# 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_spkb44131 # _entry.id spkb44131 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=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 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" "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 MET 1 1 n TYR 2 1 n SER 3 1 n MET 4 1 n ALA 5 1 n PHE 6 1 n LEU 7 1 n ALA 8 1 n SER 9 1 n SER 10 1 n GLY 11 1 n LEU 12 1 n VAL 13 1 n ALA 14 1 n ASN 15 1 n SER 16 1 n SER 17 1 n ALA 18 # _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 @ 2025-07-10 01:55:15)" _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 79.00 _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 75.91 1 1 A TYR 2 2 73.62 1 2 A SER 3 2 80.52 1 3 A MET 4 2 79.41 1 4 A ALA 5 2 84.77 1 5 A PHE 6 2 79.56 1 6 A LEU 7 2 80.16 1 7 A ALA 8 2 85.73 1 8 A SER 9 2 84.08 1 9 A SER 10 2 83.76 1 10 A GLY 11 2 84.64 1 11 A LEU 12 2 80.85 1 12 A VAL 13 2 81.53 1 13 A ALA 14 2 83.73 1 14 A ASN 15 2 74.52 1 15 A SER 16 2 77.26 1 16 A SER 17 2 71.98 1 17 A ALA 18 2 70.59 1 18 # _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 TYR . 2 A 2 A 3 1 n SER . 3 A 3 A 4 1 n MET . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ASN . 15 A 15 A 16 1 n SER . 16 A 16 A 17 1 n SER . 17 A 17 A 18 1 n ALA . 18 A 18 # _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 ? -13.088 0.952 6.228 1.00 76.49 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.786 1.618 6.390 1.00 81.59 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.631 0.676 6.082 1.00 82.85 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.526 1.119 5.796 1.00 79.93 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.630 2.152 7.820 1.00 75.90 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.543 3.332 8.094 1.00 73.54 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.277 4.032 9.720 1.00 71.85 1 A 1 ATOM 8 C CE . MET A 1 1 ? -13.402 5.422 9.648 1.00 65.10 1 A 1 ATOM 9 N N . TYR A 1 2 ? -10.901 -0.608 6.136 1.00 73.90 2 A 1 ATOM 10 C CA . TYR A 1 2 ? -9.858 -1.593 5.847 1.00 78.09 2 A 1 ATOM 11 C C . TYR A 1 2 ? -9.344 -1.440 4.421 1.00 80.88 2 A 1 ATOM 12 O O . TYR A 1 2 ? -8.143 -1.543 4.159 1.00 78.06 2 A 1 ATOM 13 C CB . TYR A 1 2 ? -10.413 -3.002 6.056 1.00 75.10 2 A 1 ATOM 14 C CG . TYR A 1 2 ? -10.810 -3.263 7.492 1.00 73.58 2 A 1 ATOM 15 C CD1 . TYR A 1 2 ? -9.862 -3.202 8.505 1.00 72.87 2 A 1 ATOM 16 C CD2 . TYR A 1 2 ? -12.118 -3.577 7.823 1.00 70.65 2 A 1 ATOM 17 C CE1 . TYR A 1 2 ? -10.215 -3.445 9.825 1.00 70.71 2 A 1 ATOM 18 C CE2 . TYR A 1 2 ? -12.479 -3.821 9.141 1.00 71.06 2 A 1 ATOM 19 C CZ . TYR A 1 2 ? -11.525 -3.755 10.135 1.00 70.29 2 A 1 ATOM 20 O OH . TYR A 1 2 ? -11.880 -4.000 11.438 1.00 68.24 2 A 1 ATOM 21 N N . SER A 1 3 ? -10.237 -1.161 3.499 1.00 81.98 3 A 1 ATOM 22 C CA . SER A 1 3 ? -9.864 -0.965 2.102 1.00 82.60 3 A 1 ATOM 23 C C . SER A 1 3 ? -8.960 0.251 1.946 1.00 84.09 3 A 1 ATOM 24 O O . SER A 1 3 ? -8.005 0.232 1.172 1.00 82.76 3 A 1 ATOM 25 C CB . SER A 1 3 ? -11.112 -0.805 1.239 1.00 79.07 3 A 1 ATOM 26 O OG . SER A 1 3 ? -11.854 -2.008 1.211 1.00 72.63 3 A 1 ATOM 27 N N . MET A 1 4 ? -9.255 1.300 2.706 1.00 84.32 4 A 1 ATOM 28 C CA . MET A 1 4 ? -8.453 2.520 2.663 1.00 84.63 4 A 1 ATOM 29 C C . MET A 1 4 ? -7.049 2.267 3.205 1.00 86.28 4 A 1 ATOM 30 O O . MET A 1 4 ? -6.063 2.696 2.611 1.00 84.53 4 A 1 ATOM 31 C CB . MET A 1 4 ? -9.127 3.627 3.474 1.00 80.69 4 A 1 ATOM 32 C CG . MET A 1 4 ? -10.338 4.210 2.767 1.00 77.94 4 A 1 ATOM 33 S SD . MET A 1 4 ? -11.080 5.547 3.699 1.00 72.88 4 A 1 ATOM 34 C CE . MET A 1 4 ? -12.202 6.195 2.463 1.00 64.04 4 A 1 ATOM 35 N N . ALA A 1 5 ? -6.972 1.561 4.328 1.00 83.62 5 A 1 ATOM 36 C CA . ALA A 1 5 ? -5.689 1.246 4.945 1.00 85.29 5 A 1 ATOM 37 C C . ALA A 1 5 ? -4.855 0.352 4.037 1.00 86.68 5 A 1 ATOM 38 O O . ALA A 1 5 ? -3.672 0.600 3.810 1.00 84.85 5 A 1 ATOM 39 C CB . ALA A 1 5 ? -5.909 0.568 6.293 1.00 83.43 5 A 1 ATOM 40 N N . PHE A 1 6 ? -5.486 -0.689 3.506 1.00 80.96 6 A 1 ATOM 41 C CA . PHE A 1 6 ? -4.805 -1.618 2.613 1.00 82.31 6 A 1 ATOM 42 C C . PHE A 1 6 ? -4.415 -0.933 1.311 1.00 84.20 6 A 1 ATOM 43 O O . PHE A 1 6 ? -3.335 -1.177 0.770 1.00 82.97 6 A 1 ATOM 44 C CB . PHE A 1 6 ? -5.705 -2.817 2.325 1.00 80.53 6 A 1 ATOM 45 C CG . PHE A 1 6 ? -4.994 -3.893 1.550 1.00 79.47 6 A 1 ATOM 46 C CD1 . PHE A 1 6 ? -4.021 -4.665 2.162 1.00 78.63 6 A 1 ATOM 47 C CD2 . PHE A 1 6 ? -5.302 -4.125 0.221 1.00 78.00 6 A 1 ATOM 48 C CE1 . PHE A 1 6 ? -3.359 -5.656 1.457 1.00 76.57 6 A 1 ATOM 49 C CE2 . PHE A 1 6 ? -4.638 -5.116 -0.492 1.00 76.15 6 A 1 ATOM 50 C CZ . PHE A 1 6 ? -3.668 -5.881 0.126 1.00 75.40 6 A 1 ATOM 51 N N . LEU A 1 7 ? -5.286 -0.071 0.835 1.00 80.85 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -5.030 0.657 -0.408 1.00 82.27 7 A 1 ATOM 53 C C . LEU A 1 7 ? -3.836 