# 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_spkb32257 # _entry.id spkb32257 # 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" "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" "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" "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 ASN 2 1 n LEU 3 1 n ILE 4 1 n MET 5 1 n LEU 6 1 n ILE 7 1 n LEU 8 1 n ALA 9 1 n LEU 10 1 n TRP 11 1 n ALA 12 1 n PRO 13 1 n VAL 14 1 n ALA 15 1 n GLY 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 @ 2025-07-02 19:19:57)" _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 92.90 _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 81.33 1 1 A ASN 2 2 93.02 1 2 A LEU 3 2 95.04 1 3 A ILE 4 2 96.09 1 4 A MET 5 2 92.19 1 5 A LEU 6 2 95.38 1 6 A ILE 7 2 96.32 1 7 A LEU 8 2 94.88 1 8 A ALA 9 2 97.66 1 9 A LEU 10 2 95.94 1 10 A TRP 11 2 93.39 1 11 A ALA 12 2 96.79 1 12 A PRO 13 2 95.80 1 13 A VAL 14 2 93.71 1 14 A ALA 15 2 92.87 1 15 A GLY 16 2 90.00 1 16 A SER 17 2 79.10 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 ASN . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n MET . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n TRP . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n PRO . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n GLY . 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 ? -2.636 7.752 14.300 1.00 88.40 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.750 6.905 13.103 1.00 89.78 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.624 5.876 13.046 1.00 90.74 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.583 6.040 13.682 1.00 87.45 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.699 7.754 11.832 1.00 82.25 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.357 8.443 11.625 1.00 75.92 1 A 1 ATOM 7 S SD . MET A 1 1 ? -1.315 9.493 10.161 1.00 72.90 1 A 1 ATOM 8 C CE . MET A 1 1 ? -2.240 10.899 10.757 1.00 63.19 1 A 1 ATOM 9 N N . ASN A 1 2 ? -1.830 4.832 12.264 1.00 92.80 2 A 1 ATOM 10 C CA . ASN A 1 2 ? -0.842 3.772 12.111 1.00 96.15 2 A 1 ATOM 11 C C . ASN A 1 2 ? 0.112 4.074 10.956 1.00 97.20 2 A 1 ATOM 12 O O . ASN A 1 2 ? -0.317 4.460 9.869 1.00 96.68 2 A 1 ATOM 13 C CB . ASN A 1 2 ? -1.534 2.436 11.869 1.00 94.62 2 A 1 ATOM 14 C CG . ASN A 1 2 ? -2.288 1.949 13.090 1.00 91.74 2 A 1 ATOM 15 O OD1 . ASN A 1 2 ? -2.980 2.712 13.755 1.00 89.73 2 A 1 ATOM 16 N ND2 . ASN A 1 2 ? -2.167 0.669 13.389 1.00 85.26 2 A 1 ATOM 17 N N . LEU A 1 3 ? 