# 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_spkb08205 # _entry.id spkb08205 # 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 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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" # _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 ILE 5 1 n LEU 6 1 n LEU 7 1 n PHE 8 1 n LEU 9 1 n LEU 10 1 n PRO 11 1 n SER 12 1 n PRO 13 1 n LEU 14 1 n HIS 15 1 n SER 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 @ 2025-07-08 16:05:45)" _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 91.99 _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 87.94 1 1 A ALA 2 2 97.69 1 2 A LEU 3 2 94.21 1 3 A LEU 4 2 94.81 1 4 A ILE 5 2 96.72 1 5 A LEU 6 2 93.31 1 6 A LEU 7 2 93.41 1 7 A PHE 8 2 94.05 1 8 A LEU 9 2 95.36 1 9 A LEU 10 2 92.99 1 10 A PRO 11 2 95.14 1 11 A SER 12 2 93.98 1 12 A PRO 13 2 94.85 1 13 A LEU 14 2 89.60 1 14 A HIS 15 2 77.51 1 15 A SER 16 2 85.69 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 ALA . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PRO . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n PRO . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n HIS . 15 A 15 A 16 1 n SER . 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 ? -6.818 12.595 -1.795 1.00 94.21 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.997 11.696 -0.964 1.00 94.71 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.356 10.615 -1.834 1.00 94.94 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.993 9.623 -2.168 1.00 93.92 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.864 11.041 0.104 1.00 90.76 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.366 12.048 1.119 1.00 83.64 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.524 11.308 2.270 1.00 80.24 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.844 12.709 3.342 1.00 71.06 1 A 1 ATOM 9 N N . ALA A 1 2 ? -4.107 10.840 -2.193 1.00 97.32 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -3.387 9.876 -3.027 1.00 97.92 2 A 1 ATOM 11 C C . ALA A 1 2 ? -2.844 8.717 -2.195 1.00 98.18 2 A 1 ATOM 12 O O . ALA A 1 2 ? -2.504 7.671 -2.737 1.00 97.53 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -2.250 10.582 -3.753 1.00 97.48 2 A 1 ATOM 14 N N . LEU A 1 3 ? -2.762 8.916 -0.889 1.00 97.36 3 A 1 ATOM 15 C CA . LEU A 1 3 ? -2.259 7.877 0.007 1.00 97.22 3 A 1 ATOM 16 C C . LEU A 1 3 ? -3.135 6.627 -0.079 1.00 97.13 3 A 1 ATOM 17 O O . LEU A 1 3 ? -2.642 5.504 -0.094 1.00 96.19 3 A 1 ATOM 18 C CB . LEU A 1 3 ? -2.218 8.414 1.442 1.00 97.09 3 A 1 ATOM 19 C CG . LEU A 1 3 ? -1.242 7.676 2.363 1.00 91.23 3 A 1 ATOM 20 C CD1 . LEU A 1 3 ? -1.730 6.272 2.659 1.00 88.30 3 A 1 ATOM 21 C CD2 . LEU A 1 3 ? 