# 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_spkb09065 # _entry.id spkb09065 # 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 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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 LYS 2 1 n PHE 3 1 n LEU 4 1 n LEU 5 1 n VAL 6 1 n PHE 7 1 n ALA 8 1 n LEU 9 1 n ALA 10 1 n LEU 11 1 n ALA 12 1 n THR 13 1 n THR 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 @ 2025-07-08 22:54:43)" _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 90.31 _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 84.91 1 1 A LYS 2 2 88.78 1 2 A PHE 3 2 90.49 1 3 A LEU 4 2 93.33 1 4 A LEU 5 2 92.74 1 5 A VAL 6 2 95.75 1 6 A PHE 7 2 92.44 1 7 A ALA 8 2 96.36 1 8 A LEU 9 2 92.93 1 9 A ALA 10 2 96.51 1 10 A LEU 11 2 91.89 1 11 A ALA 12 2 95.20 1 12 A THR 13 2 88.10 1 13 A THR 14 2 85.48 1 14 A SER 15 2 82.62 1 15 A ALA 16 2 78.04 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 LYS . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n THR . 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 ? -10.392 -4.175 4.779 1.00 90.49 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.254 -3.324 5.156 1.00 91.55 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.958 -3.833 4.532 1.00 92.58 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.123 -4.429 5.205 1.00 90.40 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.116 -3.322 6.673 1.00 86.37 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.950 -2.247 7.322 1.00 80.63 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.779 -2.289 9.103 1.00 78.25 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.624 -0.770 9.518 1.00 69.00 1 A 1 ATOM 9 N N . LYS A 1 2 ? -7.817 -3.591 3.251 1.00 95.20 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -6.624 -4.023 2.533 1.00 95.35 2 A 1 ATOM 11 C C . LYS A 1 2 ? -5.794 -2.821 2.090 1.00 95.67 2 A 1 ATOM 12 O O . LYS A 1 2 ? -4.616 -2.955 1.771 1.00 95.10 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -7.038 -4.864 1.330 1.00 94.05 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -5.968 -5.839 0.910 1.00 88.83 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -6.342 -7.259 1.301 1.00 84.58 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -5.283 -8.235 0.838 1.00 78.39 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -5.747 -9.635 0.982 1.00 71.89 2 A 1 ATOM 18 N N . PHE A 1 3 ? -6.415 -1.665 2.085 1.00 94.38 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -5.730 -0.446 1.670 1.00 95.24 3 A 1 ATOM 20 C C . PHE A 1 3 ? -4.633 -0.056 2.654 1.00 96.47 3 A 1 ATOM 21 O O . PHE A 1 3 ? -3.696 0.655 2.292 1.00 95.36 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -6.737 0.691 1.540 1.00 94.01 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -7.222 0.874 0.124 1.00 90.21 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -6.328 1.206 -0.880 1.00 87.64 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -8.560 0.719 -0.189 1.00 86.85 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -6.757 