# 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_spkb40451 # _entry.id spkb40451 # 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 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" "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 ALA 2 1 n LEU 3 1 n LEU 4 1 n LEU 5 1 n CYS 6 1 n LEU 7 1 n VAL 8 1 n GLY 9 1 n VAL 10 1 n THR 11 1 n ALA 12 1 n ALA 13 1 n LEU 14 1 n ALA 15 # _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 @ 2025-07-09 03:16:06)" _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 94.92 _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 82.18 1 1 A ALA 2 2 95.36 1 2 A LEU 3 2 95.95 1 3 A LEU 4 2 96.96 1 4 A LEU 5 2 96.83 1 5 A CYS 6 2 97.43 1 6 A LEU 7 2 96.42 1 7 A VAL 8 2 96.95 1 8 A GLY 9 2 97.66 1 9 A VAL 10 2 96.91 1 10 A THR 11 2 96.58 1 11 A ALA 12 2 97.62 1 12 A ALA 13 2 97.57 1 13 A LEU 14 2 94.90 1 14 A ALA 15 2 87.46 1 15 # _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 ALA . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n CYS . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n GLY . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 # _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 ? -5.226 8.817 -5.007 1.00 88.85 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.735 7.553 -4.440 1.00 87.69 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.702 6.944 -3.495 1.00 87.75 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.011 5.992 -3.843 1.00 85.55 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.048 6.564 -5.565 1.00 82.92 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.176 7.058 -6.450 1.00 78.83 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.448 5.984 -7.863 1.00 77.94 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.585 7.204 -9.163 1.00 67.89 1 A 1 ATOM 9 N N . ALA A 1 2 ? -4.601 7.515 -2.318 1.00 93.28 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -3.636 7.054 -1.324 1.00 95.84 2 A 1 ATOM 11 C C . ALA A 1 2 ? -4.024 5.694 -0.752 1.00 97.27 2 A 1 ATOM 12 O O . ALA A 1 2 ? -3.159 4.906 -0.377 1.00 96.43 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -3.519 8.085 -0.210 1.00 93.98 2 A 1 ATOM 14 N N . LEU A 1 3 ? -5.324 5.426 -0.696 1.00 97.09 3 A 1 ATOM 15 C CA . LEU A 1 3 ? -5.830 4.170 -0.145 1.00 97.37 3 A 1 ATOM 16 C C . LEU A 1 3 ? -5.278 2.968 -0.905 1.00 97.95 3 A 1 ATOM 17 O O . LEU A 1 3 ? -4.785 2.013 -0.308 1.00 97.62 3 A 1 ATOM 18 C CB . LEU A 1 3 ? -7.359 4.151 -0.177 1.00 97.04 3 A 1 ATOM 19 C CG . LEU A 1 3 ? -8.019 5.157 0.767 1.00 94.96 3 A 1 ATOM 20 C CD1 . LEU A 1 3 ? -8.125 6.529 