# 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_spkb16525 # _entry.id spkb16525 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "PEPTIDE LINKING" "C6 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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" "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 HIS 2 1 n PRO 3 1 n LEU 4 1 n PRO 5 1 n SER 6 1 n VAL 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n SER 11 1 n ALA 12 1 n ILE 13 1 n GLY 14 1 n ALA 15 1 n VAL 16 1 n ALA 17 1 n ALA 18 # _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 @ 2025-07-07 07:35:10)" _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 90.30 _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 79.79 1 1 A HIS 2 2 79.13 1 2 A PRO 3 2 89.78 1 3 A LEU 4 2 86.17 1 4 A PRO 5 2 92.47 1 5 A SER 6 2 92.24 1 6 A VAL 7 2 92.82 1 7 A ALA 8 2 94.43 1 8 A LEU 9 2 90.96 1 9 A LEU 10 2 92.58 1 10 A SER 11 2 92.59 1 11 A ALA 12 2 95.53 1 12 A ILE 13 2 93.34 1 13 A GLY 14 2 96.17 1 14 A ALA 15 2 96.26 1 15 A VAL 16 2 93.79 1 16 A ALA 17 2 94.34 1 17 A ALA 18 2 87.30 1 18 # _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 HIS . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n PRO . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ILE . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n ALA . 17 A 17 A 18 1 n ALA . 18 A 18 # _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 ? -5.022 14.004 10.688 1.00 82.56 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.340 12.696 10.755 1.00 85.44 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.267 11.589 10.272 1.00 87.10 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.401 11.488 10.723 1.00 84.88 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.910 12.396 12.188 1.00 81.11 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.886 13.396 12.700 1.00 77.88 1 A 1 ATOM 7 S SD . MET A 1 1 ? -2.397 13.046 14.401 1.00 74.43 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.308 14.426 14.701 1.00 64.91 1 A 1 ATOM 9 N N . HIS A 1 2 ? -4.774 10.776 9.363 1.00 83.78 2 A 1 ATOM 10 C CA . HIS A 1 2 ? -5.570 9.674 8.832 1.00 86.83 2 A 1 ATOM 11 C C . HIS A 1 2 ? -4.730 8.402 8.790 1.00 90.07 2 A 1 ATOM 12 O O . HIS A 1 2 ? -3.637 8.388 8.235 1.00 88.21 2 A 1 ATOM 13 C CB . HIS A 1 2 ? -6.067 10.027 7.428 1.00 