1.379 -2.181 1.00 85.52 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -8.999 0.893 -1.492 1.00 85.71 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -8.096 1.223 -2.485 1.00 83.98 3 A 1 ATOM 29 N N . LEU A 1 4 ? -4.754 -0.519 3.872 1.00 96.30 4 A 1 ATOM 30 C CA . LEU A 1 4 ? -3.744 -0.215 4.886 1.00 96.65 4 A 1 ATOM 31 C C . LEU A 1 4 ? -2.366 -0.679 4.426 1.00 97.11 4 A 1 ATOM 32 O O . LEU A 1 4 ? -1.367 0.017 4.601 1.00 96.79 4 A 1 ATOM 33 C CB . LEU A 1 4 ? -4.119 -0.899 6.198 1.00 96.31 4 A 1 ATOM 34 C CG . LEU A 1 4 ? -5.254 -0.204 6.941 1.00 89.93 4 A 1 ATOM 35 C CD1 . LEU A 1 4 ? -5.769 -1.088 8.060 1.00 87.29 4 A 1 ATOM 36 C CD2 . LEU A 1 4 ? -4.775 1.126 7.510 1.00 86.24 4 A 1 ATOM 37 N N . LEU A 1 5 ? -2.330 -1.858 3.829 1.00 96.54 5 A 1 ATOM 38 C CA . LEU A 1 5 ? -1.075 -2.412 3.324 1.00 96.39 5 A 1 ATOM 39 C C . LEU A 1 5 ? -0.548 -1.568 2.168 1.00 96.83 5 A 1 ATOM 40 O O . LEU A 1 5 ? 0.646 -1.265 2.100 1.00 96.64 5 A 1 ATOM 41 C CB . LEU A 1 5 ? -1.308 -3.855 2.870 1.00 95.86 5 A 1 ATOM 42 C CG . LEU A 1 5 ? -1.474 -4.834 4.028 1.00 86.76 5 A 1 ATOM 43 C CD1 . LEU A 1 5 ? -2.235 -6.069 3.573 1.00 86.40 5 A 1 ATOM 44 C CD2 . LEU A 1 5 ? -0.111 -5.233 4.573 1.00 86.52 5 A 1 ATOM 45 N N . VAL A 1 6 ? -1.443 -1.198 1.281 1.00 96.72 6 A 1 ATOM 46 C CA . VAL A 1 6 ? -1.080 -0.378 0.124 1.00 96.76 6 A 1 ATOM 47 C C . VAL A 1 6 ? -0.688 1.027 0.572 1.00 96.97 6 A 1 ATOM 48 O O . VAL A 1 6 ? 0.239 1.632 0.028 1.00 96.65 6 A 1 ATOM 49 C CB . VAL A 1 6 ? -2.244 -0.315 -0.875 1.00 96.14 6 A 1 ATOM 50 C CG1 . VAL A 1 6 ? -1.865 0.513 -2.092 1.00 93.71 6 A 1 ATOM 51 C CG2 . VAL A 1 6 ? -2.644 -1.720 -1.306 1.00 93.33 6 A 1 ATOM 52 N N . PHE A 1 7 ? -1.394 1.521 1.561 1.00 95.53 7 A 1 ATOM 53 C CA . PHE A 1 7 ? -1.127 2.857 2.089 1.00 95.25 7 A 1 ATOM 54 C C . PHE A 1 7 ? 0.286 2.935 2.658 1.00 95.81 7 A 1 ATOM 55 O O . PHE A 1 7 ? 1.031 3.874 2.384 1.00 95.53 7 A 1 ATOM 56 C CB . PHE A 1 7 ? -2.150 3.186 3.170 1.00 94.85 7 A 1 ATOM 57 C CG . PHE A 1 7 ? -2.167 4.653 3.515 1.00 92.89 7 A 1 ATOM 58 C CD1 . PHE A 1 7 ? -2.447 5.599 2.544 1.00 90.42 7 A 1 ATOM 59 C CD2 . PHE A 1 7 ? -1.910 5.067 4.808 1.00 90.06 7 A 1 ATOM 60 C CE1 . PHE A 1 7 ? -2.466 6.950 2.853 1.00 89.07 7 A 1 ATOM 61 C CE2 . PHE A 1 7 ? -1.930 6.421 5.127 1.00 88.88 7 A 1 ATOM 62 C CZ . PHE A 1 7 ? -2.205 7.361 4.151 1.00 88.50 7 A 1 ATOM 63 N N . ALA A 1 8 ? 0.642 1.948 3.435 1.00 96.40 8 A 1 ATOM 64 C CA . ALA A 1 8 ? 1.977 1.898 4.029 1.00 96.44 8 A 1 ATOM 65 C C . ALA A 1 8 ? 3.040 1.730 2.950 1.00 96.83 8 A 1 ATOM 66 O O . ALA A 1 8 ? 4.108 2.341 3.023 1.00 96.15 8 A 1 ATOM 67 C CB . ALA A 1 8 ? 2.052 0.749 5.025 1.00 96.00 8 A 1 ATOM 68 N N . LEU A 1 9 ? 2.741 0.906 1.971 1.00 96.46 9 A 1 ATOM 69 C CA . LEU A 1 9 ? 3.666 0.663 0.867 1.00 95.90 9 A 1 ATOM 70 C C . LEU A 1 9 ? 3.858 1.928 0.043 1.00 96.18 9 A 1 ATOM 71 O O . LEU A 1 9 ? 4.985 2.280 -0.311 1.00 95.42 9 A 1 ATOM 72 C CB . LEU A 1 9 ? 3.130 -0.461 -0.016 1.00 95.22 9 A 1 ATOM 73 C CG . LEU A 1 9 ? 