# 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_spkb24372 # _entry.id spkb24372 # 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" "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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O3" 105.093 SER y SERINE C([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 LEU 2 1 n LYS 3 1 n LEU 4 1 n LEU 5 1 n CYS 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n PRO 10 1 n LEU 11 1 n VAL 12 1 n ALA 13 1 n VAL 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 @ 2025-07-09 14:18:33)" _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 87.55 _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 81.10 1 1 A LEU 2 2 86.48 1 2 A LYS 3 2 85.84 1 3 A LEU 4 2 89.69 1 4 A LEU 5 2 89.43 1 5 A CYS 6 2 91.64 1 6 A LEU 7 2 89.82 1 7 A LEU 8 2 90.09 1 8 A LEU 9 2 87.90 1 9 A PRO 10 2 91.37 1 10 A LEU 11 2 85.76 1 11 A VAL 12 2 88.79 1 12 A ALA 13 2 92.67 1 13 A VAL 14 2 84.60 1 14 A SER 15 2 85.80 1 15 A ALA 16 2 81.15 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 LEU . 2 A 2 A 3 1 n LYS . 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 LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PRO . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 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 ? -4.648 -5.513 9.770 1.00 86.53 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.373 -5.195 9.108 1.00 87.84 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.586 -4.189 7.982 1.00 88.64 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.090 -4.366 6.872 1.00 87.99 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.750 -6.472 8.539 1.00 83.28 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.391 -7.468 9.623 1.00 77.93 1 A 1 ATOM 7 S SD . MET A 1 1 ? -1.669 -8.968 8.956 1.00 73.26 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.340 -9.853 10.472 1.00 63.32 1 A 1 ATOM 9 N N . LEU A 1 2 ? -4.307 -3.113 8.272 1.00 90.01 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -4.598 -2.083 7.285 1.00 91.59 2 A 1 ATOM 11 C C . LEU A 1 2 ? -3.373 -1.221 7.004 1.00 93.39 2 A 1 ATOM 12 O O . LEU A 1 2 ? -3.357 -0.455 6.045 1.00 91.79 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -5.749 -1.194 7.766 1.00 89.12 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -5.482 -0.541 9.123 1.00 81.81 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -6.135 0.832 9.167 1.00 77.69 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -6.033 -1.398 10.243 1.00 76.41 2 A 1 ATOM 17 N N . LYS A 1 3 ? -2.350 -1.328 7.841 1.00 91.77 3 A 1 ATOM 18 C CA . LYS A 1 3 ? -1.139 -0.537 7.655 1.00 92.36 3 A 1 ATOM 19 C C . LYS A 1 3 ? -0.489 -0.861 6.312 1.00 92.73 3 A 1 ATOM 20 O O . LYS A 1 3 ? 0.068 0.015 5.658 1.00 92.66 3 A 1 ATOM 21 C CB . LYS A 1 3 ? -0.155 -0.796 8.801 1.00 91.57 3 A 1 ATOM 22 C CG . LYS A 1 3 ? 0.372 -2.222 8.823 1.00 85.07 3 A 1 ATOM 23 C CD . LYS A 1 3 ? 1.476 -2.379 9.861 1.00 81.43 3 A 1 ATOM 24 C CE . LYS A 1 3 ? 2.076 -3.774 9.825 1.00 76.13 3 A 1 ATOM 25 N NZ . LYS A 1 3 ? 