# 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_spkb25289 # _entry.id spkb25289 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 THR 3 1 n LEU 4 1 n CYS 5 1 n ILE 6 1 n PHE 7 1 n LEU 8 1 n VAL 9 1 n LEU 10 1 n VAL 11 1 n VAL 12 1 n ALA 13 1 n VAL 14 1 n ALA 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 @ 2025-07-08 06:22:31)" _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 95.03 _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 88.86 1 1 A LYS 2 2 89.99 1 2 A THR 3 2 94.92 1 3 A LEU 4 2 94.82 1 4 A CYS 5 2 96.72 1 5 A ILE 6 2 96.38 1 6 A PHE 7 2 95.85 1 7 A LEU 8 2 95.66 1 8 A VAL 9 2 97.17 1 9 A LEU 10 2 95.72 1 10 A VAL 11 2 96.80 1 11 A VAL 12 2 97.11 1 12 A ALA 13 2 98.29 1 13 A VAL 14 2 95.91 1 14 A ALA 15 2 97.05 1 15 A ALA 16 2 92.13 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 LYS . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n CYS . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 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 ? 3.344 1.727 11.014 1.00 94.89 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.199 2.864 10.081 1.00 95.67 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.893 2.715 9.295 1.00 96.13 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.815 1.925 8.358 1.00 93.68 1 A 1 ATOM 5 C CB . MET A 1 1 ? 4.383 2.910 9.117 1.00 92.69 1 A 1 ATOM 6 C CG . MET A 1 1 ? 5.720 3.115 9.840 1.00 87.36 1 A 1 ATOM 7 S SD . MET A 1 1 ? 5.879 4.740 10.554 1.00 79.80 1 A 1 ATOM 8 C CE . MET A 1 1 ? 7.532 4.647 11.221 1.00 70.67 1 A 1 ATOM 9 N N . LYS A 1 2 ? 0.861 3.450 9.677 1.00 96.66 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -0.468 3.347 9.050 1.00 97.01 2 A 1 ATOM 11 C C . LYS A 1 2 ? -0.430 3.752 7.574 1.00 97.47 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.115 3.151 6.750 1.00 96.79 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -1.465 4.222 9.818 1.00 95.82 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -1.748 3.679 11.214 1.00 89.90 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.721 4.571 11.972 1.00 85.04 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.998 4.002 13.357 1.00 78.55 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -3.872 4.901 14.150 1.00 72.63 2 A 1 ATOM 18 N N . THR A 1 3 ? 0.375 4.739 7.239 1.00 96.73 3 A 1 ATOM 19 C CA . THR A 1 3 ? 0.492 5.225 5.862 1.00 97.44 3 A 1 ATOM 20 C C . THR A 1 3 ? 1.016 4.131 4.929 1.00 97.75 3 A 1 ATOM 21 O O . THR A 1 3 ? 0.520 3.970 3.814 1.00 97.00 3 A 1 ATOM 22 C CB . THR A 1 3 ? 1.428 6.442 5.816 1.00 96.67 3 A 1 ATOM 23 O OG1 . THR A 1 3 ? 1.122 7.330 6.886 1.00 90.43 3 A 1 ATOM 24 C CG2 . THR A 1 3 ? 1.292 7.188 4.503 1.00 88.41 3 A 1 ATOM 25 N N . LEU A 1 4 ? 1.996 3.362 5.381 1.00 98.07 4 A 1 ATOM 26 C CA . LEU A 1 4 ? 2.568 2.282 4.577 1.00 98.07 4 A 1 ATOM 27 C C . LEU A 1 4 ? 1.544 1.169 4.350 1.00 98.22 4 A 1 ATOM 28 O O . LEU A 1 4 ? 1.446 0.634 3.246 1.00 97.95 4 A 1 ATOM 29 C CB . LEU A 1 4 ? 