# 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_spkb12665 # _entry.id spkb12665 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)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" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)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 LEU 2 1 n PRO 3 1 n GLY 4 1 n LEU 5 1 n ALA 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n ALA 12 1 n TRP 13 1 n THR 14 1 n ALA 15 1 n ARG 16 1 n ALA 17 # _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 02:08:17)" _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 95.40 _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 88.04 1 1 A LEU 2 2 92.93 1 2 A PRO 3 2 96.20 1 3 A GLY 4 2 97.96 1 4 A LEU 5 2 96.93 1 5 A ALA 6 2 98.15 1 6 A LEU 7 2 97.58 1 7 A LEU 8 2 97.33 1 8 A LEU 9 2 97.33 1 9 A LEU 10 2 97.15 1 10 A ALA 11 2 98.26 1 11 A ALA 12 2 98.27 1 12 A TRP 13 2 95.53 1 13 A THR 14 2 96.76 1 14 A ALA 15 2 97.98 1 15 A ARG 16 2 91.00 1 16 A ALA 17 2 90.48 1 17 # _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 LEU . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n GLY . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n TRP . 13 A 13 A 14 1 n THR . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n ARG . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? 2.789 7.008 12.636 1.00 91.34 1 A 1 ATOM 2 C CA . MET A 1 1 ? 2.613 6.243 11.386 1.00 92.42 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.192 5.701 11.275 1.00 94.19 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.498 5.568 12.278 1.00 92.99 1 A 1 ATOM 5 C CB . MET A 1 1 ? 3.598 5.073 11.357 1.00 88.89 1 A 1 ATOM 6 C CG . MET A 1 1 ? 5.026 5.528 11.130 1.00 85.07 1 A 1 ATOM 7 S SD . MET A 1 1 ? 6.118 4.112 10.922 1.00 84.05 1 A 1 ATOM 8 C CE . MET A 1 1 ? 7.649 4.954 10.576 1.00 75.40 1 A 1 ATOM 9 N N . LEU A 1 2 ? 0.781 5.366 10.066 1.00 93.45 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -0.550 4.818 9.827 1.00 95.64 2 A 1 ATOM 11 C C . LEU A 1 2 ? -0.456 3.467 9.116 1.00 97.01 2 A 1 ATOM 12 O O . LEU A 1 2 ? -0.102 3.412 7.935 1.00 96.27 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -1.366 5.809 8.999 1.00 94.56 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -2.442 6.523 9.801 1.00 92.20 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -2.681 7.919 9.246 1.00 88.41 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -3.732 5.716 9.775 1.00 85.87 2 A 1 ATOM 17 N N . PRO A 1 3 ? -0.767 2.381 9.830 1.00 97.07 3 A 1 ATOM 18 C CA . PRO A 1 3 ? -0.705 1.034 9.249 1.00 97.21 3 A 1 ATOM 19 C C . PRO A 1 3 ? -1.697 0.836 8.110 1.00 97.82 3 A 1 ATOM 20 O O . PRO A 1 3 ? -1.454 0.040 7.199 1.00 97.17 3 A 1 ATOM 21 C CB . PRO A 1 3 ? -1.037 0.112 10.435 1.00 95.50 3 A 1 ATOM 22 C CG . PRO A 1 3 ? -1.731 0.972 11.424 1.00 93.02 3 A 1 ATOM 23 C CD . PRO A 1 3 ? -1.186 2.359 11.243 1.00 95.59 3 A 1 ATOM 24 N N . GLY A 1 4 ? -2.806 1.550 8.154 1.00 97.61 4 A 1 ATOM 25 C CA . GLY A 1 4 ? -3.821 1.457 7.106 1.00 97.84 4 A 1 ATOM 26 C