0.144 7.642 1.736 1.00 89.13 3 A 1 ATOM 22 N N . LEU A 1 4 ? -4.436 6.846 -0.146 1.00 97.68 4 A 1 ATOM 23 C CA . LEU A 1 4 ? -5.375 5.727 -0.254 1.00 97.51 4 A 1 ATOM 24 C C . LEU A 1 4 ? -5.177 4.996 -1.576 1.00 97.44 4 A 1 ATOM 25 O O . LEU A 1 4 ? -5.247 3.771 -1.637 1.00 96.90 4 A 1 ATOM 26 C CB . LEU A 1 4 ? -6.804 6.256 -0.153 1.00 97.34 4 A 1 ATOM 27 C CG . LEU A 1 4 ? -7.151 6.762 1.246 1.00 91.88 4 A 1 ATOM 28 C CD1 . LEU A 1 4 ? -8.419 7.589 1.199 1.00 89.22 4 A 1 ATOM 29 C CD2 . LEU A 1 4 ? -7.333 5.583 2.198 1.00 90.55 4 A 1 ATOM 30 N N . ILE A 1 5 ? -4.938 5.766 -2.628 1.00 97.86 5 A 1 ATOM 31 C CA . ILE A 1 5 ? -4.714 5.182 -3.950 1.00 97.65 5 A 1 ATOM 32 C C . ILE A 1 5 ? -3.404 4.400 -3.947 1.00 97.53 5 A 1 ATOM 33 O O . ILE A 1 5 ? -3.294 3.342 -4.572 1.00 96.72 5 A 1 ATOM 34 C CB . ILE A 1 5 ? -4.685 6.283 -5.024 1.00 97.69 5 A 1 ATOM 35 C CG1 . ILE A 1 5 ? -6.014 7.040 -5.043 1.00 96.51 5 A 1 ATOM 36 C CG2 . ILE A 1 5 ? -4.402 5.670 -6.403 1.00 95.90 5 A 1 ATOM 37 C CD1 . ILE A 1 5 ? -5.947 8.340 -5.822 1.00 93.86 5 A 1 ATOM 38 N N . LEU A 1 6 ? -2.425 4.926 -3.241 1.00 96.72 6 A 1 ATOM 39 C CA . LEU A 1 6 ? -1.128 4.254 -3.153 1.00 96.00 6 A 1 ATOM 40 C C . LEU A 1 6 ? -1.287 2.883 -2.504 1.00 95.77 6 A 1 ATOM 41 O O . LEU A 1 6 ? -0.608 1.930 -2.874 1.00 94.94 6 A 1 ATOM 42 C CB . LEU A 1 6 ? -0.162 5.106 -2.328 1.00 95.85 6 A 1 ATOM 43 C CG . LEU A 1 6 ? 1.303 4.735 -2.571 1.00 90.27 6 A 1 ATOM 44 C CD1 . LEU A 1 6 ? 1.908 5.652 -3.628 1.00 87.86 6 A 1 ATOM 45 C CD2 . LEU A 1 6 ? 2.094 4.846 -1.279 1.00 89.10 6 A 1 ATOM 46 N N . LEU A 1 7 ? -2.184 2.794 -1.549 1.00 95.98 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -2.440 1.532 -0.858 1.00 95.84 7 A 1 ATOM 48 C C . LEU A 1 7 ? -2.978 0.494 -1.834 1.00 96.16 7 A 1 ATOM 49 O O . LEU A 1 7 ? -2.695 -0.695 -1.708 1.00 95.55 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -3.433 1.775 0.274 1.00 95.74 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -3.289 0.765 1.406 1.00 90.89 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -3.520 1.445 2.743 1.00 88.04 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -4.280 -0.375 1.230 1.00 89.08 7 A 1 ATOM 54 N N . PHE A 1 8 ? -3.754 0.965 -2.813 1.00 96.38 8 A 1 ATOM 55 C CA . PHE A 1 8 ? -4.295 0.069 -3.827 1.00 96.29 8 A 1 ATOM 56 C C . PHE A 1 8 ? -3.197 -0.374 -4.786 1.00 96.65 8 A 1 ATOM 57 O O . PHE A 1 8 ? -3.206 -1.504 -5.274 1.00 95.89 8 A 1 ATOM 58 C CB . PHE A 1 8 ? -5.411 0.772 -4.594 1.00 96.35 8 A 1 ATOM 59 C CG . PHE A 1 8 ? -6.723 0.752 -3.840 1.00 94.85 8 A 1 ATOM 60 C CD1 . PHE A 1 8 ? -7.336 -0.453 -3.545 1.00 91.17 8 A 1 ATOM 61 C CD2 . PHE A 1 8 ? -7.324 1.936 -3.443 1.00 92.00 8 A 1 ATOM 62 C CE1 . PHE A 1 8 ? -8.540 -0.483 -2.856 1.00 91.39 8 A 1 ATOM 63 C CE2 . PHE A 1 8 ? -8.532 1.910 -2.751 1.00 91.53 8 A 1 ATOM 64 C CZ . PHE A 1 8 ? -9.138 0.701 -2.456 1.00 92.10 8 A 1 ATOM 65 N N . LEU A 1 9 ? -2.250 0.522 -5.055 1.00 97.21 9 A 1 ATOM 66 C CA . LEU A 1 9 ? -1.132 0.197 -5.940 1.00 97.04 9 A 1 ATOM 67 C C . LEU A 1 9 ? -0.245 -0.862 -5.297 1.00 96.98 9 A 1 ATOM 68 O O . LEU A 1 9 ? 0.336 -1.699 -5.986 1.00 95.88 9 A 1 ATOM 69 C CB . LEU A 1 9 ? -0.326 1.461 -6.229 1.00 96.99 9 A 1 ATOM 70 C CG . LEU A 1 9 ? -0.997 2.396 -7.231 1.00 94.83 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? -0.323 3.762 -7.208 1.00 92.05 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? -0.916 1.811 -8.638 1.00 91.88 9 A 1 ATOM 73 N N . LEU A 1 10 ? -0.149 -0.819 -3.983 1.00 96.09 10 A 1 ATOM 74 C CA . LEU A 1 10 ? 0.638 -1.795 -3.236 1.00 95.97 10 A 1 ATOM 75 C C . LEU A 1 10 ? -0.290 -2.755 -2.498 1.00 96.23 10 A 1 ATOM 76 O O . LEU A 1 10 ? -0.684 -2.487 -1.366 1.00 94.88 10 A 1 ATOM 77 C CB . LEU A 1 10 ? 1.543 -1.062 -2.251 1.00 95.16 10 A 1 ATOM 78 C CG . LEU A 1 10 ? 2.663 -0.286 -2.934 1.00 91.29 10 A 1 ATOM 79 C CD1 . LEU A 1 10 ? 3.226 0.758 -1.989 1.00 87.18 10 A 1 ATOM 80 C CD2 . LEU A 1 10 ? 3.766 -1.246 -3.369 1.00 87.13 10 A 1 ATOM 81 N N . PRO A 1 11 ? -0.630 -3.870 -3.134 1.00 96.16 11 A 1 ATOM 82 C CA . PRO A 1 11 ? -1.536 -4.847 -2.529 1.00 95.90 11 A 1 ATOM 83 C C . PRO A 1 11 ? -0.964 -5.481 -1.268 1.00 96.17 11 A 1 ATOM 84 O O . PRO A 1 11 ? -1.688 -6.109 -0.497 1.00 94.72 11 A 1 ATOM 85 C CB . PRO A 1 11 ? -1.737 -5.894 -3.632 1.00 94.39 11 A 1 ATOM 86 C CG . PRO A 1 11 ? -0.529 -5.773 -4.503 1.00 93.20 11 A 1 ATOM 87 C CD . PRO A 1 11 ? -0.131 -4.320 -4.446 1.00 95.45 11 A 1 ATOM 88 N N . SER A 1 12 ? 0.324 -5.321 -1.058 1.00 95.90 12 A 1 ATOM 89 C CA . SER A 1 12 ? 