1.401 3.878 11.192 1.00 97.48 3 A 1 ATOM 18 C CA . LEU A 1 3 ? 2.424 4.134 10.175 1.00 97.94 3 A 1 ATOM 19 C C . LEU A 1 3 ? 2.325 3.124 9.037 1.00 98.26 3 A 1 ATOM 20 O O . LEU A 1 3 ? 2.550 3.459 7.875 1.00 98.06 3 A 1 ATOM 21 C CB . LEU A 1 3 ? 3.818 4.073 10.805 1.00 97.52 3 A 1 ATOM 22 C CG . LEU A 1 3 ? 4.952 4.478 9.871 1.00 91.85 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? 4.837 5.948 9.492 1.00 89.86 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? 6.296 4.204 10.531 1.00 89.37 3 A 1 ATOM 25 N N . ILE A 1 4 ? 1.973 1.892 9.379 1.00 97.57 4 A 1 ATOM 26 C CA . ILE A 1 4 ? 1.839 0.821 8.395 1.00 97.49 4 A 1 ATOM 27 C C . ILE A 1 4 ? 0.717 1.126 7.411 1.00 97.71 4 A 1 ATOM 28 O O . ILE A 1 4 ? 0.844 0.896 6.208 1.00 97.45 4 A 1 ATOM 29 C CB . ILE A 1 4 ? 1.575 -0.525 9.085 1.00 97.15 4 A 1 ATOM 30 C CG1 . ILE A 1 4 ? 2.716 -0.859 10.045 1.00 95.40 4 A 1 ATOM 31 C CG2 . ILE A 1 4 ? 1.418 -1.632 8.049 1.00 94.51 4 A 1 ATOM 32 C CD1 . ILE A 1 4 ? 2.419 -2.038 10.934 1.00 91.42 4 A 1 ATOM 33 N N . MET A 1 5 ? -0.388 1.643 7.930 1.00 97.38 5 A 1 ATOM 34 C CA . MET A 1 5 ? -1.535 1.991 7.097 1.00 97.18 5 A 1 ATOM 35 C C . MET A 1 5 ? -1.194 3.114 6.123 1.00 97.32 5 A 1 ATOM 36 O O . MET A 1 5 ? -1.651 3.123 4.985 1.00 96.83 5 A 1 ATOM 37 C CB . MET A 1 5 ? -2.707 2.414 7.977 1.00 96.57 5 A 1 ATOM 38 C CG . MET A 1 5 ? -3.413 1.233 8.620 1.00 91.56 5 A 1 ATOM 39 S SD . MET A 1 5 ? -4.429 0.347 7.446 1.00 84.75 5 A 1 ATOM 40 C CE . MET A 1 5 ? -5.153 -0.889 8.514 1.00 75.94 5 A 1 ATOM 41 N N . LEU A 1 6 ? -0.405 4.059 6.581 1.00 97.08 6 A 1 ATOM 42 C CA . LEU A 1 6 ? 0.001 5.193 5.755 1.00 97.09 6 A 1 ATOM 43 C C . LEU A 1 6 ? 0.917 4.753 4.618 1.00 97.75 6 A 1 ATOM 44 O O . LEU A 1 6 ? 0.746 5.173 3.473 1.00 97.79 6 A 1 ATOM 45 C CB . LEU A 1 6 ? 0.709 6.238 6.613 1.00 96.63 6 A 1 ATOM 46 C CG . LEU A 1 6 ? 1.115 7.509 5.871 1.00 93.94 6 A 1 ATOM 47 C CD1 . LEU A 1 6 ? -0.116 8.257 5.373 1.00 91.62 6 A 1 ATOM 48 C CD2 . LEU A 1 6 ? 1.947 8.403 6.773 1.00 91.12 6 A 1 ATOM 49 N N . ILE A 1 7 ? 1.877 3.918 4.936 1.00 96.69 7 A 1 ATOM 50 C CA . ILE A 1 7 ? 2.833 3.428 3.946 1.00 96.80 7 A 1 ATOM 51 C C . ILE A 1 7 ? 2.153 2.503 2.950 1.00 97.30 7 A 1 ATOM 52 O O . ILE A 1 7 ? 2.394 2.583 1.742 1.00 97.27 7 A 1 ATOM 53 C CB . ILE A 1 7 ? 3.995 2.689 4.629 1.00 96.75 7 A 1 ATOM 54 C CG1 . ILE A 1 7 ? 