# 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_spkb38884 # _entry.id spkb38884 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "PEPTIDE LINKING" "C6 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)C[C@@H](C(=O)O)N ? "L-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" "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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 VAL 2 1 n LEU 3 1 n HIS 4 1 n VAL 5 1 n ILE 6 1 n THR 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n SER 11 1 n ILE 12 1 n GLY 13 1 n LEU 14 1 n CYS 15 1 n TYR 16 1 n GLY 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 @ 2025-07-08 06:46:34)" _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 95.79 _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 90.40 1 1 A VAL 2 2 96.60 1 2 A LEU 3 2 95.76 1 3 A HIS 4 2 94.03 1 4 A VAL 5 2 97.83 1 5 A ILE 6 2 97.25 1 6 A THR 7 2 96.62 1 7 A ALA 8 2 98.23 1 8 A LEU 9 2 96.77 1 9 A LEU 10 2 96.78 1 10 A SER 11 2 96.74 1 11 A ILE 12 2 97.07 1 12 A GLY 13 2 97.85 1 13 A LEU 14 2 96.61 1 14 A CYS 15 2 96.70 1 15 A TYR 16 2 94.64 1 16 A GLY 17 2 90.51 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 VAL . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n HIS . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n THR . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n TYR . 16 A 16 A 17 1 n GLY . 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 ? -5.655 1.710 12.610 1.00 95.63 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.656 2.343 11.728 1.00 96.45 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.796 1.299 11.020 1.00 96.68 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.260 1.559 9.948 1.00 94.91 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.750 3.293 12.528 1.00 93.13 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.509 4.499 13.066 1.00 85.01 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.460 5.637 13.976 1.00 85.02 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.650 6.901 14.405 1.00 76.38 1 A 1 ATOM 9 N N . VAL A 1 2 ? -3.677 0.133 11.634 1.00 97.30 2 A 1 ATOM 10 C CA . VAL A 1 2 ? -2.889 -0.950 11.035 1.00 98.01 2 A 1 ATOM 11 C C . VAL A 1 2 ? -3.426 -1.312 9.655 1.00 98.33 2 A 1 ATOM 12 O O . VAL A 1 2 ? -2.665 -1.497 8.697 1.00 98.02 2 A 1 ATOM 13 C CB . VAL A 1 2 ? -2.887 -2.197 11.935 1.00 97.28 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? -2.086 -3.323 