# 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_spkb44854 # _entry.id spkb44854 # 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" "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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" "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" "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 GLU 2 1 n LEU 3 1 n GLY 4 1 n LEU 5 1 n ILE 6 1 n LEU 7 1 n MET 8 1 n PHE 9 1 n ALA 10 1 n SER 11 1 n ALA 12 1 n PHE 13 1 n VAL 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 @ 2025-07-05 22:34:42)" _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 92.45 _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 82.87 1 1 A GLU 2 2 86.10 1 2 A LEU 3 2 92.47 1 3 A GLY 4 2 95.72 1 4 A LEU 5 2 94.18 1 5 A ILE 6 2 95.79 1 6 A LEU 7 2 94.68 1 7 A MET 8 2 92.32 1 8 A PHE 9 2 93.30 1 9 A ALA 10 2 96.72 1 10 A SER 11 2 94.30 1 11 A ALA 12 2 97.04 1 12 A PHE 13 2 93.94 1 13 A VAL 14 2 95.11 1 14 A SER 15 2 91.92 1 15 A ALA 16 2 86.84 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 GLU . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n GLY . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n MET . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n PHE . 13 A 13 A 14 1 n VAL . 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 ? 1.190 5.380 12.059 1.00 87.71 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.965 4.700 11.015 1.00 90.07 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.155 3.559 10.398 1.00 90.65 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.147 2.440 10.898 1.00 87.12 1 A 1 ATOM 5 C CB . MET A 1 1 ? 3.260 4.156 11.598 1.00 84.81 1 A 1 ATOM 6 C CG . MET A 1 1 ? 3.049 3.236 12.792 1.00 79.58 1 A 1 ATOM 7 S SD . MET A 1 1 ? 4.591 2.827 13.606 1.00 76.66 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.069 2.806 15.300 1.00 66.36 1 A 1 ATOM 9 N N . GLU A 1 2 ? 0.484 3.845 9.322 1.00 89.17 2 A 1 ATOM 10 C CA . GLU A 1 2 ? -0.327 2.850 8.640 1.00 94.06 2 A 1 ATOM 11 C C . GLU A 1 2 ? 0.431 2.261 7.457 1.00 95.67 2 A 1 ATOM 12 O O . GLU A 1 2 ? 0.089 2.507 6.298 1.00 94.18 2 A 1 ATOM 13 C CB . GLU A 1 2 ? -1.632 3.477 8.166 1.00 90.45 2 A 1 ATOM 14 C CG . GLU A 1 2 ? -2.527 3.921 9.297 1.00 83.02 2 A 1 ATOM 15 C CD . GLU A 1 2 ? -2.301 5.369 9.661 1.00 80.21 2 A 1 ATOM 16 O OE1 . GLU A 1 2 ? -2.264 6.198 8.744 1.00 72.27 2 A 1 ATOM 17 O OE2 . GLU A 1 2 ? -2.150 5.664 10.849 1.00 75.89 2 A 1 ATOM 18 N N . LEU A 1 3 ? 1.452 1.488 7.758 1.00 94.38 3 A 1 ATOM 19 C CA . LEU A 1 3 ? 2.257 0.856 6.714 1.00 95.37 3 A 1 ATOM 20 C C . LEU A 1 3 ? 1.421 -0.096 5.874 1.00 96.17 3 A 1 ATOM 21 O O . LEU A 1 3 ? 1.643 -0.237 4.674 1.00 94.85 3 A 1 ATOM 22 C CB . LEU A 1 3 ? 3.429 0.108 7.345 1.00 94.33 3 A 1 ATOM 23 C CG . LEU A 1 3 ? 4.699 0.929 7.477 1.00 91.06 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? 5.567 0.388 8.598 1.00 87.58 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? 5.468 0.922 6.168 1.00 86.06 3 A 1 ATOM 26 N N . GLY A 1 4 ? 