# 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_spkb34028 # _entry.id spkb34028 # 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" "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" "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" "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 LYS 2 1 n PHE 3 1 n LEU 4 1 n THR 5 1 n VAL 6 1 n ALA 7 1 n ILE 8 1 n VAL 9 1 n LEU 10 1 n ALA 11 1 n ALA 12 1 n ALA 13 1 n ALA 14 1 n SER 15 1 n ALA 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 @ 2025-07-12 13:42:41)" _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 95.52 _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 90.95 1 1 A LYS 2 2 93.61 1 2 A PHE 3 2 95.10 1 3 A LEU 4 2 96.17 1 4 A THR 5 2 97.15 1 5 A VAL 6 2 97.79 1 6 A ALA 7 2 98.21 1 7 A ILE 8 2 96.48 1 8 A VAL 9 2 97.82 1 9 A LEU 10 2 96.19 1 10 A ALA 11 2 98.18 1 11 A ALA 12 2 98.05 1 12 A ALA 13 2 97.96 1 13 A ALA 14 2 97.62 1 14 A SER 15 2 93.57 1 15 A ALA 16 2 86.49 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 LYS . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n ALA . 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 ? -6.188 11.349 5.653 1.00 95.08 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.887 10.792 4.314 1.00 95.79 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.818 9.269 4.383 1.00 96.40 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.132 8.723 5.235 1.00 94.99 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.553 11.318 3.809 1.00 93.41 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.484 12.832 3.865 1.00 90.30 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.034 13.445 3.014 1.00 85.93 1 A 1 ATOM 8 C CE . MET A 1 1 ? -2.705 14.914 3.976 1.00 75.72 1 A 1 ATOM 9 N N . LYS A 1 2 ? -6.523 8.595 3.490 1.00 97.37 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -6.538 7.135 3.475 1.00 97.67 2 A 1 ATOM 11 C C . LYS A 1 2 ? -5.568 6.590 2.426 1.00 97.97 2 A 1 ATOM 12 O O . LYS A 1 2 ? -4.939 5.557 2.631 1.00 97.62 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -7.960 6.647 3.185 1.00 96.94 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -8.295 5.372 3.921 1.00 94.11 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -9.410 5.609 4.933 1.00 91.43 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -9.639 4.369 5.770 1.00 86.91 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -10.873 4.489 6.596 1.00 82.45 2 A 1 ATOM 18 N N . PHE A 1 3 ? -5.462 7.281 1.302 1.00 97.40 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -4.556 6.865 0.233 1.00 97.80 3 A 1 ATOM 20 C C . PHE A 1 3 ? -3.106 6.877 0.711 1.00 98.19 3 A 1 ATOM 21 O O . PHE A 1 3 ? -2.294 6.052 0.292 1.00 97.62 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -4.712 7.795 -0.971 1.00 97.29 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -5.596 7.200 -2.041 