# 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_spkb32486 # _entry.id spkb32486 # 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" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])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" "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 ASN 2 1 n LYS 3 1 n ILE 4 1 n VAL 5 1 n LEU 6 1 n TYR 7 1 n LEU 8 1 n LEU 9 1 n VAL 10 1 n TYR 11 1 n GLY 12 1 n ALA 13 1 n THR 14 1 n LEU 15 1 n GLY 16 # _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 @ 2025-07-13 07:46:46)" _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 94.69 _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 86.27 1 1 A ASN 2 2 93.33 1 2 A LYS 3 2 92.88 1 3 A ILE 4 2 96.35 1 4 A VAL 5 2 97.64 1 5 A LEU 6 2 95.26 1 6 A TYR 7 2 95.99 1 7 A LEU 8 2 96.00 1 8 A LEU 9 2 95.94 1 9 A VAL 10 2 97.25 1 10 A TYR 11 2 94.78 1 11 A GLY 12 2 97.90 1 12 A ALA 13 2 97.66 1 13 A THR 14 2 95.86 1 14 A LEU 15 2 93.50 1 15 A GLY 16 2 89.52 1 16 # _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 LYS . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n TYR . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n TYR . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n THR . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n GLY . 16 A 16 # _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 ? -1.735 7.667 9.189 1.00 91.93 1 A 1 ATOM 2 C CA . MET A 1 1 ? -0.738 7.069 8.281 1.00 93.94 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.077 7.375 6.827 1.00 94.18 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.244 7.516 6.478 1.00 91.72 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.675 5.549 8.474 1.00 88.33 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.444 4.884 7.699 1.00 80.94 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.565 3.118 8.045 1.00 79.28 1 A 1 ATOM 8 C CE . MET A 1 1 ? 1.976 2.693 7.025 1.00 69.84 1 A 1 ATOM 9 N N . ASN A 1 2 ? -0.063 7.456 5.975 1.00 95.64 2 A 1 ATOM 10 C CA . ASN A 1 2 ? -0.271 7.764 4.563 1.00 96.68 2 A 1 ATOM 11 C C . ASN A 1 2 ? -0.923 6.579 3.843 1.00 97.20 2 A 1 ATOM 12 O O . ASN A 1 2 ? -0.416 5.462 3.887 1.00 96.36 2 A 1 ATOM 13 C CB . ASN A 1 2 ? 1.061 8.103 3.902 1.00 95.14 2 A 1 ATOM 14 C CG . ASN A 1 2 ? 0.857 8.722 2.533 1.00 91.20 2 A 1 ATOM 15 O OD1 . ASN A 1 2 ? 0.221 8.149 1.670 1.00 88.92 2 A 1 ATOM 16 N ND2 . ASN A 1 2 ? 