# 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_spkb39140 # _entry.id spkb39140 # 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" "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" "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" "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" # _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 ASN 2 1 n LEU 3 1 n TYR 4 1 n PHE 5 1 n LEU 6 1 n PHE 7 1 n PHE 8 1 n ILE 9 1 n SER 10 1 n THR 11 1 n ILE 12 1 n LEU 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 @ 2025-07-10 15:01:32)" _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 96.08 _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 88.21 1 1 A ASN 2 2 92.37 1 2 A LEU 3 2 96.49 1 3 A TYR 4 2 96.50 1 4 A PHE 5 2 97.53 1 5 A LEU 6 2 96.95 1 6 A PHE 7 2 96.92 1 7 A PHE 8 2 96.99 1 8 A ILE 9 2 97.51 1 9 A SER 10 2 97.87 1 10 A THR 11 2 97.77 1 11 A ILE 12 2 97.93 1 12 A LEU 13 2 96.93 1 13 A ALA 14 2 93.94 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 MET . 1 A 1 A 2 1 n ASN . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n TYR . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n LEU . 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 . MET A 1 1 ? 8.543 -6.178 3.147 1.00 92.62 1 A 1 ATOM 2 C CA . MET A 1 1 ? 7.167 -6.225 3.671 1.00 94.48 1 A 1 ATOM 3 C C . MET A 1 1 ? 6.702 -4.828 4.072 1.00 94.87 1 A 1 ATOM 4 O O . MET A 1 1 ? 6.841 -4.422 5.226 1.00 93.83 1 A 1 ATOM 5 C CB . MET A 1 1 ? 7.092 -7.174 4.867 1.00 91.42 1 A 1 ATOM 6 C CG . MET A 1 1 ? 5.715 -7.247 5.502 1.00 85.09 1 A 1 ATOM 7 S SD . MET A 1 1 ? 5.671 -8.404 6.869 1.00 80.83 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.033 -8.128 7.496 1.00 72.56 1 A 1 ATOM 9 N N . ASN A 1 2 ? 6.140 -4.104 3.125 1.00 94.03 2 A 1 ATOM 10 C CA . ASN A 1 2 ? 5.667 -2.749 3.372 1.00 96.45 2 A 1 ATOM 11 C C . ASN A 1 2 ? 4.135 -2.739 3.442 1.00 97.46 2 A 1 ATOM 12 O O . ASN A 1 2 ? 3.456 -2.448 2.457 1.00 96.56 2 A 1 ATOM 13 C CB . ASN A 1 2 ? 6.168 -1.815 2.269 1.00 94.40 2 A 1 ATOM 14 C CG . ASN A 1 2 ? 6.479 -0.427 2.787 1.00 89.07 2 A 1 ATOM 15 O OD1 . ASN A 1 2 ? 5.647 0.218 3.414 1.00 86.59 2 A 1 ATOM 16 N ND2 . ASN A 1 2 ? 7.687 0.037 2.523 1.00 84.39 2 A 1 ATOM 17 N N . LEU A 1 3 ? 