# 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_spkb20303 # _entry.id spkb20303 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)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 PHE 2 1 n GLN 3 1 n VAL 4 1 n ALA 5 1 n GLY 6 1 n LEU 7 1 n ILE 8 1 n VAL 9 1 n PHE 10 1 n CYS 11 1 n GLY 12 1 n LEU 13 1 n LEU 14 1 n ALA 15 # _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 @ 2025-07-03 14:19:14)" _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 90.46 _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 80.46 1 1 A PHE 2 2 83.18 1 2 A GLN 3 2 84.53 1 3 A VAL 4 2 90.58 1 4 A ALA 5 2 95.35 1 5 A GLY 6 2 96.51 1 6 A LEU 7 2 92.70 1 7 A ILE 8 2 94.25 1 8 A VAL 9 2 95.16 1 9 A PHE 10 2 92.57 1 10 A CYS 11 2 94.55 1 11 A GLY 12 2 95.86 1 12 A LEU 13 2 92.57 1 13 A LEU 14 2 91.98 1 14 A ALA 15 2 87.89 1 15 # _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 PHE . 2 A 2 A 3 1 n GLN . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 # _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 ? -3.835 15.428 2.108 1.00 82.79 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.256 14.156 1.616 1.00 86.94 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.988 13.205 2.778 1.00 89.11 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.429 13.606 3.786 1.00 86.53 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.934 14.435 0.899 1.00 81.04 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.115 15.362 -0.289 1.00 76.23 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.563 15.633 -1.147 1.00 74.56 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.029 16.983 -2.213 1.00 66.49 1 A 1 ATOM 9 N N . PHE A 1 2 ? -3.392 11.953 2.616 1.00 83.39 2 A 1 ATOM 10 C CA . PHE A 1 2 ? -3.201 10.951 3.664 1.00 87.50 2 A 1 ATOM 11 C C . PHE A 1 2 ? -2.256 9.840 3.218 1.00 91.48 2 A 1 ATOM 12 O O . PHE A 1 2 ? -2.134 8.814 3.881 1.00 89.05 2 A 1 ATOM 13 C CB . PHE A 1 2 ? -4.557 10.361 4.055 1.00 84.12 2 A 1 ATOM 14 C CG . PHE A 1 2 ? -5.513 11.398 4.573 1.00 81.95 2 A 1 ATOM 15 C CD1 . PHE A 1 2 ? -6.461 11.952 3.735 1.00 81.02 2 A 1 ATOM 16 C CD2 . PHE A 1 2 ? -5.452 11.808 5.891 1.00 79.39 2 A 1 ATOM 17 C CE1 . PHE A 1 2 ? -7.348 12.909 4.204 1.00 79.49 2 A 1 ATOM 18 C CE2 . PHE A 1 2 ? -6.332 12.764 6.372 1.00 78.81 2 A 1 ATOM 19 C CZ . PHE A 1 2 ? -7.283 13.315 5.526 1.00 78.80 2 A 1 ATOM 20 N N . GLN A 1 3 ? -1.584 10.041 2.100 1.00 84.97 3 A 1 ATOM 21 C CA . GLN A 1 3 ? -0.644 9.055 1.569 1.00 90.30 3 A 1 ATOM 22 C C . GLN A 1 3 ? -1.287 7.671 1.446 1.00 93.10 3 A 1 ATOM 23 O O . GLN A 1 3 ? -0.758 6.679 1.947 1.00 91.03 3 A 1 ATOM 24 C CB . GLN A 1 3 ? 0.589 8.995 2.469 1.00 88.07 3 A 1 ATOM 25 C CG . GLN A 1 3 ? 1.772 9.748 1.905 1.00 83.15 3 A 1 ATOM 26 C CD . GLN A 1 3 ? 