3.210 -3.902 10.776 1.00 68.83 3 A 1 ATOM 26 N N . LEU A 1 4 ? -0.579 -2.117 5.901 1.00 92.93 4 A 1 ATOM 27 C CA . LEU A 1 4 ? -0.010 -2.551 4.633 1.00 93.68 4 A 1 ATOM 28 C C . LEU A 1 4 ? -0.831 -2.026 3.461 1.00 94.46 4 A 1 ATOM 29 O O . LEU A 1 4 ? -0.346 -1.963 2.331 1.00 93.42 4 A 1 ATOM 30 C CB . LEU A 1 4 ? 0.064 -4.085 4.573 1.00 93.46 4 A 1 ATOM 31 C CG . LEU A 1 4 ? 1.323 -4.689 5.199 1.00 84.85 4 A 1 ATOM 32 C CD1 . LEU A 1 4 ? 2.553 -4.266 4.418 1.00 82.20 4 A 1 ATOM 33 C CD2 . LEU A 1 4 ? 1.456 -4.275 6.650 1.00 82.52 4 A 1 ATOM 34 N N . LEU A 1 5 ? -2.080 -1.656 3.729 1.00 94.66 5 A 1 ATOM 35 C CA . LEU A 1 5 ? -2.975 -1.162 2.692 1.00 93.54 5 A 1 ATOM 36 C C . LEU A 1 5 ? -3.064 0.360 2.710 1.00 94.19 5 A 1 ATOM 37 O O . LEU A 1 5 ? -3.034 1.005 1.660 1.00 93.38 5 A 1 ATOM 38 C CB . LEU A 1 5 ? -4.372 -1.767 2.886 1.00 92.71 5 A 1 ATOM 39 C CG . LEU A 1 5 ? -4.395 -3.297 2.932 1.00 84.24 5 A 1 ATOM 40 C CD1 . LEU A 1 5 ? -5.809 -3.794 3.182 1.00 81.39 5 A 1 ATOM 41 C CD2 . LEU A 1 5 ? -3.848 -3.879 1.640 1.00 81.32 5 A 1 ATOM 42 N N . CYS A 1 6 ? -3.174 0.935 3.905 1.00 93.19 6 A 1 ATOM 43 C CA . CYS A 1 6 ? -3.329 2.377 4.050 1.00 93.08 6 A 1 ATOM 44 C C . CYS A 1 6 ? -1.986 3.109 4.010 1.00 93.14 6 A 1 ATOM 45 O O . CYS A 1 6 ? -1.939 4.318 3.819 1.00 92.03 6 A 1 ATOM 46 C CB . CYS A 1 6 ? -4.056 2.690 5.364 1.00 91.83 6 A 1 ATOM 47 S SG . CYS A 1 6 ? -5.739 2.038 5.425 1.00 86.58 6 A 1 ATOM 48 N N . LEU A 1 7 ? -0.906 2.395 4.199 1.00 93.25 7 A 1 ATOM 49 C CA . LEU A 1 7 ? 0.417 3.013 4.211 1.00 92.96 7 A 1 ATOM 50 C C . LEU A 1 7 ? 1.272 2.579 3.026 1.00 94.08 7 A 1 ATOM 51 O O . LEU A 1 7 ? 2.077 3.359 2.512 1.00 92.66 7 A 1 ATOM 52 C CB . LEU A 1 7 ? 1.142 2.660 5.511 1.00 92.57 7 A 1 ATOM 53 C CG . LEU A 1 7 ? 0.420 3.100 6.783 1.00 85.69 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? 1.226 2.687 8.012 1.00 83.55 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? 0.196 4.598 6.785 1.00 83.82 7 A 1 ATOM 56 N N . LEU A 1 8 ? 1.103 1.349 2.604 1.00 93.11 8 A 1 ATOM 57 C CA . LEU A 1 8 ? 1.886 0.825 1.488 1.00 92.77 8 A 1 ATOM 58 C C . LEU A 1 8 ? 1.466 1.433 0.158 1.00 93.70 8 A 1 ATOM 59 O O . LEU A 1 8 ? 2.298 1.971 -0.576 1.00 92.59 8 A 1 ATOM 60 C CB . LEU A 1 8 ? 1.747 -0.697 1.426 1.00 92.48 8 A 1 ATOM 61 C CG . LEU A 1 8 ? 2.519 -1.359 0.291 1.00 87.34 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? 4.006 -1.077 0.422 1.00 84.37 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? 2.265 -2.857 0.289 1.00 84.35 8 A 1 ATOM 64 N N . LEU A 1 9 ? 0.180 1.343 -0.149 1.00 92.62 9 A 1 ATOM 65 C CA . LEU A 1 9 ? -0.342 1.858 -1.413 1.00 91.84 9 A 1 ATOM 66 C C . LEU A 1 9 ? -0.069 3.352 -1.594 1.00 92.91 9 A 1 ATOM 67 O O . LEU A 1 9 ? 0.536 3.753 -2.596 1.00 91.36 9 A 1 ATOM 68 C CB . LEU A 1 9 ? -1.840 1.567 -1.509 1.00 90.39 9 A 1 ATOM 69 C CG . LEU A 1 9 ? -2.500 2.104 -2.771 1.00 84.04 9 A 1 ATOM 70 C CD1 . LEU A 1 9 ? -1.895 1.457 -4.005 1.00 80.09 9 A 1 ATOM 71 C CD2 . LEU A 1 9 ? -4.001 1.850 -2.719 1.00 79.94 9 A 1 ATOM 72 N N . PRO A 1 10 ? -0.506 4.201 -0.656 1.00 92.76 10 A 1 ATOM 73 C CA . PRO A 1 10 ? -0.290 5.649 -0.785 1.00 92.42 10 A 1 ATOM 74 C C . PRO A 1 10 ? 