# 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_spkb09587 # _entry.id spkb09587 # 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 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 ALA 2 1 n LEU 3 1 n PRO 4 1 n SER 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n VAL 9 1 n VAL 10 1 n ALA 11 1 n ALA 12 1 n LEU 13 1 n ALA 14 1 n GLY 15 1 n GLY 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 @ 2025-07-02 14:55:16)" _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 95.04 _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 86.25 1 1 A ALA 2 2 92.65 1 2 A LEU 3 2 93.64 1 3 A PRO 4 2 96.93 1 4 A SER 5 2 97.24 1 5 A LEU 6 2 96.73 1 6 A LEU 7 2 96.78 1 7 A LEU 8 2 96.38 1 8 A VAL 9 2 97.85 1 9 A VAL 10 2 97.61 1 10 A ALA 11 2 97.75 1 11 A ALA 12 2 98.17 1 12 A LEU 13 2 97.04 1 13 A ALA 14 2 97.22 1 14 A GLY 15 2 94.22 1 15 A GLY 16 2 82.68 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 PRO . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n GLY . 15 A 15 A 16 1 n GLY . 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 ? -9.434 2.077 10.448 1.00 92.91 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.627 0.881 10.162 1.00 92.25 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.599 1.182 9.076 1.00 92.22 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.961 1.503 7.945 1.00 89.22 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.522 -0.280 9.712 1.00 88.67 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.757 -1.554 9.443 1.00 82.95 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.810 -2.917 8.923 1.00 80.89 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.734 -3.206 10.434 1.00 70.86 1 A 1 ATOM 9 N N . ALA A 1 2 ? -6.308 1.092 9.412 1.00 90.62 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -5.231 1.360 8.461 1.00 93.32 2 A 1 ATOM 11 C C . ALA A 1 2 ? -4.603 0.052 7.984 1.00 95.13 2 A 1 ATOM 12 O O . ALA A 1 2 ? -4.074 -0.716 8.788 1.00 93.33 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -4.169 2.249 9.100 1.00 90.86 2 A 1 ATOM 14 N N . LEU A 1 3 ? -4.649 -0.190 6.669 1.00 96.08 3 A 1 ATOM 15 C CA . LEU A 1 3 ? -4.069 -1.389 6.083 1.00 96.69 3 A 1 ATOM 16 C C . LEU A 1 3 ? -2.572 -1.179 5.842 1.00 97.44 3 A 1 ATOM 17 O O . LEU A 1 3 ? -2.187 -0.221 5.159 1.00 96.82 3 A 1 ATOM 18 C CB . LEU A 1 3 ? -4.768 -1.729 4.767 1.00 95.35 3 A 1 ATOM 19 C CG . LEU A 1 3 ? -6.252 -2.069 4.897 1.00 91.78 3 A 1 ATOM 20 C CD1 . LEU A 1 3 ? -6.878 -2.261 3.523 1.00 89.16 3 A 1 ATOM 21 C CD2 . LEU A 1 3 ? -6.443 -3.321 5.747 1.00 85.83 3 A 1 ATOM 22 N N . PRO A 1 4 ? -1.711 -2.070 6.387 1.00 97.51 4 A 1 ATOM 23 C CA . PRO A 1 4 ? -0.255 -1.942 6.225 1.00 97.72 4 A 1 ATOM 24 C C . PRO A 1 4 ? 