# 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_spkb12607 # _entry.id spkb12607 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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 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" "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 GLN 2 1 n PHE 3 1 n SER 4 1 n SER 5 1 n ALA 6 1 n VAL 7 1 n VAL 8 1 n LEU 9 1 n SER 10 1 n ALA 11 1 n VAL 12 1 n ALA 13 1 n GLY 14 1 n SER 15 1 n ALA 16 1 n LEU 17 1 n ALA 18 # _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 @ 2025-07-08 06:24:24)" _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 91.60 _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 85.36 1 1 A GLN 2 2 86.88 1 2 A PHE 3 2 86.65 1 3 A SER 4 2 92.37 1 4 A SER 5 2 94.23 1 5 A ALA 6 2 96.09 1 6 A VAL 7 2 95.99 1 7 A VAL 8 2 95.14 1 8 A LEU 9 2 93.57 1 9 A SER 10 2 93.43 1 10 A ALA 11 2 96.17 1 11 A VAL 12 2 95.53 1 12 A ALA 13 2 95.46 1 13 A GLY 14 2 94.33 1 14 A SER 15 2 92.66 1 15 A ALA 16 2 92.93 1 16 A LEU 17 2 88.89 1 17 A ALA 18 2 83.22 1 18 # _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 GLN . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n ALA . 16 A 16 A 17 1 n LEU . 17 A 17 A 18 1 n ALA . 18 A 18 # _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 ? -12.328 2.051 5.262 1.00 88.69 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.483 2.353 4.091 1.00 91.23 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.070 1.803 4.300 1.00 92.53 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.082 2.539 4.266 1.00 90.21 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.417 3.864 3.877 1.00 87.44 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.784 4.473 3.690 1.00 83.58 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.779 6.244 4.010 1.00 80.04 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.515 6.536 4.209 1.00 69.12 1 A 1 ATOM 9 N N . GLN A 1 2 ? -10.005 0.498 4.511 1.00 91.57 2 A 1 ATOM 10 C CA . GLN A 1 2 ? -8.725 -0.160 4.759 1.00 93.86 2 A 1 ATOM 11 C C . GLN A 1 2 ? -7.832 -0.116 3.524 1.00 95.10 2 A 1 ATOM 12 O O . GLN A 1 2 ? -6.615 0.028 3.636 1.00 93.17 2 A 1 ATOM 13 C CB . GLN A 1 2 ? -8.967 -1.613 5.176 1.00 91.01 2 A 1 ATOM 14 C CG . GLN A 1 2 ? -9.613 -1.743 6.544 1.00 84.16 2 A 1 ATOM 15 C CD . GLN A 1 2 ? -8.664 -1.390 7.670 1.00 83.14 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? -7.590 -0.850 7.444 1.00 75.88 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? -9.037 -1.691 8.895 1.00 74.04 2 A 1 ATOM 18 N N . PHE A 1 3 ? -8.451 -0.238 2.331 1.00 90.53 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -7.698 -0.205 1.082 1.00 91.13 3 A 1 ATOM 20 C C . PHE A 1 3 ? -6.994 1.131 0.889 1.00 93.77 3 A 1 ATOM 21 O O . PHE A 1 3 ? -5.815 1.174 0.529 1.00 92.46 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -8.624 -0.480 -0.102 1.00 89.21 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -8.778 -1.953 -0.390 1.00 85.20 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -7.766 -2.637 -1.040 1.00 82.78 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -9.917 -2.637 -0.009 1.00 82.95 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -7.883 -3.991 -1.305 1.00 82.29 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -10.044 -3.994 -0.268 1.00 81.92 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -9.025 -4.674 -0.919 1.00 80.89 3 A 1 ATOM 29 N N . SER A 1 4 ? -7.707 2.226 1.138 1.00 93.72 4 A 1 ATOM 30 C CA . SER A 1 4 ? -7.132 3.562 1.005 1.00 94.03 4 A 1 ATOM 31 C C . SER A 1 4 ? -5.936 3.726 1.937 1.00 95.57 4 A 1 ATOM 32 O O . SER A 1 4 ? -4.891 4.243 1.547 1.00 94.56 4 A 1 ATOM 33 C CB . SER A 1 4 ? -8.181 4.626 1.310 1.00 91.95 4 A 1 ATOM 34 O OG . SER A 1 4 ? -9.240 4.568 0.378 1.00 84.40 4 A 1 ATOM 35 N N . SER A 1 5 ? -6.099 3.251 3.169 1.00 94.97 5 A 1 ATOM 36 C CA . SER A 1 5 ? -5.029 3.310 4.160 1.00 95.98 5 A 1 ATOM 37 C C . SER A 1 5 ? -3.859 2.427 3.740 1.00 96.80 5 A 1 ATOM 38 O O . SER A 1 5 ? -2.695 2.801 3.889 1.00 95.80 5 A 1 ATOM 39 C CB . SER A 1 5 ? -5.545 2.866 5.527 1.00 94.44 5 A 1 ATOM 40 O OG . SER A 1 5 ? -4.545 3.040 6.504 1.00 87.38 5 A 1 ATOM 41 N N . ALA A 1 6 ? -4.179 1.251 3.191 1.00 95.66 6 A 1 ATOM 42 C CA . ALA A 1 6 ? -3.165 0.312 2.729 1.00 96.28 6 A 1 ATOM 43 C C . ALA A 1 6 ? -2.337 0.910 1.597 1.00 97.10 6 A 1 ATOM 44 O O . ALA A 1 6 ? -1.127 0.693 1.520 1.00 96.16 6 A 1 ATOM 45 C CB . ALA A 1 6 ? -3.823 -0.981 2.264 1.00 95.25 6 A 1 ATOM 46 N N . VAL A 1 7 ? -2.996 1.663 0.722 1.00 96.64 7 A 1 ATOM 47 C CA . VAL A 1 7 ? -2.315 2.315 -0.397 1.00 96.85 7 A 1 ATOM 48 C C . VAL A 1 7 ? -1.259 3.285 0.119 1.00 97.28 7 A 1 ATOM 49 O O . VAL A 1 7 ? -0.139 3.339 -0.396 1.00 97.07 7 A 1 ATOM 50 C CB . VAL A 1 7 ? -3.314 3.062 -1.294 1.00 96.09 7 A 1 ATOM 51 C CG1 . VAL A 1 7 ? -2.578 3.867 -2.361 1.00 93.96 7 A 1 ATOM 52 C CG2 . VAL A 1 7 ? -4.271 2.080 -1.945 1.00 94.03 7 A 1 ATOM 53 N N . VAL A 1 8 ? -1.619 4.035 1.140 1.00 95.67 8 A 1 ATOM 54 C CA . VAL A 1 8 ? -0.695 4.995 1.742 1.00 95.88 8 A 1 ATOM 55 C C . VAL A 1 8 ? 0.513 4.272 2.325 1.00 96.29 8 A 1 ATOM 56 O O . VAL A 1 8 ? 1.659 4.681 2.119 1.00 95.96 8 A 1 ATOM 57 C CB . VAL A 1 8 ? -1.386 5.818 2.842 1.00 95.32 8 A 1 ATOM 58 C CG1 . VAL A 1 8 ? -0.393 6.768 3.501 1.00 93.19 8 A 1 ATOM 59 C CG2 . VAL A 1 8 ? -2.560 6.592 2.268 1.00 93.68 8 A 1 ATOM 60 N N . LEU A 1 9 ? 0.248 3.183 3.044 1.00 95.73 9 A 1 ATOM 61 C CA . LEU A 1 9 ? 1.316 2.391 3.641 1.00 95.20 9 A 1 ATOM 62 C C . LEU A 1 9 ? 2.219 1.803 2.565 1.00 95.79 9 A 1 ATOM 63 O O . LEU A 1 9 ? 3.438 1.748 2.725 1.00 95.33 9 A 1 ATOM 64 C CB . LEU A 1 9 ? 0.731 1.273 4.501 1.00 94.59 9 A 1 ATOM 65 C CG . LEU A 1 9 ? 0.509 1.664 5.965 1.00 91.32 9 A 1 ATOM 66 C CD1 . LEU A 1 9 ? -0.527 2.770 6.090 1.00 90.53 9 A 1 ATOM 67 C CD2 . LEU A 1 9 ? 0.097 0.449 6.779 1.00 90.08 9 A 1 ATOM 68 N N . SER A 1 10 ? 1.611 1.369 1.462 1.00 95.69 10 A 1 ATOM 69 C CA . SER A 1 10 ? 2.356 0.802 0.344 1.00 95.23 10 A 1 ATOM 70 C C . SER A 1 10 ? 3.294 1.839 -0.260 1.00 95.88 10 A 1 ATOM 71 O O . SER A 1 10 ? 4.445 1.542 -0.582 1.00 94.63 10 A 1 ATOM 72 C CB . SER A 1 10 ? 1.399 0.284 -0.724 1.00 93.99 10 A 1 ATOM 73 O OG . SER A 1 10 ? 