C . GLY A 1 4 ? -3.285 1.874 5.749 1.00 98.27 4 A 1 ATOM 27 O O . GLY A 1 4 ? -3.604 1.266 4.727 1.00 98.11 4 A 1 ATOM 28 N N . LEU A 1 5 ? -2.450 2.904 5.738 1.00 98.09 5 A 1 ATOM 29 C CA . LEU A 1 5 ? -1.839 3.399 4.504 1.00 98.20 5 A 1 ATOM 30 C C . LEU A 1 5 ? -0.925 2.347 3.895 1.00 98.41 5 A 1 ATOM 31 O O . LEU A 1 5 ? -0.908 2.153 2.679 1.00 98.34 5 A 1 ATOM 32 C CB . LEU A 1 5 ? -1.052 4.671 4.797 1.00 98.05 5 A 1 ATOM 33 C CG . LEU A 1 5 ? -0.853 5.538 3.571 1.00 96.28 5 A 1 ATOM 34 C CD1 . LEU A 1 5 ? -1.574 6.864 3.727 1.00 94.05 5 A 1 ATOM 35 C CD2 . LEU A 1 5 ? 0.619 5.761 3.312 1.00 93.99 5 A 1 ATOM 36 N N . ALA A 1 6 ? -0.161 1.676 4.741 1.00 98.14 6 A 1 ATOM 37 C CA . ALA A 1 6 ? 0.751 0.623 4.293 1.00 98.15 6 A 1 ATOM 38 C C . ALA A 1 6 ? -0.018 -0.511 3.624 1.00 98.29 6 A 1 ATOM 39 O O . ALA A 1 6 ? 0.436 -1.072 2.628 1.00 98.20 6 A 1 ATOM 40 C CB . ALA A 1 6 ? 1.540 0.094 5.483 1.00 97.96 6 A 1 ATOM 41 N N . LEU A 1 7 ? -1.176 -0.829 4.163 1.00 98.35 7 A 1 ATOM 42 C CA . LEU A 1 7 ? -2.029 -1.881 3.613 1.00 98.39 7 A 1 ATOM 43 C C . LEU A 1 7 ? -2.492 -1.512 2.210 1.00 98.49 7 A 1 ATOM 44 O O . LEU A 1 7 ? -2.472 -2.346 1.301 1.00 98.48 7 A 1 ATOM 45 C CB . LEU A 1 7 ? -3.233 -2.093 4.533 1.00 98.30 7 A 1 ATOM 46 C CG . LEU A 1 7 ? -3.960 -3.404 4.286 1.00 97.09 7 A 1 ATOM 47 C CD1 . LEU A 1 7 ? -3.296 -4.534 5.064 1.00 95.79 7 A 1 ATOM 48 C CD2 . LEU A 1 7 ? -5.416 -3.285 4.677 1.00 95.71 7 A 1 ATOM 49 N N . LEU A 1 8 ? -2.895 -0.263 2.036 1.00 98.15 8 A 1 ATOM 50 C CA . LEU A 1 8 ? -3.345 0.235 0.739 1.00 98.17 8 A 1 ATOM 51 C C . LEU A 1 8 ? -2.209 0.205 -0.273 1.00 98.25 8 A 1 ATOM 52 O O . LEU A 1 8 ? -2.401 -0.179 -1.428 1.00 98.27 8 A 1 ATOM 53 C CB . LEU A 1 8 ? -3.872 1.663 0.901 1.00 98.22 8 A 1 ATOM 54 C CG . LEU A 1 8 ? -5.392 1.764 0.842 1.00 96.98 8 A 1 ATOM 55 C CD1 . LEU A 1 8 ? -5.888 2.988 1.582 1.00 95.22 8 A 1 ATOM 56 C CD2 . LEU A 1 8 ? -5.841 1.815 -0.618 1.00 95.37 8 A 1 ATOM 57 N N . LEU A 1 9 ? -1.037 0.600 0.168 1.00 98.14 9 A 1 ATOM 58 C CA . LEU A 1 9 ? 0.150 0.606 -0.684 1.00 98.04 9 A 1 ATOM 59 C C . LEU A 1 9 ? 0.489 -0.804 -1.143 1.00 98.14 9 A 1 ATOM 60 O O . LEU A 1 9 ? 0.824 -1.020 -2.310 1.00 98.21 9 A 1 ATOM 61 C CB . LEU A 1 9 ? 1.324 1.208 0.088 1.00 98.02 9 A 1 ATOM 62 C CG . LEU A 1 9 ? 2.540 1.518 -0.773 1.00 96.91 9 A 1 ATOM 63 C CD1 . LEU A 1 9 ? 2.335 2.836 -1.523 1.00 95.56 9 A 1 ATOM 64 C CD2 . LEU A 1 9 ? 3.782 1.596 0.080 1.00 95.62 9 A 1 ATOM 65 N N . LEU A 1 10 ? 0.404 -1.754 -0.231 1.00 98.22 10 A 1 ATOM 66 C CA . LEU A 1 10 ? 0.688 -3.153 -0.537 1.00 98.13 10 A 1 ATOM 67 C C . LEU A 1 10 ? -0.299 -3.687 -1.562 1.00 98.27 10 A 1 ATOM 68 O O . LEU A 1 10 ? 0.091 -4.369 -2.514 1.00 98.26 10 A 1 ATOM 69 C CB . LEU A 1 10 ? 0.616 -3.981 0.748 1.00 97.97 10 A 1 ATOM 70 C CG . LEU A 1 10 ? 1.546 -5.186 0.748 1.00 96.32 10 A 1 ATOM 71 C CD1 . LEU A 1 10 ? 2.393 -5.211 2.009 1.00 95.08 10 A 1 ATOM 72 C CD2 . LEU A 1 10 ? 