# 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_spkb07332 # _entry.id spkb07332 # 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 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" "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" # _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 ILE 3 1 n ILE 4 1 n ILE 5 1 n LEU 6 1 n LEU 7 1 n GLY 8 1 n PHE 9 1 n LEU 10 1 n GLY 11 1 n ALA 12 1 n THR 13 1 n LEU 14 1 n SER 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 @ 2025-07-07 13:03:55)" _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 95.83 _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 92.71 1 1 A LYS 2 2 93.39 1 2 A ILE 3 2 97.10 1 3 A ILE 4 2 97.47 1 4 A ILE 5 2 97.43 1 5 A LEU 6 2 96.47 1 6 A LEU 7 2 96.81 1 7 A GLY 8 2 98.26 1 8 A PHE 9 2 96.16 1 9 A LEU 10 2 96.68 1 10 A GLY 11 2 98.32 1 11 A ALA 12 2 98.40 1 12 A THR 13 2 96.27 1 13 A LEU 14 2 95.32 1 14 A SER 15 2 89.56 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 LYS . 2 A 2 A 3 1 n ILE . 3 A 3 A 4 1 n ILE . 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 GLY . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n SER . 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 ? -7.736 -4.499 11.665 1.00 96.54 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.376 -3.352 10.823 1.00 97.03 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.755 -3.827 9.513 1.00 97.18 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.702 -4.453 9.519 1.00 95.77 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.389 -2.442 11.544 1.00 94.89 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.970 -1.845 12.813 1.00 90.69 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.781 -0.840 13.708 1.00 89.36 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.795 -0.281 15.062 1.00 80.20 1 A 1 ATOM 9 N N . LYS A 1 2 ? -7.417 -3.525 8.412 1.00 97.87 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -6.963 -3.924 7.087 1.00 98.16 2 A 1 ATOM 11 C C . LYS A 1 2 ? -6.183 -2.810 6.399 1.00 98.35 2 A 1 ATOM 12 O O . LYS A 1 2 ? -5.525 -3.037 5.387 1.00 98.05 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -8.169 -4.315 6.237 1.00 97.61 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -9.266 -3.274 6.253 1.00 93.68 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -10.482 -3.741 5.466 1.00 90.79 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -10.248 -3.637 3.980 1.00 85.55 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -11.505 -3.905 3.227 1.00 80.43 2 A 1 ATOM 18 N N . ILE A 1 3 ? -6.267 -1.623 6.950 1.00 98.17 3 A 1 ATOM 19 C CA . ILE A 1 3 ? -5.604 -0.457 6.380 1.00 98.32 3 A 1 ATOM 20 C C . ILE A 1 3 ? -4.084 -0.602 6.385 1.00 98.49 3 A 1 ATOM 21 O O . ILE A 1 3 ? -3.391 0.002 5.573 1.00 98.20 3 A 1 ATOM 22 C CB . ILE A 1 3 ? -5.999 0.818 7.133 1.00 98.13 3 A 1 ATOM 23 C CG1 . ILE A 1 3 ? -5.688 0.679 8.615 1.00 96.52 3 A 1 ATOM 24 C CG2 . ILE A 1 3 ? -7.470 1.128 6.908 1.00 96.04 3 A 1 ATOM 25 C CD1 . ILE A 1 3 ? -5.966 1.936 9.412 1.00 92.96 3 A 1 ATOM 26 N N . ILE A 1 4 ? -3.588 -1.410 7.300 1.00 98.40 4 A 1 ATOM 27 C CA . ILE A 1 4 ? -2.152 -1.634 7.404 1.00 98.34 4 A 1 ATOM 28 C C . ILE A 1 4 ? -1.594 -2.221 6.113 1.00 98.35 4 A 1 ATOM 29 O O . ILE A 1 4 ? -0.456 -1.955 5.733 1.00 98.05 4 A 1 ATOM 30 C CB . ILE A 1 4 ? -1.820 -2.563 8.584 1.00 98.22 4 A 1 ATOM 31 C CG1 . ILE A 1 4 ? -2.620 -3.857 8.492 1.00 97.10 4 A 1 ATOM 32 C CG2 . ILE A 1 4 ? -2.091 -1.853 9.902 1.00 96.89 4 A 1 ATOM 33 C CD1 . ILE A 1 4 ? -2.289 -4.854 9.584 1.00 94.37 4 A 1 ATOM 34 N N . ILE A 1 5 ? -2.410 -3.023 5.450 1.00 98.47 5 A 1 ATOM 35 C CA . ILE A 1 5 ? -2.015 -3.646 4.198 1.00 98.39 5 A 1 ATOM 36 C C . ILE A 1 5 ? -1.875 -2.592 3.109 1.00 98.40 5 A 1 ATOM 37 O O . ILE A 1 5 ? -0.936 -2.605 2.312 1.00 98.15 5 A 1 ATOM 38 C CB . ILE A 1 5 ? -3.041 -4.702 3.759 1.00 98.25 5 A 1 ATOM 39 C CG1 . ILE A 1 5 ? -3.331 -5.682 4.898 1.00 96.99 5 A 1 ATOM 40 C CG2 . ILE A 1 5 ? -2.531 -5.433 2.525 1.00 96.68 5 A 1 ATOM 41 C CD1 . ILE A 1 5 ? -2.092 -6.381 5.417 1.00 94.07 5 A 1 ATOM 42 N N . LEU A 1 6 ? -2.830 -1.688 3.094 1.00 98.58 6 A 1 ATOM 43 C CA . LEU A 1 6 ? -2.834 -0.617 2.109 1.00 98.53 6 A 1 ATOM 44 C C . LEU A 1 6 ? -1.663 0.330 2.330 1.00 98.61 6 A 1 ATOM 45 O O . LEU A 1 6 ? -1.055 0.813 1.377 1.00 98.48 6 A 1 ATOM 46 C CB . LEU A 1 6 ? -4.146 0.160 2.192 1.00 98.36 6 A 1 ATOM 47 C CG . LEU A 1 6 ? -5.402 -0.684 2.023 1.00 94.42 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? -6.642 0.173 2.218 1.00 91.92 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? -5.419 -1.348 0.658 1.00 92.88 6 A 1 ATOM 50 N N . LEU A 1 7 ? -1.364 0.580 3.586 1.00 98.43 7 A 1 ATOM 51 C CA . LEU A 1 7 ? -0.269 1.475 3.939 1.00 98.35 7 A 1 ATOM 52 C C . LEU A 1 7 ? 1.064 0.936 3.443 1.00 98.45 7 A 1 ATOM 53 O O . LEU A 1 7 ? 1.862 1.665 2.853 1.00 98.19 7 A 1 ATOM 54 C CB . LEU A 1 7 ? -0.225 1.664 5.453 1.00 98.06 7 A 1 ATOM 55 C CG . LEU A 1 7 ? 0.841 2.637 5.934 1.00 95.75 7 A 1 ATOM 56 C CD1 . LEU A 1 7 ? 0.599 4.021 5.364 1.00 93.65 7 A 1 ATOM 57 C CD2 . LEU A 1 7 ? 0.870 2.679 7.452 1.00 93.62 7 A 1 ATOM 58 N N . GLY A 1 8 ? 1.291 -0.347 3.688 1.00 98.28 8 A 1 ATOM 59 C CA . GLY A 1 8 ? 2.529 -0.976 3.245 1.00 98.21 8 A 1 ATOM 60 C C . GLY A 1 8 ? 2.607 -1.078 1.738 1.00 98.38 8 A 1 ATOM 61 O O . GLY A 1 8 ? 3.650 -0.815 1.135 1.00 98.16 8 A 1 ATOM 62 N N . PHE A 1 9 ? 1.494 -1.464 1.127 1.00 98.42 9 A 1 ATOM 63 C CA . PHE A 1 9 ? 1.427 -1.607 -0.322 1.00 98.35 9 A 1 ATOM 64 C C . PHE A 1 9 ? 1.608 -0.266 -1.017 1.00 98.51 9 A 1 ATOM 65 O O . PHE A 1 9 ? 2.358 -0.158 -1.987 1.00 98.16 9 A 1 ATOM 66 C CB . PHE A 1 9 ? 0.086 -2.215 -0.722 1.00 98.01 9 A 1 ATOM 67 C CG . PHE A 1 9 ? -0.061 -2.378 -2.205 1.00 96.43 9 A 1 ATOM 68 C CD1 . PHE A 1 9 ? 