1.184 6.030 -0.722 1.00 93.13 10 A 1 ATOM 75 O O . PRO A 1 10 ? 1.601 7.000 -1.351 1.00 91.08 10 A 1 ATOM 76 C CB . PRO A 1 10 ? -1.066 6.239 0.401 1.00 90.48 10 A 1 ATOM 77 C CG . PRO A 1 10 ? -1.142 5.135 1.398 1.00 88.45 10 A 1 ATOM 78 C CD . PRO A 1 10 ? -1.235 3.871 0.584 1.00 91.28 10 A 1 ATOM 79 N N . LEU A 1 11 ? 1.968 5.283 0.010 1.00 90.51 11 A 1 ATOM 80 C CA . LEU A 1 11 ? 3.397 5.557 0.125 1.00 90.30 11 A 1 ATOM 81 C C . LEU A 1 11 ? 4.081 5.463 -1.229 1.00 91.78 11 A 1 ATOM 82 O O . LEU A 1 11 ? 4.867 6.334 -1.607 1.00 89.35 11 A 1 ATOM 83 C CB . LEU A 1 11 ? 4.040 4.571 1.090 1.00 88.94 11 A 1 ATOM 84 C CG . LEU A 1 11 ? 5.544 4.750 1.252 1.00 81.54 11 A 1 ATOM 85 C CD1 . LEU A 1 11 ? 5.859 6.150 1.750 1.00 76.90 11 A 1 ATOM 86 C CD2 . LEU A 1 11 ? 6.094 3.709 2.211 1.00 76.79 11 A 1 ATOM 87 N N . VAL A 1 12 ? 3.788 4.407 -1.960 1.00 92.04 12 A 1 ATOM 88 C CA . VAL A 1 12 ? 4.370 4.211 -3.282 1.00 91.18 12 A 1 ATOM 89 C C . VAL A 1 12 ? 3.901 5.289 -4.246 1.00 91.69 12 A 1 ATOM 90 O O . VAL A 1 12 ? 4.681 5.797 -5.055 1.00 89.54 12 A 1 ATOM 91 C CB . VAL A 1 12 ? 4.001 2.831 -3.840 1.00 89.36 12 A 1 ATOM 92 C CG1 . VAL A 1 12 ? 4.558 2.660 -5.243 1.00 83.06 12 A 1 ATOM 93 C CG2 . VAL A 1 12 ? 4.529 1.745 -2.923 1.00 84.63 12 A 1 ATOM 94 N N . ALA A 1 13 ? 2.631 5.638 -4.167 1.00 93.18 13 A 1 ATOM 95 C CA . ALA A 1 13 ? 2.054 6.654 -5.039 1.00 93.29 13 A 1 ATOM 96 C C . ALA A 1 13 ? 2.679 8.021 -4.782 1.00 93.60 13 A 1 ATOM 97 O O . ALA A 1 13 ? 3.009 8.749 -5.714 1.00 91.24 13 A 1 ATOM 98 C CB . ALA A 1 13 ? 0.546 6.722 -4.833 1.00 92.03 13 A 1 ATOM 99 N N . VAL A 1 14 ? 2.852 8.376 -3.523 1.00 89.74 14 A 1 ATOM 100 C CA . VAL A 1 14 ? 3.439 9.661 -3.154 1.00 88.25 14 A 1 ATOM 101 C C . VAL A 1 14 ? 4.924 9.701 -3.486 1.00 89.09 14 A 1 ATOM 102 O O . VAL A 1 14 ? 5.482 10.754 -3.795 1.00 84.20 14 A 1 ATOM 103 C CB . VAL A 1 14 ? 3.233 9.937 -1.660 1.00 84.84 14 A 1 ATOM 104 C CG1 . VAL A 1 14 ? 3.957 11.209 -1.241 1.00 77.25 14 A 1 ATOM 105 C CG2 . VAL A 1 14 ? 1.762 10.039 -1.339 1.00 78.80 14 A 1 ATOM 106 N N . SER A 1 15 ? 5.568 8.556 -3.419 1.00 89.48 15 A 1 ATOM 107 C CA . SER A 1 15 ? 6.990 8.459 -3.722 1.00 89.08 15 A 1 ATOM 108 C C . SER A 1 15 ? 7.277 8.875 -5.157 1.00 88.42 15 A 1 ATOM 109 O O . SER A 1 15 ? 8.370 9.344 -5.472 1.00 85.47 15 A 1 ATOM 110 C CB . SER A 1 15 ? 7.480 7.033 -3.491 1.00 86.98 15 A 1 ATOM 111 O OG . SER A 1 15 ? 7.389 6.692 -2.122 1.00 75.35 15 A 1 ATOM 112 N N . ALA A 1 16 ? 6.294 8.709 -6.033 1.00 89.31 16 A 1 ATOM 113 C CA . ALA A 1 16 ? 6.434 9.075 -7.437 1.00 86.01 16 A 1 ATOM 114 C C . ALA A 1 16 ? 6.015 10.530 -7.654 1.00 83.56 16 A 1 ATOM 115 O O . ALA A 1 16 ? 6.785 11.435 -7.312 1.00 76.68 16 A 1 ATOM 116 C CB . ALA A 1 16 ? 5.604 8.137 -8.304 1.00 80.76 16 A 1 ATOM 117 O OXT . ALA A 1 16 ? 4.916 10.774 -8.142 1.00 70.59 16 A 1 #