# 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_spkb33097 # _entry.id spkb33097 # 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 "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N ? "L-PEPTIDE LINKING" "C4 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "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 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" "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 ASP 2 1 n ARG 3 1 n VAL 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n SER 9 1 n VAL 10 1 n LEU 11 1 n THR 12 1 n LEU 13 1 n GLY 14 1 n VAL 15 1 n SER 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 @ 2025-07-12 09:03:01)" _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 89.65 _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 80.07 1 1 A ASP 2 2 84.99 1 2 A ARG 3 2 85.51 1 3 A VAL 4 2 92.80 1 4 A LEU 5 2 91.36 1 5 A LEU 6 2 91.07 1 6 A LEU 7 2 91.60 1 7 A LEU 8 2 92.17 1 8 A SER 9 2 92.95 1 9 A VAL 10 2 95.31 1 10 A LEU 11 2 94.19 1 11 A THR 12 2 94.69 1 12 A LEU 13 2 93.64 1 13 A GLY 14 2 94.05 1 14 A VAL 15 2 89.83 1 15 A SER 16 2 86.56 1 16 A SER 17 2 77.21 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 ASP . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n SER . 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 ? -2.449 3.768 12.715 1.00 85.88 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.141 4.402 12.958 1.00 89.23 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.197 4.202 11.772 1.00 89.31 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.534 5.118 11.407 1.00 84.83 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.514 3.846 14.233 1.00 83.15 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.276 4.307 15.475 1.00 76.34 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.415 3.938 17.005 1.00 70.69 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.489 4.753 18.176 1.00 61.11 1 A 1 ATOM 9 N N . ASP A 1 2 ? -0.223 3.011 11.164 1.00 89.10 2 A 1 ATOM 10 C CA . ASP A 1 2 ? 0.618 2.728 10.001 1.00 93.26 2 A 1 ATOM 11 C C . ASP A 1 2 ? -0.131 3.065 8.711 1.00 94.73 2 A 1 ATOM 12 O O . ASP A 1 2 ? -0.781 2.213 8.103 1.00 91.85 2 A 1 ATOM 13 C CB . ASP A 1 2 ? 1.040 1.261 10.012 1.00 87.95 2 A 1 ATOM 14 C CG . ASP A 1 2 ? 1.921 0.931 11.203 1.00 76.27 2 A 1 ATOM 15 O OD1 . ASP A 1 2 ? 2.885 1.678 11.445 1.00 74.85 2 A 1 ATOM 16 O OD2 . ASP A 1 2 ? 