4.754 3.640 5.557 1.00 96.15 7 A 1 ATOM 55 C CG2 . ILE A 1 7 ? 4.945 2.106 3.589 1.00 95.61 7 A 1 ATOM 56 C CD1 . ILE A 1 7 ? 5.732 2.933 6.464 1.00 93.96 7 A 1 ATOM 57 N N . LEU A 1 8 ? 1.295 1.632 3.456 1.00 97.27 8 A 1 ATOM 58 C CA . LEU A 1 8 ? 0.587 0.676 2.615 1.00 97.22 8 A 1 ATOM 59 C C . LEU A 1 8 ? -0.360 1.385 1.654 1.00 97.57 8 A 1 ATOM 60 O O . LEU A 1 8 ? -0.508 0.980 0.503 1.00 97.55 8 A 1 ATOM 61 C CB . LEU A 1 8 ? -0.199 -0.302 3.488 1.00 96.79 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -0.867 -1.440 2.730 1.00 91.23 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? 0.164 -2.340 2.083 1.00 90.78 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? -1.765 -2.238 3.664 1.00 90.63 8 A 1 ATOM 65 N N . ALA A 1 9 ? -0.995 2.440 2.120 1.00 97.77 9 A 1 ATOM 66 C CA . ALA A 1 9 ? -1.934 3.202 1.304 1.00 97.74 9 A 1 ATOM 67 C C . ALA A 1 9 ? -1.235 3.853 0.115 1.00 97.89 9 A 1 ATOM 68 O O . ALA A 1 9 ? -1.795 3.943 -0.975 1.00 97.42 9 A 1 ATOM 69 C CB . ALA A 1 9 ? -2.617 4.268 2.153 1.00 97.48 9 A 1 ATOM 70 N N . LEU A 1 10 ? -0.015 4.307 0.315 1.00 97.63 10 A 1 ATOM 71 C CA . LEU A 1 10 ? 0.759 4.952 -0.743 1.00 97.39 10 A 1 ATOM 72 C C . LEU A 1 10 ? 1.376 3.927 -1.685 1.00 97.54 10 A 1 ATOM 73 O O . LEU A 1 10 ? 1.622 4.219 -2.858 1.00 97.05 10 A 1 ATOM 74 C CB . LEU A 1 10 ? 1.862 5.811 -0.126 1.00 97.00 10 A 1 ATOM 75 C CG . LEU A 1 10 ? 1.360 7.010 0.675 1.00 94.99 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? 2.495 7.626 1.480 1.00 93.23 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? 0.746 8.045 -0.248 1.00 92.66 10 A 1 ATOM 78 N N . TRP A 1 11 ? 1.621 2.721 -1.165 1.00 97.02 11 A 1 ATOM 79 C CA . TRP A 1 11 ? 2.245 1.669 -1.952 1.00 96.90 11 A 1 ATOM 80 C C . TRP A 1 11 ? 1.222 0.893 -2.766 1.00 97.20 11 A 1 ATOM 81 O O . TRP A 1 11 ? 1.562 0.294 -3.784 1.00 96.46 11 A 1 ATOM 82 C CB . TRP A 1 11 ? 3.019 0.721 -1.039 1.00 96.15 11 A 1 ATOM 83 C CG . TRP A 1 11 ? 4.387 0.410 -1.546 1.00 94.74 11 A 1 ATOM 84 C CD1 . TRP A 1 11 ? 5.448 1.257 -1.591 1.00 92.26 11 A 1 ATOM 85 C CD2 . TRP A 1 11 ? 4.844 -0.837 -2.093 1.00 94.00 11 A 1 ATOM 86 N NE1 . TRP A 1 11 ? 6.534 0.624 -2.139 1.00 91.26 11 A 1 ATOM 87 C CE2 . TRP A 1 11 ? 6.196 -0.666 -2.455 1.00 92.72 11 A 1 ATOM 88 C CE3 . TRP A 1 11 ? 4.240 -2.074 -2.313 1.00 91.20 11 A 1 ATOM 89 C CZ2 . TRP A 1 11 ? 6.945 -1.690 -3.023 1.00 91.11 11 A 1 ATOM 90 C CZ3 . TRP A 1 11 ? 