# 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_560 # _entry.id 560 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=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" "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 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" "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 ILE 2 1 n LEU 3 1 n PRO 4 1 n PHE 5 1 n LEU 6 1 n VAL 7 1 n LEU 8 1 n ALA 9 1 n ILE 10 1 n GLY 11 1 n THR 12 1 n CYS 13 1 n LEU 14 1 n THR 15 1 n ASN 16 1 n SER 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 @ 2025-05-30 12:25:22)" _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 89.36 _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 84.91 1 1 A ILE 2 2 87.90 1 2 A LEU 3 2 88.13 1 3 A PRO 4 2 92.67 1 4 A PHE 5 2 87.12 1 5 A LEU 6 2 90.06 1 6 A VAL 7 2 92.50 1 7 A LEU 8 2 91.42 1 8 A ALA 9 2 94.39 1 9 A ILE 10 2 92.29 1 10 A GLY 11 2 93.57 1 11 A THR 12 2 91.35 1 12 A CYS 13 2 92.04 1 13 A LEU 14 2 90.79 1 14 A THR 15 2 90.72 1 15 A ASN 16 2 85.35 1 16 A SER 17 2 79.36 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 ILE . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n CYS . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n THR . 15 A 15 A 16 1 n ASN . 16 A 16 A 17 1 n SER . 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 ? -11.199 -3.202 7.459 1.00 90.48 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.881 -3.851 7.334 1.00 91.63 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.804 -2.834 6.954 1.00 91.70 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.079 -1.890 6.217 1.00 89.86 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.943 -4.964 6.277 1.00 85.88 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.091 -6.167 6.622 1.00 79.56 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.617 -7.641 5.755 1.00 78.79 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.592 -8.870 6.556 1.00 71.34 1 A 1 ATOM 9 N N . ILE A 1 2 ? -7.592 -3.021 7.449 1.00 89.14 2 A 1 ATOM 10 C CA . ILE A 1 2 ? -6.492 -2.083 7.225 1.00 91.37 2 A 1 ATOM 11 C C . ILE A 1 2 ? -5.582 -2.513 6.068 1.00 92.96 2 A 1 ATOM 12 O O . ILE A 1 2 ? -4.594 -1.838 5.759 1.00 92.27 2 A 1 ATOM 13 C CB . ILE A 1 2 ? -5.681 -1.910 8.524 1.00 89.74 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -4.788 -0.676 8.453 1.00 85.50 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? -4.873 -3.171 8.825 1.00 83.73 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -4.245 -0.236 9.786 1.00 78.47 2 A 1 ATOM 17 N N . LEU A 1 3 ? -5.919 -3.618 5.423 1.00 92.27 3 A 1 ATOM 18 C CA . LEU A 1 3 ? -5.123 -4.143 4.309 1.00 92.74 3 A 1 ATOM 19 C C . LEU A 1 3 ? -4.938 -3.125 3.176 1.00 93.83 3 A 1 ATOM 20 O O . LEU A 1 3 ? -3.804 -2.904 2.739 1.00 93.76 3 A 1 ATOM 21 C CB . LEU A 1 3 ? -5.753 -5.441 3.785 1.00 91.18 3 A 1 ATOM 22 C CG . LEU A 1 3 ? -4.942 -6.162 2.715 1.00 83.00 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? -3.660 -6.730 3.309 1.00 80.04 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? -5.774 -7.271 2.092 1.00 78.23 3 A 1 ATOM 25 N N . PRO A 1 4 ? -6.020 -2.495 2.684 1.00 94.04 4 A 1 ATOM 26 C CA . PRO A 1 4 ? -5.871 -1.487 1.621 1.00 93.99 4 A 1 ATOM 27 C C . PRO A 1 4 ? -5.091 -0.261 2.085 1.00 94.85 4 A 1 ATOM 28 O O . PRO A 1 4 ? -4.382 0.369 1.302 1.00 93.17 4 A 1 ATOM 29 C CB . PRO A 1 4 ? -7.320 -1.120 1.258 1.00 91.11 4 A 1 ATOM 30 C CG . PRO A 1 4 ? -8.121 -1.499 2.450 1.00 89.22 4 A 1 ATOM 31 C CD . PRO A 1 4 ? -7.430 -2.693 3.044 1.00 92.33 4 A 1 ATOM 32 N N . PHE A 1 5 ? -5.214 0.063 3.353 1.00 90.77 5 A 1 ATOM 33 C CA . PHE A 1 5 ? -4.495 1.195 3.928 1.00 91.28 5 A 1 ATOM 34 C C . PHE A 1 5 ? -2.992 0.921 3.978 1.00 93.14 5 A 1 ATOM 35 O O . PHE A 1 5 ? -2.181 1.821 3.758 1.00 91.95 5 A 1 ATOM 36 C CB . PHE A 1 5 ? -5.028 1.496 5.329 1.00 90.13 5 A 1 ATOM 37 C CG . PHE A 1 5 ? -4.457 2.756 5.918 1.00 86.83 5 A 1 ATOM 38 C CD1 . PHE A 1 5 ? -4.850 3.998 5.440 1.00 84.37 5 A 1 ATOM 39 C CD2 . PHE A 1 5 ? -3.531 2.690 6.945 1.00 84.04 5 A 1 ATOM 40 C CE1 . PHE A 1 5 ? -4.324 5.162 5.977 1.00 81.86 5 A 1 ATOM 41 C CE2 . PHE A 1 5 ? -2.999 3.856 7.486 1.00 81.11 5 A 1 ATOM 42 C CZ . PHE A 1 5 ? -3.396 5.091 7.001 1.00 82.82 5 A 1 ATOM 43 N N . LEU A 1 6 ? -2.635 -0.320 4.245 1.00 92.31 6 A 1 ATOM 44 C CA . LEU A 1 6 ? -1.231 -0.725 4.268 1.00 92.95 6 A 1 ATOM 45 C C . LEU A 1 6 ? -0.591 -0.547 2.896 1.00 94.39 6 A 1 ATOM 46 O O . LEU A 1 6 ? 0.538 -0.067 2.785 1.00 94.30 6 A 1 ATOM 47 C CB . LEU A 1 6 ? -1.117 -2.184 4.711 1.00 92.41 6 A 1 ATOM 48 C CG . LEU A 1 6 ? -1.272 -2.412 6.212 1.00 87.09 6 A 1 ATOM 49 C CD1 . LEU A 1 6 ? -1.422 -3.896 6.508 1.00 83.57 6 A 1 ATOM 50 C CD2 . LEU A 1 6 ? -0.077 -1.849 6.965 1.00 83.46 6 A 1 ATOM 51 N N . VAL A 1 7 ? -1.327 -0.918 1.861 1.00 93.79 7 A 1 ATOM 52 C CA . VAL A 1 7 ? -0.855 -0.770 0.485 1.00 93.91 7 A 1 ATOM 53 C C . VAL A 1 7 ? -0.639 0.705 0.156 1.00 94.34 7 A 1 ATOM 54 O O . VAL A 1 7 ? 