 C CA . ALA A 1 16 ? 7.793 -7.524 3.320 1.00 92.78 16 A 1 ATOM 108 C C . ALA A 1 16 ? 7.974 -9.018 3.612 1.00 91.00 16 A 1 ATOM 109 O O . ALA A 1 16 ? 7.271 -9.847 3.016 1.00 87.07 16 A 1 ATOM 110 C CB . ALA A 1 16 ? 7.202 -6.814 4.529 1.00 89.03 16 A 1 ATOM 111 O OXT . ALA A 1 16 ? 8.826 -9.350 4.444 1.00 81.60 16 A 1 #