11.296 1.00 93.35 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? -2.321 -1.861 13.308 1.00 93.88 2 A 1 ATOM 16 N N . LEU A 1 3 ? -4.747 -1.398 9.543 1.00 98.05 3 A 1 ATOM 17 C CA . LEU A 1 3 ? -5.383 -1.729 8.269 1.00 98.09 3 A 1 ATOM 18 C C . LEU A 1 3 ? -5.101 -0.660 7.218 1.00 98.31 3 A 1 ATOM 19 O O . LEU A 1 3 ? -4.963 -0.960 6.031 1.00 98.07 3 A 1 ATOM 20 C CB . LEU A 1 3 ? -6.897 -1.885 8.463 1.00 97.74 3 A 1 ATOM 21 C CG . LEU A 1 3 ? -7.646 -2.328 7.209 1.00 93.89 3 A 1 ATOM 22 C CD1 . LEU A 1 3 ? -7.210 -3.729 6.791 1.00 91.39 3 A 1 ATOM 23 C CD2 . LEU A 1 3 ? -9.146 -2.296 7.459 1.00 90.56 3 A 1 ATOM 24 N N . HIS A 1 4 ? -5.009 0.586 7.659 1.00 97.85 4 A 1 ATOM 25 C CA . HIS A 1 4 ? -4.725 1.702 6.755 1.00 97.95 4 A 1 ATOM 26 C C . HIS A 1 4 ? -3.339 1.557 6.135 1.00 98.31 4 A 1 ATOM 27 O O . HIS A 1 4 ? -3.135 1.883 4.961 1.00 98.07 4 A 1 ATOM 28 C CB . HIS A 1 4 ? -4.819 3.035 7.503 1.00 97.47 4 A 1 ATOM 29 C CG . HIS A 1 4 ? -6.225 3.398 7.884 1.00 95.25 4 A 1 ATOM 30 N ND1 . HIS A 1 4 ? -6.792 3.077 9.089 1.00 87.56 4 A 1 ATOM 31 C CD2 . HIS A 1 4 ? -7.178 4.071 7.193 1.00 88.37 4 A 1 ATOM 32 C CE1 . HIS A 1 4 ? -8.038 3.541 9.116 1.00 89.20 4 A 1 ATOM 33 N NE2 . HIS A 1 4 ? -8.302 4.151 7.981 1.00 90.24 4 A 1 ATOM 34 N N . VAL A 1 5 ? -2.374 1.061 6.919 1.00 98.33 5 A 1 ATOM 35 C CA . VAL A 1 5 ? -1.010 0.853 6.431 1.00 98.43 5 A 1 ATOM 36 C C . VAL A 1 5 ? -0.996 -0.205 5.333 1.00 98.50 5 A 1 ATOM 37 O O . VAL A 1 5 ? -0.389 -0.013 4.274 1.00 98.19 5 A 1 ATOM 38 C CB . VAL A 1 5 ? -0.072 0.429 7.573 1.00 98.19 5 A 1 ATOM 39 C CG1 . VAL A 1 5 ? 1.331 0.161 7.046 1.00 96.54 5 A 1 ATOM 40 C CG2 . VAL A 1 5 ? -0.032 1.503 8.651 1.00 96.64 5 A 1 ATOM 41 N N . ILE A 1 6 ? -1.668 -1.322 5.589 1.00 98.37 6 A 1 ATOM 42 C CA . ILE A 1 6 ? -1.737 -2.412 4.622 1.00 98.17 6 A 1 ATOM 43 C C . ILE A 1 6 ? -2.448 -1.954 3.353 1.00 98.24 6 A 1 ATOM 44 O O . ILE A 1 6 ? -2.005 -2.236 2.235 1.00 98.17 6 A 1 ATOM 45 C CB . ILE A 1 6 ? -2.468 -3.628 5.226 1.00 98.10 6 A 1 ATOM 46 C CG1 . ILE A 1 6 ? -1.746 -4.120 6.489 1.00 96.77 6 A 1 ATOM 47 C CG2 . ILE A 1 6 ? -2.562 -4.758 4.197 1.00 96.68 6 A 1 ATOM 48 C CD1 . ILE A 1 6 ? -0.316 -4.577 6.228 1.00 93.48 6 A 1 ATOM 49 N N . THR A 1 7 ? -3.552 -1.248 3.526 1.00 98.30 7 A 1 ATOM 50 C CA . THR A 1 7 ? -4.332 -0.741 2.397 1.00 98.15 7 A 1 ATOM 51 C C . THR A 1 7 ? -3.520 0.251 1.568 1.00 98.30 7 A 1 ATOM 52 O O . THR A 1 7 ? -3.573 0.234 