# 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_spkb13089 # _entry.id spkb13089 # 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" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[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 ALA 2 1 n VAL 3 1 n LEU 4 1 n VAL 5 1 n VAL 6 1 n LEU 7 1 n LEU 8 1 n SER 9 1 n SER 10 1 n LEU 11 1 n VAL 12 1 n SER 13 1 n SER 14 1 n ALA 15 1 n LEU 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 @ 2025-07-07 13:27:40)" _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 94.80 _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 81.56 1 1 A ALA 2 2 93.86 1 2 A VAL 3 2 96.00 1 3 A LEU 4 2 96.05 1 4 A VAL 5 2 97.36 1 5 A VAL 6 2 97.61 1 6 A LEU 7 2 96.26 1 7 A LEU 8 2 95.44 1 8 A SER 9 2 96.03 1 9 A SER 10 2 96.55 1 10 A LEU 11 2 95.88 1 11 A VAL 12 2 97.04 1 12 A SER 13 2 96.38 1 13 A SER 14 2 96.76 1 14 A ALA 15 2 97.44 1 15 A LEU 16 2 94.70 1 16 A ALA 17 2 88.41 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 ALA . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n LEU . 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 ? -6.940 -6.504 8.699 1.00 88.35 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.299 -5.842 7.423 1.00 87.77 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.032 -5.393 6.692 1.00 87.83 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.519 -4.298 6.935 1.00 86.55 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.180 -4.639 7.699 1.00 83.01 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.581 -5.037 8.173 1.00 78.29 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.605 -6.453 9.259 1.00 74.83 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.235 -6.308 9.959 1.00 65.83 1 A 1 ATOM 9 N N . ALA A 1 2 ? -5.563 -6.260 5.795 1.00 90.67 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -4.336 -5.990 5.041 1.00 94.80 2 A 1 ATOM 11 C C . ALA A 1 2 ? -4.521 -4.862 4.029 1.00 96.56 2 A 1 ATOM 12 O O . ALA A 1 2 ? -3.557 -4.193 3.650 1.00 95.22 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -3.874 -7.262 4.329 1.00 92.03 2 A 1 ATOM 14 N N . VAL A 1 3 ? -5.769 -4.668 3.587 1.00 96.81 3 A 1 ATOM 15 C CA . VAL A 1 3 ? -6.071 -3.628 2.597 1.00 97.37 3 A 1 ATOM 16 C C . VAL A 1 3 ? -5.619 -2.256 3.087 1.00 97.91 3 A 1 ATOM 17 O O . VAL A 1 3 ? -5.031 -1.471 2.334 1.00 97.50 3 A 1 ATOM 18 C CB . VAL A 1 3 ? -7.576 -3.593 2.276 1.00 96.59 3 A 1 ATOM 19 C CG1 . VAL A 1 3 ? -7.875 -2.508 1.249 1.00 93.10 3 A 1 ATOM 20 C CG2 . VAL A 1 3 ? -8.044 -4.950 1.763 1.00 92.74 3 A 1 ATOM 21 N N . LEU A 1 4 ? -5.888 -1.972 4.352 1.00 96.94 4 A 1 ATOM 22 C CA . LEU A 1 4 ? -5.505 -0.694 4.945 1.00 97.45 4 A 1 ATOM 23 C C . LEU A 1 4 ? -3.990 -0.532 4.926 1.00 97.84 4 A 1 ATOM 24 O O . LEU A 1 4 ? -3.460 0.540 4.631 1.00 97.59 4 A 1 ATOM 25 C CB . LEU A 1 4 ? -6.033 -0.600 6.384 1.00 97.26 4 A 1 ATOM 26 C CG . LEU A 1 4 ? -6.649 0.752 6.743 1.00 