# 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_spkb42407 # _entry.id spkb42407 # 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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 ALA 2 1 n THR 3 1 n VAL 4 1 n PHE 5 1 n SER 6 1 n ARG 7 1 n ALA 8 1 n LEU 9 1 n GLY 10 1 n ALA 11 1 n LEU 12 1 n VAL 13 1 n LEU 14 1 n GLY 15 1 n VAL 16 1 n ALA 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 @ 2025-07-06 22:35:11)" _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 94.32 _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 83.08 1 1 A ALA 2 2 93.85 1 2 A THR 3 2 96.22 1 3 A VAL 4 2 96.80 1 4 A PHE 5 2 93.60 1 5 A SER 6 2 96.64 1 6 A ARG 7 2 91.56 1 7 A ALA 8 2 97.90 1 8 A LEU 9 2 95.76 1 9 A GLY 10 2 97.77 1 10 A ALA 11 2 98.01 1 11 A LEU 12 2 96.54 1 12 A VAL 13 2 97.49 1 13 A LEU 14 2 95.67 1 14 A GLY 15 2 97.44 1 15 A VAL 16 2 94.84 1 16 A ALA 17 2 87.19 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 ALA . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n ARG . 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 ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n GLY . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n ALA . 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 ? -3.490 -12.681 3.247 1.00 88.76 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.200 -11.447 3.635 1.00 89.38 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.115 -10.404 2.523 1.00 89.70 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.201 -9.587 2.498 1.00 87.19 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.596 -10.877 4.913 1.00 82.92 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.067 -11.634 6.140 1.00 79.73 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.702 -10.741 7.653 1.00 78.11 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.679 -11.694 8.816 1.00 68.85 1 A 1 ATOM 9 N N . ALA A 1 2 ? -5.074 -10.465 1.630 1.00 90.43 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -5.122 -9.511 0.524 1.00 94.54 2 A 1 ATOM 11 C C . ALA A 1 2 ? -5.390 -8.100 1.035 1.00 96.50 2 A 1 ATOM 12 O O . ALA A 1 2 ? -5.055 -7.114 0.385 1.00 95.40 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -6.205 -9.927 -0.455 1.00 92.37 2 A 1 ATOM 14 N N . THR A 1 3 ? -6.000 -8.030 2.214 1.00 97.29 3 A 1 ATOM 15 C CA . THR A 1 3 ? -6.299 -6.735 2.830 1.00 97.55 3 A 1 ATOM 16 C C . THR A 1 3 ? -5.017 -5.949 3.070 1.00 97.97 3 A 1 ATOM 17 O O . THR A 1 3 ? -4.990 -4.727 2.922 1.00 97.43 3 A 1 ATOM 18 C CB . THR A 1 3 ? -7.020 -6.939 4.167 1.00 96.88 3 A 1 ATOM 19 O OG1 . THR A 1 3 ? -6.361 -7.957 4.910 1.00 93.52 3 A 1 ATOM 20 C CG2 . THR A 1 3 ? -8.463 -7.336 3.943 1.00 92.88 3 A 1 ATOM 21 N N . VAL A 1 4 ? -3.964 -6.671 3.429 1.00 97.73 4 A 1 ATOM 22 C CA . VAL A 1 4 ? -2.670 -6.034 3.664 1.00 97.93 4 A 1 ATOM 23 C C . VAL A 1 4 ? -2.146 -5.428 2.370 1.00 98.12 4 A 1 ATOM 24 O O . VAL A 1 4 ? -1.513 -4.372 2.368 1.00 97.73 4 A 1 ATOM 25 C CB . VAL A 1 4 ? -1.654 -7.044 4.205 1.00 97.37 4 