4.137 -0.950 -1.056 1.00 89.55 9 A 1 ATOM 74 C CD1 . LEU A 1 9 ? 5.035 -2.019 -0.459 1.00 87.40 9 A 1 ATOM 75 C CD2 . LEU A 1 9 ? 3.420 -1.485 -2.278 1.00 87.30 9 A 1 ATOM 76 N N . ALA A 1 10 ? 2.772 2.602 -0.266 1.00 96.76 10 A 1 ATOM 77 C CA . ALA A 1 10 ? 2.817 3.830 -1.055 1.00 96.68 10 A 1 ATOM 78 C C . ALA A 1 10 ? 3.583 4.921 -0.318 1.00 97.01 10 A 1 ATOM 79 O O . ALA A 1 10 ? 4.356 5.662 -0.921 1.00 96.07 10 A 1 ATOM 80 C CB . ALA A 1 10 ? 1.402 4.293 -1.365 1.00 96.02 10 A 1 ATOM 81 N N . LEU A 1 11 ? 3.371 5.002 0.967 1.00 95.94 11 A 1 ATOM 82 C CA . LEU A 1 11 ? 4.048 6.000 1.789 1.00 95.41 11 A 1 ATOM 83 C C . LEU A 1 11 ? 5.543 5.720 1.856 1.00 95.56 11 A 1 ATOM 84 O O . LEU A 1 11 ? 6.362 6.632 1.743 1.00 94.71 11 A 1 ATOM 85 C CB . LEU A 1 11 ? 3.457 5.995 3.193 1.00 94.37 11 A 1 ATOM 86 C CG . LEU A 1 11 ? 3.798 7.253 3.985 1.00 88.41 11 A 1 ATOM 87 C CD1 . LEU A 1 11 ? 2.911 8.405 3.548 1.00 85.79 11 A 1 ATOM 88 C CD2 . LEU A 1 11 ? 3.637 6.996 5.473 1.00 84.91 11 A 1 ATOM 89 N N . ALA A 1 12 ? 5.893 4.469 2.042 1.00 96.02 12 A 1 ATOM 90 C CA . ALA A 1 12 ? 7.297 4.069 2.115 1.00 95.69 12 A 1 ATOM 91 C C . ALA A 1 12 ? 7.979 4.227 0.763 1.00 95.94 12 A 1 ATOM 92 O O . ALA A 1 12 ? 9.151 4.594 0.696 1.00 94.13 12 A 1 ATOM 93 C CB . ALA A 1 12 ? 7.395 2.630 2.593 1.00 94.24 12 A 1 ATOM 94 N N . THR A 1 13 ? 7.246 3.945 -0.293 1.00 93.36 13 A 1 ATOM 95 C CA . THR A 1 13 ? 7.773 4.053 -1.654 1.00 92.38 13 A 1 ATOM 96 C C . THR A 1 13 ? 8.125 5.495 -1.985 1.00 91.92 13 A 1 ATOM 97 O O . THR A 1 13 ? 9.183 5.767 -2.554 1.00 87.28 13 A 1 ATOM 98 C CB . THR A 1 13 ? 6.749 3.520 -2.657 1.00 89.79 13 A 1 ATOM 99 O OG1 . THR A 1 13 ? 6.698 2.099 -2.539 1.00 81.75 13 A 1 ATOM 100 C CG2 . THR A 1 13 ? 7.140 3.853 -4.084 1.00 80.25 13 A 1 ATOM 101 N N . THR A 1 14 ? 7.258 6.406 -1.630 1.00 91.78 14 A 1 ATOM 102 C CA . THR A 1 14 ? 7.469 7.826 -1.894 1.00 90.04 14 A 1 ATOM 103 C C . THR A 1 14 ? 8.093 8.523 -0.687 1.00 89.22 14 A 1 ATOM 104 O O . THR A 1 14 ? 7.667 9.601 -0.277 1.00 83.66 14 A 1 ATOM 105 C CB . THR A 1 14 ? 6.148 8.500 -2.277 1.00 86.72 14 A 1 ATOM 106 O OG1 . THR A 1 14 ? 6.400 9.870 -2.589 1.00 79.06 14 A 1 ATOM 107 C CG2 . THR A 1 14 ? 5.135 8.425 -1.150 1.00 77.89 14 A 1 ATOM 108 N N . SER A 1 15 ? 9.099 7.906 -0.133 1.00 89.21 15 A 1 ATOM 109 C CA . SER A 1 15 ? 9.780 8.447 1.043 1.00 86.46 15 A 1 ATOM 110 C C . SER A 1 15 ? 10.699 9.611 0.674 1.00 85.40 15 A 1 ATOM 111 O O . SER A 1 15 ? 11.305 10.234 1.544 1.00 80.34 15 A 1 ATOM 112 C CB . SER A 1 15 ? 10.589 7.347 1.730 1.00 82.65 15 A 1 ATOM 113 O OG . SER A 1 15 ? 10.820 7.666 3.085 1.00 71.67 15 A 1 ATOM 114 N N . ALA A 1 16 ? 10.809 9.890 -0.607 1.00 86.53 16 A 1 ATOM 115 C CA . ALA A 1 16 ? 11.662 10.971 -1.098 1.00 83.02 16 A 1 ATOM 116 C C . ALA A 1 16 ? 11.074 12.325 -0.719 1.00 79.94 16 A 1 ATOM 117 O O . ALA A 1 16 ? 11.718 13.069 0.044 1.00 73.63 16 A 1 ATOM 118 C CB . ALA A 1 16 ? 11.829 10.855 -2.607 1.00 76.22 16 A 1 ATOM 119 O OXT . ALA A 1 16 ? 9.990 12.658 -1.185 1.00 68.92 16 A 1 #