1.405 9.908 2.330 1.00 85.52 2 A 1 ATOM 17 N N . LYS A 1 3 ? -2.040 6.844 3.152 1.00 98.11 3 A 1 ATOM 18 C CA . LYS A 1 3 ? -2.779 5.799 2.446 1.00 98.22 3 A 1 ATOM 19 C C . LYS A 1 3 ? -1.983 5.234 1.274 1.00 98.31 3 A 1 ATOM 20 O O . LYS A 1 3 ? -2.068 4.041 0.982 1.00 97.60 3 A 1 ATOM 21 C CB . LYS A 1 3 ? -4.109 6.356 1.946 1.00 97.61 3 A 1 ATOM 22 C CG . LYS A 1 3 ? -5.055 6.757 3.069 1.00 93.64 3 A 1 ATOM 23 C CD . LYS A 1 3 ? -5.470 5.557 3.894 1.00 90.19 3 A 1 ATOM 24 C CE . LYS A 1 3 ? -6.475 5.943 4.969 1.00 84.67 3 A 1 ATOM 25 N NZ . LYS A 1 3 ? -6.867 4.765 5.789 1.00 77.54 3 A 1 ATOM 26 N N . ILE A 1 4 ? -1.224 6.071 0.602 1.00 98.10 4 A 1 ATOM 27 C CA . ILE A 1 4 ? -0.425 5.640 -0.544 1.00 98.09 4 A 1 ATOM 28 C C . ILE A 1 4 ? 0.557 4.550 -0.135 1.00 98.17 4 A 1 ATOM 29 O O . ILE A 1 4 ? 0.722 3.544 -0.831 1.00 97.71 4 A 1 ATOM 30 C CB . ILE A 1 4 ? 0.338 6.825 -1.154 1.00 97.78 4 A 1 ATOM 31 C CG1 . ILE A 1 4 ? -0.647 7.880 -1.657 1.00 95.46 4 A 1 ATOM 32 C CG2 . ILE A 1 4 ? 1.225 6.336 -2.297 1.00 94.98 4 A 1 ATOM 33 C CD1 . ILE A 1 4 ? 0.031 9.142 -2.145 1.00 90.55 4 A 1 ATOM 34 N N . VAL A 1 5 ? 1.200 4.741 0.986 1.00 98.27 5 A 1 ATOM 35 C CA . VAL A 1 5 ? 2.161 3.764 1.493 1.00 98.25 5 A 1 ATOM 36 C C . VAL A 1 5 ? 1.465 2.447 1.811 1.00 98.28 5 A 1 ATOM 37 O O . VAL A 1 5 ? 1.991 1.365 1.536 1.00 98.08 5 A 1 ATOM 38 C CB . VAL A 1 5 ? 2.866 4.289 2.752 1.00 97.99 5 A 1 ATOM 39 C CG1 . VAL A 1 5 ? 3.816 3.242 3.309 1.00 96.40 5 A 1 ATOM 40 C CG2 . VAL A 1 5 ? 3.617 5.571 2.430 1.00 96.23 5 A 1 ATOM 41 N N . LEU A 1 6 ? 0.276 2.543 2.378 1.00 97.82 6 A 1 ATOM 42 C CA . LEU A 1 6 ? -0.505 1.363 2.730 1.00 97.78 6 A 1 ATOM 43 C C . LEU A 1 6 ? -0.866 0.560 1.484 1.00 97.91 6 A 1 ATOM 44 O O . LEU A 1 6 ? -0.762 -0.669 1.476 1.00 97.85 6 A 1 ATOM 45 C CB . LEU A 1 6 ? -1.779 1.779 3.462 1.00 97.48 6 A 1 ATOM 46 C CG . LEU A 1 6 ? -2.664 0.609 3.890 1.00 92.05 6 A 1 ATOM 47 C CD1 . LEU A 1 6 ? -1.925 -0.292 4.870 1.00 90.39 6 A 1 ATOM 48 C CD2 . LEU A 1 6 ? -3.944 1.129 4.526 1.00 90.78 6 A 1 ATOM 49 N N . TYR A 1 7 ? -1.297 1.249 0.435 1.00 97.86 7 A 1 ATOM 50 C CA . TYR A 1 7 ? -1.673 0.587 -0.813 1.00 97.92 7 A 1 ATOM 51 C C . TYR A 1 7 ? -0.480 -0.139 -1.419 1.00 97.98 7 A 1 ATOM 52 O O . TYR A 1 7 ? -0.591 -1.270 -1.899 1.00 97.78 7 A 1 ATOM 53 C CB . TYR A 1 7 ? -2.205 