0.463 -0.736 6.519 1.00 94.72 4 A 1 ATOM 27 C CA . GLY A 1 4 ? -0.425 -1.660 5.826 1.00 95.65 4 A 1 ATOM 28 C C . GLY A 1 4 ? -1.257 -0.968 4.774 1.00 96.61 4 A 1 ATOM 29 O O . GLY A 1 4 ? -1.441 -1.484 3.673 1.00 95.88 4 A 1 ATOM 30 N N . LEU A 1 5 ? -1.764 0.201 5.122 1.00 95.78 5 A 1 ATOM 31 C CA . LEU A 1 5 ? -2.574 0.982 4.190 1.00 96.52 5 A 1 ATOM 32 C C . LEU A 1 5 ? -1.707 1.560 3.078 1.00 97.12 5 A 1 ATOM 33 O O . LEU A 1 5 ? -2.106 1.580 1.912 1.00 96.46 5 A 1 ATOM 34 C CB . LEU A 1 5 ? -3.328 2.081 4.954 1.00 95.48 5 A 1 ATOM 35 C CG . LEU A 1 5 ? -3.065 3.527 4.531 1.00 92.11 5 A 1 ATOM 36 C CD1 . LEU A 1 5 ? -3.633 3.807 3.153 1.00 90.49 5 A 1 ATOM 37 C CD2 . LEU A 1 5 ? -3.678 4.478 5.546 1.00 89.48 5 A 1 ATOM 38 N N . ILE A 1 6 ? -0.523 2.023 3.454 1.00 96.70 6 A 1 ATOM 39 C CA . ILE A 1 6 ? 0.415 2.580 2.483 1.00 97.11 6 A 1 ATOM 40 C C . ILE A 1 6 ? 0.840 1.510 1.488 1.00 97.33 6 A 1 ATOM 41 O O . ILE A 1 6 ? 0.959 1.760 0.288 1.00 96.76 6 A 1 ATOM 42 C CB . ILE A 1 6 ? 1.645 3.167 3.192 1.00 96.82 6 A 1 ATOM 43 C CG1 . ILE A 1 6 ? 1.248 4.379 4.034 1.00 95.30 6 A 1 ATOM 44 C CG2 . ILE A 1 6 ? 2.698 3.579 2.165 1.00 94.50 6 A 1 ATOM 45 C CD1 . ILE A 1 6 ? 2.315 4.781 5.021 1.00 91.77 6 A 1 ATOM 46 N N . LEU A 1 7 ? 1.052 0.321 2.005 1.00 96.66 7 A 1 ATOM 47 C CA . LEU A 1 7 ? 1.440 -0.804 1.162 1.00 96.76 7 A 1 ATOM 48 C C . LEU A 1 7 ? 0.309 -1.165 0.210 1.00 96.98 7 A 1 ATOM 49 O O . LEU A 1 7 ? 0.541 -1.538 -0.937 1.00 96.40 7 A 1 ATOM 50 C CB . LEU A 1 7 ? 1.801 -2.003 2.039 1.00 96.17 7 A 1 ATOM 51 C CG . LEU A 1 7 ? 2.672 -3.053 1.360 1.00 93.20 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? 4.015 -2.466 0.972 1.00 90.98 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? 2.858 -4.250 2.275 1.00 90.27 7 A 1 ATOM 54 N N . MET A 1 8 ? -0.913 -1.043 0.698 1.00 96.22 8 A 1 ATOM 55 C CA . MET A 1 8 ? -2.095 -1.309 -0.115 1.00 96.31 8 A 1 ATOM 56 C C . MET A 1 8 ? -2.204 -0.297 -1.249 1.00 96.65 8 A 1 ATOM 57 O O . MET A 1 8 ? -2.634 -0.625 -2.350 1.00 95.42 8 A 1 ATOM 58 C CB . MET A 1 8 ? -3.353 -1.253 0.748 1.00 95.46 8 A 1 ATOM 59 C CG . MET A 1 8 ? -3.952 -2.620 1.007 1.00 91.89 8 A 1 ATOM 60 S SD . MET A 1 8 ? -5.591 -2.516 1.723 1.00 87.14 8 A 1 ATOM 61 C CE . MET A 1 8 ? -6.280 -4.074 1.195 1.00 79.45 8 A 1 ATOM 62 N N . PHE A 1 9 ? -1.805 0.923 -0.949 1.00 95.24 9 A 1 ATOM 63 C CA . PHE A 1 9 ? -1.834 1.994 -1.936 1.00 95.76 9 A 1 ATOM 64 C C . PHE A 1 9 ? -0.910 1.668 -3.102 1.00 96.58 9 A 1 ATOM 65 O O . PHE A 1 9 ? -1.294 1.775 -4.268 1.00 96.12 9 A 1 ATOM 66 C CB . PHE A 1 9 ? -1.410 3.303 -1.283 1.00 95.29 9 A 1 ATOM 67 C CG . PHE A 1 9 ? -2.160 4.497 -1.810 1.00 93.22 9 A 1 ATOM 68 C CD1 . PHE A 1 9 ? -1.997 4.911 -3.118 1.00 90.96 9 A 1 ATOM 69 C CD2 . PHE A 1 9 ? -3.020 5.199 -0.986 1.00 91.30 9 A 1 ATOM 70 C CE1 . PHE A 1 9 ? -2.686 6.005 -3.610 1.00 90.93 9 A 1 ATOM 71 C CE2 . PHE A 1 9 ? -3.711 6.298 -1.469 1.00 90.59 9 A 1 ATOM 72 C CZ . PHE A 1 9 ? -3.545 6.701 -2.781 1.00 90.34 9 A 1 ATOM 73 N N . ALA A 1 10 ? 0.301 1.273 -2.773 1.00 96.46 10 A 1 ATOM 74 C CA . ALA A 1 10 ? 