0.978 -5.884 0.117 1.00 96.16 12 A 1 ATOM 90 C C . SER A 1 12 ? 2.019 -4.922 0.682 1.00 96.31 12 A 1 ATOM 91 O O . SER A 1 12 ? 3.218 -5.126 0.508 1.00 95.09 12 A 1 ATOM 92 C CB . SER A 1 12 ? 1.622 -7.212 -0.247 1.00 94.63 12 A 1 ATOM 93 O OG . SER A 1 12 ? 2.356 -7.104 -1.441 1.00 85.77 12 A 1 ATOM 94 N N . PRO A 1 13 ? 1.557 -3.867 1.365 1.00 95.83 13 A 1 ATOM 95 C CA . PRO A 1 13 ? 2.477 -2.909 1.984 1.00 95.82 13 A 1 ATOM 96 C C . PRO A 1 13 ? 3.171 -3.497 3.205 1.00 96.21 13 A 1 ATOM 97 O O . PRO A 1 13 ? 4.154 -2.938 3.690 1.00 94.43 13 A 1 ATOM 98 C CB . PRO A 1 13 ? 1.568 -1.743 2.371 1.00 94.22 13 A 1 ATOM 99 C CG . PRO A 1 13 ? 0.225 -2.367 2.537 1.00 92.62 13 A 1 ATOM 100 C CD . PRO A 1 13 ? 0.164 -3.508 1.555 1.00 94.79 13 A 1 ATOM 101 N N . LEU A 1 14 ? 2.668 -4.604 3.693 1.00 95.26 14 A 1 ATOM 102 C CA . LEU A 1 14 ? 3.248 -5.281 4.847 1.00 94.02 14 A 1 ATOM 103 C C . LEU A 1 14 ? 4.432 -6.137 4.412 1.00 93.76 14 A 1 ATOM 104 O O . LEU A 1 14 ? 4.422 -7.366 4.557 1.00 92.05 14 A 1 ATOM 105 C CB . LEU A 1 14 ? 2.181 -6.142 5.525 1.00 93.39 14 A 1 ATOM 106 C CG . LEU A 1 14 ? 2.319 -6.253 7.038 1.00 88.76 14 A 1 ATOM 107 C CD1 . LEU A 1 14 ? 3.644 -6.870 7.431 1.00 81.21 14 A 1 ATOM 108 C CD2 . LEU A 1 14 ? 2.173 -4.873 7.656 1.00 78.38 14 A 1 ATOM 109 N N . HIS A 1 15 ? 5.441 -5.468 3.864 1.00 90.80 15 A 1 ATOM 110 C CA . HIS A 1 15 ? 6.626 -6.173 3.387 1.00 90.17 15 A 1 ATOM 111 C C . HIS A 1 15 ? 7.874 -5.353 3.723 1.00 90.17 15 A 1 ATOM 112 O O . HIS A 1 15 ? 8.104 -4.295 3.136 1.00 85.00 15 A 1 ATOM 113 C CB . HIS A 1 15 ? 6.525 -6.411 1.875 1.00 85.58 15 A 1 ATOM 114 C CG . HIS A 1 15 ? 7.330 -7.592 1.422 1.00 77.98 15 A 1 ATOM 115 N ND1 . HIS A 1 15 ? 8.692 -7.585 1.349 1.00 66.51 15 A 1 ATOM 116 C CD2 . HIS A 1 15 ? 6.930 -8.817 1.022 1.00 64.21 15 A 1 ATOM 117 C CE1 . HIS A 1 15 ? 9.110 -8.775 0.924 1.00 60.49 15 A 1 ATOM 118 N NE2 . HIS A 1 15 ? 8.059 -9.545 0.710 1.00 64.19 15 A 1 ATOM 119 N N . SER A 1 16 ? 8.644 -5.851 4.652 1.00 92.34 16 A 1 ATOM 120 C CA . SER A 1 16 ? 9.871 -5.160 5.062 1.00 91.86 16 A 1 ATOM 121 C C . SER A 1 16 ? 11.091 -5.754 4.370 1.00 88.16 16 A 1 ATOM 122 O O . SER A 1 16 ? 12.108 -5.053 4.250 1.00 83.01 16 A 1 ATOM 123 C CB . SER A 1 16 ? 10.038 -5.260 6.580 1.00 87.73 16 A 1 ATOM 124 O OG . SER A 1 16 ? 10.006 -6.607 6.993 1.00 77.88 16 A 1 ATOM 125 O OXT . SER A 1 16 ? 11.046 -6.935 3.977 1.00 78.83 16 A 1 #