1.635 -0.067 11.884 1.00 71.92 2 A 1 ATOM 17 N N . ARG A 1 3 ? -0.052 4.325 8.296 1.00 92.58 3 A 1 ATOM 18 C CA . ARG A 1 3 ? -0.723 4.787 7.073 1.00 94.48 3 A 1 ATOM 19 C C . ARG A 1 3 ? 0.085 4.446 5.824 1.00 95.33 3 A 1 ATOM 20 O O . ARG A 1 3 ? -0.487 4.259 4.755 1.00 93.30 3 A 1 ATOM 21 C CB . ARG A 1 3 ? -0.956 6.299 7.155 1.00 92.47 3 A 1 ATOM 22 C CG . ARG A 1 3 ? -2.017 6.650 8.190 1.00 87.20 3 A 1 ATOM 23 C CD . ARG A 1 3 ? -2.175 8.155 8.287 1.00 84.18 3 A 1 ATOM 24 N NE . ARG A 1 3 ? -3.225 8.525 9.240 1.00 80.09 3 A 1 ATOM 25 C CZ . ARG A 1 3 ? -3.475 9.758 9.640 1.00 77.54 3 A 1 ATOM 26 N NH1 . ARG A 1 3 ? -2.760 10.778 9.194 1.00 72.36 3 A 1 ATOM 27 N NH2 . ARG A 1 3 ? -4.447 9.989 10.495 1.00 71.03 3 A 1 ATOM 28 N N . VAL A 1 4 ? 1.395 4.351 5.962 1.00 94.32 4 A 1 ATOM 29 C CA . VAL A 1 4 ? 2.288 4.043 4.839 1.00 95.35 4 A 1 ATOM 30 C C . VAL A 1 4 ? 2.011 2.635 4.306 1.00 96.05 4 A 1 ATOM 31 O O . VAL A 1 4 ? 1.914 2.430 3.095 1.00 94.67 4 A 1 ATOM 32 C CB . VAL A 1 4 ? 3.764 4.192 5.260 1.00 94.00 4 A 1 ATOM 33 C CG1 . VAL A 1 4 ? 4.693 3.896 4.091 1.00 87.04 4 A 1 ATOM 34 C CG2 . VAL A 1 4 ? 4.036 5.598 5.785 1.00 88.15 4 A 1 ATOM 35 N N . LEU A 1 5 ? 1.851 1.681 5.206 1.00 95.13 5 A 1 ATOM 36 C CA . LEU A 1 5 ? 1.553 0.297 4.829 1.00 95.36 5 A 1 ATOM 37 C C . LEU A 1 5 ? 0.184 0.188 4.155 1.00 96.06 5 A 1 ATOM 38 O O . LEU A 1 5 ? 0.020 -0.564 3.195 1.00 95.27 5 A 1 ATOM 39 C CB . LEU A 1 5 ? 1.609 -0.595 6.076 1.00 94.24 5 A 1 ATOM 40 C CG . LEU A 1 5 ? 3.030 -1.010 6.454 1.00 87.07 5 A 1 ATOM 41 C CD1 . LEU A 1 5 ? 3.081 -1.472 7.905 1.00 84.22 5 A 1 ATOM 42 C CD2 . LEU A 1 5 ? 3.502 -2.151 5.550 1.00 83.50 5 A 1 ATOM 43 N N . LEU A 1 6 ? -0.786 0.956 4.636 1.00 95.12 6 A 1 ATOM 44 C CA . LEU A 1 6 ? -2.130 0.979 4.059 1.00 95.16 6 A 1 ATOM 45 C C . LEU A 1 6 ? -2.103 1.503 2.624 1.00 95.84 6 A 1 ATOM 46 O O . LEU A 1 6 ? -2.690 0.898 1.728 1.00 95.23 6 A 1 ATOM 47 C CB . LEU A 1 6 ? -3.047 1.839 4.936 1.00 94.38 6 A 1 ATOM 48 C CG . LEU A 1 6 ? -4.079 1.021 5.709 1.00 86.39 6 A 1 ATOM 49 C CD1 . LEU A 1 6 ? -4.590 1.809 6.910 1.00 83.40 6 A 1 ATOM 50 C CD2 . LEU A 1 6 ? -5.248 0.656 4.804 1.00 83.04 6 A 1 ATOM 51 N N . LEU A 1 7 ? -1.397 2.599 2.401 1.00 94.88 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -1.278 3.187 1.066 1.00 95.43 7 A 1 ATOM 53 C C . LEU A 1 7 ? -0.583 2.233 0.099 1.00 96.28 7 A 1 ATOM 54 O O . LEU A 1 7 ? -1.015 2.079 -1.046 1.00 95.86 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -0.507 4.508 1.169 1.00 94.89 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -1.383 5.677 1.614 1.00 86.86 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -0.544 6.773 2.258 1.00 84.29 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -2.138 6.258 0.422 1.00 84.30 7 A 1 ATOM 59 N N . LEU A 1 8 ? 