# 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_spkb24609 # _entry.id spkb24609 # 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" "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" "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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 THR 1 1 n PHE 2 1 n ALA 3 1 n GLY 4 1 n LEU 5 1 n VAL 6 1 n LEU 7 1 n LEU 8 1 n PHE 9 1 n VAL 10 1 n VAL 11 1 n CYS 12 1 n TYR 13 1 n ALA 14 # _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 @ 2025-07-06 07:51:06)" _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 96.91 _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 THR 1 2 93.69 1 1 A PHE 2 2 95.41 1 2 A ALA 3 2 97.98 1 3 A GLY 4 2 98.44 1 4 A LEU 5 2 97.59 1 5 A VAL 6 2 98.33 1 6 A LEU 7 2 97.71 1 7 A LEU 8 2 97.62 1 8 A PHE 9 2 97.24 1 9 A VAL 10 2 98.30 1 10 A VAL 11 2 98.02 1 11 A CYS 12 2 97.81 1 12 A TYR 13 2 96.35 1 13 A ALA 14 2 93.70 1 14 # _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 THR . 1 A 1 A 2 1 n PHE . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n GLY . 4 A 4 A 5 1 n LEU . 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 PHE . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n CYS . 12 A 12 A 13 1 n TYR . 13 A 13 A 14 1 n ALA . 14 A 14 # _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 . THR A 1 1 ? -8.336 6.717 -5.141 1.00 94.40 1 A 1 ATOM 2 C CA . THR A 1 1 ? -8.347 5.597 -4.176 1.00 96.22 1 A 1 ATOM 3 C C . THR A 1 1 ? -7.018 5.518 -3.430 1.00 97.05 1 A 1 ATOM 4 O O . THR A 1 1 ? -6.123 4.767 -3.811 1.00 95.79 1 A 1 ATOM 5 C CB . THR A 1 1 ? -8.578 4.269 -4.902 1.00 93.72 1 A 1 ATOM 6 O OG1 . THR A 1 1 ? -9.587 4.450 -5.889 1.00 89.35 1 A 1 ATOM 7 C CG2 . THR A 1 1 ? -9.001 3.182 -3.933 1.00 89.33 1 A 1 ATOM 8 N N . PHE A 1 2 ? -6.910 6.302 -2.382 1.00 97.28 2 A 1 ATOM 9 C CA . PHE A 1 2 ? -5.688 6.337 -1.584 1.00 97.79 2 A 1 ATOM 10 C C . PHE A 1 2 ? -5.609 5.156 -0.622 1.00 98.35 2 A 1 ATOM 11 O O . PHE A 1 2 ? -4.531 4.798 -0.145 1.00 98.26 2 A 1 ATOM 12 C CB . PHE A 1 2 ? -5.631 7.652 -0.809 1.00 97.21 2 A 1 ATOM 13 C CG . PHE A 1 2 ? -5.247 8.820 -1.684 1.00 95.35 2 A 1 ATOM 14 C CD1 . PHE A 1 2 ? -3.920 9.019 -2.027 1.00 93.73 2 A 1 ATOM 15 C CD2 . PHE A 1 2 ? -6.207 9.697 -2.153 1.00 93.57 2 A 1 ATOM 16 C CE1 . PHE A 1 2 ? -3.549 10.083 -2.831 1.00 93.06 2 A 1 ATOM 17 C CE2 . PHE A 1 2 ? -5.845 10.766 -2.961 1.00 92.18 2 A 1 ATOM 18 C CZ . PHE A 1 2 ? -4.514 10.959 -3.299 1.00 92.68 2 A 1 ATOM 19 N N . ALA A 1 3 ? -6.746 4.559 -0.339 1.00 97.64 3 A 1 ATOM 20 C CA . ALA A 1 3 ? -6.799 3.407 0.562 1.00 98.04 3 A 1 ATOM 21 C C . ALA A 1 3 ? -5.979 2.239 0.020 1.00 98.39 3 A 1 ATOM 22 O O . ALA A 1 3 ? -5.429 1.447 0.782 1.00 98.15 3 A 1 ATOM 