# 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_spkb25252 # _entry.id spkb25252 # 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 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" "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 LYS 2 1 n SER 3 1 n VAL 4 1 n VAL 5 1 n PHE 6 1 n ALA 7 1 n SER 8 1 n LEU 9 1 n ILE 10 1 n ALA 11 1 n SER 12 1 n ALA 13 1 n LEU 14 1 n ALA 15 # _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 04:38:05)" _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 92.73 _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 83.30 1 1 A LYS 2 2 85.94 1 2 A SER 3 2 92.71 1 3 A VAL 4 2 95.58 1 4 A VAL 5 2 95.92 1 5 A PHE 6 2 93.11 1 6 A ALA 7 2 96.59 1 7 A SER 8 2 94.74 1 8 A LEU 9 2 95.00 1 9 A ILE 10 2 94.96 1 10 A ALA 11 2 96.83 1 11 A SER 12 2 95.20 1 12 A ALA 13 2 96.82 1 13 A LEU 14 2 92.68 1 14 A ALA 15 2 87.34 1 15 # _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 SER . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 # _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 ? 2.423 10.959 9.739 1.00 86.78 1 A 1 ATOM 2 C CA . MET A 1 1 ? 2.634 10.969 8.273 1.00 88.84 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.529 10.186 7.569 1.00 90.62 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.314 9.017 7.865 1.00 87.65 1 A 1 ATOM 5 C CB . MET A 1 1 ? 3.984 10.351 7.929 1.00 83.76 1 A 1 ATOM 6 C CG . MET A 1 1 ? 5.145 11.207 8.402 1.00 81.45 1 A 1 ATOM 7 S SD . MET A 1 1 ? 6.728 10.467 7.998 1.00 78.79 1 A 1 ATOM 8 C CE . MET A 1 1 ? 7.841 11.656 8.724 1.00 68.54 1 A 1 ATOM 9 N N . LYS A 1 2 ? 0.823 10.854 6.658 1.00 91.13 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -0.271 10.227 5.922 1.00 92.29 2 A 1 ATOM 11 C C . LYS A 1 2 ? 0.254 9.389 4.758 1.00 93.11 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.349 8.385 4.386 1.00 92.36 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -1.230 11.306 5.417 1.00 89.47 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -2.646 11.152 5.946 1.00 84.42 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.748 11.568 7.411 1.00 82.43 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -4.175 11.487 7.895 1.00 77.50 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -4.270 11.693 9.357 1.00 70.79 2 A 1 ATOM 18 N N . SER A 1 3 ? 1.370 9.801 4.182 1.00 92.52 3 A 1 ATOM 19 C CA . SER A 1 3 ? 1.978 9.102 3.050 1.00 94.77 3 A 1 ATOM 20 C C . SER A 1 3 ? 2.405 7.688 3.431 1.00 96.19 3 A 1 ATOM 21 O O . SER A 1 3 ? 2.390 6.778 2.607 1.00 94.54 3 A 1 ATOM 22 C CB . SER A 1 3 ? 3.182 9.882 2.531 1.00 92.57 3 A 1 ATOM 23 O OG . SER A 1 3 ? 