0.621 -0.779 -0.213 1.00 85.14 10 A 1 ATOM 74 N N . ALA A 1 11 ? 2.789 3.061 -0.408 1.00 96.22 11 A 1 ATOM 75 C CA . ALA A 1 11 ? 3.585 4.151 -0.959 1.00 96.32 11 A 1 ATOM 76 C C . ALA A 1 11 ? 4.775 4.458 -0.056 1.00 96.87 11 A 1 ATOM 77 O O . ALA A 1 11 ? 5.893 4.668 -0.531 1.00 95.76 11 A 1 ATOM 78 C CB . ALA A 1 11 ? 2.720 5.395 -1.132 1.00 95.69 11 A 1 ATOM 79 N N . VAL A 1 12 ? 4.523 4.469 1.245 1.00 96.55 12 A 1 ATOM 80 C CA . VAL A 1 12 ? 5.574 4.729 2.225 1.00 96.27 12 A 1 ATOM 81 C C . VAL A 1 12 ? 6.627 3.633 2.178 1.00 96.65 12 A 1 ATOM 82 O O . VAL A 1 12 ? 7.830 3.909 2.206 1.00 96.11 12 A 1 ATOM 83 C CB . VAL A 1 12 ? 4.996 4.832 3.647 1.00 95.35 12 A 1 ATOM 84 C CG1 . VAL A 1 12 ? 6.116 4.998 4.670 1.00 93.54 12 A 1 ATOM 85 C CG2 . VAL A 1 12 ? 4.023 5.998 3.746 1.00 94.22 12 A 1 ATOM 86 N N . ALA A 1 13 ? 6.161 2.389 2.100 1.00 96.07 13 A 1 ATOM 87 C CA . ALA A 1 13 ? 7.061 1.244 2.047 1.00 95.81 13 A 1 ATOM 88 C C . ALA A 1 13 ? 7.943 1.303 0.808 1.00 96.23 13 A 1 ATOM 89 O O . ALA A 1 13 ? 9.147 1.056 0.882 1.00 94.69 13 A 1 ATOM 90 C CB . ALA A 1 13 ? 6.255 -0.049 2.060 1.00 94.50 13 A 1 ATOM 91 N N . GLY A 1 14 ? 7.337 1.627 -0.330 1.00 94.31 14 A 1 ATOM 92 C CA . GLY A 1 14 ? 8.083 1.733 -1.579 1.00 93.42 14 A 1 ATOM 93 C C . GLY A 1 14 ? 9.122 2.832 -1.527 1.00 94.92 14 A 1 ATOM 94 O O . GLY A 1 14 ? 10.252 2.662 -1.991 1.00 94.68 14 A 1 ATOM 95 N N . SER A 1 15 ? 8.738 3.960 -0.954 1.00 95.07 15 A 1 ATOM 96 C CA . SER A 1 15 ? 9.644 5.097 -0.815 1.00 94.99 15 A 1 ATOM 97 C C . SER A 1 15 ? 10.775 4.782 0.160 1.00 95.57 15 A 1 ATOM 98 O O . SER A 1 15 ? 11.925 5.168 -0.060 1.00 93.23 15 A 1 ATOM 99 C CB . SER A 1 15 ? 8.884 6.334 -0.336 1.00 93.16 15 A 1 ATOM 100 O OG . SER A 1 15 ? 9.740 7.451 -0.280 1.00 83.96 15 A 1 ATOM 101 N N . ALA A 1 16 ? 10.437 4.078 1.236 1.00 93.10 16 A 1 ATOM 102 C CA . ALA A 1 16 ? 11.419 3.705 2.249 1.00 93.20 16 A 1 ATOM 103 C C . ALA A 1 16 ? 12.421 2.696 1.700 1.00 94.52 16 A 1 ATOM 104 O O . ALA A 1 16 ? 13.606 2.744 2.037 1.00 92.52 16 A 1 ATOM 105 C CB . ALA A 1 16 ? 10.719 3.131 3.476 1.00 91.31 16 A 1 ATOM 106 N N . LEU A 1 17 ? 11.931 1.775 0.861 1.00 92.48 17 A 1 ATOM 107 C CA . LEU A 1 17 ? 12.788 0.755 0.263 1.00 92.75 17 A 1 ATOM 108 C C . LEU A 1 17 ? 13.765 1.368 -0.729 1.00 93.90 17 A 1 ATOM 109 O O . LEU A 1 17 ? 14.897 0.903 -0.880 1.00 91.92 17 A 1 ATOM 110 C CB . LEU A 1 17 ? 11.937 -0.321 -0.424 1.00 90.02 17 A 1 ATOM 111 C CG . LEU A 1 17 ? 11.718 -1.589 0.399 1.00 85.33 17 A 1 ATOM 112 C CD1 . LEU A 1 17 ? 13.046 -2.291 0.632 1.00 83.64 17 A 1 ATOM 113 C CD2 . LEU A 1 17 ? 11.056 -1.259 1.724 1.00 81.07 17 A 1 ATOM 114 N N . ALA A 1 18 ? 13.315 2.414 -1.426 1.00 88.38 18 A 1 ATOM 115 C CA . ALA A 1 18 ? 14.136 3.085 -2.422 1.00 87.57 18 A 1 ATOM 116 C C . ALA A 1 18 ? 15.154 4.016 -1.762 1.00 85.44 18 A 1 ATOM 117 O O . ALA A 1 18 ? 14.892 4.516 -0.658 1.00 80.88 18 A 1 ATOM 118 C CB . ALA A 1 18 ? 13.256 3.849 -3.400 1.00 82.11 18 A 1 ATOM 119 O OXT . ALA A 1 18 ? 16.219 4.262 -2.344 1.00 74.92 18 A 1 #