0.604 -3.388 -2.868 1.00 94.33 9 A 1 ATOM 69 C CD2 . PHE A 1 9 ? -0.859 -1.515 -2.927 1.00 94.49 9 A 1 ATOM 70 C CE1 . PHE A 1 9 ? 0.476 -3.541 -4.233 1.00 93.70 9 A 1 ATOM 71 C CE2 . PHE A 1 9 ? -0.988 -1.659 -4.300 1.00 93.45 9 A 1 ATOM 72 C CZ . PHE A 1 9 ? -0.320 -2.674 -4.949 1.00 93.92 9 A 1 ATOM 73 N N . LEU A 1 10 ? 0.920 0.739 -0.509 1.00 98.48 10 A 1 ATOM 74 C CA . LEU A 1 10 ? 1.003 2.072 -1.091 1.00 98.40 10 A 1 ATOM 75 C C . LEU A 1 10 ? 2.422 2.615 -1.012 1.00 98.49 10 A 1 ATOM 76 O O . LEU A 1 10 ? 2.910 3.248 -1.945 1.00 98.11 10 A 1 ATOM 77 C CB . LEU A 1 10 ? 0.045 3.015 -0.375 1.00 98.04 10 A 1 ATOM 78 C CG . LEU A 1 10 ? -0.006 4.421 -0.946 1.00 95.58 10 A 1 ATOM 79 C CD1 . LEU A 1 10 ? -0.452 4.392 -2.394 1.00 93.06 10 A 1 ATOM 80 C CD2 . LEU A 1 10 ? -0.929 5.295 -0.115 1.00 93.29 10 A 1 ATOM 81 N N . GLY A 1 11 ? 3.076 2.368 0.098 1.00 98.39 11 A 1 ATOM 82 C CA . GLY A 1 11 ? 4.445 2.825 0.272 1.00 98.30 11 A 1 ATOM 83 C C . GLY A 1 11 ? 5.403 2.139 -0.676 1.00 98.45 11 A 1 ATOM 84 O O . GLY A 1 11 ? 6.350 2.750 -1.170 1.00 98.14 11 A 1 ATOM 85 N N . ALA A 1 12 ? 5.155 0.858 -0.932 1.00 98.56 12 A 1 ATOM 86 C CA . ALA A 1 12 ? 5.997 0.076 -1.830 1.00 98.53 12 A 1 ATOM 87 C C . ALA A 1 12 ? 5.772 0.456 -3.287 1.00 98.64 12 A 1 ATOM 88 O O . ALA A 1 12 ? 6.726 0.617 -4.045 1.00 98.17 12 A 1 ATOM 89 C CB . ALA A 1 12 ? 5.732 -1.407 -1.633 1.00 98.10 12 A 1 ATOM 90 N N . THR A 1 13 ? 4.511 0.584 -3.671 1.00 98.17 13 A 1 ATOM 91 C CA . THR A 1 13 ? 4.171 0.913 -5.051 1.00 98.08 13 A 1 ATOM 92 C C . THR A 1 13 ? 4.569 2.335 -5.404 1.00 98.00 13 A 1 ATOM 93 O O . THR A 1 13 ? 5.062 2.598 -6.498 1.00 96.71 13 A 1 ATOM 94 C CB . THR A 1 13 ? 2.671 0.725 -5.310 1.00 97.39 13 A 1 ATOM 95 O OG1 . THR A 1 13 ? 2.408 0.925 -6.700 1.00 93.17 13 A 1 ATOM 96 C CG2 . THR A 1 13 ? 1.844 1.702 -4.512 1.00 92.38 13 A 1 ATOM 97 N N . LEU A 1 14 ? 4.367 3.240 -4.481 1.00 97.96 14 A 1 ATOM 98 C CA . LEU A 1 14 ? 4.703 4.640 -4.708 1.00 97.62 14 A 1 ATOM 99 C C . LEU A 1 14 ? 6.206 4.842 -4.688 1.00 97.44 14 A 1 ATOM 100 O O . LEU A 1 14 ? 6.770 5.485 -5.578 1.00 96.23 14 A 1 ATOM 101 C CB . LEU A 1 14 ? 4.048 5.515 -3.639 1.00 96.88 14 A 1 ATOM 102 C CG . LEU A 1 14 ? 4.280 7.006 -3.813 1.00 94.76 14 A 1 ATOM 103 C CD1 . LEU A 1 14 ? 3.711 7.484 -5.130 1.00 91.40 14 A 1 ATOM 104 C CD2 . LEU A 1 14 ? 3.661 7.767 -2.653 1.00 90.24 14 A 1 ATOM 105 N N . SER A 1 15 ? 6.847 4.287 -3.669 1.00 95.85 15 A 1 ATOM 106 C CA . SER A 1 15 ? 8.297 4.377 -3.521 1.00 94.46 15 A 1 ATOM 107 C C . SER A 1 15 ? 8.779 5.794 -3.828 1.00 92.36 15 A 1 ATOM 108 O O . SER A 1 15 ? 8.452 6.706 -3.033 1.00 86.59 15 A 1 ATOM 109 C CB . SER A 1 15 ? 8.979 3.363 -4.438 1.00 91.20 15 A 1 ATOM 110 O OG . SER A 1 15 ? 8.598 2.048 -4.114 1.00 82.88 15 A 1 ATOM 111 O OXT . SER A 1 15 ? 9.443 6.033 -4.826 1.00 83.55 15 A 1 #