0.172 -1.998 4.763 1.00 98.17 4 A 1 ATOM 25 O O . PRO A 1 4 ? 1.073 -1.258 4.344 1.00 97.69 4 A 1 ATOM 26 C CB . PRO A 1 4 ? 0.307 -3.133 7.017 1.00 96.52 4 A 1 ATOM 27 C CG . PRO A 1 4 ? -0.832 -4.109 7.085 1.00 94.50 4 A 1 ATOM 28 C CD . PRO A 1 4 ? -2.079 -3.263 7.144 1.00 96.41 4 A 1 ATOM 29 N N . SER A 1 5 ? -0.473 -2.862 3.975 1.00 98.02 5 A 1 ATOM 30 C CA . SER A 1 5 ? -0.162 -2.990 2.553 1.00 98.22 5 A 1 ATOM 31 C C . SER A 1 5 ? -0.485 -1.703 1.802 1.00 98.49 5 A 1 ATOM 32 O O . SER A 1 5 ? 0.261 -1.288 0.911 1.00 98.14 5 A 1 ATOM 33 C CB . SER A 1 5 ? -0.942 -4.156 1.946 1.00 97.55 5 A 1 ATOM 34 O OG . SER A 1 5 ? -2.326 -3.968 2.114 1.00 93.00 5 A 1 ATOM 35 N N . LEU A 1 6 ? -1.594 -1.061 2.177 1.00 98.21 6 A 1 ATOM 36 C CA . LEU A 1 6 ? -2.008 0.192 1.550 1.00 98.20 6 A 1 ATOM 37 C C . LEU A 1 6 ? -0.981 1.292 1.811 1.00 98.38 6 A 1 ATOM 38 O O . LEU A 1 6 ? -0.622 2.049 0.905 1.00 98.17 6 A 1 ATOM 39 C CB . LEU A 1 6 ? -3.380 0.622 2.081 1.00 97.96 6 A 1 ATOM 40 C CG . LEU A 1 6 ? -3.924 1.910 1.470 1.00 95.27 6 A 1 ATOM 41 C CD1 . LEU A 1 6 ? -4.114 1.760 -0.034 1.00 93.92 6 A 1 ATOM 42 C CD2 . LEU A 1 6 ? -5.241 2.285 2.137 1.00 93.73 6 A 1 ATOM 43 N N . LEU A 1 7 ? -0.505 1.377 3.056 1.00 98.02 7 A 1 ATOM 44 C CA . LEU A 1 7 ? 0.489 2.378 3.433 1.00 97.98 7 A 1 ATOM 45 C C . LEU A 1 7 ? 1.783 2.191 2.644 1.00 98.12 7 A 1 ATOM 46 O O . LEU A 1 7 ? 2.396 3.164 2.194 1.00 98.03 7 A 1 ATOM 47 C CB . LEU A 1 7 ? 0.780 2.294 4.935 1.00 97.75 7 A 1 ATOM 48 C CG . LEU A 1 7 ? -0.404 2.658 5.832 1.00 95.69 7 A 1 ATOM 49 C CD1 . LEU A 1 7 ? -0.051 2.424 7.295 1.00 94.47 7 A 1 ATOM 50 C CD2 . LEU A 1 7 ? -0.818 4.107 5.618 1.00 94.15 7 A 1 ATOM 51 N N . LEU A 1 8 ? 2.192 0.936 2.462 1.00 97.98 8 A 1 ATOM 52 C CA . LEU A 1 8 ? 3.407 0.621 1.716 1.00 97.91 8 A 1 ATOM 53 C C . LEU A 1 8 ? 3.270 1.016 0.248 1.00 98.07 8 A 1 ATOM 54 O O . LEU A 1 8 ? 4.203 1.566 -0.345 1.00 97.88 8 A 1 ATOM 55 C CB . LEU A 1 8 ? 3.716 -0.875 1.825 1.00 97.55 8 A 1 ATOM 56 C CG . LEU A 1 8 ? 4.132 -1.340 3.222 1.00 94.21 8 A 1 ATOM 57 C CD1 . LEU A 1 8 ? 4.269 -2.857 3.253 1.00 93.77 8 A 1 ATOM 58 C CD2 . LEU A 1 8 ? 5.442 -0.686 3.641 1.00 93.67 8 A 1 ATOM 59 N N . VAL A 1 9 ? 2.105 0.747 -0.340 1.00 98.01 9 A 1 ATOM 60 C CA . VAL A 1 9 ? 1.849 1.090 -1.737 1.00 98.05 9 A 1 ATOM 61 C C . VAL A 1 9 ? 1.899 2.601 -1.939 1.00 98.26 9 A 1 ATOM 62 O O . VAL A 1 9 ? 2.529 3.093 -2.881 1.00 98.06 9 A 1 ATOM 63 C CB . VAL A 1 9 ? 0.490 0.540 -2.203 1.00 97.82 9 A 1 ATOM 64 C CG1 . VAL A 1 9 ? 