0.355 1.073 -0.480 1.00 93.56 7 A 1 ATOM 55 C CB . VAL A 1 7 ? -1.852 -1.395 -0.509 1.00 92.77 7 A 1 ATOM 56 C CG1 . VAL A 1 7 ? -1.354 -1.251 -1.942 1.00 89.22 7 A 1 ATOM 57 C CG2 . VAL A 1 7 ? -2.081 -2.862 -0.183 1.00 89.88 7 A 1 ATOM 58 N N . LEU A 1 8 ? -1.557 1.534 0.606 1.00 94.62 8 A 1 ATOM 59 C CA . LEU A 1 8 ? -1.464 2.976 0.391 1.00 94.24 8 A 1 ATOM 60 C C . LEU A 1 8 ? -0.233 3.550 1.088 1.00 94.83 8 A 1 ATOM 61 O O . LEU A 1 8 ? 0.483 4.380 0.531 1.00 94.52 8 A 1 ATOM 62 C CB . LEU A 1 8 ? -2.735 3.670 0.903 1.00 93.66 8 A 1 ATOM 63 C CG . LEU A 1 8 ? -3.677 4.216 -0.170 1.00 88.13 8 A 1 ATOM 64 C CD1 . LEU A 1 8 ? -2.998 5.299 -0.982 1.00 85.41 8 A 1 ATOM 65 C CD2 . LEU A 1 8 ? -4.176 3.098 -1.061 1.00 85.95 8 A 1 ATOM 66 N N . ALA A 1 9 ? 0.004 3.104 2.307 1.00 94.55 9 A 1 ATOM 67 C CA . ALA A 1 9 ? 1.144 3.564 3.090 1.00 94.58 9 A 1 ATOM 68 C C . ALA A 1 9 ? 2.465 3.209 2.412 1.00 95.08 9 A 1 ATOM 69 O O . ALA A 1 9 ? 3.365 4.043 2.317 1.00 93.98 9 A 1 ATOM 70 C CB . ALA A 1 9 ? 1.085 2.960 4.489 1.00 93.77 9 A 1 ATOM 71 N N . ILE A 1 10 ? 2.569 1.985 1.924 1.00 94.69 10 A 1 ATOM 72 C CA . ILE A 1 10 ? 3.772 1.523 1.235 1.00 94.50 10 A 1 ATOM 73 C C . ILE A 1 10 ? 3.955 2.267 -0.082 1.00 94.69 10 A 1 ATOM 74 O O . ILE A 1 10 ? 5.067 2.679 -0.425 1.00 93.81 10 A 1 ATOM 75 C CB . ILE A 1 10 ? 3.712 0.004 0.990 1.00 93.95 10 A 1 ATOM 76 C CG1 . ILE A 1 10 ? 3.673 -0.751 2.324 1.00 91.08 10 A 1 ATOM 77 C CG2 . ILE A 1 10 ? 4.917 -0.449 0.165 1.00 90.32 10 A 1 ATOM 78 C CD1 . ILE A 1 10 ? 3.247 -2.198 2.195 1.00 85.27 10 A 1 ATOM 79 N N . GLY A 1 11 ? 2.862 2.441 -0.804 1.00 93.84 11 A 1 ATOM 80 C CA . GLY A 1 11 ? 2.903 3.152 -2.079 1.00 93.32 11 A 1 ATOM 81 C C . GLY A 1 11 ? 3.355 4.590 -1.920 1.00 94.13 11 A 1 ATOM 82 O O . GLY A 1 11 ? 4.167 5.087 -2.706 1.00 93.01 11 A 1 ATOM 83 N N . THR A 1 12 ? 2.855 5.253 -0.898 1.00 94.68 12 A 1 ATOM 84 C CA . THR A 1 12 ? 3.226 6.636 -0.611 1.00 94.19 12 A 1 ATOM 85 C C . THR A 1 12 ? 4.692 6.726 -0.197 1.00 94.49 12 A 1 ATOM 86 O O . THR A 1 12 ? 5.414 7.621 -0.636 1.00 92.37 12 A 1 ATOM 87 C CB . THR A 1 12 ? 2.342 7.217 0.498 1.00 92.73 12 A 1 ATOM 88 O OG1 . THR A 1 12 ? 0.970 7.089 0.137 1.00 85.86 12 A 1 ATOM 89 C CG2 . THR A 1 12 ? 