3.822 1.727 5.267 1.00 97.84 4 A 1 ATOM 30 C CG . LEU A 1 4 ? 4.994 2.711 5.337 1.00 92.63 4 A 1 ATOM 31 C CD1 . LEU A 1 4 ? 6.125 2.112 6.170 1.00 87.59 4 A 1 ATOM 32 C CD2 . LEU A 1 4 ? 5.518 3.050 3.944 1.00 88.19 4 A 1 ATOM 33 N N . CYS A 1 5 ? 0.769 0.838 5.377 1.00 97.59 5 A 1 ATOM 34 C CA . CYS A 1 5 ? -0.264 -0.189 5.267 1.00 97.77 5 A 1 ATOM 35 C C . CYS A 1 5 ? -1.329 0.215 4.245 1.00 97.83 5 A 1 ATOM 36 O O . CYS A 1 5 ? -1.735 -0.591 3.414 1.00 97.47 5 A 1 ATOM 37 C CB . CYS A 1 5 ? -0.903 -0.423 6.638 1.00 97.30 5 A 1 ATOM 38 S SG . CYS A 1 5 ? 0.273 -1.171 7.796 1.00 92.34 5 A 1 ATOM 39 N N . ILE A 1 6 ? -1.762 1.459 4.291 1.00 97.81 6 A 1 ATOM 40 C CA . ILE A 1 6 ? -2.763 1.968 3.351 1.00 97.87 6 A 1 ATOM 41 C C . ILE A 1 6 ? -2.209 1.946 1.924 1.00 98.05 6 A 1 ATOM 42 O O . ILE A 1 6 ? -2.908 1.555 0.987 1.00 97.89 6 A 1 ATOM 43 C CB . ILE A 1 6 ? -3.200 3.387 3.761 1.00 97.74 6 A 1 ATOM 44 C CG1 . ILE A 1 6 ? -3.959 3.336 5.098 1.00 95.86 6 A 1 ATOM 45 C CG2 . ILE A 1 6 ? -4.092 4.011 2.679 1.00 95.33 6 A 1 ATOM 46 C CD1 . ILE A 1 6 ? -4.137 4.700 5.738 1.00 90.46 6 A 1 ATOM 47 N N . PHE A 1 7 ? -0.959 2.338 1.763 1.00 97.59 7 A 1 ATOM 48 C CA . PHE A 1 7 ? -0.317 2.348 0.450 1.00 97.67 7 A 1 ATOM 49 C C . PHE A 1 7 ? -0.248 0.934 -0.135 1.00 97.82 7 A 1 ATOM 50 O O . PHE A 1 7 ? -0.588 0.723 -1.298 1.00 97.59 7 A 1 ATOM 51 C CB . PHE A 1 7 ? 1.083 2.957 0.578 1.00 97.67 7 A 1 ATOM 52 C CG . PHE A 1 7 ? 1.439 3.838 -0.594 1.00 96.37 7 A 1 ATOM 53 C CD1 . PHE A 1 7 ? 2.021 3.299 -1.737 1.00 93.84 7 A 1 ATOM 54 C CD2 . PHE A 1 7 ? 1.174 5.206 -0.540 1.00 94.35 7 A 1 ATOM 55 C CE1 . PHE A 1 7 ? 2.341 4.113 -2.822 1.00 93.70 7 A 1 ATOM 56 C CE2 . PHE A 1 7 ? 1.494 6.027 -1.624 1.00 93.76 7 A 1 ATOM 57 C CZ . PHE A 1 7 ? 2.078 5.482 -2.764 1.00 93.99 7 A 1 ATOM 58 N N . LEU A 1 8 ? 0.148 -0.036 0.682 1.00 97.86 8 A 1 ATOM 59 C CA . LEU A 1 8 ? 0.225 -1.433 0.249 1.00 97.76 8 A 1 ATOM 60 C C . LEU A 1 8 ? -1.153 -1.968 -0.140 1.00 98.00 8 A 1 ATOM 61 O O . LEU A 1 8 ? -1.309 -2.592 -1.187 1.00 97.82 8 A 1 ATOM 62 C CB . LEU A 1 8 ? 0.828 -2.294 1.367 1.00 97.57 8 A 1 ATOM 63 C CG . LEU A 1 8 ? 2.171 -2.911 0.969 1.00 93.81 8 A 1 ATOM 64 C CD1 . LEU A 1 8 ? 3.321 -1.973 1.312 1.00 90.71 8 A 1 ATOM 65 C CD2 . LEU A 1 8 ? 2.375 -4.242 1.684 1.00 91.77 8 A 1 ATOM 66 N N . VAL A 1 9 ? -2.146 -1.714 0.698 1.00 97.95 9 A 1 ATOM 67 C CA . VAL A 1 9 ? -3.509 -2.185 0.441 1.00 97.96 9 A 1 ATOM 68 C C . VAL A 1 9 ? -4.057 -1.567 -0.845 1.00 98.21 9 A 1 ATOM 69 O O . VAL A 1 9 ? -4.704 -2.253 -1.639 1.00 97.87 9 A 1 ATOM 70 C CB . VAL A 1 9 ? -4.415 -1.858 1.641 1.00 97.45 9 A 1 ATOM 71 C CG1 . VAL A 1 9 ? -5.880 -2.140 1.329 1.00 95.52 9 A 1 ATOM 72 C CG2 . VAL A 1 9 ? -3.995 -2.686 2.850 1.00 95.22 9 A 1 ATOM 73 N N . LEU A 1 10 ? -3.785 -0.304 -1.057 1.00 97.75 10 A 1 ATOM 74 C CA . LEU A 1 10 ? -4.242 0.387 -2.265 1.00 97.87 10 A 1 