0.134 1.065 -3.592 1.00 97.42 9 A 1 ATOM 65 C CG2 . VAL A 1 9 ? 0.518 -0.981 -2.217 1.00 97.32 9 A 1 ATOM 66 N N . VAL A 1 10 ? 1.247 3.336 -1.050 1.00 98.01 10 A 1 ATOM 67 C CA . VAL A 1 10 ? 1.229 4.796 -1.135 1.00 97.95 10 A 1 ATOM 68 C C . VAL A 1 10 ? 2.643 5.362 -1.034 1.00 98.18 10 A 1 ATOM 69 O O . VAL A 1 10 ? 3.026 6.249 -1.803 1.00 98.06 10 A 1 ATOM 70 C CB . VAL A 1 10 ? 0.343 5.407 -0.036 1.00 97.60 10 A 1 ATOM 71 C CG1 . VAL A 1 10 ? 0.450 6.931 -0.031 1.00 96.63 10 A 1 ATOM 72 C CG2 . VAL A 1 10 ? -1.107 4.994 -0.245 1.00 96.86 10 A 1 ATOM 73 N N . ALA A 1 11 ? 3.423 4.848 -0.088 1.00 98.01 11 A 1 ATOM 74 C CA . ALA A 1 11 ? 4.801 5.298 0.100 1.00 97.82 11 A 1 ATOM 75 C C . ALA A 1 11 ? 5.648 5.012 -1.134 1.00 98.06 11 A 1 ATOM 76 O O . ALA A 1 11 ? 6.466 5.841 -1.544 1.00 97.58 11 A 1 ATOM 77 C CB . ALA A 1 11 ? 5.411 4.613 1.319 1.00 97.30 11 A 1 ATOM 78 N N . ALA A 1 12 ? 5.455 3.840 -1.739 1.00 98.26 12 A 1 ATOM 79 C CA . ALA A 1 12 ? 6.198 3.455 -2.934 1.00 98.25 12 A 1 ATOM 80 C C . ALA A 1 12 ? 5.869 4.374 -4.107 1.00 98.43 12 A 1 ATOM 81 O O . ALA A 1 12 ? 6.763 4.797 -4.845 1.00 97.95 12 A 1 ATOM 82 C CB . ALA A 1 12 ? 5.889 2.002 -3.297 1.00 97.95 12 A 1 ATOM 83 N N . LEU A 1 13 ? 4.588 4.686 -4.285 1.00 98.44 13 A 1 ATOM 84 C CA . LEU A 1 13 ? 4.150 5.560 -5.369 1.00 98.30 13 A 1 ATOM 85 C C . LEU A 1 13 ? 4.669 6.978 -5.174 1.00 98.29 13 A 1 ATOM 86 O O . LEU A 1 13 ? 5.032 7.658 -6.142 1.00 97.60 13 A 1 ATOM 87 C CB . LEU A 1 13 ? 2.623 5.572 -5.450 1.00 97.90 13 A 1 ATOM 88 C CG . LEU A 1 13 ? 1.996 4.255 -5.908 1.00 96.21 13 A 1 ATOM 89 C CD1 . LEU A 1 13 ? 0.482 4.320 -5.792 1.00 94.98 13 A 1 ATOM 90 C CD2 . LEU A 1 13 ? 2.405 3.931 -7.339 1.00 94.58 13 A 1 ATOM 91 N N . ALA A 1 14 ? 4.716 7.421 -3.927 1.00 98.05 14 A 1 ATOM 92 C CA . ALA A 1 14 ? 5.200 8.758 -3.596 1.00 97.75 14 A 1 ATOM 93 C C . ALA A 1 14 ? 6.715 8.847 -3.719 1.00 97.62 14 A 1 ATOM 94 O O . ALA A 1 14 ? 7.267 9.936 -3.890 1.00 95.86 14 A 1 ATOM 95 C CB . ALA A 1 14 ? 4.764 9.140 -2.184 1.00 96.80 14 A 1 ATOM 96 N N . GLY A 1 15 ? 7.384 7.696 -3.647 1.00 96.58 15 A 1 ATOM 97 C CA . GLY A 1 15 ? 8.840 7.658 -3.745 1.00 95.56 15 A 1 ATOM 98 C C . GLY A 1 15 ? 9.517 8.201 -2.501 1.00 94.55 15 A 1 ATOM 99 O O . GLY A 1 15 ? 10.564 8.854 -2.594 1.00 90.18 15 A 1 ATOM 100 N N . GLY A 1 16 ? 8.892 7.924 -1.369 1.00 91.10 16 A 1 ATOM 101 C CA . GLY A 1 16 ? 9.428 8.400 -0.102 1.00 85.92 16 A 1 ATOM 102 C C . GLY A 1 16 ? 8.690 7.806 1.079 1.00 81.75 16 A 1 ATOM 103 O O . GLY A 1 16 ? 9.090 8.087 2.232 1.00 75.33 16 A 1 ATOM 104 O OXT . GLY A 1 16 ? 7.709 7.061 0.882 1.00 79.32 16 A 1 #