# 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_spkb30333 # _entry.id spkb30333 # 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 "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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" "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 PHE 2 1 n LEU 3 1 n MET 4 1 n TYR 5 1 n LEU 6 1 n LEU 7 1 n VAL 8 1 n GLN 9 1 n THR 10 1 n THR 11 1 n GLU 12 1 n SER 13 # _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 @ 2025-07-12 15:03:20)" _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 89.05 _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 86.95 1 1 A PHE 2 2 92.07 1 2 A LEU 3 2 92.41 1 3 A MET 4 2 90.98 1 4 A TYR 5 2 93.29 1 5 A LEU 6 2 94.23 1 6 A LEU 7 2 93.56 1 7 A VAL 8 2 93.62 1 8 A GLN 9 2 90.46 1 9 A THR 10 2 92.04 1 10 A THR 11 2 88.94 1 11 A GLU 12 2 73.89 1 12 A SER 13 2 72.53 1 13 # _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 LEU . 3 A 3 A 4 1 n MET . 4 A 4 A 5 1 n TYR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n GLN . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n GLU . 12 A 12 A 13 1 n SER . 13 A 13 # _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 ? -1.488 12.377 5.749 1.00 90.74 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.157 11.729 4.466 1.00 92.64 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.001 10.475 4.241 1.00 94.07 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.943 9.527 5.019 1.00 92.49 1 A 1 ATOM 5 C CB . MET A 1 1 ? 0.326 11.335 4.420 1.00 88.76 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.230 12.493 4.013 1.00 83.72 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.195 12.772 2.250 1.00 80.57 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.404 14.089 2.104 1.00 72.63 1 A 1 ATOM 9 N N . PHE A 1 2 ? -2.781 10.482 3.176 1.00 93.03 2 A 1 ATOM 10 C CA . PHE A 1 2 ? -3.639 9.350 2.829 1.00 94.89 2 A 1 ATOM 11 C C . PHE A 1 2 ? -2.860 8.297 2.041 1.00 96.45 2 A 1 ATOM 12 O O . PHE A 1 2 ? -3.064 7.100 2.220 1.00 96.07 2 A 1 ATOM 13 C CB . PHE A 1 2 ? -4.834 9.845 2.008 1.00 94.11 2 A 1 ATOM 14 C CG . PHE A 1 2 ? -5.511 8.734 1.243 1.00 93.07 2 A 1 ATOM 15 C CD1 . PHE A 1 2 ? -6.178 7.721 1.913 1.00 90.08 2 A 1 ATOM 16 C CD2 . PHE A 1 2 ? -5.462 8.707 -0.140 1.00 90.24 2 A 1 ATOM 17 C CE1 . PHE A 1 2 ? -6.805 6.695 1.216 1.00 88.66 2 A 1 ATOM 18 C CE2 . PHE A 1 2 ? -6.086 7.678 -0.847 1.00 87.89 2 A 1 ATOM 19 C CZ . PHE A 1 2 ? -6.757 6.678 -0.167 1.00 88.25 2 A 1 ATOM 20 N N . LEU A 1 3 ? -1.963 8.734 1.172 1.00 94.23 3 A 1 ATOM 21 C CA . LEU A 1 3 ? -1.152 7.828 0.357 1.00 95.31 3 A 1 ATOM 22 C C . LEU A 1 3 ? -0.203 7.008 1.227 1.00 96.29 3 A 1 ATOM 23 O O . LEU A 1 3 ? 