3.593 -3.098 4.610 1.00 97.61 3 A 1 ATOM 18 C CA . LEU A 1 3 ? 2.144 -3.171 4.817 1.00 97.97 3 A 1 ATOM 19 C C . LEU A 1 3 ? 1.484 -1.821 4.569 1.00 98.22 3 A 1 ATOM 20 O O . LEU A 1 3 ? 0.366 -1.740 4.059 1.00 97.89 3 A 1 ATOM 21 C CB . LEU A 1 3 ? 1.848 -3.659 6.237 1.00 97.66 3 A 1 ATOM 22 C CG . LEU A 1 3 ? 0.952 -4.897 6.324 1.00 96.01 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? -0.422 -4.611 5.747 1.00 93.68 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? 1.618 -6.051 5.583 1.00 92.86 3 A 1 ATOM 25 N N . TYR A 1 4 ? 2.193 -0.753 4.924 1.00 98.53 4 A 1 ATOM 26 C CA . TYR A 1 4 ? 1.708 0.610 4.723 1.00 98.51 4 A 1 ATOM 27 C C . TYR A 1 4 ? 1.478 0.872 3.236 1.00 98.56 4 A 1 ATOM 28 O O . TYR A 1 4 ? 0.512 1.531 2.844 1.00 98.27 4 A 1 ATOM 29 C CB . TYR A 1 4 ? 2.733 1.602 5.289 1.00 98.16 4 A 1 ATOM 30 C CG . TYR A 1 4 ? 2.137 2.945 5.648 1.00 96.68 4 A 1 ATOM 31 C CD1 . TYR A 1 4 ? 1.708 3.822 4.667 1.00 94.98 4 A 1 ATOM 32 C CD2 . TYR A 1 4 ? 2.012 3.329 6.979 1.00 95.22 4 A 1 ATOM 33 C CE1 . TYR A 1 4 ? 1.156 5.054 4.991 1.00 94.79 4 A 1 ATOM 34 C CE2 . TYR A 1 4 ? 1.464 4.564 7.317 1.00 94.91 4 A 1 ATOM 35 C CZ . TYR A 1 4 ? 1.039 5.419 6.315 1.00 95.16 4 A 1 ATOM 36 O OH . TYR A 1 4 ? 0.499 6.646 6.644 1.00 94.17 4 A 1 ATOM 37 N N . PHE A 1 5 ? 2.360 0.331 2.408 1.00 98.55 5 A 1 ATOM 38 C CA . PHE A 1 5 ? 2.282 0.481 0.955 1.00 98.60 5 A 1 ATOM 39 C C . PHE A 1 5 ? 1.093 -0.294 0.389 1.00 98.65 5 A 1 ATOM 40 O O . PHE A 1 5 ? 0.296 0.246 -0.378 1.00 98.55 5 A 1 ATOM 41 C CB . PHE A 1 5 ? 3.589 -0.001 0.316 1.00 98.43 5 A 1 ATOM 42 C CG . PHE A 1 5 ? 3.576 0.035 -1.188 1.00 97.82 5 A 1 ATOM 43 C CD1 . PHE A 1 5 ? 3.591 1.243 -1.861 1.00 96.62 5 A 1 ATOM 44 C CD2 . PHE A 1 5 ? 3.556 -1.142 -1.913 1.00 96.93 5 A 1 ATOM 45 C CE1 . PHE A 1 5 ? 3.578 1.292 -3.247 1.00 96.29 5 A 1 ATOM 46 C CE2 . PHE A 1 5 ? 3.543 -1.106 -3.308 1.00 96.13 5 A 1 ATOM 47 C CZ . PHE A 1 5 ? 3.553 0.109 -3.970 1.00 96.22 5 A 1 ATOM 48 N N . LEU A 1 6 ? 0.967 -1.560 0.767 1.00 98.45 6 A 1 ATOM 49 C CA . LEU A 1 6 ? -0.118 -2.412 0.291 1.00 98.43 6 A 1 ATOM 50 C C . LEU A 1 6 ? -1.476 -1.891 0.750 1.00 98.52 6 A 1 ATOM 51 O O . LEU A 1 6 ? -2.450 -1.924 0.000 1.00 98.42 6 A 1 ATOM 52 C CB . LEU A 1 6 ? 