1.612 -1.815 1.00 97.79 7 A 1 ATOM 54 C CG . TYR A 1 7 ? -3.512 2.241 -1.382 1.00 96.96 7 A 1 ATOM 55 C CD1 . TYR A 1 7 ? -4.549 1.456 -0.900 1.00 94.64 7 A 1 ATOM 56 C CD2 . TYR A 1 7 ? -3.697 3.616 -1.470 1.00 94.97 7 A 1 ATOM 57 C CE1 . TYR A 1 7 ? -5.750 2.031 -0.507 1.00 93.87 7 A 1 ATOM 58 C CE2 . TYR A 1 7 ? -4.896 4.197 -1.080 1.00 94.16 7 A 1 ATOM 59 C CZ . TYR A 1 7 ? -5.913 3.399 -0.598 1.00 94.77 7 A 1 ATOM 60 O OH . TYR A 1 7 ? -7.097 3.969 -0.209 1.00 93.19 7 A 1 ATOM 61 N N . LEU A 1 8 ? 0.662 0.498 -1.389 1.00 97.79 8 A 1 ATOM 62 C CA . LEU A 1 8 ? 1.880 -0.093 -1.937 1.00 97.79 8 A 1 ATOM 63 C C . LEU A 1 8 ? 2.247 -1.367 -1.182 1.00 98.04 8 A 1 ATOM 64 O O . LEU A 1 8 ? 2.649 -2.365 -1.785 1.00 97.79 8 A 1 ATOM 65 C CB . LEU A 1 8 ? 3.029 0.909 -1.841 1.00 97.51 8 A 1 ATOM 66 C CG . LEU A 1 8 ? 4.349 0.403 -2.426 1.00 94.49 8 A 1 ATOM 67 C CD1 . LEU A 1 8 ? 4.201 0.127 -3.914 1.00 91.90 8 A 1 ATOM 68 C CD2 . LEU A 1 8 ? 5.449 1.423 -2.189 1.00 92.68 8 A 1 ATOM 69 N N . LEU A 1 9 ? 2.102 -1.329 0.122 1.00 97.83 9 A 1 ATOM 70 C CA . LEU A 1 9 ? 2.413 -2.479 0.967 1.00 97.77 9 A 1 ATOM 71 C C . LEU A 1 9 ? 1.486 -3.651 0.665 1.00 97.99 9 A 1 ATOM 72 O O . LEU A 1 9 ? 1.938 -4.793 0.528 1.00 97.79 9 A 1 ATOM 73 C CB . LEU A 1 9 ? 2.286 -2.086 2.437 1.00 97.40 9 A 1 ATOM 74 C CG . LEU A 1 9 ? 2.602 -3.215 3.417 1.00 93.73 9 A 1 ATOM 75 C CD1 . LEU A 1 9 ? 4.063 -3.620 3.308 1.00 92.47 9 A 1 ATOM 76 C CD2 . LEU A 1 9 ? 2.289 -2.776 4.839 1.00 92.56 9 A 1 ATOM 77 N N . VAL A 1 10 ? 0.190 -3.367 0.557 1.00 98.04 10 A 1 ATOM 78 C CA . VAL A 1 10 ? -0.806 -4.399 0.280 1.00 97.97 10 A 1 ATOM 79 C C . VAL A 1 10 ? -0.570 -5.035 -1.083 1.00 98.06 10 A 1 ATOM 80 O O . VAL A 1 10 ? -0.597 -6.262 -1.221 1.00 97.81 10 A 1 ATOM 81 C CB . VAL A 1 10 ? -2.227 -3.816 0.334 1.00 97.48 10 A 1 ATOM 82 C CG1 . VAL A 1 10 ? -3.250 -4.869 -0.063 1.00 95.64 10 A 1 ATOM 83 C CG2 . VAL A 1 10 ? -2.527 -3.305 1.734 1.00 95.78 10 A 1 ATOM 84 N N . TYR A 1 11 ? -0.338 -4.212 -2.085 1.00 97.99 11 A 1 ATOM 85 C CA . TYR A 1 11 ? -0.116 -4.711 -3.439 1.00 97.87 11 A 1 ATOM 86 C C . TYR A 1 11 ? 1.147 -5.557 -3.509 1.00 98.03 11 A 1 ATOM 87 O O . TYR A 1 11 ? 