1.646 11.242 2.094 1.00 81.72 3 A 1 ATOM 27 O OE1 . GLN A 1 3 ? 0.819 11.883 1.467 1.00 75.32 3 A 1 ATOM 28 N NE2 . GLN A 1 3 ? 2.482 11.805 2.942 1.00 73.08 3 A 1 ATOM 29 N N . VAL A 1 4 ? -2.424 7.617 0.775 1.00 89.66 4 A 1 ATOM 30 C CA . VAL A 1 4 ? -3.155 6.360 0.592 1.00 92.80 4 A 1 ATOM 31 C C . VAL A 1 4 ? -2.328 5.373 -0.224 1.00 94.39 4 A 1 ATOM 32 O O . VAL A 1 4 ? -2.223 4.198 0.123 1.00 93.62 4 A 1 ATOM 33 C CB . VAL A 1 4 ? -4.502 6.614 -0.105 1.00 90.61 4 A 1 ATOM 34 C CG1 . VAL A 1 4 ? -5.276 5.319 -0.251 1.00 85.37 4 A 1 ATOM 35 C CG2 . VAL A 1 4 ? -5.320 7.630 0.678 1.00 87.61 4 A 1 ATOM 36 N N . ALA A 1 5 ? -1.745 5.853 -1.315 1.00 95.02 5 A 1 ATOM 37 C CA . ALA A 1 5 ? -0.926 5.013 -2.185 1.00 95.45 5 A 1 ATOM 38 C C . ALA A 1 5 ? 0.289 4.469 -1.444 1.00 96.29 5 A 1 ATOM 39 O O . ALA A 1 5 ? 0.663 3.311 -1.612 1.00 95.66 5 A 1 ATOM 40 C CB . ALA A 1 5 ? -0.482 5.819 -3.400 1.00 94.33 5 A 1 ATOM 41 N N . GLY A 1 6 ? 0.896 5.309 -0.627 1.00 96.17 6 A 1 ATOM 42 C CA . GLY A 1 6 ? 2.067 4.903 0.144 1.00 96.27 6 A 1 ATOM 43 C C . GLY A 1 6 ? 1.750 3.798 1.130 1.00 96.99 6 A 1 ATOM 44 O O . GLY A 1 6 ? 2.514 2.848 1.279 1.00 96.60 6 A 1 ATOM 45 N N . LEU A 1 7 ? 0.598 3.916 1.792 1.00 94.99 7 A 1 ATOM 46 C CA . LEU A 1 7 ? 0.165 2.921 2.774 1.00 95.38 7 A 1 ATOM 47 C C . LEU A 1 7 ? -0.133 1.588 2.097 1.00 96.44 7 A 1 ATOM 48 O O . LEU A 1 7 ? 0.257 0.531 2.581 1.00 96.04 7 A 1 ATOM 49 C CB . LEU A 1 7 ? -1.086 3.421 3.499 1.00 94.85 7 A 1 ATOM 50 C CG . LEU A 1 7 ? -1.270 2.779 4.864 1.00 89.93 7 A 1 ATOM 51 C CD1 . LEU A 1 7 ? -0.798 3.724 5.960 1.00 87.28 7 A 1 ATOM 52 C CD2 . LEU A 1 7 ? -2.722 2.400 5.084 1.00 86.66 7 A 1 ATOM 53 N N . ILE A 1 8 ? -0.824 1.646 0.965 1.00 95.77 8 A 1 ATOM 54 C CA . ILE A 1 8 ? -1.185 0.443 0.220 1.00 95.70 8 A 1 ATOM 55 C C . ILE A 1 8 ? 0.061 -0.271 -0.291 1.00 96.14 8 A 1 ATOM 56 O O . ILE A 1 8 ? 0.171 -1.493 -0.198 1.00 95.59 8 A 1 ATOM 57 C CB . ILE A 1 8 ? -2.115 0.805 -0.949 1.00 95.31 8 A 1 ATOM 58 C CG1 . ILE A 1 8 ? -3.479 1.260 -0.421 1.00 93.64 8 A 1 ATOM 59 C CG2 . ILE A 1 8 ? -2.301 -0.402 -1.878 1.00 93.42 8 A 1 ATOM 60 C CD1 . ILE A 1 8 ? -4.302 1.976 -1.473 1.00 88.41 8 A 1 ATOM 61 N N . VAL A 1 9 ? 0.987 0.490 -0.836 1.00 95.90 9 A 1 ATOM 62 C CA . VAL A 1 9 ? 2.229 -0.077 -1.369 1.00 95.89 9 A 1 ATOM 63 C C . VAL A 1 9 ? 3.044 -0.725 -0.254 1.00 96.34 9 A 1 ATOM 64 O O . VAL A 1 9 ? 3.594 -1.814 -0.424 1.00 96.01 9 A 1 ATOM 65 C CB . VAL A 1 9 ? 3.062 1.010 -2.062 1.00 95.28 9 A 1 ATOM 66 C CG1 . VAL A 1 9 ? 4.426 0.476 -2.476 1.00 93.36 9 A 1 ATOM 67 C CG2 . VAL A 1 9 ? 2.326 1.537 -3.285 1.00 93.31 9 A 1 ATOM 68 N N . PHE A 1 10 ? 3.111 -0.058 0.878 1.00 94.31 10 A 1 ATOM 69 C CA . PHE A 1 10 ? 