1.00 95.85 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -5.209 6.041 -2.694 1.00 93.57 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -6.798 7.801 -2.386 1.00 93.05 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -6.013 5.479 -3.680 1.00 92.03 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -7.608 7.246 -3.371 1.00 91.75 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -7.215 6.084 -4.020 1.00 91.59 3 A 1 ATOM 29 N N . LEU A 1 4 ? -2.784 7.809 1.587 1.00 98.28 4 A 1 ATOM 30 C CA . LEU A 1 4 ? -1.428 7.917 2.128 1.00 98.35 4 A 1 ATOM 31 C C . LEU A 1 4 ? -1.058 6.642 2.879 1.00 98.51 4 A 1 ATOM 32 O O . LEU A 1 4 ? 0.034 6.102 2.724 1.00 98.27 4 A 1 ATOM 33 C CB . LEU A 1 4 ? -1.327 9.132 3.060 1.00 98.10 4 A 1 ATOM 34 C CG . LEU A 1 4 ? -0.369 10.214 2.562 1.00 93.89 4 A 1 ATOM 35 C CD1 . LEU A 1 4 ? 1.039 9.657 2.426 1.00 91.97 4 A 1 ATOM 36 C CD2 . LEU A 1 4 ? -0.849 10.763 1.229 1.00 91.97 4 A 1 ATOM 37 N N . THR A 1 5 ? -1.987 6.161 3.690 1.00 98.07 5 A 1 ATOM 38 C CA . THR A 1 5 ? -1.764 4.946 4.474 1.00 98.10 5 A 1 ATOM 39 C C . THR A 1 5 ? -1.574 3.747 3.549 1.00 98.33 5 A 1 ATOM 40 O O . THR A 1 5 ? -0.703 2.905 3.776 1.00 98.19 5 A 1 ATOM 41 C CB . THR A 1 5 ? -2.958 4.683 5.398 1.00 97.77 5 A 1 ATOM 42 O OG1 . THR A 1 5 ? -3.230 5.849 6.168 1.00 95.40 5 A 1 ATOM 43 C CG2 . THR A 1 5 ? -2.656 3.529 6.345 1.00 94.19 5 A 1 ATOM 44 N N . VAL A 1 6 ? -2.385 3.668 2.509 1.00 98.31 6 A 1 ATOM 45 C CA . VAL A 1 6 ? -2.303 2.570 1.543 1.00 98.39 6 A 1 ATOM 46 C C . VAL A 1 6 ? -0.948 2.590 0.838 1.00 98.54 6 A 1 ATOM 47 O O . VAL A 1 6 ? -0.356 1.541 0.575 1.00 98.44 6 A 1 ATOM 48 C CB . VAL A 1 6 ? -3.426 2.676 0.500 1.00 98.11 6 A 1 ATOM 49 C CG1 . VAL A 1 6 ? -3.329 1.541 -0.513 1.00 96.62 6 A 1 ATOM 50 C CG2 . VAL A 1 6 ? -4.783 2.647 1.191 1.00 96.13 6 A 1 ATOM 51 N N . ALA A 1 7 ? -0.475 3.779 0.532 1.00 98.19 7 A 1 ATOM 52 C CA . ALA A 1 7 ? 0.809 3.933 -0.151 1.00 98.26 7 A 1 ATOM 53 C C . ALA A 1 7 ? 1.944 3.389 0.715 1.00 98.40 7 A 1 ATOM 54 O O . ALA A 1 7 ? 2.869 2.747 0.217 1.00 98.18 7 A 1 ATOM 55 C CB . ALA A 1 7 ? 1.051 5.404 -0.468 1.00 98.03 7 A 1 ATOM 56 N N . ILE A 1 8 ? 1.866 3.634 2.009 1.00 98.09 8 A 1 ATOM 57 C CA . ILE A 1 8 ? 2.892 3.172 2.945 1.00 97.98 8 A 1 ATOM 58 C C . ILE A 1 8 ? 2.883 1.649 3.027 1.00 98.15 8 A 1 ATOM 59 O O . ILE A 1 8 ? 3.936 1.004 3.000 1.00 98.02 8 A 1 ATOM 60 C CB . ILE A 1 8 ? 2.651 3.770 4.341 1.00 97.82 8 A 1 ATOM 61 C CG1 . ILE A 1 8 ? 2.754 5.295 4.291 1.00 96.02 8 A 1 ATOM 62 C CG2 . ILE A 1 8 ? 3.687 3.217 5.329 1.00 95.17 8 A 1 ATOM 63 C CD1 . ILE A 1 8 ? 2.189 5.954 5.538 1.00 90.56 8 A 1 ATOM 64 N N . VAL A 1 9 ? 1.701 1.077 3.130 1.00 98.22 9 A 1 ATOM 65 C CA . VAL A 1 9 ? 1.557 -0.378 3.214 1.00 98.24 9 A 1 ATOM 66 C C . VAL A 1 9 ? 2.029 -1.031 1.920 1.00 98.39 9 A 1 ATOM 67 O O . VAL A 1 9 ? 