0.118 1.00 93.20 3 A 1 ATOM 21 C CD2 . LEU A 1 3 ? -9.397 4.670 1.181 1.00 92.38 3 A 1 ATOM 22 N N . LEU A 1 4 ? -5.355 3.022 -2.227 1.00 97.93 4 A 1 ATOM 23 C CA . LEU A 1 4 ? -4.853 1.939 -3.072 1.00 97.97 4 A 1 ATOM 24 C C . LEU A 1 4 ? -3.351 1.778 -2.905 1.00 98.16 4 A 1 ATOM 25 O O . LEU A 1 4 ? -2.850 0.668 -2.722 1.00 97.97 4 A 1 ATOM 26 C CB . LEU A 1 4 ? -5.195 2.232 -4.536 1.00 97.78 4 A 1 ATOM 27 C CG . LEU A 1 4 ? -6.681 2.099 -4.849 1.00 96.06 4 A 1 ATOM 28 C CD1 . LEU A 1 4 ? -6.989 2.702 -6.212 1.00 95.18 4 A 1 ATOM 29 C CD2 . LEU A 1 4 ? -7.102 0.640 -4.821 1.00 94.66 4 A 1 ATOM 30 N N . LEU A 1 5 ? -2.636 2.891 -2.947 1.00 98.04 5 A 1 ATOM 31 C CA . LEU A 1 5 ? -1.186 2.877 -2.806 1.00 97.94 5 A 1 ATOM 32 C C . LEU A 1 5 ? -0.773 2.398 -1.420 1.00 98.09 5 A 1 ATOM 33 O O . LEU A 1 5 ? 0.223 1.694 -1.272 1.00 97.75 5 A 1 ATOM 34 C CB . LEU A 1 5 ? -0.635 4.277 -3.070 1.00 97.60 5 A 1 ATOM 35 C CG . LEU A 1 5 ? -0.794 4.726 -4.526 1.00 95.91 5 A 1 ATOM 36 C CD1 . LEU A 1 5 ? -0.415 6.197 -4.664 1.00 94.95 5 A 1 ATOM 37 C CD2 . LEU A 1 5 ? 0.070 3.878 -5.449 1.00 94.38 5 A 1 ATOM 38 N N . CYS A 1 6 ? -1.540 2.769 -0.418 1.00 97.88 6 A 1 ATOM 39 C CA . CYS A 1 6 ? -1.261 2.352 0.952 1.00 97.98 6 A 1 ATOM 40 C C . CYS A 1 6 ? -1.335 0.835 1.087 1.00 97.99 6 A 1 ATOM 41 O O . CYS A 1 6 ? -0.464 0.215 1.688 1.00 97.21 6 A 1 ATOM 42 C CB . CYS A 1 6 ? -2.247 3.015 1.910 1.00 97.77 6 A 1 ATOM 43 S SG . CYS A 1 6 ? -1.852 4.754 2.221 1.00 95.76 6 A 1 ATOM 44 N N . LEU A 1 7 ? -2.376 0.251 0.511 1.00 97.91 7 A 1 ATOM 45 C CA . LEU A 1 7 ? -2.555 -1.197 0.561 1.00 97.81 7 A 1 ATOM 46 C C . LEU A 1 7 ? -1.406 -1.911 -0.139 1.00 98.00 7 A 1 ATOM 47 O O . LEU A 1 7 ? -0.866 -2.895 0.372 1.00 97.71 7 A 1 ATOM 48 C CB . LEU A 1 7 ? -3.885 -1.579 -0.095 1.00 97.54 7 A 1 ATOM 49 C CG . LEU A 1 7 ? -5.110 -1.140 0.709 1.00 95.16 7 A 1 ATOM 50 C CD1 . LEU A 1 7 ? -6.377 -1.320 -0.110 1.00 93.96 7 A 1 ATOM 51 C CD2 . LEU A 1 7 ? -5.206 -1.932 2.007 1.00 93.27 7 A 1 ATOM 52 N N . VAL A 1 8 ? -1.031 -1.411 -1.298 1.00 97.68 8 A 1 ATOM 53 C CA . VAL A 1 8 ? 0.081 -1.979 -2.058 1.00 97.47 8 A 1 ATOM 54 C C . VAL A 1 8 ? 1.377 -1.857 -1.272 1.00 97.64 8 A 1 ATOM 55 O O . VAL A 1 8 ? 2.188 -2.785 -1.240 1.00 97.34 8 A 1 ATOM 56 C CB . VAL A 1 8 ? 0.215 -1.285 -3.421 1.00 97.00 8 A 1 ATOM 57 C CG1 . VAL A 1 8 ? 1.437 -1.793 -4.176 1.00 95.68 8 A 1 ATOM 58 C CG2 . VAL A 1 8 ? -1.039 -1.519 -4.253 1.00 95.83 8 A 1 ATOM 59 N N . GLY A 1 9 ? 1.564 -0.716 -0.628 1.00 97.67 9 A 1 ATOM 60 C CA . GLY A 1 9 ? 2.766 -0.475 0.162 1.00 97.57 9 A 1 ATOM 61 C C . GLY A 1 9 ? 