3.865 -0.566 2.025 1.00 93.91 10 A 1 ATOM 70 C C . PHE A 1 10 ? 3.290 -1.892 2.507 1.00 94.89 10 A 1 ATOM 71 O O . PHE A 1 10 ? 4.024 -2.845 2.756 1.00 94.12 10 A 1 ATOM 72 C CB . PHE A 1 10 ? 3.810 0.461 3.155 1.00 93.58 10 A 1 ATOM 73 C CG . PHE A 1 10 ? 5.026 0.412 4.038 1.00 93.11 10 A 1 ATOM 74 C CD1 . PHE A 1 10 ? 6.186 1.078 3.668 1.00 91.15 10 A 1 ATOM 75 C CD2 . PHE A 1 10 ? 4.999 -0.289 5.231 1.00 91.34 10 A 1 ATOM 76 C CE1 . PHE A 1 10 ? 7.309 1.041 4.478 1.00 90.86 10 A 1 ATOM 77 C CE2 . PHE A 1 10 ? 6.124 -0.333 6.048 1.00 90.14 10 A 1 ATOM 78 C CZ . PHE A 1 10 ? 7.281 0.333 5.670 1.00 90.85 10 A 1 ATOM 79 N N . CYS A 1 11 ? 1.969 -1.948 2.625 1.00 95.48 11 A 1 ATOM 80 C CA . CYS A 1 11 ? 1.291 -3.167 3.074 1.00 95.31 11 A 1 ATOM 81 C C . CYS A 1 11 ? 1.403 -4.268 2.025 1.00 95.99 11 A 1 ATOM 82 O O . CYS A 1 11 ? 1.576 -5.437 2.352 1.00 94.54 11 A 1 ATOM 83 C CB . CYS A 1 11 ? -0.181 -2.862 3.357 1.00 94.03 11 A 1 ATOM 84 S SG . CYS A 1 11 ? -0.936 -4.125 4.395 1.00 91.97 11 A 1 ATOM 85 N N . GLY A 1 12 ? 1.297 -3.885 0.758 1.00 95.19 12 A 1 ATOM 86 C CA . GLY A 1 12 ? 1.394 -4.841 -0.342 1.00 95.46 12 A 1 ATOM 87 C C . GLY A 1 12 ? 2.768 -5.481 -0.415 1.00 96.69 12 A 1 ATOM 88 O O . GLY A 1 12 ? 2.897 -6.670 -0.694 1.00 96.10 12 A 1 ATOM 89 N N . LEU A 1 13 ? 3.797 -4.699 -0.163 1.00 94.35 13 A 1 ATOM 90 C CA . LEU A 1 13 ? 5.177 -5.190 -0.182 1.00 94.70 13 A 1 ATOM 91 C C . LEU A 1 13 ? 5.407 -6.196 0.942 1.00 95.70 13 A 1 ATOM 92 O O . LEU A 1 13 ? 6.117 -7.187 0.764 1.00 94.43 13 A 1 ATOM 93 C CB . LEU A 1 13 ? 6.144 -4.010 -0.030 1.00 94.03 13 A 1 ATOM 94 C CG . LEU A 1 13 ? 7.584 -4.352 -0.393 1.00 91.42 13 A 1 ATOM 95 C CD1 . LEU A 1 13 ? 7.791 -4.264 -1.902 1.00 88.78 13 A 1 ATOM 96 C CD2 . LEU A 1 13 ? 8.547 -3.418 0.318 1.00 87.16 13 A 1 ATOM 97 N N . LEU A 1 14 ? 4.817 -5.943 2.091 1.00 94.53 14 A 1 ATOM 98 C CA . LEU A 1 14 ? 4.937 -6.832 3.250 1.00 94.28 14 A 1 ATOM 99 C C . LEU A 1 14 ? 4.260 -8.170 2.989 1.00 94.92 14 A 1 ATOM 100 O O . LEU A 1 14 ? 4.786 -9.225 3.355 1.00 93.94 14 A 1 ATOM 101 C CB . LEU A 1 14 ? 4.303 -6.163 4.474 1.00 93.12 14 A 1 ATOM 102 C CG . LEU A 1 14 ? 4.534 -6.916 5.774 1.00 91.16 14 A 1 ATOM 103 C CD1 . LEU A 1 14 ? 5.840 -6.467 6.425 1.00 88.05 14 A 1 ATOM 104 C CD2 . LEU A 1 14 ? 3.379 -6.688 6.730 1.00 85.82 14 A 1 ATOM 105 N N . ALA A 1 15 ? 3.090 -8.138 2.358 1.00 92.99 15 A 1 ATOM 106 C CA . ALA A 1 15 ? 2.314 -9.338 2.070 1.00 91.57 15 A 1 ATOM 107 C C . ALA A 1 15 ? 2.918 -10.138 0.922 1.00 90.24 15 A 1 ATOM 108 O O . ALA A 1 15 ? 3.386 -9.525 -0.053 1.00 86.60 15 A 1 ATOM 109 C CB . ALA A 1 15 ? 0.872 -8.966 1.761 1.00 86.76 15 A 1 ATOM 110 O OXT . ALA A 1 15 ? 2.892 -11.383 0.976 1.00 79.21 15 A 1 #