1.284 0.919 -3.791 1.00 96.87 10 A 1 ATOM 75 C C . ALA A 1 10 ? 0.889 -0.362 -4.512 1.00 97.28 10 A 1 ATOM 76 O O . ALA A 1 10 ? 1.067 -0.485 -5.724 1.00 96.57 10 A 1 ATOM 77 C CB . ALA A 1 10 ? 2.658 0.762 -3.154 1.00 96.41 10 A 1 ATOM 78 N N . SER A 1 11 ? 0.355 -1.307 -3.756 1.00 96.67 11 A 1 ATOM 79 C CA . SER A 1 11 ? -0.077 -2.583 -4.312 1.00 96.54 11 A 1 ATOM 80 C C . SER A 1 11 ? -1.228 -2.388 -5.287 1.00 96.74 11 A 1 ATOM 81 O O . SER A 1 11 ? -1.267 -3.002 -6.351 1.00 95.32 11 A 1 ATOM 82 C CB . SER A 1 11 ? -0.489 -3.534 -3.195 1.00 95.12 11 A 1 ATOM 83 O OG . SER A 1 11 ? -0.356 -4.869 -3.603 1.00 85.39 11 A 1 ATOM 84 N N . ALA A 1 12 ? -2.162 -1.529 -4.909 1.00 97.12 12 A 1 ATOM 85 C CA . ALA A 1 12 ? -3.312 -1.233 -5.758 1.00 97.27 12 A 1 ATOM 86 C C . ALA A 1 12 ? -2.879 -0.512 -7.027 1.00 97.59 12 A 1 ATOM 87 O O . ALA A 1 12 ? -3.445 -0.723 -8.096 1.00 96.65 12 A 1 ATOM 88 C CB . ALA A 1 12 ? -4.319 -0.392 -4.994 1.00 96.56 12 A 1 ATOM 89 N N . PHE A 1 13 ? -1.884 0.337 -6.893 1.00 96.70 13 A 1 ATOM 90 C CA . PHE A 1 13 ? -1.353 1.090 -8.026 1.00 96.59 13 A 1 ATOM 91 C C . PHE A 1 13 ? -0.744 0.162 -9.069 1.00 96.89 13 A 1 ATOM 92 O O . PHE A 1 13 ? -0.948 0.335 -10.269 1.00 96.13 13 A 1 ATOM 93 C CB . PHE A 1 13 ? -0.304 2.086 -7.539 1.00 95.75 13 A 1 ATOM 94 C CG . PHE A 1 13 ? -0.168 3.291 -8.429 1.00 94.01 13 A 1 ATOM 95 C CD1 . PHE A 1 13 ? -1.249 4.128 -8.643 1.00 91.89 13 A 1 ATOM 96 C CD2 . PHE A 1 13 ? 1.041 3.584 -9.031 1.00 91.84 13 A 1 ATOM 97 C CE1 . PHE A 1 13 ? -1.128 5.240 -9.455 1.00 91.21 13 A 1 ATOM 98 C CE2 . PHE A 1 13 ? 1.170 4.700 -9.845 1.00 91.07 13 A 1 ATOM 99 C CZ . PHE A 1 13 ? 0.083 5.529 -10.057 1.00 91.25 13 A 1 ATOM 100 N N . VAL A 1 14 ? 0.002 -0.819 -8.600 1.00 96.74 14 A 1 ATOM 101 C CA . VAL A 1 14 ? 0.644 -1.786 -9.488 1.00 96.69 14 A 1 ATOM 102 C C . VAL A 1 14 ? -0.342 -2.856 -9.944 1.00 96.78 14 A 1 ATOM 103 O O . VAL A 1 14 ? -0.255 -3.353 -11.069 1.00 95.62 14 A 1 ATOM 104 C CB . VAL A 1 14 ? 1.851 -2.445 -8.801 1.00 95.46 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? 2.558 -3.396 -9.752 1.00 92.18 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? 2.822 -1.393 -8.301 1.00 92.27 14 A 1 ATOM 107 N N . SER A 1 15 ? -1.259 -3.206 -9.067 1.00 94.61 15 A 1 ATOM 108 C CA . SER A 1 15 ? -2.263 -4.228 -9.367 1.00 94.49 15 A 1 ATOM 109 C C . SER A 1 15 ? -3.275 -3.733 -10.394 1.00 94.62 15 A 1 ATOM 110 O O . SER A 1 15 ? -3.746 -4.500 -11.233 1.00 91.68 15 A 1 ATOM 111 C CB . SER A 1 15 ? -2.983 -4.655 -8.095 1.00 92.02 15 A 1 ATOM 112 O OG . SER A 1 15 ? -3.665 -5.869 -8.289 1.00 84.12 15 A 1 ATOM 113 N N . ALA A 1 16 ? -3.599 -2.460 -10.314 1.00 92.82 16 A 1 ATOM 114 C CA . ALA A 1 16 ? -4.572 -1.846 -11.223 1.00 90.69 16 A 1 ATOM 115 C C . ALA A 1 16 ? -3.935 -1.483 -12.562 1.00 88.41 16 A 1 ATOM 116 O O . ALA A 1 16 ? -4.082 -0.349 -13.027 1.00 84.84 16 A 1 ATOM 117 C CB . ALA A 1 16 ? -5.187 -0.627 -10.565 1.00 86.05 16 A 1 ATOM 118 O OXT . ALA A 1 16 ? -3.299 -2.366 -13.171 1.00 78.24 16 A 1 #