1.587 -0.254 1.00 82.97 7 A 1 ATOM 54 O O . LEU A 1 7 ? -2.958 1.635 -1.117 1.00 82.01 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -6.279 1.449 -0.806 1.00 81.08 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -6.706 1.233 -2.260 1.00 78.37 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -8.172 1.588 -2.445 1.00 77.50 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -5.845 2.053 -3.195 1.00 76.20 7 A 1 ATOM 59 N N . ALA A 1 8 ? -3.793 2.310 0.862 1.00 85.68 8 A 1 ATOM 60 C CA . ALA A 1 8 ? -2.700 3.239 1.134 1.00 86.09 8 A 1 ATOM 61 C C . ALA A 1 8 ? -1.380 2.496 1.294 1.00 87.00 8 A 1 ATOM 62 O O . ALA A 1 8 ? -0.382 2.841 0.660 1.00 84.89 8 A 1 ATOM 63 C CB . ALA A 1 8 ? -3.006 4.051 2.387 1.00 84.97 8 A 1 ATOM 64 N N . SER A 1 9 ? -1.381 1.466 2.130 1.00 86.71 9 A 1 ATOM 65 C CA . SER A 1 9 ? -0.178 0.680 2.374 1.00 85.87 9 A 1 ATOM 66 C C . SER A 1 9 ? 0.237 -0.094 1.133 1.00 87.16 9 A 1 ATOM 67 O O . SER A 1 9 ? 1.411 -0.116 0.768 1.00 84.40 9 A 1 ATOM 68 C CB . SER A 1 9 ? -0.405 -0.285 3.534 1.00 83.46 9 A 1 ATOM 69 O OG . SER A 1 9 ? -0.400 0.420 4.764 1.00 76.90 9 A 1 ATOM 70 N N . SER A 1 10 ? -0.722 -0.714 0.474 1.00 86.30 10 A 1 ATOM 71 C CA . SER A 1 10 ? -0.455 -1.497 -0.728 1.00 85.73 10 A 1 ATOM 72 C C . SER A 1 10 ? 0.122 -0.620 -1.829 1.00 86.64 10 A 1 ATOM 73 O O . SER A 1 10 ? 1.052 -1.023 -2.528 1.00 83.41 10 A 1 ATOM 74 C CB . SER A 1 10 ? -1.733 -2.170 -1.221 1.00 83.16 10 A 1 ATOM 75 O OG . SER A 1 10 ? -1.448 -3.006 -2.313 1.00 77.32 10 A 1 ATOM 76 N N . GLY A 1 11 ? -0.419 0.579 -1.962 1.00 84.76 11 A 1 ATOM 77 C CA . GLY A 1 11 ? 0.061 1.510 -2.976 1.00 84.39 11 A 1 ATOM 78 C C . GLY A 1 11 ? 1.494 1.931 -2.735 1.00 85.99 11 A 1 ATOM 79 O O . GLY A 1 11 ? 2.333 1.861 -3.633 1.00 83.41 11 A 1 ATOM 80 N N . LEU A 1 12 ? 1.788 2.348 -1.514 1.00 84.68 12 A 1 ATOM 81 C CA . LEU A 1 12 ? 3.132 2.796 -1.160 1.00 84.35 12 A 1 ATOM 82 C C . LEU A 1 12 ? 4.120 1.637 -1.142 1.00 85.72 12 A 1 ATOM 83 O O . LEU A 1 12 ? 5.224 1.745 -1.677 1.00 83.78 12 A 1 ATOM 84 C CB . LEU A 1 12 ? 3.114 3.486 0.207 1.00 81.69 12 A 1 ATOM 85 C CG . LEU A 1 12 ? 4.453 4.101 0.608 1.00 77.65 12 A 1 ATOM 86 C CD1 . LEU A 1 12 ? 4.789 5.287 -0.285 1.00 75.14 12 A 1 ATOM 87 C CD2 . LEU A 1 12 ? 4.421 4.534 2.067 1.00 73.82 12 A 1 ATOM 88 N N . VAL A 1 13 ? 3.726 0.535 -0.536 1.00 84.09 13 A 1 ATOM 89 C CA . VAL A 1 13 ? 