A 1 ATOM 26 C CG1 . VAL A 1 4 ? -0.334 -6.358 4.498 1.00 94.52 4 A 1 ATOM 27 C CG2 . VAL A 1 4 ? -2.194 -7.705 5.463 1.00 94.20 4 A 1 ATOM 28 N N . PHE A 1 5 ? -2.423 -6.127 1.285 1.00 97.72 5 A 1 ATOM 29 C CA . PHE A 1 5 ? -2.011 -5.649 -0.032 1.00 97.39 5 A 1 ATOM 30 C C . PHE A 1 5 ? -2.683 -4.324 -0.345 1.00 97.58 5 A 1 ATOM 31 O O . PHE A 1 5 ? -2.047 -3.379 -0.805 1.00 97.15 5 A 1 ATOM 32 C CB . PHE A 1 5 ? -2.393 -6.679 -1.088 1.00 96.92 5 A 1 ATOM 33 C CG . PHE A 1 5 ? -1.187 -7.306 -1.724 1.00 93.46 5 A 1 ATOM 34 C CD1 . PHE A 1 5 ? -0.384 -8.174 -1.006 1.00 90.74 5 A 1 ATOM 35 C CD2 . PHE A 1 5 ? -0.868 -7.029 -3.044 1.00 90.41 5 A 1 ATOM 36 C CE1 . PHE A 1 5 ? 0.728 -8.757 -1.592 1.00 89.78 5 A 1 ATOM 37 C CE2 . PHE A 1 5 ? 0.242 -7.609 -3.639 1.00 89.13 5 A 1 ATOM 38 C CZ . PHE A 1 5 ? 1.047 -8.476 -2.912 1.00 89.34 5 A 1 ATOM 39 N N . SER A 1 6 ? -3.964 -4.273 -0.080 1.00 97.92 6 A 1 ATOM 40 C CA . SER A 1 6 ? -4.736 -3.057 -0.321 1.00 97.87 6 A 1 ATOM 41 C C . SER A 1 6 ? -4.268 -1.930 0.588 1.00 98.07 6 A 1 ATOM 42 O O . SER A 1 6 ? -4.148 -0.780 0.172 1.00 97.53 6 A 1 ATOM 43 C CB . SER A 1 6 ? -6.218 -3.328 -0.089 1.00 97.25 6 A 1 ATOM 44 O OG . SER A 1 6 ? -6.971 -2.187 -0.407 1.00 91.23 6 A 1 ATOM 45 N N . ARG A 1 7 ? -3.990 -2.288 1.831 1.00 97.60 7 A 1 ATOM 46 C CA . ARG A 1 7 ? -3.537 -1.302 2.811 1.00 97.66 7 A 1 ATOM 47 C C . ARG A 1 7 ? -2.165 -0.762 2.426 1.00 98.03 7 A 1 ATOM 48 O O . ARG A 1 7 ? -1.923 0.441 2.488 1.00 97.65 7 A 1 ATOM 49 C CB . ARG A 1 7 ? -3.477 -1.951 4.189 1.00 97.22 7 A 1 ATOM 50 C CG . ARG A 1 7 ? -3.481 -0.905 5.289 1.00 92.59 7 A 1 ATOM 51 C CD . ARG A 1 7 ? -3.174 -1.541 6.624 1.00 91.18 7 A 1 ATOM 52 N NE . ARG A 1 7 ? -2.903 -0.523 7.645 1.00 88.54 7 A 1 ATOM 53 C CZ . ARG A 1 7 ? -2.140 -0.750 8.703 1.00 85.97 7 A 1 ATOM 54 N NH1 . ARG A 1 7 ? -1.582 -1.925 8.891 1.00 80.58 7 A 1 ATOM 55 N NH2 . ARG A 1 7 ? -1.920 0.214 9.580 1.00 80.09 7 A 1 ATOM 56 N N . ALA A 1 8 ? -1.280 -1.665 2.025 1.00 97.74 8 A 1 ATOM 57 C CA . ALA A 1 8 ? 0.061 -1.271 1.608 1.00 97.91 8 A 1 ATOM 58 C C . ALA A 1 8 ? -0.013 -0.359 0.392 1.00 98.21 8 A 1 ATOM 59 O O . ALA A 1 8 ? 0.695 0.642 0.306 1.00 97.89 8 A 1 ATOM 60 C CB . ALA A 1 8 ? 0.886 -2.507 1.288 1.00 97.75 8 A 1 ATOM 61 N N . LEU A 1 9 ? -0.884 -0.724 -0.525 1.00 97.65 9 A 1 ATOM 62 C CA . LEU A 1 9 ? -1.068 0.074 -1.732 1.00 97.49 9 A 1 ATOM 63 C C . LEU A 1 9 ? -1.630 1.438 -1.373 1.00 97.77 9 A 1 ATOM 64 O O . LEU A 1 9 ? -1.241 2.455 -1.947 1.00 97.49 9 A 1 ATOM 65 C CB . LEU A 1 9 ? -2.005 -0.655 -2.690 1.00 97.07 9 A 1 ATOM 66 C CG . LEU A 1 9 ? -1.736 -0.308 -4.144 1.00 94.13 9 A 1 ATOM 67 C CD1 . LEU A 1 9 ? -1.901 -1.538 -5.020 1.00 92.70 9 A 1 ATOM 68 C CD2 . LEU A 1 9 ? -2.667 0.793 -4.611 1.00 91.81 9 A 1 ATOM 69 N N . GLY A 1 10 ? -2.542 1.441 -0.414 1.00 97.57 10 A 1 ATOM 70 C CA . GLY A 1 10 ? -3.133 2.696 0.036 1.00 97.51 10 A 1 ATOM 71 C C . GLY A 1 10 ? -2.088 3.612 0.632 1.00 98.09 10 A 1 ATOM 72 O O . GLY A 1 10 ? -2.103 4.820 0.412 1.00 97.93 10 A 1 ATOM 73 N N . ALA A 1 11 ? -1.178 3.020 1.391 1.00 98.04 11 A 1 ATOM 74 C CA . ALA A 1 11 ? -0.097 3.788 2.000 1.00 98.12 11 A 1 ATOM 75 C C . ALA A 1 11 ? 