2.768 10.873 1.619 1.00 85.66 3 A 1 ATOM 24 N N . VAL A 1 4 ? 2.777 7.504 4.686 1.00 95.77 4 A 1 ATOM 25 C CA . VAL A 1 4 ? 3.214 6.198 5.181 1.00 96.74 4 A 1 ATOM 26 C C . VAL A 1 4 ? 2.075 5.188 5.106 1.00 97.32 4 A 1 ATOM 27 O O . VAL A 1 4 ? 2.281 4.025 4.743 1.00 96.56 4 A 1 ATOM 28 C CB . VAL A 1 4 ? 3.725 6.300 6.628 1.00 96.01 4 A 1 ATOM 29 C CG1 . VAL A 1 4 ? 4.213 4.951 7.126 1.00 93.62 4 A 1 ATOM 30 C CG2 . VAL A 1 4 ? 4.846 7.327 6.725 1.00 93.04 4 A 1 ATOM 31 N N . VAL A 1 5 ? 0.880 5.634 5.447 1.00 96.33 5 A 1 ATOM 32 C CA . VAL A 1 5 ? -0.301 4.771 5.425 1.00 96.79 5 A 1 ATOM 33 C C . VAL A 1 5 ? -0.604 4.324 3.999 1.00 97.07 5 A 1 ATOM 34 O O . VAL A 1 5 ? -0.928 3.158 3.753 1.00 96.64 5 A 1 ATOM 35 C CB . VAL A 1 5 ? -1.522 5.493 6.016 1.00 96.37 5 A 1 ATOM 36 C CG1 . VAL A 1 5 ? -2.721 4.565 6.075 1.00 94.34 5 A 1 ATOM 37 C CG2 . VAL A 1 5 ? -1.202 6.025 7.408 1.00 93.92 5 A 1 ATOM 38 N N . PHE A 1 6 ? -0.499 5.262 3.070 1.00 95.86 6 A 1 ATOM 39 C CA . PHE A 1 6 ? -0.770 4.972 1.665 1.00 95.62 6 A 1 ATOM 40 C C . PHE A 1 6 ? 0.279 4.014 1.111 1.00 96.32 6 A 1 ATOM 41 O O . PHE A 1 6 ? -0.041 3.067 0.393 1.00 96.00 6 A 1 ATOM 42 C CB . PHE A 1 6 ? -0.774 6.269 0.857 1.00 94.98 6 A 1 ATOM 43 C CG . PHE A 1 6 ? -1.932 6.341 -0.109 1.00 93.14 6 A 1 ATOM 44 C CD1 . PHE A 1 6 ? -1.898 5.643 -1.301 1.00 90.84 6 A 1 ATOM 45 C CD2 . PHE A 1 6 ? -3.048 7.104 0.195 1.00 91.13 6 A 1 ATOM 46 C CE1 . PHE A 1 6 ? -2.964 5.694 -2.191 1.00 90.30 6 A 1 ATOM 47 C CE2 . PHE A 1 6 ? -4.120 7.165 -0.687 1.00 90.18 6 A 1 ATOM 48 C CZ . PHE A 1 6 ? -4.079 6.460 -1.882 1.00 89.83 6 A 1 ATOM 49 N N . ALA A 1 7 ? 1.532 4.259 1.458 1.00 96.55 7 A 1 ATOM 50 C CA . ALA A 1 7 ? 2.634 3.415 1.002 1.00 96.62 7 A 1 ATOM 51 C C . ALA A 1 7 ? 2.467 1.984 1.500 1.00 97.24 7 A 1 ATOM 52 O O . ALA A 1 7 ? 2.788 1.029 0.796 1.00 96.62 7 A 1 ATOM 53 C CB . ALA A 1 7 ? 3.957 3.989 1.484 1.00 95.94 7 A 1 ATOM 54 N N . SER A 1 8 ? 1.951 1.844 2.705 1.00 96.30 8 A 1 ATOM 55 C CA . SER A 1 8 ? 1.730 0.532 3.307 1.00 96.28 8 A 1 ATOM 56 C C . SER A 1 8 ? 0.655 -0.236 2.543 1.00 96.90 8 A 1 ATOM 57 O O . SER A 1 8 ? 0.767 -1.443 2.329 1.00 96.21 8 A 1 ATOM 58 C CB . SER A 1 8 ? 1.315 0.696 4.766 1.00 95.65 8 A 1 ATOM 59 O OG . SER A 1 8 ? 1.837 -0.346 5.553 1.00 87.08 8 A 1 ATOM 60 N N . LEU A 1 9 ? -0.378 0.478 2.128 1.00 96.41 9 A 1 ATOM 61 C CA . LEU A 1 9 ? -1.474 -0.128 1.375 1.00 96.73 9 A 1 ATOM 62 C C . LEU A 1 9 ? -0.995 -0.593 0.003 1.00 97.33 9 A 1 ATOM 63 O O . LEU A 1 9 ? -1.347 -1.680 -0.458 1.00 97.03 9 A 1 ATOM 64 C CB . LEU A 1 9 ? -2.617 0.879 1.215 1.00 96.46 9 A 1 ATOM 65 C CG . LEU A 1 9 ? -3.990 0.310 1.559 1.00 93.25 9 A 1 ATOM 66 C CD1 . LEU A 1 9 ? -4.532 0.937 2.836 1.00 91.25 9 A 1 ATOM 67 C CD2 . LEU A 1 9 ? -4.969 0.521 0.419 1.00 91.54 9 A 1 ATOM 68 N N . ILE A 1 10 ? -0.204 0.245 -0.646 1.00 96.57 10 A 1 ATOM 69 C CA . ILE A 1 10 ? 