0.466 1.575 0.561 1.00 95.56 8 A 1 ATOM 60 C CA . LEU A 1 8 ? 1.198 0.611 -0.259 1.00 95.91 8 A 1 ATOM 61 C C . LEU A 1 8 ? 0.323 -0.591 -0.611 1.00 96.52 8 A 1 ATOM 62 O O . LEU A 1 8 ? 0.328 -1.056 -1.750 1.00 96.10 8 A 1 ATOM 63 C CB . LEU A 1 8 ? 2.465 0.151 0.478 1.00 95.23 8 A 1 ATOM 64 C CG . LEU A 1 8 ? 3.735 0.332 -0.355 1.00 87.69 8 A 1 ATOM 65 C CD1 . LEU A 1 8 ? 4.525 1.553 0.127 1.00 85.22 8 A 1 ATOM 66 C CD2 . LEU A 1 8 ? 4.618 -0.903 -0.271 1.00 85.12 8 A 1 ATOM 67 N N . SER A 1 9 ? -0.445 -1.080 0.347 1.00 94.89 9 A 1 ATOM 68 C CA . SER A 1 9 ? -1.319 -2.234 0.130 1.00 95.03 9 A 1 ATOM 69 C C . SER A 1 9 ? -2.417 -1.917 -0.888 1.00 95.80 9 A 1 ATOM 70 O O . SER A 1 9 ? -2.729 -2.748 -1.739 1.00 94.52 9 A 1 ATOM 71 C CB . SER A 1 9 ? -1.923 -2.689 1.461 1.00 93.65 9 A 1 ATOM 72 O OG . SER A 1 9 ? -2.837 -1.747 1.959 1.00 83.82 9 A 1 ATOM 73 N N . VAL A 1 10 ? -2.967 -0.717 -0.840 1.00 96.60 10 A 1 ATOM 74 C CA . VAL A 1 10 ? -3.997 -0.280 -1.791 1.00 96.73 10 A 1 ATOM 75 C C . VAL A 1 10 ? -3.423 -0.221 -3.206 1.00 97.17 10 A 1 ATOM 76 O O . VAL A 1 10 ? -4.077 -0.646 -4.162 1.00 96.27 10 A 1 ATOM 77 C CB . VAL A 1 10 ? -4.574 1.084 -1.372 1.00 95.62 10 A 1 ATOM 78 C CG1 . VAL A 1 10 ? -5.498 1.654 -2.445 1.00 92.02 10 A 1 ATOM 79 C CG2 . VAL A 1 10 ? -5.350 0.957 -0.067 1.00 92.77 10 A 1 ATOM 80 N N . LEU A 1 11 ? -2.208 0.276 -3.336 1.00 97.13 11 A 1 ATOM 81 C CA . LEU A 1 11 ? -1.535 0.359 -4.631 1.00 97.04 11 A 1 ATOM 82 C C . LEU A 1 11 ? -1.294 -1.033 -5.209 1.00 97.13 11 A 1 ATOM 83 O O . LEU A 1 11 ? -1.535 -1.267 -6.393 1.00 95.98 11 A 1 ATOM 84 C CB . LEU A 1 11 ? -0.212 1.119 -4.465 1.00 96.39 11 A 1 ATOM 85 C CG . LEU A 1 11 ? 0.498 1.440 -5.783 1.00 92.33 11 A 1 ATOM 86 C CD1 . LEU A 1 11 ? -0.268 2.496 -6.572 1.00 88.92 11 A 1 ATOM 87 C CD2 . LEU A 1 11 ? 1.908 1.942 -5.503 1.00 88.59 11 A 1 ATOM 88 N N . THR A 1 12 ? -0.841 -1.956 -4.380 1.00 97.33 12 A 1 ATOM 89 C CA . THR A 1 12 ? -0.575 -3.336 -4.803 1.00 97.11 12 A 1 ATOM 90 C C . THR A 1 12 ? -1.863 -4.029 -5.254 1.00 96.93 12 A 1 ATOM 91 O O . THR A 1 12 ? -1.874 -4.723 -6.272 1.00 95.18 12 A 1 ATOM 92 C CB . THR A 1 12 ? 