23 C CB . ALA A 1 3 ? -8.246 2.984 0.765 1.00 97.68 3 A 1 ATOM 24 N N . GLY A 1 4 ? -5.899 2.147 -1.304 1.00 98.40 4 A 1 ATOM 25 C CA . GLY A 1 4 ? -5.121 1.086 -1.944 1.00 98.45 4 A 1 ATOM 26 C C . GLY A 1 4 ? -3.640 1.215 -1.659 1.00 98.60 4 A 1 ATOM 27 O O . GLY A 1 4 ? -2.949 0.225 -1.421 1.00 98.29 4 A 1 ATOM 28 N N . LEU A 1 5 ? -3.154 2.449 -1.674 1.00 98.54 5 A 1 ATOM 29 C CA . LEU A 1 5 ? -1.744 2.714 -1.397 1.00 98.58 5 A 1 ATOM 30 C C . LEU A 1 5 ? -1.397 2.370 0.047 1.00 98.69 5 A 1 ATOM 31 O O . LEU A 1 5 ? -0.350 1.787 0.325 1.00 98.53 5 A 1 ATOM 32 C CB . LEU A 1 5 ? -1.438 4.185 -1.666 1.00 98.40 5 A 1 ATOM 33 C CG . LEU A 1 5 ? -1.296 4.510 -3.151 1.00 96.82 5 A 1 ATOM 34 C CD1 . LEU A 1 5 ? -1.425 6.006 -3.380 1.00 95.62 5 A 1 ATOM 35 C CD2 . LEU A 1 5 ? 0.049 4.014 -3.666 1.00 95.51 5 A 1 ATOM 36 N N . VAL A 1 6 ? -2.286 2.741 0.951 1.00 98.62 6 A 1 ATOM 37 C CA . VAL A 1 6 ? -2.083 2.469 2.377 1.00 98.61 6 A 1 ATOM 38 C C . VAL A 1 6 ? -2.089 0.967 2.635 1.00 98.69 6 A 1 ATOM 39 O O . VAL A 1 6 ? -1.323 0.462 3.456 1.00 98.62 6 A 1 ATOM 40 C CB . VAL A 1 6 ? -3.171 3.148 3.220 1.00 98.45 6 A 1 ATOM 41 C CG1 . VAL A 1 6 ? -2.942 2.887 4.698 1.00 97.72 6 A 1 ATOM 42 C CG2 . VAL A 1 6 ? -3.188 4.644 2.943 1.00 97.62 6 A 1 ATOM 43 N N . LEU A 1 7 ? -2.959 0.259 1.922 1.00 98.55 7 A 1 ATOM 44 C CA . LEU A 1 7 ? -3.062 -1.193 2.073 1.00 98.52 7 A 1 ATOM 45 C C . LEU A 1 7 ? -1.751 -1.865 1.681 1.00 98.64 7 A 1 ATOM 46 O O . LEU A 1 7 ? -1.280 -2.776 2.365 1.00 98.58 7 A 1 ATOM 47 C CB . LEU A 1 7 ? -4.200 -1.724 1.200 1.00 98.38 7 A 1 ATOM 48 C CG . LEU A 1 7 ? -4.434 -3.228 1.315 1.00 96.67 7 A 1 ATOM 49 C CD1 . LEU A 1 7 ? -5.013 -3.575 2.680 1.00 96.08 7 A 1 ATOM 50 C CD2 . LEU A 1 7 ? -5.365 -3.703 0.213 1.00 96.25 7 A 1 ATOM 51 N N . LEU A 1 8 ? -1.166 -1.403 0.583 1.00 98.58 8 A 1 ATOM 52 C CA . LEU A 1 8 ? 0.097 -1.960 0.109 1.00 98.55 8 A 1 ATOM 53 C C . LEU A 1 8 ? 1.210 -1.702 1.119 1.00 98.62 8 A 1 ATOM 54 O O . LEU A 1 8 ? 2.092 -2.540 1.324 1.00 98.49 8 A 1 ATOM 55 C CB . LEU A 1 8 ? 0.450 -1.337 -1.246 1.00 98.41 8 A 1 ATOM 56 C CG . LEU A 1 8 ? 0.749 -2.362 -2.335 1.00 96.78 8 A 1 ATOM 57 C CD1 . LEU A 1 8 ? 0.533 -1.750 -3.718 1.00 95.66 8 A 1 ATOM 58 C CD2 . LEU A 1 8 ? 2.173 -2.874 -2.213 1.00 95.88 8 A 1 ATOM 59 N N . PHE A 1 9 ? 1.153 -0.543 1.758 1.00 98.50 9 A 1 ATOM 60 C CA . PHE A 1 9 ? 2.141 -0.174 2.770 1.00 98.47 9 A 1 ATOM 61 C C . PHE A 1 9 ? 2.081 -1.125 3.961 1.00 98.57 9 A 1 ATOM 62 O O . PHE A 1 9 ? 3.110 -1.569 4.469 1.00 98.40 9 A 1 ATOM 63 C CB . PHE A 1 9 ? 1.888 1.260 3.230 1.00 98.28 9 A 1 ATOM 64 C CG . PHE A 1 9 ? 2.985 1.785 4.116 1.00 97.49 9 A 1 ATOM 65 C CD1 . PHE A 1 9 ? 4.232 2.081 3.588 1.00 96.16 9 A 1 ATOM 66 C CD2 . PHE A 1 9 ? 