0.163 5.889 0.888 1.00 96.10 3 A 1 ATOM 24 C CB . LEU A 1 3 ? -0.360 8.626 -0.687 1.00 94.70 3 A 1 ATOM 25 C CG . LEU A 1 3 ? -0.614 8.200 -2.138 1.00 89.28 3 A 1 ATOM 26 C CD1 . LEU A 1 3 ? -0.231 6.751 -2.357 1.00 86.66 3 A 1 ATOM 27 C CD2 . LEU A 1 3 ? -2.091 8.416 -2.463 1.00 86.67 3 A 1 ATOM 28 N N . MET A 1 4 ? 0.201 7.581 2.367 1.00 95.51 4 A 1 ATOM 29 C CA . MET A 1 4 ? 1.100 6.893 3.296 1.00 95.96 4 A 1 ATOM 30 C C . MET A 1 4 ? 0.419 5.665 3.900 1.00 96.36 4 A 1 ATOM 31 O O . MET A 1 4 ? 1.061 4.653 4.155 1.00 95.62 4 A 1 ATOM 32 C CB . MET A 1 4 ? 1.545 7.843 4.414 1.00 95.24 4 A 1 ATOM 33 C CG . MET A 1 4 ? 2.664 8.780 3.980 1.00 90.90 4 A 1 ATOM 34 S SD . MET A 1 4 ? 3.331 9.730 5.355 1.00 83.40 4 A 1 ATOM 35 C CE . MET A 1 4 ? 4.720 10.543 4.569 1.00 74.83 4 A 1 ATOM 36 N N . TYR A 1 5 ? -0.875 5.759 4.110 1.00 95.37 5 A 1 ATOM 37 C CA . TYR A 1 5 ? -1.648 4.652 4.672 1.00 95.73 5 A 1 ATOM 38 C C . TYR A 1 5 ? -1.642 3.455 3.720 1.00 96.20 5 A 1 ATOM 39 O O . TYR A 1 5 ? -1.417 2.319 4.134 1.00 95.75 5 A 1 ATOM 40 C CB . TYR A 1 5 ? -3.081 5.114 4.945 1.00 95.48 5 A 1 ATOM 41 C CG . TYR A 1 5 ? -4.084 3.985 4.860 1.00 94.49 5 A 1 ATOM 42 C CD1 . TYR A 1 5 ? -4.056 2.941 5.780 1.00 92.43 5 A 1 ATOM 43 C CD2 . TYR A 1 5 ? -5.047 3.971 3.862 1.00 92.36 5 A 1 ATOM 44 C CE1 . TYR A 1 5 ? -4.978 1.904 5.701 1.00 90.86 5 A 1 ATOM 45 C CE2 . TYR A 1 5 ? -5.971 2.933 3.781 1.00 90.84 5 A 1 ATOM 46 C CZ . TYR A 1 5 ? -5.929 1.906 4.698 1.00 90.65 5 A 1 ATOM 47 O OH . TYR A 1 5 ? -6.836 0.880 4.612 1.00 89.26 5 A 1 ATOM 48 N N . LEU A 1 6 ? -1.887 3.711 2.451 1.00 95.91 6 A 1 ATOM 49 C CA . LEU A 1 6 ? -1.907 2.665 1.434 1.00 95.89 6 A 1 ATOM 50 C C . LEU A 1 6 ? -0.503 2.124 1.185 1.00 96.23 6 A 1 ATOM 51 O O . LEU A 1 6 ? -0.322 0.965 0.835 1.00 95.99 6 A 1 ATOM 52 C CB . LEU A 1 6 ? -2.491 3.217 0.133 1.00 95.63 6 A 1 ATOM 53 C CG . LEU A 1 6 ? -3.744 2.498 -0.353 1.00 93.07 6 A 1 ATOM 54 C CD1 . LEU A 1 6 ? -3.459 1.025 -0.598 1.00 90.57 6 A 1 ATOM 55 C CD2 . LEU A 1 6 ? -4.841 2.655 0.694 1.00 90.52 6 A 1 ATOM 56 N N . LEU A 1 7 ? 0.484 2.975 1.370 1.00 95.91 7 A 1 ATOM 57 C CA . LEU A 1 7 ? 1.879 2.599 1.160 1.00 95.57 7 A 1 ATOM 58 C C . LEU A 1 7 ? 2.304 1.483 2.109 1.00 95.30 7 A 1 ATOM 59 O O . LEU A 1 7 ? 3.109 0.623 1.748 1.00 94.26 7 A 1 ATOM 60 C CB . LEU A 1 7 ? 2.782 3.830 1.342 1.00 95.06 7 A 1 ATOM 61 C CG . LEU A 1 7 ? 4.285 3.536 1.336 1.00 92.58 7 A 1 ATOM 62 C CD1 . LEU A 1 7 ? 5.052 4.685 0.712 1.00 89.99 7 A 1 ATOM 63 C CD2 . LEU A 1 7 ? 4.775 3.312 2.765 1.00 89.84 7 A 1 ATOM 64 N N . VAL A 1 8 ? 1.772 1.482 3.325 1.00 95.66 8 A 1 ATOM 65 C CA . VAL A 1 8 ? 2.118 0.475 4.325 1.00 95.25 8 A 1 ATOM 66 C C . VAL A 1 8 ? 1.506 -0.879 3.989 1.00 94.71 8 A 1 ATOM 67 O O . VAL A 1 8 ? 2.041 -1.920 4.371 1.00 92.83 8 A 1 ATOM 68 C CB . VAL A 1 8 ? 