83.16 2 A 1 ATOM 14 C CG . HIS A 1 2 ? -5.090 10.857 6.655 1.00 77.97 2 A 1 ATOM 15 N ND1 . HIS A 1 2 ? -5.093 12.231 6.678 1.00 71.56 2 A 1 ATOM 16 C CD2 . HIS A 1 2 ? -4.074 10.496 5.836 1.00 69.56 2 A 1 ATOM 17 C CE1 . HIS A 1 2 ? -4.119 12.681 5.898 1.00 70.07 2 A 1 ATOM 18 N NE2 . HIS A 1 2 ? -3.477 11.641 5.369 1.00 70.11 2 A 1 ATOM 19 N N . PRO A 1 3 ? -5.255 7.322 9.397 1.00 89.44 3 A 1 ATOM 20 C CA . PRO A 1 3 ? -4.550 6.038 9.431 1.00 91.57 3 A 1 ATOM 21 C C . PRO A 1 3 ? -4.446 5.414 8.044 1.00 93.22 3 A 1 ATOM 22 O O . PRO A 1 3 ? -5.272 5.678 7.165 1.00 90.74 3 A 1 ATOM 23 C CB . PRO A 1 3 ? -5.414 5.173 10.357 1.00 88.27 3 A 1 ATOM 24 C CG . PRO A 1 3 ? -6.785 5.756 10.241 1.00 85.91 3 A 1 ATOM 25 C CD . PRO A 1 3 ? -6.574 7.244 10.024 1.00 89.30 3 A 1 ATOM 26 N N . LEU A 1 4 ? -3.434 4.576 7.855 1.00 86.66 4 A 1 ATOM 27 C CA . LEU A 1 4 ? -3.235 3.910 6.574 1.00 88.96 4 A 1 ATOM 28 C C . LEU A 1 4 ? -4.256 2.796 6.388 1.00 90.90 4 A 1 ATOM 29 O O . LEU A 1 4 ? -4.418 1.954 7.272 1.00 89.26 4 A 1 ATOM 30 C CB . LEU A 1 4 ? -1.820 3.339 6.508 1.00 86.44 4 A 1 ATOM 31 C CG . LEU A 1 4 ? -0.752 4.391 6.234 1.00 83.89 4 A 1 ATOM 32 C CD1 . LEU A 1 4 ? 0.613 3.894 6.686 1.00 83.44 4 A 1 ATOM 33 C CD2 . LEU A 1 4 ? -0.722 4.728 4.751 1.00 79.83 4 A 1 ATOM 34 N N . PRO A 1 5 ? -4.949 2.787 5.246 1.00 93.07 5 A 1 ATOM 35 C CA . PRO A 1 5 ? -5.948 1.765 4.955 1.00 93.54 5 A 1 ATOM 36 C C . PRO A 1 5 ? -5.288 0.432 4.618 1.00 94.39 5 A 1 ATOM 37 O O . PRO A 1 5 ? -4.133 0.391 4.203 1.00 93.18 5 A 1 ATOM 38 C CB . PRO A 1 5 ? -6.701 2.328 3.748 1.00 91.19 5 A 1 ATOM 39 C CG . PRO A 1 5 ? -5.706 3.218 3.067 1.00 89.57 5 A 1 ATOM 40 C CD . PRO A 1 5 ? -4.855 3.795 4.190 1.00 92.38 5 A 1 ATOM 41 N N . SER A 1 6 ? -6.037 -0.647 4.786 1.00 92.97 6 A 1 ATOM 42 C CA . SER A 1 6 ? -5.523 -1.981 4.487 1.00 93.94 6 A 1 ATOM 43 C C . SER A 1 6 ? -5.056 -2.069 3.038 1.00 94.70 6 A 1 ATOM 44 O O . SER A 1 6 ? -4.098 -2.772 2.719 1.00 93.17 6 A 1 ATOM 45 C CB . SER A 1 6 ? -6.611 -3.021 4.743 1.00 92.45 6 A 1 ATOM 46 O OG . SER A 1 6 ? -7.771 -2.703 4.008 1.00 86.22 6 A 1 ATOM 47 N N . VAL A 1 7 ? -5.738 -1.342 2.176 1.00 93.48 7 A 1 ATOM 48 C CA . VAL A 1 7 ? -5.394 -1.323 0.752 1.00 94.04 7 A 1 ATOM 49 C C . VAL A 1 7 ? -3.989 -0.765 0.551 1.00 94.69 7 A 1 ATOM 50 O O . VAL A 1 7 ? -3.228 -1.248 -0.292 1.00 94.04 7 A 1 ATOM 51 C CB . VAL A 1 7 ? -6.402 -0.474 -0.036 1.00 93.14 7 A 1 ATOM 52 C CG1 . VAL A 1 7 ? -6.036 -0.445 -1.512 1.00 90.09 7 A 1 ATOM 53 C CG2 . VAL A 1 7 ? -7.810 -1.012 0.154 1.00 90.24 7 A 1 ATOM 54 N N . ALA A 1 8 ? -3.659 0.256 1.329 1.00 94.77 8 A 1 ATOM 55 C CA . ALA A 1 8 ? -2.347 0.882 1.236 1.00 94.55 8 A 1 ATOM 56 C C . ALA A 1 8 ? -1.255 -0.112 1.616 1.00 95.06 8 A 1 ATOM 57 O O . ALA A 1 8 ? -0.204 -0.170 0.978 1.00 93.80 8 A 1 ATOM 58 C CB . ALA A 1 8 ? -2.285 2.101 2.150 1.00 93.95 8 A 1 ATOM 59 N N . LEU A 1 9 ? -1.512 -0.888 2.658 1.00 93.29 9 A 1 ATOM 60 C CA . LEU A 1 9 ? -0.553 -1.897 3.107 1.00 92.79 9 A 1 ATOM 61 C C . LEU A 1 9 ? -0.361 -2.959 2.031 1.00 93.72 9 A 1 ATOM 62 O O . LEU A 1 9 ? 0.761 -3.375 1.745 1.00 93.04 9 A 1 ATOM 63 C CB . LEU A 1 9 ? -1.041 -2.535 4.407 1.00 92.35 9 A 1 ATOM 64 C CG . LEU A 1 9 ? -0.804 -1.656 5.635 1.00 88.37 9 A 1 ATOM 65 C CD1 . LEU A 1 9 ? -2.113 -1.043 6.109 1.00 87.62 9 A 1 ATOM 66 C CD2 . LEU A 1 9 ? -0.157 -2.449 6.758 1.00 86.50 9 A 1 ATOM 67 N N . LEU A 1 10 ? -1.463 -3.385 1.446 1.00 93.91 10 A 1 ATOM 68 C CA . LEU A 1 10 ? -1.414 -4.392 0.390 1.00 93.99 10 A 1 ATOM 69 C C . LEU A 1 10 ? -0.644 -3.859 -0.812 1.00 94.99 10 A 1 ATOM 70 O O . LEU A 1 10 ? 0.139 -4.570 -1.441 1.00 94.50 10 A 1 ATOM 71 C CB . LEU A 1 10 ? -2.839 -4.788 -0.024 1.00 93.87 10 A 1 ATOM 72 C CG . LEU A 1 10 ? -3.317 -6.113 0.577 1.00 90.81 10 A 1 ATOM 73 C CD1 . LEU A 1 10 ? -2.462 -7.259 0.065 1.00 89.70 10 A 1 ATOM 74 C CD2 . LEU A 1 10 ? -3.280 -6.054 2.091 1.00 88.86 10 A 1 ATOM 75 N N . SER A 1 11 ? -0.879 -2.594 -1.112 1.00 94.44 11 A 1 ATOM 76 C CA . SER A 1 11 ? -0.209 -1.946 -2.234 1.00 93.97 11 A 1 ATOM 77 C C . SER A 1 11 ? 1.296 -1.900 -1.999 1.00 95.15 11 A 1 ATOM 78 O O . SER A 1 11 ? 2.088 -2.106 -2.920 1.00 94.81 11 A 1 ATOM 79 C CB . SER A 1 11 ? -0.746 -0.530 -2.418 1.00 92.73 11 A 1 ATOM 80 O OG . SER A 1 11 ? -0.186 0.059 -3.563 1.00 84.45 11 A 1 ATOM 81 N N . ALA A 1 12 ? 1.675 -1.635 -0.749 1.00 95.27 12 A 1 ATOM 82 C CA . ALA A 1 12 ? 3.086 -1.573 -0.384 1.00 95.58 12 A 1 ATOM 83 C C . ALA A 1 12 ? 3.753 -2.929 -0.606 1.00 96.64 12 A 1 ATOM 84 O O . ALA A 1 12 ? 4.867 -3.013 -1.123 1.00 95.46 12 A 1 ATOM 85 C CB . ALA A 1 12 ? 3.229 -1.144 1.073 1.00 94.70 12 A 1 ATOM 86 N N . ILE A 1 13 ? 