0.326 -0.069 -1.969 1.00 96.34 10 A 1 ATOM 70 C C . ILE A 1 10 ? 1.248 -1.280 -1.900 1.00 96.65 10 A 1 ATOM 71 O O . ILE A 1 10 ? 1.215 -2.157 -2.764 1.00 96.40 10 A 1 ATOM 72 C CB . ILE A 1 10 ? 1.083 1.133 -2.554 1.00 95.77 10 A 1 ATOM 73 C CG1 . ILE A 1 10 ? 0.175 2.374 -2.598 1.00 94.12 10 A 1 ATOM 74 C CG2 . ILE A 1 10 ? 1.586 0.806 -3.963 1.00 93.64 10 A 1 ATOM 75 C CD1 . ILE A 1 10 ? -1.067 2.172 -3.444 1.00 90.18 10 A 1 ATOM 76 N N . ALA A 1 11 ? 2.083 -1.315 -0.881 1.00 97.11 11 A 1 ATOM 77 C CA . ALA A 1 11 ? 3.022 -2.418 -0.697 1.00 96.96 11 A 1 ATOM 78 C C . ALA A 1 11 ? 2.283 -3.731 -0.457 1.00 97.52 11 A 1 ATOM 79 O O . ALA A 1 11 ? 2.709 -4.786 -0.922 1.00 96.63 11 A 1 ATOM 80 C CB . ALA A 1 11 ? 3.948 -2.113 0.469 1.00 95.95 11 A 1 ATOM 81 N N . SER A 1 12 ? 1.176 -3.664 0.257 1.00 97.14 12 A 1 ATOM 82 C CA . SER A 1 12 ? 0.360 -4.840 0.555 1.00 97.01 12 A 1 ATOM 83 C C . SER A 1 12 ? -0.270 -5.402 -0.711 1.00 97.43 12 A 1 ATOM 84 O O . SER A 1 12 ? -0.364 -6.618 -0.884 1.00 96.25 12 A 1 ATOM 85 C CB . SER A 1 12 ? -0.729 -4.482 1.561 1.00 96.02 12 A 1 ATOM 86 O OG . SER A 1 12 ? -1.376 -5.639 2.027 1.00 87.33 12 A 1 ATOM 87 N N . ALA A 1 13 ? -0.705 -4.517 -1.589 1.00 97.03 13 A 1 ATOM 88 C CA . ALA A 1 13 ? -1.336 -4.913 -2.845 1.00 97.00 13 A 1 ATOM 89 C C . ALA A 1 13 ? -0.327 -5.553 -3.797 1.00 97.46 13 A 1 ATOM 90 O O . ALA A 1 13 ? -0.656 -6.483 -4.535 1.00 96.48 13 A 1 ATOM 91 C CB . ALA A 1 13 ? -1.988 -3.701 -3.507 1.00 96.11 13 A 1 ATOM 92 N N . LEU A 1 14 ? 0.891 -5.049 -3.775 1.00 96.44 14 A 1 ATOM 93 C CA . LEU A 1 14 ? 1.949 -5.564 -4.648 1.00 96.22 14 A 1 ATOM 94 C C . LEU A 1 14 ? 2.444 -6.926 -4.179 1.00 96.50 14 A 1 ATOM 95 O O . LEU A 1 14 ? 2.692 -7.821 -4.989 1.00 94.90 14 A 1 ATOM 96 C CB . LEU A 1 14 ? 3.103 -4.567 -4.700 1.00 94.49 14 A 1 ATOM 97 C CG . LEU A 1 14 ? 2.838 -3.362 -5.598 1.00 89.91 14 A 1 ATOM 98 C CD1 . LEU A 1 14 ? 3.837 -2.250 -5.307 1.00 87.16 14 A 1 ATOM 99 C CD2 . LEU A 1 14 ? 2.919 -3.768 -7.061 1.00 85.84 14 A 1 ATOM 100 N N . ALA A 1 15 ? 2.593 -7.070 -2.862 1.00 93.54 15 A 1 ATOM 101 C CA . ALA A 1 15 ? 3.091 -8.310 -2.285 1.00 91.34 15 A 1 ATOM 102 C C . ALA A 1 15 ? 2.395 -8.615 -0.963 1.00 89.67 15 A 1 ATOM 103 O O . ALA A 1 15 ? 2.327 -7.734 -0.102 1.00 85.55 15 A 1 ATOM 104 C CB . ALA A 1 15 ? 4.592 -8.222 -2.066 1.00 85.58 15 A 1 ATOM 105 O OXT . ALA A 1 15 ? 1.936 -9.751 -0.771 1.00 78.35 15 A 1 #