0.808 4.374 0.923 1.00 98.42 11 A 1 ATOM 76 O O . ALA A 1 11 ? 1.242 5.521 1.020 1.00 97.87 11 A 1 ATOM 77 C CB . ALA A 1 11 ? 0.709 2.898 2.936 1.00 97.60 11 A 1 ATOM 78 N N . LEU A 1 12 ? 1.073 3.566 -0.093 1.00 97.99 12 A 1 ATOM 79 C CA . LEU A 1 12 ? 1.901 4.004 -1.210 1.00 97.90 12 A 1 ATOM 80 C C . LEU A 1 12 ? 1.224 5.150 -1.943 1.00 98.23 12 A 1 ATOM 81 O O . LEU A 1 12 ? 1.847 6.158 -2.264 1.00 97.79 12 A 1 ATOM 82 C CB . LEU A 1 12 ? 2.145 2.834 -2.171 1.00 97.62 12 A 1 ATOM 83 C CG . LEU A 1 12 ? 3.587 2.337 -2.192 1.00 95.30 12 A 1 ATOM 84 C CD1 . LEU A 1 12 ? 4.521 3.410 -2.700 1.00 93.82 12 A 1 ATOM 85 C CD2 . LEU A 1 12 ? 4.009 1.876 -0.807 1.00 93.69 12 A 1 ATOM 86 N N . VAL A 1 13 ? -0.053 4.965 -2.198 1.00 98.18 13 A 1 ATOM 87 C CA . VAL A 1 13 ? -0.833 5.990 -2.888 1.00 98.10 13 A 1 ATOM 88 C C . VAL A 1 13 ? -0.876 7.267 -2.064 1.00 98.23 13 A 1 ATOM 89 O O . VAL A 1 13 ? -0.799 8.370 -2.604 1.00 97.83 13 A 1 ATOM 90 C CB . VAL A 1 13 ? -2.262 5.493 -3.146 1.00 97.58 13 A 1 ATOM 91 C CG1 . VAL A 1 13 ? -3.108 6.601 -3.756 1.00 96.24 13 A 1 ATOM 92 C CG2 . VAL A 1 13 ? -2.235 4.290 -4.073 1.00 96.29 13 A 1 ATOM 93 N N . LEU A 1 14 ? -0.993 7.102 -0.754 1.00 97.77 14 A 1 ATOM 94 C CA . LEU A 1 14 ? -1.059 8.252 0.141 1.00 97.48 14 A 1 ATOM 95 C C . LEU A 1 14 ? 0.265 9.002 0.143 1.00 97.80 14 A 1 ATOM 96 O O . LEU A 1 14 ? 0.301 10.232 0.186 1.00 96.63 14 A 1 ATOM 97 C CB . LEU A 1 14 ? -1.409 7.777 1.555 1.00 96.86 14 A 1 ATOM 98 C CG . LEU A 1 14 ? -2.426 8.676 2.245 1.00 94.64 14 A 1 ATOM 99 C CD1 . LEU A 1 14 ? -3.343 7.862 3.140 1.00 92.78 14 A 1 ATOM 100 C CD2 . LEU A 1 14 ? -1.718 9.747 3.052 1.00 91.39 14 A 1 ATOM 101 N N . GLY A 1 15 ? 1.348 8.249 0.104 1.00 97.50 15 A 1 ATOM 102 C CA . GLY A 1 15 ? 2.672 8.862 0.088 1.00 97.32 15 A 1 ATOM 103 C C . GLY A 1 15 ? 3.050 9.385 -1.282 1.00 97.76 15 A 1 ATOM 104 O O . GLY A 1 15 ? 3.654 10.449 -1.407 1.00 97.16 15 A 1 ATOM 105 N N . VAL A 1 16 ? 2.697 8.619 -2.298 1.00 96.92 16 A 1 ATOM 106 C CA . VAL A 1 16 ? 3.008 8.999 -3.677 1.00 96.83 16 A 1 ATOM 107 C C . VAL A 1 16 ? 1.933 9.903 -4.267 1.00 97.23 16 A 1 ATOM 108 O O . VAL A 1 16 ? 2.176 10.622 -5.238 1.00 96.17 16 A 1 ATOM 109 C CB . VAL A 1 16 ? 3.171 7.749 -4.558 1.00 95.45 16 A 1 ATOM 110 C CG1 . VAL A 1 16 ? 3.507 8.133 -5.992 1.00 90.62 16 A 1 ATOM 111 C CG2 . VAL A 1 16 ? 4.267 6.852 -3.998 1.00 90.69 16 A 1 ATOM 112 N N . ALA A 1 17 ? 0.757 9.870 -3.668 1.00 93.14 17 A 1 ATOM 113 C CA . ALA A 1 17 ? -0.374 10.655 -4.154 1.00 91.22 17 A 1 ATOM 114 C C . ALA A 1 17 ? -0.061 12.150 -4.165 1.00 89.69 17 A 1 ATOM 115 O O . ALA A 1 17 ? 0.962 12.569 -3.600 1.00 85.09 17 A 1 ATOM 116 C CB . ALA A 1 17 ? -1.599 10.385 -3.298 1.00 85.78 17 A 1 ATOM 117 O OXT . ALA A 1 17 ? -0.852 12.905 -4.731 1.00 78.25 17 A 1 #