3.058 -3.982 -0.206 1.00 95.01 13 A 1 ATOM 87 C CA . ILE A 1 13 ? 3.576 -5.335 -0.370 1.00 94.77 13 A 1 ATOM 88 C C . ILE A 1 13 ? 3.743 -5.657 -1.850 1.00 95.10 13 A 1 ATOM 89 O O . ILE A 1 13 ? 4.732 -6.268 -2.264 1.00 93.85 13 A 1 ATOM 90 C CB . ILE A 1 13 ? 2.633 -6.359 0.289 1.00 94.42 13 A 1 ATOM 91 C CG1 . ILE A 1 13 ? 2.548 -6.106 1.796 1.00 92.63 13 A 1 ATOM 92 C CG2 . ILE A 1 13 ? 3.141 -7.781 0.028 1.00 92.03 13 A 1 ATOM 93 C CD1 . ILE A 1 13 ? 1.374 -6.817 2.443 1.00 88.94 13 A 1 ATOM 94 N N . GLY A 1 14 ? 2.766 -5.241 -2.628 1.00 95.84 14 A 1 ATOM 95 C CA . GLY A 1 14 ? 2.818 -5.481 -4.068 1.00 95.75 14 A 1 ATOM 96 C C . GLY A 1 14 ? 3.980 -4.755 -4.711 1.00 96.70 14 A 1 ATOM 97 O O . GLY A 1 14 ? 4.618 -5.267 -5.631 1.00 96.40 14 A 1 ATOM 98 N N . ALA A 1 15 ? 4.256 -3.557 -4.216 1.00 96.52 15 A 1 ATOM 99 C CA . ALA A 1 15 ? 5.359 -2.754 -4.737 1.00 96.49 15 A 1 ATOM 100 C C . ALA A 1 15 ? 6.694 -3.445 -4.474 1.00 97.11 15 A 1 ATOM 101 O O . ALA A 1 15 ? 7.586 -3.435 -5.321 1.00 95.65 15 A 1 ATOM 102 C CB . ALA A 1 15 ? 5.346 -1.374 -4.090 1.00 95.55 15 A 1 ATOM 103 N N . VAL A 1 16 ? 6.824 -4.036 -3.294 1.00 95.57 16 A 1 ATOM 104 C CA . VAL A 1 16 ? 8.047 -4.750 -2.928 1.00 95.71 16 A 1 ATOM 105 C C . VAL A 1 16 ? 8.199 -6.006 -3.774 1.00 95.98 16 A 1 ATOM 106 O O . VAL A 1 16 ? 9.312 -6.402 -4.134 1.00 94.85 16 A 1 ATOM 107 C CB . VAL A 1 16 ? 8.035 -5.127 -1.435 1.00 93.98 16 A 1 ATOM 108 C CG1 . VAL A 1 16 ? 9.283 -5.927 -1.074 1.00 89.71 16 A 1 ATOM 109 C CG2 . VAL A 1 16 ? 7.945 -3.878 -0.573 1.00 90.76 16 A 1 ATOM 110 N N . ALA A 1 17 ? 7.080 -6.637 -4.074 1.00 94.74 17 A 1 ATOM 111 C CA . ALA A 1 17 ? 7.078 -7.860 -4.874 1.00 94.60 17 A 1 ATOM 112 C C . ALA A 1 17 ? 7.526 -7.580 -6.303 1.00 95.24 17 A 1 ATOM 113 O O . ALA A 1 17 ? 7.969 -8.489 -7.012 1.00 94.32 17 A 1 ATOM 114 C CB . ALA A 1 17 ? 5.683 -8.481 -4.875 1.00 92.79 17 A 1 ATOM 115 N N . ALA A 1 18 ? 7.401 -6.326 -6.740 1.00 92.52 18 A 1 ATOM 116 C CA . ALA A 1 18 ? 7.792 -5.937 -8.088 1.00 90.86 18 A 1 ATOM 117 C C . ALA A 1 18 ? 9.299 -6.065 -8.294 1.00 89.37 18 A 1 ATOM 118 O O . ALA A 1 18 ? 10.052 -6.067 -7.305 1.00 85.77 18 A 1 ATOM 119 C CB . ALA A 1 18 ? 7.332 -4.510 -8.369 1.00 86.46 18 A 1 ATOM 120 O OXT . ALA A 1 18 ? 9.743 -6.154 -9.451 1.00 78.83 18 A 1 #