1.660 0.906 5.723 1.00 94.42 8 A 1 ATOM 69 C CG1 . VAL A 1 8 ? 2.066 -0.136 6.755 1.00 91.16 8 A 1 ATOM 70 C CG2 . VAL A 1 8 ? 2.266 2.254 6.084 1.00 91.31 8 A 1 ATOM 71 N N . GLN A 1 9 ? 0.386 -0.876 3.283 1.00 94.97 9 A 1 ATOM 72 C CA . GLN A 1 9 ? -0.300 -2.111 2.919 1.00 94.76 9 A 1 ATOM 73 C C . GLN A 1 9 ? 0.089 -2.597 1.526 1.00 94.58 9 A 1 ATOM 74 O O . GLN A 1 9 ? -0.183 -3.741 1.172 1.00 92.70 9 A 1 ATOM 75 C CB . GLN A 1 9 ? -1.811 -1.911 2.983 1.00 93.86 9 A 1 ATOM 76 C CG . GLN A 1 9 ? -2.309 -1.630 4.384 1.00 89.32 9 A 1 ATOM 77 C CD . GLN A 1 9 ? -3.813 -1.764 4.471 1.00 88.78 9 A 1 ATOM 78 O OE1 . GLN A 1 9 ? -4.451 -2.346 3.599 1.00 83.68 9 A 1 ATOM 79 N NE2 . GLN A 1 9 ? -4.399 -1.227 5.525 1.00 81.51 9 A 1 ATOM 80 N N . THR A 1 10 ? 0.720 -1.736 0.747 1.00 94.52 10 A 1 ATOM 81 C CA . THR A 1 10 ? 1.131 -2.080 -0.611 1.00 94.38 10 A 1 ATOM 82 C C . THR A 1 10 ? 2.644 -2.249 -0.703 1.00 93.89 10 A 1 ATOM 83 O O . THR A 1 10 ? 3.251 -1.986 -1.738 1.00 91.37 10 A 1 ATOM 84 C CB . THR A 1 10 ? 0.688 -1.012 -1.615 1.00 92.91 10 A 1 ATOM 85 O OG1 . THR A 1 10 ? 0.979 -1.478 -2.935 1.00 89.01 10 A 1 ATOM 86 C CG2 . THR A 1 10 ? 1.405 0.300 -1.373 1.00 88.23 10 A 1 ATOM 87 N N . THR A 1 11 ? 3.256 -2.702 0.384 1.00 92.85 11 A 1 ATOM 88 C CA . THR A 1 11 ? 4.703 -2.884 0.425 1.00 92.44 11 A 1 ATOM 89 C C . THR A 1 11 ? 5.132 -4.137 -0.332 1.00 91.17 11 A 1 ATOM 90 O O . THR A 1 11 ? 4.475 -5.171 -0.266 1.00 87.84 11 A 1 ATOM 91 C CB . THR A 1 11 ? 5.203 -2.989 1.871 1.00 90.60 11 A 1 ATOM 92 O OG1 . THR A 1 11 ? 6.617 -3.202 1.869 1.00 84.70 11 A 1 ATOM 93 C CG2 . THR A 1 11 ? 4.527 -4.132 2.601 1.00 83.01 11 A 1 ATOM 94 N N . GLU A 1 12 ? 6.263 -4.048 -1.041 1.00 85.63 12 A 1 ATOM 95 C CA . GLU A 1 12 ? 6.793 -5.180 -1.808 1.00 83.13 12 A 1 ATOM 96 C C . GLU A 1 12 ? 8.096 -5.674 -1.190 1.00 80.37 12 A 1 ATOM 97 O O . GLU A 1 12 ? 9.146 -5.075 -1.394 1.00 74.51 12 A 1 ATOM 98 C CB . GLU A 1 12 ? 7.043 -4.778 -3.260 1.00 78.94 12 A 1 ATOM 99 C CG . GLU A 1 12 ? 5.773 -4.583 -4.048 1.00 70.54 12 A 1 ATOM 100 C CD . GLU A 1 12 ? 6.053 -4.419 -5.525 1.00 65.99 12 A 1 ATOM 101 O OE1 . GLU A 1 12 ? 7.227 -4.233 -5.892 1.00 62.44 12 A 1 ATOM 102 O OE2 . GLU A 1 12 ? 5.096 -4.471 -6.313 1.00 63.46 12 A 1 ATOM 103 N N . SER A 1 13 ? 8.019 -6.774 -0.416 1.00 81.45 13 A 1 ATOM 104 C CA . SER A 1 13 ? 9.192 -7.345 0.253 1.00 78.31 13 A 1 ATOM 105 C C . SER A 1 13 ? 10.349 -7.579 -0.728 1.00 73.97 13 A 1 ATOM 106 O O . SER A 1 13 ? 11.479 -7.182 -0.423 1.00 69.28 13 A 1 ATOM 107 C CB . SER A 1 13 ? 8.808 -8.672 0.915 1.00 72.24 13 A 1 ATOM 108 O OG . SER A 1 13 ? 8.124 -9.508 0.018 1.00 67.11 13 A 1 ATOM 109 O OXT . SER A 1 13 ? 10.149 -8.138 -1.782 1.00 65.36 13 A 1 #