# 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_spkb07942 # _entry.id spkb07942 # 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 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" "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 LYS 2 1 n PHE 3 1 n SER 4 1 n ALA 5 1 n PRO 6 1 n VAL 7 1 n LEU 8 1 n ALA 9 1 n ILE 10 1 n PHE 11 1 n LEU 12 1 n ALA 13 1 n SER 14 1 n ALA 15 1 n SER 16 1 n ALA 17 # _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 17:01:24)" _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 92.64 _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 82.88 1 1 A LYS 2 2 84.04 1 2 A PHE 3 2 88.15 1 3 A SER 4 2 93.81 1 4 A ALA 5 2 96.64 1 5 A PRO 6 2 96.60 1 6 A VAL 7 2 96.95 1 7 A LEU 8 2 94.56 1 8 A ALA 9 2 97.22 1 9 A ILE 10 2 95.76 1 10 A PHE 11 2 94.22 1 11 A LEU 12 2 94.89 1 12 A ALA 13 2 97.52 1 13 A SER 14 2 95.53 1 14 A ALA 15 2 96.67 1 15 A SER 16 2 91.51 1 16 A ALA 17 2 86.99 1 17 # _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 SER . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n PRO . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n SER . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? -11.229 9.220 0.607 1.00 87.75 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.867 8.864 0.165 1.00 89.38 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.862 7.494 -0.493 1.00 90.55 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.175 6.499 0.152 1.00 87.00 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.916 8.848 1.349 1.00 84.61 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.706 10.235 1.921 1.00 80.74 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.590 10.232 3.326 1.00 76.22 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.539 11.975 3.686 1.00 66.75 1 A 1 ATOM 9 N N . LYS A 1 2 ? -9.539 7.461 -1.775 1.00 90.26 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -9.527 6.216 -2.534 1.00 92.20 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.117 5.647 -2.636 1.00 92.43 2 A 1 ATOM 12 O O . LYS A 1 2 ? -7.930 4.524 -3.093 1.00 91.32 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -10.105 6.467 -3.927 1.00 89.02 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -10.738 5.234 -4.547 1.00 81.51 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -12.131 4.995 -3.983 1.00 80.01 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -12.776 3.795 -4.638 1.00 73.03 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -14.131 3.535 -4.081 1.00 66.57 2 A 1 ATOM 18 N N . PHE A 1 3 ? -7.122 6.407 -2.221 1.00 91.47 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -5.724 6.010 -2.321 1.00 92.49 3 A 1 ATOM 20 C C . PHE A 1 3 ? -5.204 5.429 -1.009 1.00 94.58 3 A 1 ATOM 21 O O . PHE A 1 3 ? -3.993 5.355 -0.792 1.00 93.57 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -4.874 7.207 -2.727 1.00 90.96 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -5.290 7.813 -4.038 1.00 88.01 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -4.935 7.208 -5.228 1.00 85.41 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -6.033 8.979 -4.070 1.00 84.82 