2.895 -1.443 1.319 1.00 97.84 9 A 1 ATOM 62 O O . GLY A 1 9 ? 3.975 -1.978 1.580 1.00 97.56 9 A 1 ATOM 63 N N . VAL A 1 10 ? 1.789 -1.689 2.003 1.00 97.77 10 A 1 ATOM 64 C CA . VAL A 1 10 ? 1.780 -2.624 3.127 1.00 97.69 10 A 1 ATOM 65 C C . VAL A 1 10 ? 2.134 -4.028 2.656 1.00 98.00 10 A 1 ATOM 66 O O . VAL A 1 10 ? 2.919 -4.736 3.291 1.00 97.58 10 A 1 ATOM 67 C CB . VAL A 1 10 ? 0.412 -2.635 3.817 1.00 97.05 10 A 1 ATOM 68 C CG1 . VAL A 1 10 ? 0.368 -3.692 4.911 1.00 95.07 10 A 1 ATOM 69 C CG2 . VAL A 1 10 ? 0.113 -1.266 4.403 1.00 95.24 10 A 1 ATOM 70 N N . THR A 1 11 ? 1.558 -4.425 1.536 1.00 97.67 11 A 1 ATOM 71 C CA . THR A 1 11 ? 1.830 -5.743 0.963 1.00 97.73 11 A 1 ATOM 72 C C . THR A 1 11 ? 3.294 -5.861 0.564 1.00 97.91 11 A 1 ATOM 73 O O . THR A 1 11 ? 3.924 -6.898 0.774 1.00 97.56 11 A 1 ATOM 74 C CB . THR A 1 11 ? 0.953 -5.995 -0.264 1.00 97.05 11 A 1 ATOM 75 O OG1 . THR A 1 11 ? -0.415 -5.791 0.080 1.00 94.16 11 A 1 ATOM 76 C CG2 . THR A 1 11 ? 1.129 -7.418 -0.767 1.00 93.95 11 A 1 ATOM 77 N N . ALA A 1 12 ? 3.842 -4.800 0.002 1.00 97.82 12 A 1 ATOM 78 C CA . ALA A 1 12 ? 5.239 -4.779 -0.416 1.00 97.74 12 A 1 ATOM 79 C C . ALA A 1 12 ? 6.164 -4.934 0.781 1.00 98.02 12 A 1 ATOM 80 O O . ALA A 1 12 ? 7.180 -5.623 0.707 1.00 97.50 12 A 1 ATOM 81 C CB . ALA A 1 12 ? 5.545 -3.481 -1.149 1.00 97.03 12 A 1 ATOM 82 N N . ALA A 1 13 ? 5.809 -4.312 1.894 1.00 97.72 13 A 1 ATOM 83 C CA . ALA A 1 13 ? 6.598 -4.404 3.117 1.00 97.71 13 A 1 ATOM 84 C C . ALA A 1 13 ? 6.598 -5.830 3.654 1.00 98.00 13 A 1 ATOM 85 O O . ALA A 1 13 ? 7.596 -6.297 4.205 1.00 97.29 13 A 1 ATOM 86 C CB . ALA A 1 13 ? 6.047 -3.445 4.165 1.00 97.11 13 A 1 ATOM 87 N N . LEU A 1 14 ? 5.471 -6.502 3.503 1.00 97.31 14 A 1 ATOM 88 C CA . LEU A 1 14 ? 5.341 -7.884 3.944 1.00 97.00 14 A 1 ATOM 89 C C . LEU A 1 14 ? 6.205 -8.805 3.096 1.00 97.14 14 A 1 ATOM 90 O O . LEU A 1 14 ? 6.847 -9.723 3.617 1.00 95.90 14 A 1 ATOM 91 C CB . LEU A 1 14 ? 3.881 -8.327 3.839 1.00 96.11 14 A 1 ATOM 92 C CG . LEU A 1 14 ? 3.629 -9.749 4.322 1.00 94.09 14 A 1 ATOM 93 C CD1 . LEU A 1 14 ? 3.582 -9.798 5.838 1.00 91.76 14 A 1 ATOM 94 C CD2 . LEU A 1 14 ? 2.324 -10.287 3.740 1.00 89.87 14 A 1 ATOM 95 N N . ALA A 1 15 ? 6.203 -8.569 1.795 1.00 93.66 15 A 1 ATOM 96 C CA . ALA A 1 15 ? 6.964 -9.378 0.842 1.00 91.39 15 A 1 ATOM 97 C C . ALA A 1 15 ? 8.455 -9.173 1.056 1.00 89.53 15 A 1 ATOM 98 O O . ALA A 1 15 ? 9.177 -10.172 1.267 1.00 84.82 15 A 1 ATOM 99 C CB . ALA A 1 15 ? 6.574 -9.012 -0.587 1.00 86.84 15 A 1 ATOM 100 O OXT . ALA A 1 15 ? 8.902 -8.030 1.008 1.00 78.53 15 A 1 #