1.167 -6.609 -4.146 1.00 97.46 11 A 1 ATOM 88 C CB . TYR A 1 11 ? -0.008 -3.541 -4.416 1.00 97.34 11 A 1 ATOM 89 C CG . TYR A 1 11 ? -1.357 -3.060 -4.904 1.00 95.90 11 A 1 ATOM 90 C CD1 . TYR A 1 11 ? -2.266 -2.473 -4.039 1.00 92.90 11 A 1 ATOM 91 C CD2 . TYR A 1 11 ? -1.712 -3.209 -6.237 1.00 93.02 11 A 1 ATOM 92 C CE1 . TYR A 1 11 ? -3.504 -2.042 -4.484 1.00 91.66 11 A 1 ATOM 93 C CE2 . TYR A 1 11 ? -2.950 -2.776 -6.694 1.00 92.17 11 A 1 ATOM 94 C CZ . TYR A 1 11 ? -3.840 -2.195 -5.810 1.00 92.46 11 A 1 ATOM 95 O OH . TYR A 1 11 ? -5.064 -1.768 -6.257 1.00 90.53 11 A 1 ATOM 96 N N . GLY A 1 12 ? 2.186 -5.116 -2.859 1.00 97.98 12 A 1 ATOM 97 C CA . GLY A 1 12 ? 3.445 -5.839 -2.865 1.00 97.93 12 A 1 ATOM 98 C C . GLY A 1 12 ? 3.343 -7.205 -2.214 1.00 98.12 12 A 1 ATOM 99 O O . GLY A 1 12 ? 3.982 -8.161 -2.654 1.00 97.55 12 A 1 ATOM 100 N N . ALA A 1 13 ? 2.537 -7.311 -1.177 1.00 98.03 13 A 1 ATOM 101 C CA . ALA A 1 13 ? 2.376 -8.566 -0.449 1.00 97.92 13 A 1 ATOM 102 C C . ALA A 1 13 ? 1.307 -9.466 -1.059 1.00 98.10 13 A 1 ATOM 103 O O . ALA A 1 13 ? 1.390 -10.692 -0.951 1.00 97.11 13 A 1 ATOM 104 C CB . ALA A 1 13 ? 2.029 -8.275 1.006 1.00 97.14 13 A 1 ATOM 105 N N . THR A 1 14 ? 0.307 -8.869 -1.695 1.00 98.08 14 A 1 ATOM 106 C CA . THR A 1 14 ? -0.798 -9.628 -2.280 1.00 97.91 14 A 1 ATOM 107 C C . THR A 1 14 ? -0.542 -10.015 -3.730 1.00 97.88 14 A 1 ATOM 108 O O . THR A 1 14 ? -0.623 -11.190 -4.096 1.00 96.28 14 A 1 ATOM 109 C CB . THR A 1 14 ? -2.099 -8.827 -2.204 1.00 96.99 14 A 1 ATOM 110 O OG1 . THR A 1 14 ? -2.355 -8.459 -0.850 1.00 92.27 14 A 1 ATOM 111 C CG2 . THR A 1 14 ? -3.259 -9.648 -2.724 1.00 91.60 14 A 1 ATOM 112 N N . LEU A 1 15 ? -0.261 -9.031 -4.557 1.00 97.04 15 A 1 ATOM 113 C CA . LEU A 1 15 ? -0.021 -9.257 -5.976 1.00 96.71 15 A 1 ATOM 114 C C . LEU A 1 15 ? 1.308 -9.969 -6.202 1.00 96.67 15 A 1 ATOM 115 O O . LEU A 1 15 ? 2.339 -9.567 -5.666 1.00 94.94 15 A 1 ATOM 116 C CB . LEU A 1 15 ? -0.059 -7.913 -6.714 1.00 95.60 15 A 1 ATOM 117 C CG . LEU A 1 15 ? -0.163 -8.012 -8.232 1.00 92.33 15 A 1 ATOM 118 C CD1 . LEU A 1 15 ? -0.743 -6.720 -8.790 1.00 88.53 15 A 1 ATOM 119 C CD2 . LEU A 1 15 ? 1.200 -8.269 -8.855 1.00 86.20 15 A 1 ATOM 120 N N . GLY A 1 16 ? 1.270 -11.027 -7.032 1.00 94.70 16 A 1 ATOM 121 C CA . GLY A 1 16 ? 2.494 -11.769 -7.339 1.00 92.08 16 A 1 ATOM 122 C C . GLY A 1 16 ? 2.425 -13.203 -6.858 1.00 89.71 16 A 1 ATOM 123 O O . GLY A 1 16 ? 3.073 -14.075 -7.471 1.00 82.84 16 A 1 ATOM 124 O OXT . GLY A 1 16 ? 1.753 -13.482 -5.880 1.00 88.27 16 A 1 #