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -5.309 7.758 -6.441 1.00 82.91 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -6.417 9.538 -5.278 1.00 83.57 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -6.051 8.926 -6.466 1.00 81.87 3 A 1 ATOM 29 N N . SER A 1 4 ? -6.112 5.017 -0.139 1.00 95.23 4 A 1 ATOM 30 C CA . SER A 1 4 ? -5.736 4.465 1.159 1.00 95.90 4 A 1 ATOM 31 C C . SER A 1 4 ? -4.988 3.144 1.015 1.00 96.64 4 A 1 ATOM 32 O O . SER A 1 4 ? -4.035 2.876 1.744 1.00 95.97 4 A 1 ATOM 33 C CB . SER A 1 4 ? -6.980 4.262 2.017 1.00 94.12 4 A 1 ATOM 34 O OG . SER A 1 4 ? -7.673 5.479 2.173 1.00 85.01 4 A 1 ATOM 35 N N . ALA A 1 5 ? -5.440 2.310 0.068 1.00 96.08 5 A 1 ATOM 36 C CA . ALA A 1 5 ? -4.810 1.011 -0.171 1.00 96.93 5 A 1 ATOM 37 C C . ALA A 1 5 ? -3.362 1.145 -0.658 1.00 97.49 5 A 1 ATOM 38 O O . ALA A 1 5 ? -2.457 0.552 -0.066 1.00 96.91 5 A 1 ATOM 39 C CB . ALA A 1 5 ? -5.647 0.199 -1.155 1.00 95.80 5 A 1 ATOM 40 N N . PRO A 1 6 ? -3.121 1.902 -1.738 1.00 97.16 6 A 1 ATOM 41 C CA . PRO A 1 6 ? -1.756 2.068 -2.251 1.00 97.21 6 A 1 ATOM 42 C C . PRO A 1 6 ? -0.831 2.727 -1.238 1.00 97.77 6 A 1 ATOM 43 O O . PRO A 1 6 ? 0.349 2.389 -1.161 1.00 97.33 6 A 1 ATOM 44 C CB . PRO A 1 6 ? -1.932 2.948 -3.497 1.00 96.07 6 A 1 ATOM 45 C CG . PRO A 1 6 ? -3.292 3.539 -3.380 1.00 94.58 6 A 1 ATOM 46 C CD . PRO A 1 6 ? -4.109 2.563 -2.590 1.00 96.05 6 A 1 ATOM 47 N N . VAL A 1 7 ? -1.351 3.644 -0.468 1.00 97.35 7 A 1 ATOM 48 C CA . VAL A 1 7 ? -0.562 4.327 0.555 1.00 97.63 7 A 1 ATOM 49 C C . VAL A 1 7 ? -0.078 3.329 1.600 1.00 97.83 7 A 1 ATOM 50 O O . VAL A 1 7 ? 1.068 3.386 2.049 1.00 97.45 7 A 1 ATOM 51 C CB . VAL A 1 7 ? -1.392 5.434 1.222 1.00 97.22 7 A 1 ATOM 52 C CG1 . VAL A 1 7 ? -0.729 5.928 2.493 1.00 95.78 7 A 1 ATOM 53 C CG2 . VAL A 1 7 ? -1.589 6.585 0.256 1.00 95.39 7 A 1 ATOM 54 N N . LEU A 1 8 ? -0.946 2.413 1.973 1.00 96.82 8 A 1 ATOM 55 C CA . LEU A 1 8 ? -0.605 1.393 2.957 1.00 96.63 8 A 1 ATOM 56 C C . LEU A 1 8 ? 0.488 0.475 2.425 1.00 97.20 8 A 1 ATOM 57 O O . LEU A 1 8 ? 1.404 0.097 3.150 1.00 97.24 8 A 1 ATOM 58 C CB . LEU A 1 8 ? -1.842 0.570 3.304 1.00 96.23 8 A 1 ATOM 59 C CG . LEU A 1 8 ? -1.686 -0.249 4.578 1.00 92.22 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? -1.899 0.627 5.803 1.00 89.77 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? -2.657 -1.416 4.589 1.00 90.34 8 A 1 ATOM 62 N N . ALA A 1 9 ? 0.378 0.102 1.157 1.00 97.00 9 A 1 ATOM 63 C CA . ALA A 1 9 ? 1.358 -0.775 0.522 1.00 97.25 9 A 1 ATOM 64 C C . ALA A 1 9 ? 2.741 -0.128 0.508 1.00 97.76 9 A 1 ATOM 65 O O . ALA A 1 9 ? 3.745 -0.778 0.807 1.00 97.40 9 A 1 ATOM 66 C CB . ALA A 1 9 ? 0.914 -1.101 -0.898 1.00 96.68 9 A 1 ATOM 67 N N . ILE A 1 10 ? 2.786 1.139 0.173 1.00 97.08 10 A 1 ATOM 68 C CA . ILE A 1 10 ? 4.042 1.886 0.130 1.00 96.94 10 A 1 ATOM 69 C C . ILE A 1 10 ? 4.635 1.999 1.531 1.00 97.21 10 A 1 ATOM 70 O O . ILE A 1 10 ? 5.844 1.840 1.729 1.00 96.82 10 A 1 ATOM 71 C CB . ILE A 1 10 ? 3.818 3.283 -0.471 1.00 96.62 10 A 1 ATOM 72 C CG1 . ILE A 1 10 ? 3.396 3.179 -1.939 1.00 95.09 10 A 1 ATOM 73 C CG2 . ILE A 1 10 ? 5.094 4.125 -0.355 1.00 94.61 10 A 1 ATOM 74 C CD1 . ILE A 1 10 ? 