2.670 -2.083 1.939 1.00 98.23 9 A 1 ATOM 68 C CB . VAL A 1 9 ? 0.094 -0.764 3.482 1.00 97.98 9 A 1 ATOM 69 C CG1 . VAL A 1 9 ? -0.052 -2.275 3.558 1.00 96.92 9 A 1 ATOM 70 C CG2 . VAL A 1 9 ? -0.388 -0.131 4.779 1.00 96.73 9 A 1 ATOM 71 N N . LEU A 1 10 ? 1.700 -0.412 0.809 1.00 98.39 10 A 1 ATOM 72 C CA . LEU A 1 10 ? 2.092 -0.933 -0.500 1.00 98.25 10 A 1 ATOM 73 C C . LEU A 1 10 ? 3.609 -0.955 -0.635 1.00 98.37 10 A 1 ATOM 74 O O . LEU A 1 10 ? 4.190 -1.929 -1.117 1.00 98.24 10 A 1 ATOM 75 C CB . LEU A 1 10 ? 1.482 -0.065 -1.602 1.00 97.88 10 A 1 ATOM 76 C CG . LEU A 1 10 ? 0.336 -0.757 -2.346 1.00 93.12 10 A 1 ATOM 77 C CD1 . LEU A 1 10 ? -0.503 0.263 -3.099 1.00 92.34 10 A 1 ATOM 78 C CD2 . LEU A 1 10 ? 0.885 -1.803 -3.295 1.00 92.93 10 A 1 ATOM 79 N N . ALA A 1 11 ? 4.244 0.113 -0.214 1.00 98.36 11 A 1 ATOM 80 C CA . ALA A 1 11 ? 5.699 0.208 -0.284 1.00 98.25 11 A 1 ATOM 81 C C . ALA A 1 11 ? 6.348 -0.847 0.602 1.00 98.34 11 A 1 ATOM 82 O O . ALA A 1 11 ? 7.352 -1.454 0.228 1.00 98.00 11 A 1 ATOM 83 C CB . ALA A 1 11 ? 6.143 1.599 0.148 1.00 97.93 11 A 1 ATOM 84 N N . ALA A 1 12 ? 5.778 -1.074 1.773 1.00 98.28 12 A 1 ATOM 85 C CA . ALA A 1 12 ? 6.304 -2.066 2.705 1.00 98.11 12 A 1 ATOM 86 C C . ALA A 1 12 ? 6.141 -3.470 2.142 1.00 98.29 12 A 1 ATOM 87 O O . ALA A 1 12 ? 7.033 -4.307 2.276 1.00 97.89 12 A 1 ATOM 88 C CB . ALA A 1 12 ? 5.576 -1.949 4.037 1.00 97.68 12 A 1 ATOM 89 N N . ALA A 1 13 ? 5.007 -3.732 1.505 1.00 98.30 13 A 1 ATOM 90 C CA . ALA A 1 13 ? 4.736 -5.041 0.918 1.00 98.13 13 A 1 ATOM 91 C C . ALA A 1 13 ? 5.690 -5.324 -0.232 1.00 98.27 13 A 1 ATOM 92 O O . ALA A 1 13 ? 6.145 -6.453 -0.407 1.00 97.62 13 A 1 ATOM 93 C CB . ALA A 1 13 ? 3.295 -5.090 0.419 1.00 97.46 13 A 1 ATOM 94 N N . ALA A 1 14 ? 5.989 -4.313 -1.021 1.00 98.11 14 A 1 ATOM 95 C CA . ALA A 1 14 ? 6.899 -4.456 -2.156 1.00 97.84 14 A 1 ATOM 96 C C . ALA A 1 14 ? 8.303 -4.810 -1.688 1.00 98.01 14 A 1 ATOM 97 O O . ALA A 1 14 ? 9.011 -5.580 -2.338 1.00 97.10 14 A 1 ATOM 98 C CB . ALA A 1 14 ? 6.931 -3.163 -2.959 1.00 97.05 14 A 1 ATOM 99 N N . SER A 1 15 ? 8.697 -4.254 -0.564 1.00 97.05 15 A 1 ATOM 100 C CA . SER A 1 15 ? 10.025 -4.507 0.001 1.00 96.70 15 A 1 ATOM 101 C C . SER A 1 15 ? 9.986 -5.639 1.030 1.00 95.79 15 A 1 ATOM 102 O O . SER A 1 15 ? 11.001 -5.966 1.642 1.00 92.04 15 A 1 ATOM 103 C CB . SER A 1 15 ? 10.568 -3.238 0.655 1.00 95.15 15 A 1 ATOM 104 O OG . SER A 1 15 ? 11.921 -3.407 1.029 1.00 84.70 15 A 1 ATOM 105 N N . ALA A 1 16 ? 8.804 -6.218 1.197 1.00 93.46 16 A 1 ATOM 106 C CA . ALA A 1 16 ? 8.571 -7.276 2.181 1.00 90.55 16 A 1 ATOM 107 C C . ALA A 1 16 ? 8.621 -6.712 3.596 1.00 89.34 16 A 1 ATOM 108 O O . ALA A 1 16 ? 9.714 -6.611 4.165 1.00 83.10 16 A 1 ATOM 109 C CB . ALA A 1 16 ? 9.586 -8.400 2.021 1.00 85.18 16 A 1 ATOM 110 O OXT . ALA A 1 16 ? 7.542 -6.322 4.098 1.00 77.32 16 A 1 #