95.05 4 A 1 ATOM 27 C CD1 . LEU A 1 4 ? -5.626 1.864 6.617 1.00 93.28 4 A 1 ATOM 28 C CD2 . LEU A 1 4 ? -7.858 1.022 5.861 1.00 93.02 4 A 1 ATOM 29 N N . VAL A 1 5 ? -3.296 -1.613 5.236 1.00 98.00 5 A 1 ATOM 30 C CA . VAL A 1 5 ? -1.832 -1.623 5.245 1.00 98.04 5 A 1 ATOM 31 C C . VAL A 1 5 ? -1.284 -1.372 3.843 1.00 98.19 5 A 1 ATOM 32 O O . VAL A 1 5 ? -0.290 -0.660 3.668 1.00 97.91 5 A 1 ATOM 33 C CB . VAL A 1 5 ? -1.290 -2.964 5.775 1.00 97.64 5 A 1 ATOM 34 C CG1 . VAL A 1 5 ? 0.233 -2.962 5.777 1.00 95.93 5 A 1 ATOM 35 C CG2 . VAL A 1 5 ? -1.823 -3.232 7.177 1.00 95.82 5 A 1 ATOM 36 N N . VAL A 1 6 ? -1.925 -1.971 2.852 1.00 98.18 6 A 1 ATOM 37 C CA . VAL A 1 6 ? -1.498 -1.806 1.461 1.00 98.15 6 A 1 ATOM 38 C C . VAL A 1 6 ? -1.618 -0.348 1.031 1.00 98.28 6 A 1 ATOM 39 O O . VAL A 1 6 ? -0.731 0.189 0.361 1.00 98.03 6 A 1 ATOM 40 C CB . VAL A 1 6 ? -2.330 -2.696 0.521 1.00 97.86 6 A 1 ATOM 41 C CG1 . VAL A 1 6 ? -1.974 -2.419 -0.934 1.00 96.42 6 A 1 ATOM 42 C CG2 . VAL A 1 6 ? -2.100 -4.164 0.846 1.00 96.32 6 A 1 ATOM 43 N N . LEU A 1 7 ? -2.717 0.282 1.421 1.00 97.92 7 A 1 ATOM 44 C CA . LEU A 1 7 ? -2.941 1.684 1.078 1.00 97.85 7 A 1 ATOM 45 C C . LEU A 1 7 ? -1.847 2.564 1.672 1.00 97.98 7 A 1 ATOM 46 O O . LEU A 1 7 ? -1.289 3.431 0.993 1.00 97.86 7 A 1 ATOM 47 C CB . LEU A 1 7 ? -4.306 2.140 1.594 1.00 97.83 7 A 1 ATOM 48 C CG . LEU A 1 7 ? -5.498 1.502 0.888 1.00 94.66 7 A 1 ATOM 49 C CD1 . LEU A 1 7 ? -6.788 1.844 1.621 1.00 93.07 7 A 1 ATOM 50 C CD2 . LEU A 1 7 ? -5.579 1.969 -0.559 1.00 92.94 7 A 1 ATOM 51 N N . LEU A 1 8 ? -1.545 2.317 2.929 1.00 97.60 8 A 1 ATOM 52 C CA . LEU A 1 8 ? -0.508 3.078 3.621 1.00 97.52 8 A 1 ATOM 53 C C . LEU A 1 8 ? 0.855 2.834 2.985 1.00 97.72 8 A 1 ATOM 54 O O . LEU A 1 8 ? 1.643 3.762 2.790 1.00 97.63 8 A 1 ATOM 55 C CB . LEU A 1 8 ? -0.472 2.683 5.096 1.00 97.30 8 A 1 ATOM 56 C CG . LEU A 1 8 ? -0.111 3.833 6.036 1.00 92.80 8 A 1 ATOM 57 C CD1 . LEU A 1 8 ? -1.230 4.865 6.067 1.00 91.53 8 A 1 ATOM 58 C CD2 . LEU A 1 8 ? 0.163 3.305 7.435 1.00 91.45 8 A 1 ATOM 59 N N . SER A 1 9 ? 1.123 1.576 2.655 1.00 97.17 9 A 1 ATOM 60 C CA . SER A 1 9 ? 2.391 1.187 2.044 1.00 97.01 9 A 1 ATOM 61 C C . SER A 1 9 ? 2.567 1.834 0.676 1.00 97.30 9 A 1 ATOM 62 O O . SER A 1 9 ? 3.663 2.268 0.322 1.00 96.54 9 A 1 ATOM 63 C CB . SER A 1 9 ? 2.468 -0.334 1.909 1.00 96.52 9 A 1 ATOM 64 O OG . SER A 1 9 ? 3.700 -0.717 1.345 1.00 91.65 9 A 1 ATOM 65 N N . SER A 1 10 ? 1.488 1.903 -0.090 1.00 97.51 10 A 1 ATOM 66 C CA . SER A 1 10 ? 1.543 2.499 -1.422 1.00 97.54 10 A 1 ATOM 67 C C . SER A 1 10 ? 1.890 3.982 -1.338 1.00 97.80 10 A 1 ATOM 68 O O . SER A 1 10 ? 2.676 4.498 -2.136 1.00 96.77 10 A 1 ATOM 69 C CB . SER A 1 10 ? 0.207 2.314 -2.150 1.00 97.18 10 A 1 ATOM 70 O OG . SER A 1 10 ? -0.789 3.147 -1.603 1.00 92.52 10 A 1 ATOM 71 N N . LEU A 1 11 ? 1.305 4.654 -0.369 1.00 97.99 11 A 1 ATOM 72 C CA . LEU A 1 11 ? 