0.073 -4.131 -3.659 1.00 95.94 12 A 1 ATOM 93 O OG1 . THR A 1 12 ? 1.179 -3.413 -3.135 1.00 90.25 12 A 1 ATOM 94 C CG2 . THR A 1 12 ? 0.586 -5.477 -4.149 1.00 90.10 12 A 1 ATOM 95 N N . LEU A 1 13 ? -2.950 -3.819 -4.530 1.00 97.21 13 A 1 ATOM 96 C CA . LEU A 1 13 ? -4.247 -4.395 -4.880 1.00 96.83 13 A 1 ATOM 97 C C . LEU A 1 13 ? -4.779 -3.810 -6.189 1.00 96.77 13 A 1 ATOM 98 O O . LEU A 1 13 ? -5.344 -4.537 -7.007 1.00 94.85 13 A 1 ATOM 99 C CB . LEU A 1 13 ? -5.236 -4.149 -3.737 1.00 95.83 13 A 1 ATOM 100 C CG . LEU A 1 13 ? -5.037 -5.089 -2.548 1.00 92.13 13 A 1 ATOM 101 C CD1 . LEU A 1 13 ? -5.667 -4.503 -1.293 1.00 88.52 13 A 1 ATOM 102 C CD2 . LEU A 1 13 ? -5.660 -6.452 -2.845 1.00 86.98 13 A 1 ATOM 103 N N . GLY A 1 14 ? -4.579 -2.525 -6.399 1.00 94.87 14 A 1 ATOM 104 C CA . GLY A 1 14 ? -5.014 -1.855 -7.624 1.00 94.25 14 A 1 ATOM 105 C C . GLY A 1 14 ? -4.287 -2.366 -8.859 1.00 94.33 14 A 1 ATOM 106 O O . GLY A 1 14 ? -4.877 -2.460 -9.933 1.00 92.77 14 A 1 ATOM 107 N N . VAL A 1 15 ? -3.012 -2.712 -8.721 1.00 94.87 15 A 1 ATOM 108 C CA . VAL A 1 15 ? -2.210 -3.248 -9.828 1.00 93.65 15 A 1 ATOM 109 C C . VAL A 1 15 ? -2.616 -4.686 -10.153 1.00 92.98 15 A 1 ATOM 110 O O . VAL A 1 15 ? -2.636 -5.078 -11.323 1.00 89.25 15 A 1 ATOM 111 C CB . VAL A 1 15 ? -0.706 -3.166 -9.496 1.00 90.94 15 A 1 ATOM 112 C CG1 . VAL A 1 15 ? 0.144 -3.868 -10.551 1.00 82.90 15 A 1 ATOM 113 C CG2 . VAL A 1 15 ? -0.261 -1.714 -9.397 1.00 84.23 15 A 1 ATOM 114 N N . SER A 1 16 ? -2.941 -5.460 -9.143 1.00 91.07 16 A 1 ATOM 115 C CA . SER A 1 16 ? -3.339 -6.862 -9.309 1.00 90.62 16 A 1 ATOM 116 C C . SER A 1 16 ? -4.777 -7.011 -9.813 1.00 89.88 16 A 1 ATOM 117 O O . SER A 1 16 ? -5.159 -8.071 -10.313 1.00 85.64 16 A 1 ATOM 118 C CB . SER A 1 16 ? -3.168 -7.609 -7.990 1.00 86.48 16 A 1 ATOM 119 O OG . SER A 1 16 ? -3.226 -8.999 -8.199 1.00 75.67 16 A 1 ATOM 120 N N . SER A 1 17 ? -5.585 -5.970 -9.681 1.00 88.30 17 A 1 ATOM 121 C CA . SER A 1 17 ? -6.987 -5.984 -10.082 1.00 83.81 17 A 1 ATOM 122 C C . SER A 1 17 ? -7.277 -4.980 -11.198 1.00 78.47 17 A 1 ATOM 123 O O . SER A 1 17 ? -6.487 -4.043 -11.391 1.00 71.49 17 A 1 ATOM 124 C CB . SER A 1 17 ? -7.891 -5.703 -8.882 1.00 76.69 17 A 1 ATOM 125 O OG . SER A 1 17 ? -9.248 -5.917 -9.229 1.00 69.73 17 A 1 ATOM 126 O OXT . SER A 1 17 ? -8.317 -5.106 -11.859 1.00 71.95 17 A 1 #