2.760 1.986 5.466 1.00 96.31 9 A 1 ATOM 67 C CE1 . PHE A 1 9 ? 5.250 2.562 4.396 1.00 95.74 9 A 1 ATOM 68 C CE2 . PHE A 1 9 ? 3.780 2.469 6.283 1.00 95.68 9 A 1 ATOM 69 C CZ . PHE A 1 9 ? 5.025 2.756 5.750 1.00 96.01 9 A 1 ATOM 70 N N . VAL A 1 10 ? 0.872 -1.428 4.393 1.00 98.64 10 A 1 ATOM 71 C CA . VAL A 1 10 ? 0.675 -2.333 5.529 1.00 98.60 10 A 1 ATOM 72 C C . VAL A 1 10 ? 1.098 -3.754 5.168 1.00 98.66 10 A 1 ATOM 73 O O . VAL A 1 10 ? 1.737 -4.445 5.962 1.00 98.45 10 A 1 ATOM 74 C CB . VAL A 1 10 ? -0.794 -2.327 5.985 1.00 98.36 10 A 1 ATOM 75 C CG1 . VAL A 1 10 ? -1.007 -3.289 7.147 1.00 97.65 10 A 1 ATOM 76 C CG2 . VAL A 1 10 ? -1.208 -0.920 6.395 1.00 97.71 10 A 1 ATOM 77 N N . VAL A 1 11 ? 0.735 -4.190 3.968 1.00 98.59 11 A 1 ATOM 78 C CA . VAL A 1 11 ? 1.077 -5.538 3.508 1.00 98.51 11 A 1 ATOM 79 C C . VAL A 1 11 ? 2.589 -5.693 3.371 1.00 98.56 11 A 1 ATOM 80 O O . VAL A 1 11 ? 3.149 -6.748 3.682 1.00 98.27 11 A 1 ATOM 81 C CB . VAL A 1 11 ? 0.392 -5.843 2.165 1.00 98.16 11 A 1 ATOM 82 C CG1 . VAL A 1 11 ? 0.800 -7.219 1.645 1.00 97.00 11 A 1 ATOM 83 C CG2 . VAL A 1 11 ? -1.121 -5.786 2.320 1.00 97.08 11 A 1 ATOM 84 N N . CYS A 1 12 ? 3.243 -4.653 2.909 1.00 98.40 12 A 1 ATOM 85 C CA . CYS A 1 12 ? 4.697 -4.680 2.742 1.00 98.38 12 A 1 ATOM 86 C C . CYS A 1 12 ? 5.409 -4.682 4.095 1.00 98.43 12 A 1 ATOM 87 O O . CYS A 1 12 ? 6.517 -5.198 4.229 1.00 97.95 12 A 1 ATOM 88 C CB . CYS A 1 12 ? 5.146 -3.470 1.918 1.00 97.87 12 A 1 ATOM 89 S SG . CYS A 1 12 ? 6.855 -3.642 1.352 1.00 95.80 12 A 1 ATOM 90 N N . TYR A 1 13 ? 4.752 -4.105 5.089 1.00 98.40 13 A 1 ATOM 91 C CA . TYR A 1 13 ? 5.314 -4.051 6.443 1.00 98.33 13 A 1 ATOM 92 C C . TYR A 1 13 ? 5.040 -5.341 7.220 1.00 98.36 13 A 1 ATOM 93 O O . TYR A 1 13 ? 5.528 -5.513 8.335 1.00 97.82 13 A 1 ATOM 94 C CB . TYR A 1 13 ? 4.730 -2.851 7.196 1.00 97.93 13 A 1 ATOM 95 C CG . TYR A 1 13 ? 5.761 -1.775 7.469 1.00 96.93 13 A 1 ATOM 96 C CD1 . TYR A 1 13 ? 6.324 -1.044 6.431 1.00 95.53 13 A 1 ATOM 97 C CD2 . TYR A 1 13 ? 6.162 -1.498 8.773 1.00 95.21 13 A 1 ATOM 98 C CE1 . TYR A 1 13 ? 7.269 -0.061 6.678 1.00 94.69 13 A 1 ATOM 99 C CE2 . TYR A 1 13 ? 7.107 -0.509 9.033 1.00 94.48 13 A 1 ATOM 100 C CZ . TYR A 1 13 ? 7.657 0.205 7.981 1.00 94.84 13 A 1 ATOM 101 O OH . TYR A 1 13 ? 8.594 1.180 8.230 1.00 93.73 13 A 1 ATOM 102 N N . ALA A 1 14 ? 4.268 -6.225 6.607 1.00 96.94 14 A 1 ATOM 103 C CA . ALA A 1 14 ? 3.899 -7.487 7.256 1.00 96.30 14 A 1 ATOM 104 C C . ALA A 1 14 ? 4.593 -8.661 6.583 1.00 95.42 14 A 1 ATOM 105 O O . ALA A 1 14 ? 4.083 -9.157 5.571 1.00 92.67 14 A 1 ATOM 106 C CB . ALA A 1 14 ? 2.393 -7.665 7.234 1.00 94.20 14 A 1 ATOM 107 O OXT . ALA A 1 14 ? 5.669 -9.050 7.072 1.00 86.70 14 A 1 #