1.566 6.073 -0.163 1.00 97.90 11 A 1 ATOM 73 C C . LEU A 1 11 ? 3.017 6.303 0.232 1.00 98.03 11 A 1 ATOM 74 O O . LEU A 1 11 ? 3.674 7.216 -0.277 1.00 97.53 11 A 1 ATOM 75 C CB . LEU A 1 11 ? 0.639 6.632 0.917 1.00 97.65 11 A 1 ATOM 76 C CG . LEU A 1 11 ? 0.712 8.146 1.079 1.00 94.10 11 A 1 ATOM 77 C CD1 . LEU A 1 11 ? 0.146 8.841 -0.150 1.00 91.80 11 A 1 ATOM 78 C CD2 . LEU A 1 11 ? -0.031 8.583 2.330 1.00 92.07 11 A 1 ATOM 79 N N . VAL A 1 12 ? 3.508 5.471 1.138 1.00 98.10 12 A 1 ATOM 80 C CA . VAL A 1 12 ? 4.893 5.570 1.594 1.00 97.96 12 A 1 ATOM 81 C C . VAL A 1 12 ? 5.856 5.315 0.444 1.00 98.09 12 A 1 ATOM 82 O O . VAL A 1 12 ? 6.888 5.983 0.324 1.00 97.77 12 A 1 ATOM 83 C CB . VAL A 1 12 ? 5.167 4.579 2.736 1.00 97.34 12 A 1 ATOM 84 C CG1 . VAL A 1 12 ? 6.644 4.596 3.112 1.00 94.96 12 A 1 ATOM 85 C CG2 . VAL A 1 12 ? 4.311 4.911 3.942 1.00 95.08 12 A 1 ATOM 86 N N . SER A 1 13 ? 5.521 4.355 -0.409 1.00 98.08 13 A 1 ATOM 87 C CA . SER A 1 13 ? 6.358 4.014 -1.554 1.00 98.00 13 A 1 ATOM 88 C C . SER A 1 13 ? 6.516 5.202 -2.496 1.00 98.16 13 A 1 ATOM 89 O O . SER A 1 13 ? 7.622 5.521 -2.934 1.00 97.42 13 A 1 ATOM 90 C CB . SER A 1 13 ? 5.761 2.832 -2.309 1.00 97.23 13 A 1 ATOM 91 O OG . SER A 1 13 ? 5.755 1.672 -1.499 1.00 89.41 13 A 1 ATOM 92 N N . SER A 1 14 ? 5.405 5.872 -2.805 1.00 98.01 14 A 1 ATOM 93 C CA . SER A 1 14 ? 5.430 7.035 -3.687 1.00 98.06 14 A 1 ATOM 94 C C . SER A 1 14 ? 6.137 8.212 -3.029 1.00 98.24 14 A 1 ATOM 95 O O . SER A 1 14 ? 6.819 8.991 -3.697 1.00 97.30 14 A 1 ATOM 96 C CB . SER A 1 14 ? 4.007 7.441 -4.075 1.00 97.29 14 A 1 ATOM 97 O OG . SER A 1 14 ? 3.303 7.935 -2.961 1.00 91.67 14 A 1 ATOM 98 N N . ALA A 1 15 ? 5.957 8.348 -1.721 1.00 97.65 15 A 1 ATOM 99 C CA . ALA A 1 15 ? 6.582 9.431 -0.967 1.00 97.59 15 A 1 ATOM 100 C C . ALA A 1 15 ? 8.097 9.262 -0.913 1.00 97.81 15 A 1 ATOM 101 O O . ALA A 1 15 ? 8.844 10.234 -1.040 1.00 97.11 15 A 1 ATOM 102 C CB . ALA A 1 15 ? 6.015 9.494 0.450 1.00 97.03 15 A 1 ATOM 103 N N . LEU A 1 16 ? 8.544 8.020 -0.731 1.00 97.51 16 A 1 ATOM 104 C CA . LEU A 1 16 ? 9.972 7.718 -0.666 1.00 97.32 16 A 1 ATOM 105 C C . LEU A 1 16 ? 10.622 7.868 -2.029 1.00 97.37 16 A 1 ATOM 106 O O . LEU A 1 16 ? 11.764 8.330 -2.134 1.00 96.41 16 A 1 ATOM 107 C CB . LEU A 1 16 ? 10.187 6.301 -0.136 1.00 96.29 16 A 1 ATOM 108 C CG . LEU A 1 16 ? 9.956 6.144 1.365 1.00 93.60 16 A 1 ATOM 109 C CD1 . LEU A 1 16 ? 9.923 4.675 1.749 1.00 90.65 16 A 1 ATOM 110 C CD2 . LEU A 1 16 ? 11.038 6.872 2.146 1.00 88.48 16 A 1 ATOM 111 N N . ALA A 1 17 ? 9.898 7.474 -3.062 1.00 94.40 17 A 1 ATOM 112 C CA . ALA A 1 17 ? 10.400 7.545 -4.433 1.00 92.25 17 A 1 ATOM 113 C C . ALA A 1 17 ? 10.434 8.988 -4.923 1.00 90.29 17 A 1 ATOM 114 O O . ALA A 1 17 ? 9.429 9.470 -5.462 1.00 86.71 17 A 1 ATOM 115 C CB . ALA A 1 17 ? 9.550 6.683 -5.342 1.00 87.22 17 A 1 ATOM 116 O OXT . ALA A 1 17 ? 11.472 9.646 -4.738 1.00 79.58 17 A 1 #