0.332 1.00 98.07 7 A 1 ATOM 53 C CB . THR A 1 7 ? -5.616 -0.061 2.890 1.00 97.65 7 A 1 ATOM 54 O OG1 . THR A 1 7 ? -6.385 -0.981 3.663 1.00 93.21 7 A 1 ATOM 55 C CG2 . THR A 1 7 ? -6.461 0.411 1.714 1.00 92.65 7 A 1 ATOM 56 N N . ALA A 1 8 ? -2.761 1.113 2.240 1.00 98.31 8 A 1 ATOM 57 C CA . ALA A 1 8 ? -1.936 2.111 1.564 1.00 98.26 8 A 1 ATOM 58 C C . ALA A 1 8 ? -0.868 1.439 0.704 1.00 98.39 8 A 1 ATOM 59 O O . ALA A 1 8 ? -0.668 1.807 -0.454 1.00 98.09 8 A 1 ATOM 60 C CB . ALA A 1 8 ? -1.277 3.036 2.586 1.00 98.11 8 A 1 ATOM 61 N N . LEU A 1 9 ? -0.183 0.436 1.272 1.00 98.22 9 A 1 ATOM 62 C CA . LEU A 1 9 ? 0.860 -0.290 0.551 1.00 98.11 9 A 1 ATOM 63 C C . LEU A 1 9 ? 0.274 -1.029 -0.643 1.00 98.21 9 A 1 ATOM 64 O O . LEU A 1 9 ? 0.880 -1.076 -1.718 1.00 97.81 9 A 1 ATOM 65 C CB . LEU A 1 9 ? 1.554 -1.285 1.485 1.00 97.89 9 A 1 ATOM 66 C CG . LEU A 1 9 ? 2.392 -0.637 2.586 1.00 96.12 9 A 1 ATOM 67 C CD1 . LEU A 1 9 ? 2.875 -1.689 3.574 1.00 93.95 9 A 1 ATOM 68 C CD2 . LEU A 1 9 ? 3.585 0.098 1.983 1.00 93.86 9 A 1 ATOM 69 N N . LEU A 1 10 ? -0.904 -1.607 -0.454 1.00 98.42 10 A 1 ATOM 70 C CA . LEU A 1 10 ? -1.586 -2.335 -1.520 1.00 98.30 10 A 1 ATOM 71 C C . LEU A 1 10 ? -1.958 -1.386 -2.655 1.00 98.43 10 A 1 ATOM 72 O O . LEU A 1 10 ? -1.824 -1.729 -3.835 1.00 98.22 10 A 1 ATOM 73 C CB . LEU A 1 10 ? -2.823 -3.036 -0.951 1.00 98.11 10 A 1 ATOM 74 C CG . LEU A 1 10 ? -3.425 -4.111 -1.863 1.00 95.86 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? -4.159 -5.150 -1.023 1.00 93.18 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? -4.385 -3.505 -2.866 1.00 93.69 10 A 1 ATOM 77 N N . SER A 1 11 ? -2.417 -0.191 -2.307 1.00 98.34 11 A 1 ATOM 78 C CA . SER A 1 11 ? -2.789 0.822 -3.289 1.00 98.26 11 A 1 ATOM 79 C C . SER A 1 11 ? -1.590 1.224 -4.140 1.00 98.38 11 A 1 ATOM 80 O O . SER A 1 11 ? -1.694 1.359 -5.358 1.00 97.83 11 A 1 ATOM 81 C CB . SER A 1 11 ? -3.359 2.056 -2.594 1.00 97.58 11 A 1 ATOM 82 O OG . SER A 1 11 ? -3.774 3.008 -3.545 1.00 90.04 11 A 1 ATOM 83 N N . ILE A 1 12 ? -0.430 1.398 -3.490 1.00 98.45 12 A 1 ATOM 84 C CA . ILE A 1 12 ? 0.802 1.755 -4.190 1.00 98.26 12 A 1 ATOM 85 C C . ILE A 1 12 ? 1.191 0.643 -5.159 1.00 98.40 12 A 1 ATOM 86 O O . ILE A 1 12 ? 1.604 0.904 -6.294 1.00 98.05 12 A 1 ATOM 87 C CB . ILE A 1 12 ? 1.946 2.010 -3.194 1.00 97.84 12 A 1 ATOM 88 C CG1 . ILE A 1 12 ? 1.631 3.229 -2.320 1.00 96.29 12 A 1 ATOM 89 C CG2 . ILE A 1 12 ? 