0.085 -3.842 0.789 1.00 98.19 6 A 1 ATOM 53 C CG . LEU A 1 6 ? 1.331 -4.530 0.251 1.00 95.25 6 A 1 ATOM 54 C CD1 . LEU A 1 6 ? 1.545 -5.849 0.975 1.00 93.79 6 A 1 ATOM 55 C CD2 . LEU A 1 6 ? 1.211 -4.765 -1.248 1.00 94.55 6 A 1 ATOM 56 N N . PHE A 1 7 ? -1.539 -1.407 1.965 1.00 98.51 7 A 1 ATOM 57 C CA . PHE A 1 7 ? -2.762 -0.847 2.534 1.00 98.46 7 A 1 ATOM 58 C C . PHE A 1 7 ? -3.210 0.382 1.751 1.00 98.53 7 A 1 ATOM 59 O O . PHE A 1 7 ? -4.378 0.505 1.379 1.00 98.31 7 A 1 ATOM 60 C CB . PHE A 1 7 ? -2.527 -0.488 4.001 1.00 98.23 7 A 1 ATOM 61 C CG . PHE A 1 7 ? -3.655 0.295 4.625 1.00 97.00 7 A 1 ATOM 62 C CD1 . PHE A 1 7 ? -4.808 -0.344 5.050 1.00 95.42 7 A 1 ATOM 63 C CD2 . PHE A 1 7 ? -3.554 1.665 4.777 1.00 96.00 7 A 1 ATOM 64 C CE1 . PHE A 1 7 ? -5.853 0.371 5.620 1.00 95.25 7 A 1 ATOM 65 C CE2 . PHE A 1 7 ? -4.601 2.395 5.342 1.00 95.21 7 A 1 ATOM 66 C CZ . PHE A 1 7 ? -5.749 1.745 5.765 1.00 95.23 7 A 1 ATOM 67 N N . PHE A 1 8 ? -2.284 1.274 1.506 1.00 98.43 8 A 1 ATOM 68 C CA . PHE A 1 8 ? -2.538 2.508 0.773 1.00 98.45 8 A 1 ATOM 69 C C . PHE A 1 8 ? -2.975 2.225 -0.667 1.00 98.56 8 A 1 ATOM 70 O O . PHE A 1 8 ? -3.942 2.812 -1.156 1.00 98.41 8 A 1 ATOM 71 C CB . PHE A 1 8 ? -1.278 3.386 0.823 1.00 98.19 8 A 1 ATOM 72 C CG . PHE A 1 8 ? -1.061 4.245 -0.396 1.00 97.31 8 A 1 ATOM 73 C CD1 . PHE A 1 8 ? -1.836 5.377 -0.603 1.00 95.66 8 A 1 ATOM 74 C CD2 . PHE A 1 8 ? -0.078 3.923 -1.313 1.00 96.14 8 A 1 ATOM 75 C CE1 . PHE A 1 8 ? -1.638 6.175 -1.721 1.00 95.08 8 A 1 ATOM 76 C CE2 . PHE A 1 8 ? 0.124 4.719 -2.440 1.00 95.21 8 A 1 ATOM 77 C CZ . PHE A 1 8 ? -0.656 5.841 -2.643 1.00 95.41 8 A 1 ATOM 78 N N . ILE A 1 9 ? -2.272 1.322 -1.335 1.00 98.43 9 A 1 ATOM 79 C CA . ILE A 1 9 ? -2.580 0.962 -2.719 1.00 98.36 9 A 1 ATOM 80 C C . ILE A 1 9 ? -3.957 0.309 -2.816 1.00 98.47 9 A 1 ATOM 81 O O . ILE A 1 9 ? -4.733 0.599 -3.726 1.00 98.35 9 A 1 ATOM 82 C CB . ILE A 1 9 ? -1.496 0.026 -3.294 1.00 98.10 9 A 1 ATOM 83 C CG1 . ILE A 1 9 ? -0.153 0.765 -3.409 1.00 97.14 9 A 1 ATOM 84 C CG2 . ILE A 1 9 ? -1.907 -0.517 -4.658 1.00 97.06 9 A 1 ATOM 85 C CD1 . ILE A 1 9 ? -0.196 1.950 -4.362 1.00 94.14 9 A 1 ATOM 86 N N . SER A 1 10 ? -4.266 -0.580 -1.892 1.00 98.56 10 A 1 ATOM 87 C CA . SER A 1 10 ? -5.545 -1.284 -1.872 1.00 98.54 10 A 1 ATOM 88 C C . SER A 1 10 ? -6.709 -0.322 -1.656 1.00 98.63 10 A 1 ATOM 89 O O . SER A 1 10 ? -7.807 -0.539 -2.173 1.00 98.30 10 A 1 ATOM 90 C CB . SER A 1 10 ? -5.542 -2.349 -0.782 1.00 98.11 10 A 1 ATOM 91 O OG . SER A 1 10 ? -6.672 -3.174 -0.912 1.00 95.08 10 A 1 ATOM 92 N N . THR A 1 11 ? -6.481 0.738 -0.915 1.00 98.66 11 A 1 ATOM 93 C CA . THR A 1 11 ? -7.502 1.747 -0.639 1.00 98.60 11 A 1 ATOM 94 C C . THR A 1 11 ? -7.793 2.597 -1.870 1.00 98.67 11 A 1 ATOM 95 O O . THR A 1 11 ? -8.939 2.978 -2.115 1.00 98.21 11 A 1 ATOM 96 C CB . THR A 1 11 ? -7.064 2.663 0.512 1.00 98.19 11 A 1 ATOM 97 O OG1 . THR A 1 11 ? -6.766 1.881 1.665 1.00 96.17 11 A 1 ATOM 98 C CG2 . THR A 1 11 ? -8.153 3.657 0.858 1.00 95.92 11 A 1 ATOM 99 N N . ILE A 1 12 ? -6.767 2.896 -2.642 1.00 98.70 12 A 1 ATOM 100 C CA . ILE A 1 12 ? -6.903 3.708 -3.848 1.00 98.63 12 A 1 ATOM 101 C C . ILE A 1 12 ? -7.652 2.947 -4.941 1.00 98.65 12 A 1 ATOM 102 O O . ILE A 1 12 ? -8.457 3.521 -5.675 1.00 98.26 12 A 1 ATOM 103 C CB . ILE A 1 12 ? -5.517 4.156 -4.377 1.00 98.38 12 A 1 ATOM 104 C CG1 . ILE A 1 12 ? -4.738 4.924 -3.295 1.00 97.59 12 A 1 ATOM 105 C CG2 . ILE A 1 12 ? -5.657 5.011 -5.633 1.00 97.07 12 A 1 ATOM 106 C CD1 . ILE A 1 12 ? -5.478 6.138 -2.767 1.00 96.16 12 A 1 ATOM 107 N N . LEU A 1 13 ? -7.374 1.655 -5.068 1.00 98.46 13 A 1 ATOM 108 C CA . LEU A 1 13 ? -7.969 0.818 -6.103 1.00 98.36 13 A 1 ATOM 109 C C . LEU A 1 13 ? -9.427 0.474 -5.801 1.00 98.41 13 A 1 ATOM 110 O O . LEU A 1 13 ? -10.299 0.591 -6.671 1.00 98.05 13 A 1 ATOM 111 C CB . LEU A 1 13 ? -7.143 -0.463 -6.266 1.00 97.95 13 A 1 ATOM 112 C CG . LEU A 1 13 ? -5.707 -0.247 -6.742 1.00 96.33 13 A 1 ATOM 113 C CD1 . LEU A 1 13 ? -4.928 -1.556 -6.679 1.00 94.15 13 A 1 ATOM 114 C CD2 . LEU A 1 13 ? -5.688 0.307 -8.156 1.00 93.72 13 A 1 ATOM 115 N N . ALA A 1 14 ? -9.685 0.042 -4.591 1.00 97.46 14 A 1 ATOM 116 C CA . ALA A 1 14 ? -11.027 -0.369 -4.180 1.00 96.61 14 A 1 ATOM 117 C C . ALA A 1 14 ? -11.672 0.689 -3.291 1.00 95.98 14 A 1 ATOM 118 O O . ALA A 1 14 ? -12.447 1.525 -3.817 1.00 93.27 14 A 1 ATOM 119 C CB . ALA A 1 14 ? -10.957 -1.717 -3.469 1.00 94.59 14 A 1 ATOM 120 O OXT . ALA A 1 14 ? -11.451 0.683 -2.095 1.00 85.76 14 A 1 #