2.726 4.431 -2.444 1.00 91.68 10 A 1 ATOM 75 N N . PHE A 1 11 ? 3.774 2.261 2.492 1.00 96.67 11 A 1 ATOM 76 C CA . PHE A 1 11 ? 4.202 2.378 3.881 1.00 96.41 11 A 1 ATOM 77 C C . PHE A 1 11 ? 4.784 1.061 4.376 1.00 96.81 11 A 1 ATOM 78 O O . PHE A 1 11 ? 5.808 1.036 5.061 1.00 96.41 11 A 1 ATOM 79 C CB . PHE A 1 11 ? 3.013 2.785 4.749 1.00 96.04 11 A 1 ATOM 80 C CG . PHE A 1 11 ? 3.369 2.904 6.205 1.00 94.53 11 A 1 ATOM 81 C CD1 . PHE A 1 11 ? 4.078 4.000 6.667 1.00 92.35 11 A 1 ATOM 82 C CD2 . PHE A 1 11 ? 2.991 1.920 7.106 1.00 92.63 11 A 1 ATOM 83 C CE1 . PHE A 1 11 ? 4.407 4.109 8.011 1.00 91.56 11 A 1 ATOM 84 C CE2 . PHE A 1 11 ? 3.321 2.026 8.452 1.00 91.41 11 A 1 ATOM 85 C CZ . PHE A 1 11 ? 4.030 3.124 8.902 1.00 91.55 11 A 1 ATOM 86 N N . LEU A 1 12 ? 4.126 -0.030 4.028 1.00 97.42 12 A 1 ATOM 87 C CA . LEU A 1 12 ? 4.582 -1.359 4.429 1.00 97.28 12 A 1 ATOM 88 C C . LEU A 1 12 ? 5.945 -1.666 3.825 1.00 97.50 12 A 1 ATOM 89 O O . LEU A 1 12 ? 6.826 -2.204 4.493 1.00 97.08 12 A 1 ATOM 90 C CB . LEU A 1 12 ? 3.574 -2.416 3.982 1.00 96.78 12 A 1 ATOM 91 C CG . LEU A 1 12 ? 3.778 -3.771 4.659 1.00 92.11 12 A 1 ATOM 92 C CD1 . LEU A 1 12 ? 3.066 -3.808 6.002 1.00 90.32 12 A 1 ATOM 93 C CD2 . LEU A 1 12 ? 3.282 -4.899 3.773 1.00 90.60 12 A 1 ATOM 94 N N . ALA A 1 13 ? 6.112 -1.334 2.561 1.00 97.87 13 A 1 ATOM 95 C CA . ALA A 1 13 ? 7.377 -1.561 1.865 1.00 97.64 13 A 1 ATOM 96 C C . ALA A 1 13 ? 8.504 -0.779 2.533 1.00 97.88 13 A 1 ATOM 97 O O . ALA A 1 13 ? 9.624 -1.276 2.668 1.00 97.18 13 A 1 ATOM 98 C CB . ALA A 1 13 ? 7.241 -1.157 0.402 1.00 97.01 13 A 1 ATOM 99 N N . SER A 1 14 ? 8.201 0.424 2.962 1.00 97.71 14 A 1 ATOM 100 C CA . SER A 1 14 ? 9.173 1.276 3.638 1.00 97.44 14 A 1 ATOM 101 C C . SER A 1 14 ? 9.510 0.728 5.021 1.00 97.43 14 A 1 ATOM 102 O O . SER A 1 14 ? 10.660 0.778 5.457 1.00 96.23 14 A 1 ATOM 103 C CB . SER A 1 14 ? 8.623 2.696 3.762 1.00 96.56 14 A 1 ATOM 104 O OG . SER A 1 14 ? 9.605 3.564 4.265 1.00 87.79 14 A 1 ATOM 105 N N . ALA A 1 15 ? 8.504 0.203 5.699 1.00 97.33 15 A 1 ATOM 106 C CA . ALA A 1 15 ? 8.682 -0.375 7.026 1.00 96.90 15 A 1 ATOM 107 C C . ALA A 1 15 ? 9.556 -1.619 6.967 1.00 97.15 15 A 1 ATOM 108 O O . ALA A 1 15 ? 10.354 -1.877 7.865 1.00 96.20 15 A 1 ATOM 109 C CB . ALA A 1 15 ? 7.326 -0.711 7.629 1.00 95.77 15 A 1 ATOM 110 N N . SER A 1 16 ? 9.408 -2.394 5.903 1.00 95.12 16 A 1 ATOM 111 C CA . SER A 1 16 ? 10.196 -3.606 5.703 1.00 94.70 16 A 1 ATOM 112 C C . SER A 1 16 ? 11.606 -3.235 5.251 1.00 94.15 16 A 1 ATOM 113 O O . SER A 1 16 ? 11.783 -2.594 4.221 1.00 91.21 16 A 1 ATOM 114 C CB . SER A 1 16 ? 9.527 -4.502 4.665 1.00 92.21 16 A 1 ATOM 115 O OG . SER A 1 16 ? 8.224 -4.856 5.093 1.00 81.69 16 A 1 ATOM 116 N N . ALA A 1 17 ? 12.596 -3.644 6.018 1.00 93.49 17 A 1 ATOM 117 C CA . ALA A 1 17 ? 13.976 -3.317 5.699 1.00 91.57 17 A 1 ATOM 118 C C . ALA A 1 17 ? 14.420 -3.935 4.372 1.00 89.78 17 A 1 ATOM 119 O O . ALA A 1 17 ? 13.755 -4.848 3.870 1.00 83.58 17 A 1 ATOM 120 C CB . ALA A 1 17 ? 14.887 -3.785 6.830 1.00 86.37 17 A 1 ATOM 121 O OXT . ALA A 1 17 ? 15.431 -3.500 3.821 1.00 77.14 17 A 1 #