4.588 -0.643 -0.443 1.00 83.32 13 A 1 ATOM 90 C C . VAL A 1 13 ? 4.866 -1.220 -1.826 1.00 83.85 13 A 1 ATOM 91 O O . VAL A 1 13 ? 6.011 -1.530 -2.160 1.00 82.15 13 A 1 ATOM 92 C CB . VAL A 1 13 ? 3.956 -1.714 0.462 1.00 80.75 13 A 1 ATOM 93 C CG1 . VAL A 1 13 ? 4.780 -2.994 0.427 1.00 77.23 13 A 1 ATOM 94 C CG2 . VAL A 1 13 ? 3.856 -1.202 1.892 1.00 79.30 13 A 1 ATOM 95 N N . ALA A 1 14 ? 3.833 -1.358 -2.623 1.00 84.38 14 A 1 ATOM 96 C CA . ALA A 1 14 ? 3.985 -1.894 -3.973 1.00 84.10 14 A 1 ATOM 97 C C . ALA A 1 14 ? 4.853 -0.981 -4.830 1.00 85.26 14 A 1 ATOM 98 O O . ALA A 1 14 ? 5.702 -1.448 -5.588 1.00 83.00 14 A 1 ATOM 99 C CB . ALA A 1 14 ? 2.619 -2.077 -4.620 1.00 81.91 14 A 1 ATOM 100 N N . ASN A 1 15 ? 4.650 0.315 -4.687 1.00 77.85 15 A 1 ATOM 101 C CA . ASN A 1 15 ? 5.432 1.291 -5.443 1.00 78.53 15 A 1 ATOM 102 C C . ASN A 1 15 ? 6.884 1.298 -4.987 1.00 79.32 15 A 1 ATOM 103 O O . ASN A 1 15 ? 7.803 1.416 -5.796 1.00 75.76 15 A 1 ATOM 104 C CB . ASN A 1 15 ? 4.837 2.691 -5.279 1.00 76.29 15 A 1 ATOM 105 C CG . ASN A 1 15 ? 5.115 3.546 -6.492 1.00 72.24 15 A 1 ATOM 106 O OD1 . ASN A 1 15 ? 5.020 3.094 -7.625 1.00 68.22 15 A 1 ATOM 107 N ND2 . ASN A 1 15 ? 5.458 4.803 -6.272 1.00 67.93 15 A 1 ATOM 108 N N . SER A 1 16 ? 7.092 1.169 -3.680 1.00 80.99 16 A 1 ATOM 109 C CA . SER A 1 16 ? 8.437 1.144 -3.107 1.00 79.48 16 A 1 ATOM 110 C C . SER A 1 16 ? 9.171 -0.133 -3.501 1.00 80.34 16 A 1 ATOM 111 O O . SER A 1 16 ? 10.396 -0.143 -3.627 1.00 76.28 16 A 1 ATOM 112 C CB . SER A 1 16 ? 8.370 1.248 -1.583 1.00 76.35 16 A 1 ATOM 113 O OG . SER A 1 16 ? 9.670 1.379 -1.048 1.00 70.10 16 A 1 ATOM 114 N N . SER A 1 17 ? 8.420 -1.202 -3.691 1.00 75.67 17 A 1 ATOM 115 C CA . SER A 1 17 ? 8.997 -2.490 -4.071 1.00 74.38 17 A 1 ATOM 116 C C . SER A 1 17 ? 9.524 -2.451 -5.502 1.00 74.94 17 A 1 ATOM 117 O O . SER A 1 17 ? 10.436 -3.198 -5.858 1.00 71.16 17 A 1 ATOM 118 C CB . SER A 1 17 ? 7.953 -3.598 -3.938 1.00 70.63 17 A 1 ATOM 119 O OG . SER A 1 17 ? 8.558 -4.863 -4.092 1.00 65.09 17 A 1 ATOM 120 N N . ALA A 1 18 ? 8.959 -1.571 -6.312 1.00 75.95 18 A 1 ATOM 121 C CA . ALA A 1 18 ? 9.357 -1.433 -7.710 1.00 74.73 18 A 1 ATOM 122 C C . ALA A 1 18 ? 10.774 -0.865 -7.808 1.00 72.32 18 A 1 ATOM 123 O O . ALA A 1 18 ? 11.625 -1.476 -8.475 1.00 68.00 18 A 1 ATOM 124 C CB . ALA A 1 18 ? 8.369 -0.537 -8.454 1.00 68.53 18 A 1 ATOM 125 O OXT . ALA A 1 18 ? 11.031 0.193 -7.225 1.00 64.01 18 A 1 #