4.985 -3.097 -2.878 1.00 88.11 11 A 1 ATOM 91 C CH2 . TRP A 1 11 ? 6.328 -2.899 -3.232 1.00 88.27 11 A 1 ATOM 92 N N . ALA A 1 12 ? -0.031 0.919 -2.325 1.00 97.30 12 A 1 ATOM 93 C CA . ALA A 1 12 ? -1.109 0.203 -3.005 1.00 97.03 12 A 1 ATOM 94 C C . ALA A 1 12 ? -1.269 0.628 -4.467 1.00 97.14 12 A 1 ATOM 95 O O . ALA A 1 12 ? -1.297 -0.226 -5.355 1.00 96.15 12 A 1 ATOM 96 C CB . ALA A 1 12 ? -2.419 0.368 -2.244 1.00 96.31 12 A 1 ATOM 97 N N . PRO A 1 13 ? -1.381 1.931 -4.755 1.00 97.12 13 A 1 ATOM 98 C CA . PRO A 1 13 ? -1.523 2.406 -6.136 1.00 96.49 13 A 1 ATOM 99 C C . PRO A 1 13 ? -0.302 2.091 -6.984 1.00 96.34 13 A 1 ATOM 100 O O . PRO A 1 13 ? -0.423 1.830 -8.180 1.00 94.04 13 A 1 ATOM 101 C CB . PRO A 1 13 ? -1.677 3.922 -5.990 1.00 95.45 13 A 1 ATOM 102 C CG . PRO A 1 13 ? -2.093 4.132 -4.578 1.00 94.55 13 A 1 ATOM 103 C CD . PRO A 1 13 ? -1.436 3.026 -3.794 1.00 96.61 13 A 1 ATOM 104 N N . VAL A 1 14 ? 0.874 2.124 -6.392 1.00 96.30 14 A 1 ATOM 105 C CA . VAL A 1 14 ? 2.120 1.847 -7.101 1.00 95.72 14 A 1 ATOM 106 C C . VAL A 1 14 ? 2.201 0.388 -7.521 1.00 95.31 14 A 1 ATOM 107 O O . VAL A 1 14 ? 2.635 0.077 -8.633 1.00 93.19 14 A 1 ATOM 108 C CB . VAL A 1 14 ? 3.335 2.196 -6.233 1.00 94.31 14 A 1 ATOM 109 C CG1 . VAL A 1 14 ? 4.623 1.913 -6.986 1.00 90.19 14 A 1 ATOM 110 C CG2 . VAL A 1 14 ? 3.279 3.643 -5.799 1.00 90.93 14 A 1 ATOM 111 N N . ALA A 1 15 ? 1.791 -0.498 -6.624 1.00 94.59 15 A 1 ATOM 112 C CA . ALA A 1 15 ? 1.829 -1.931 -6.893 1.00 93.71 15 A 1 ATOM 113 C C . ALA A 1 15 ? 0.727 -2.349 -7.857 1.00 93.25 15 A 1 ATOM 114 O O . ALA A 1 15 ? 0.884 -3.303 -8.617 1.00 90.55 15 A 1 ATOM 115 C CB . ALA A 1 15 ? 1.711 -2.711 -5.591 1.00 92.26 15 A 1 ATOM 116 N N . GLY A 1 16 ? -0.391 -1.652 -7.822 1.00 93.04 16 A 1 ATOM 117 C CA . GLY A 1 16 ? -1.520 -1.964 -8.689 1.00 90.31 16 A 1 ATOM 118 C C . GLY A 1 16 ? -1.550 -1.099 -9.933 1.00 89.50 16 A 1 ATOM 119 O O . GLY A 1 16 ? -2.519 -0.383 -10.174 1.00 87.15 16 A 1 ATOM 120 N N . SER A 1 17 ? -0.505 -1.185 -10.717 1.00 87.98 17 A 1 ATOM 121 C CA . SER A 1 17 ? -0.412 -0.386 -11.937 1.00 85.09 17 A 1 ATOM 122 C C . SER A 1 17 ? 0.112 -1.234 -13.091 1.00 80.96 17 A 1 ATOM 123 O O . SER A 1 17 ? -0.268 -0.992 -14.244 1.00 73.97 17 A 1 ATOM 124 C CB . SER A 1 17 ? 0.503 0.824 -11.705 1.00 79.51 17 A 1 ATOM 125 O OG . SER A 1 17 ? 1.792 0.419 -11.329 1.00 72.52 17 A 1 ATOM 126 O OXT . SER A 1 17 ? 0.895 -2.146 -12.851 1.00 73.65 17 A 1 #