3.266 2.226 -3.940 1.00 95.98 12 A 1 ATOM 90 C CD1 . ILE A 1 12 ? 2.547 3.364 -1.119 1.00 93.28 12 A 1 ATOM 91 N N . GLY A 1 13 ? 1.062 -0.597 -4.712 1.00 97.94 13 A 1 ATOM 92 C CA . GLY A 1 13 ? 1.384 -1.743 -5.550 1.00 97.80 13 A 1 ATOM 93 C C . GLY A 1 13 ? 0.531 -1.797 -6.803 1.00 98.09 13 A 1 ATOM 94 O O . GLY A 1 13 ? 1.025 -2.120 -7.885 1.00 97.57 13 A 1 ATOM 95 N N . LEU A 1 14 ? -0.748 -1.474 -6.672 1.00 98.26 14 A 1 ATOM 96 C CA . LEU A 1 14 ? -1.664 -1.467 -7.807 1.00 98.28 14 A 1 ATOM 97 C C . LEU A 1 14 ? -1.307 -0.368 -8.801 1.00 98.41 14 A 1 ATOM 98 O O . LEU A 1 14 ? -1.458 -0.543 -10.013 1.00 97.89 14 A 1 ATOM 99 C CB . LEU A 1 14 ? -3.103 -1.273 -7.319 1.00 97.92 14 A 1 ATOM 100 C CG . LEU A 1 14 ? -3.670 -2.467 -6.556 1.00 96.05 14 A 1 ATOM 101 C CD1 . LEU A 1 14 ? -5.029 -2.120 -5.975 1.00 93.39 14 A 1 ATOM 102 C CD2 . LEU A 1 14 ? -3.782 -3.679 -7.472 1.00 92.64 14 A 1 ATOM 103 N N . CYS A 1 15 ? -0.823 0.767 -8.303 1.00 97.97 15 A 1 ATOM 104 C CA . CYS A 1 15 ? -0.427 1.887 -9.156 1.00 97.88 15 A 1 ATOM 105 C C . CYS A 1 15 ? 0.779 1.530 -10.020 1.00 97.94 15 A 1 ATOM 106 O O . CYS A 1 15 ? 0.863 1.932 -11.178 1.00 96.96 15 A 1 ATOM 107 C CB . CYS A 1 15 ? -0.107 3.116 -8.301 1.00 96.61 15 A 1 ATOM 108 S SG . CYS A 1 15 ? -1.577 3.811 -7.507 1.00 92.87 15 A 1 ATOM 109 N N . TYR A 1 16 ? 1.729 0.787 -9.427 1.00 97.64 16 A 1 ATOM 110 C CA . TYR A 1 16 ? 2.938 0.394 -10.140 1.00 97.52 16 A 1 ATOM 111 C C . TYR A 1 16 ? 2.753 -0.918 -10.896 1.00 97.39 16 A 1 ATOM 112 O O . TYR A 1 16 ? 3.272 -1.077 -12.003 1.00 95.87 16 A 1 ATOM 113 C CB . TYR A 1 16 ? 4.111 0.268 -9.157 1.00 96.80 16 A 1 ATOM 114 C CG . TYR A 1 16 ? 4.716 1.600 -8.760 1.00 95.28 16 A 1 ATOM 115 C CD1 . TYR A 1 16 ? 4.157 2.366 -7.750 1.00 93.67 16 A 1 ATOM 116 C CD2 . TYR A 1 16 ? 5.846 2.081 -9.408 1.00 92.69 16 A 1 ATOM 117 C CE1 . TYR A 1 16 ? 4.707 3.586 -7.393 1.00 92.87 16 A 1 ATOM 118 C CE2 . TYR A 1 16 ? 6.408 3.301 -9.055 1.00 91.92 16 A 1 ATOM 119 C CZ . TYR A 1 16 ? 5.832 4.050 -8.045 1.00 92.76 16 A 1 ATOM 120 O OH . TYR A 1 16 ? 6.383 5.255 -7.694 1.00 91.26 16 A 1 ATOM 121 N N . GLY A 1 17 ? 2.023 -1.848 -10.295 1.00 94.92 17 A 1 ATOM 122 C CA . GLY A 1 17 ? 1.779 -3.167 -10.882 1.00 92.65 17 A 1 ATOM 123 C C . GLY A 1 17 ? 1.048 -3.080 -12.201 1.00 90.68 17 A 1 ATOM 124 O O . GLY A 1 17 ? 1.619 -3.498 -13.227 1.00 86.07 17 A 1 ATOM 125 O OXT . GLY A 1 17 ? -0.099 -2.632 -12.185 1.00 88.21 17 A 1 #