2.648 8.689 0.721 1.00 85.12 12 A 1 ATOM 90 N N . CYS A 1 13 ? 5.130 5.802 0.628 1.00 94.72 13 A 1 ATOM 91 C CA . CYS A 1 13 ? 6.514 5.762 1.085 1.00 94.29 13 A 1 ATOM 92 C C . CYS A 1 13 ? 7.472 5.506 -0.076 1.00 94.38 13 A 1 ATOM 93 O O . CYS A 1 13 ? 8.557 6.079 -0.135 1.00 92.01 13 A 1 ATOM 94 C CB . CYS A 1 13 ? 6.679 4.679 2.149 1.00 92.36 13 A 1 ATOM 95 S SG . CYS A 1 13 ? 8.266 4.767 2.982 1.00 84.45 13 A 1 ATOM 96 N N . LEU A 1 14 ? 7.056 4.651 -0.996 1.00 94.51 14 A 1 ATOM 97 C CA . LEU A 1 14 ? 7.858 4.309 -2.168 1.00 94.50 14 A 1 ATOM 98 C C . LEU A 1 14 ? 8.038 5.511 -3.083 1.00 95.14 14 A 1 ATOM 99 O O . LEU A 1 14 ? 9.150 5.809 -3.521 1.00 94.02 14 A 1 ATOM 100 C CB . LEU A 1 14 ? 7.191 3.167 -2.938 1.00 93.33 14 A 1 ATOM 101 C CG . LEU A 1 14 ? 8.011 2.612 -4.096 1.00 88.31 14 A 1 ATOM 102 C CD1 . LEU A 1 14 ? 9.101 1.685 -3.585 1.00 84.06 14 A 1 ATOM 103 C CD2 . LEU A 1 14 ? 7.113 1.877 -5.077 1.00 82.42 14 A 1 ATOM 104 N N . THR A 1 15 ? 6.951 6.204 -3.367 1.00 94.63 15 A 1 ATOM 105 C CA . THR A 1 15 ? 6.990 7.368 -4.252 1.00 93.99 15 A 1 ATOM 106 C C . THR A 1 15 ? 7.632 8.574 -3.574 1.00 93.23 15 A 1 ATOM 107 O O . THR A 1 15 ? 8.228 9.421 -4.242 1.00 90.23 15 A 1 ATOM 108 C CB . THR A 1 15 ? 5.581 7.740 -4.726 1.00 91.79 15 A 1 ATOM 109 O OG1 . THR A 1 15 ? 4.698 7.835 -3.619 1.00 86.49 15 A 1 ATOM 110 C CG2 . THR A 1 15 ? 5.055 6.713 -5.706 1.00 84.70 15 A 1 ATOM 111 N N . ASN A 1 16 ? 7.503 8.645 -2.269 1.00 92.03 16 A 1 ATOM 112 C CA . ASN A 1 16 ? 8.068 9.748 -1.497 1.00 89.80 16 A 1 ATOM 113 C C . ASN A 1 16 ? 9.583 9.627 -1.375 1.00 88.83 16 A 1 ATOM 114 O O . ASN A 1 16 ? 10.281 10.627 -1.194 1.00 85.48 16 A 1 ATOM 115 C CB . ASN A 1 16 ? 7.442 9.788 -0.102 1.00 87.66 16 A 1 ATOM 116 C CG . ASN A 1 16 ? 7.683 11.106 0.592 1.00 83.60 16 A 1 ATOM 117 O OD1 . ASN A 1 16 ? 7.139 12.132 0.212 1.00 78.14 16 A 1 ATOM 118 N ND2 . ASN A 1 16 ? 8.490 11.087 1.639 1.00 77.27 16 A 1 ATOM 119 N N . SER A 1 17 ? 10.078 8.413 -1.464 1.00 89.28 17 A 1 ATOM 120 C CA . SER A 1 17 ? 11.514 8.149 -1.359 1.00 85.59 17 A 1 ATOM 121 C C . SER A 1 17 ? 12.224 8.376 -2.695 1.00 81.38 17 A 1 ATOM 122 O O . SER A 1 17 ? 13.330 8.920 -2.703 1.00 73.97 17 A 1 ATOM 123 C CB . SER A 1 17 ? 11.756 6.722 -0.869 1.00 79.59 17 A 1 ATOM 124 O OG . SER A 1 17 ? 11.271 6.559 0.444 1.00 72.90 17 A 1 ATOM 125 O OXT . SER A 1 17 ? 11.696 7.987 -3.737 1.00 72.83 17 A 1 #