ATOM 75 C C . LEU A 1 10 ? -3.621 -0.231 -3.518 1.00 98.15 10 A 1 ATOM 76 O O . LEU A 1 10 ? -4.322 -0.500 -4.495 1.00 97.93 10 A 1 ATOM 77 C CB . LEU A 1 10 ? -3.878 1.871 -2.160 1.00 97.68 10 A 1 ATOM 78 C CG . LEU A 1 10 ? -4.562 2.730 -3.228 1.00 93.33 10 A 1 ATOM 79 C CD1 . LEU A 1 10 ? -6.024 2.977 -2.848 1.00 91.00 10 A 1 ATOM 80 C CD2 . LEU A 1 10 ? -3.847 4.066 -3.369 1.00 92.03 10 A 1 ATOM 81 N N . VAL A 1 11 ? -2.322 -0.480 -3.492 1.00 97.98 11 A 1 ATOM 82 C CA . VAL A 1 11 ? -1.616 -1.077 -4.632 1.00 97.92 11 A 1 ATOM 83 C C . VAL A 1 11 ? -2.153 -2.477 -4.924 1.00 98.07 11 A 1 ATOM 84 O O . VAL A 1 11 ? -2.401 -2.823 -6.080 1.00 97.54 11 A 1 ATOM 85 C CB . VAL A 1 11 ? -0.101 -1.109 -4.367 1.00 97.32 11 A 1 ATOM 86 C CG1 . VAL A 1 11 ? 0.642 -1.893 -5.443 1.00 94.29 11 A 1 ATOM 87 C CG2 . VAL A 1 11 ? 0.456 0.312 -4.330 1.00 94.45 11 A 1 ATOM 88 N N . VAL A 1 12 ? -2.355 -3.273 -3.887 1.00 98.15 12 A 1 ATOM 89 C CA . VAL A 1 12 ? -2.879 -4.633 -4.049 1.00 98.12 12 A 1 ATOM 90 C C . VAL A 1 12 ? -4.308 -4.599 -4.588 1.00 98.33 12 A 1 ATOM 91 O O . VAL A 1 12 ? -4.662 -5.398 -5.456 1.00 97.99 12 A 1 ATOM 92 C CB . VAL A 1 12 ? -2.809 -5.393 -2.713 1.00 97.60 12 A 1 ATOM 93 C CG1 . VAL A 1 12 ? -3.506 -6.746 -2.803 1.00 94.61 12 A 1 ATOM 94 C CG2 . VAL A 1 12 ? -1.353 -5.619 -2.315 1.00 94.95 12 A 1 ATOM 95 N N . ALA A 1 13 ? -5.114 -3.680 -4.105 1.00 98.43 13 A 1 ATOM 96 C CA . ALA A 1 13 ? -6.501 -3.553 -4.556 1.00 98.42 13 A 1 ATOM 97 C C . ALA A 1 13 ? -6.580 -3.172 -6.038 1.00 98.52 13 A 1 ATOM 98 O O . ALA A 1 13 ? -7.449 -3.657 -6.759 1.00 98.06 13 A 1 ATOM 99 C CB . ALA A 1 13 ? -7.215 -2.512 -3.696 1.00 98.04 13 A 1 ATOM 100 N N . VAL A 1 14 ? -5.683 -2.317 -6.496 1.00 97.75 14 A 1 ATOM 101 C CA . VAL A 1 14 ? -5.641 -1.911 -7.906 1.00 97.63 14 A 1 ATOM 102 C C . VAL A 1 14 ? -5.103 -3.037 -8.785 1.00 97.80 14 A 1 ATOM 103 O O . VAL A 1 14 ? -5.542 -3.205 -9.925 1.00 96.90 14 A 1 ATOM 104 C CB . VAL A 1 14 ? -4.791 -0.639 -8.068 1.00 96.74 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? -4.583 -0.286 -9.536 1.00 92.06 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? -5.467 0.536 -7.375 1.00 92.48 14 A 1 ATOM 107 N N . ALA A 1 15 ? -4.161 -3.804 -8.270 1.00 97.57 15 A 1 ATOM 108 C CA . ALA A 1 15 ? -3.550 -4.907 -9.012 1.00 97.33 15 A 1 ATOM 109 C C . ALA A 1 15 ? -4.444 -6.151 -9.075 1.00 97.45 15 A 1 ATOM 110 O O . ALA A 1 15 ? -4.241 -7.012 -9.934 1.00 96.37 15 A 1 ATOM 111 C CB . ALA A 1 15 ? -2.199 -5.244 -8.377 1.00 96.53 15 A 1 ATOM 112 N N . ALA A 1 16 ? -5.418 -6.271 -8.180 1.00 96.50 16 A 1 ATOM 113 C CA . ALA A 1 16 ? -6.307 -7.422 -8.117 1.00 95.30 16 A 1 ATOM 114 C C . ALA A 1 16 ? -7.332 -7.421 -9.252 1.00 94.06 16 A 1 ATOM 115 O O . ALA A 1 16 ? -7.744 -6.340 -9.703 1.00 90.28 16 A 1 ATOM 116 C CB . ALA A 1 16 ? -6.991 -7.466 -6.752 1.00 92.82 16 A 1 ATOM 117 O OXT . ALA A 1 16 ? -7.751 -8.513 -9.678 1.00 83.80 16 A 1 #