0.754 -6.475 0.631 1.00 94.97 10 A 1 ATOM 73 N N . ALA A 1 11 ? -1.571 -3.374 -1.370 1.00 98.42 11 A 1 ATOM 74 C CA . ALA A 1 11 ? -2.618 -3.813 -2.286 1.00 98.32 11 A 1 ATOM 75 C C . ALA A 1 11 ? -2.403 -3.223 -3.674 1.00 98.36 11 A 1 ATOM 76 O O . ALA A 1 11 ? -2.542 -3.924 -4.678 1.00 98.04 11 A 1 ATOM 77 C CB . ALA A 1 11 ? -3.981 -3.405 -1.738 1.00 98.14 11 A 1 ATOM 78 N N . ALA A 1 12 ? -2.058 -1.947 -3.727 1.00 98.49 12 A 1 ATOM 79 C CA . ALA A 1 12 ? -1.810 -1.265 -4.993 1.00 98.37 12 A 1 ATOM 80 C C . ALA A 1 12 ? -0.585 -1.840 -5.694 1.00 98.34 12 A 1 ATOM 81 O O . ALA A 1 12 ? -0.597 -2.055 -6.904 1.00 97.91 12 A 1 ATOM 82 C CB . ALA A 1 12 ? -1.624 0.224 -4.744 1.00 98.22 12 A 1 ATOM 83 N N . TRP A 1 13 ? 0.465 -2.089 -4.928 1.00 98.35 13 A 1 ATOM 84 C CA . TRP A 1 13 ? 1.704 -2.647 -5.470 1.00 98.14 13 A 1 ATOM 85 C C . TRP A 1 13 ? 1.466 -4.035 -6.057 1.00 98.25 13 A 1 ATOM 86 O O . TRP A 1 13 ? 1.965 -4.349 -7.136 1.00 97.83 13 A 1 ATOM 87 C CB . TRP A 1 13 ? 2.756 -2.721 -4.362 1.00 97.87 13 A 1 ATOM 88 C CG . TRP A 1 13 ? 4.056 -3.284 -4.820 1.00 97.04 13 A 1 ATOM 89 C CD1 . TRP A 1 13 ? 4.883 -2.753 -5.764 1.00 94.05 13 A 1 ATOM 90 C CD2 . TRP A 1 13 ? 4.683 -4.504 -4.371 1.00 96.06 13 A 1 ATOM 91 N NE1 . TRP A 1 13 ? 5.985 -3.562 -5.927 1.00 94.18 13 A 1 ATOM 92 C CE2 . TRP A 1 13 ? 5.888 -4.643 -5.084 1.00 95.79 13 A 1 ATOM 93 C CE3 . TRP A 1 13 ? 4.340 -5.480 -3.435 1.00 94.09 13 A 1 ATOM 94 C CZ2 . TRP A 1 13 ? 6.742 -5.727 -4.886 1.00 93.95 13 A 1 ATOM 95 C CZ3 . TRP A 1 13 ? 5.191 -6.558 -3.237 1.00 90.68 13 A 1 ATOM 96 C CH2 . TRP A 1 13 ? 6.378 -6.675 -3.965 1.00 91.20 13 A 1 ATOM 97 N N . THR A 1 14 ? 0.711 -4.847 -5.360 1.00 98.43 14 A 1 ATOM 98 C CA . THR A 1 14 ? 0.402 -6.203 -5.815 1.00 98.23 14 A 1 ATOM 99 C C . THR A 1 14 ? -0.550 -6.185 -7.008 1.00 98.19 14 A 1 ATOM 100 O O . THR A 1 14 ? -0.385 -6.968 -7.948 1.00 97.52 14 A 1 ATOM 101 C CB . THR A 1 14 ? -0.208 -7.015 -4.665 1.00 97.59 14 A 1 ATOM 102 O OG1 . THR A 1 14 ? 0.690 -7.009 -3.563 1.00 93.78 14 A 1 ATOM 103 C CG2 . THR A 1 14 ? -0.445 -8.459 -5.064 1.00 93.57 14 A 1 ATOM 104 N N . ALA A 1 15 ? -1.538 -5.317 -6.972 1.00 98.46 15 A 1 ATOM 105 C CA . ALA A 1 15 ? -2.527 -5.208 -8.042 1.00 98.29 15 A 1 ATOM 106 C C . ALA A 1 15 ? -1.923 -4.598 -9.303 1.00 98.16 15 A 1 ATOM 107 O O . ALA A 1 15 ? -2.233 -5.024 -10.413 1.00 97.11 15 A 1 ATOM 108 C CB . ALA A 1 15 ? -3.713 -4.379 -7.568 1.00 97.86 15 A 1 ATOM 109 N N . ARG A 1 16 ? -1.075 -3.583 -9.127 1.00 97.80 16 A 1 ATOM 110 C CA . ARG A 1 16 ? -0.424 -2.910 -10.251 1.00 97.18 16 A 1 ATOM 111 C C . ARG A 1 16 ? 0.670 -3.790 -10.836 1.00 97.04 16 A 1 ATOM 112 O O . ARG A 1 16 ? 1.746 -3.921 -10.263 1.00 94.79 16 A 1 ATOM 113 C CB . ARG A 1 16 ? 0.170 -1.582 -9.781 1.00 95.48 16 A 1 ATOM 114 C CG . ARG A 1 16 ? -0.689 -0.398 -10.125 1.00 91.31 16 A 1 ATOM 115 C CD . ARG A 1 16 ? -1.345 0.179 -8.889 1.00 89.96 16 A 1 ATOM 116 N NE . ARG A 1 16 ? -2.707 -0.327 -8.741 1.00 88.03 16 A 1 ATOM 117 C CZ . ARG A 1 16 ? -3.744 0.168 -9.383 1.00 86.61 16 A 1 ATOM 118 N NH1 . ARG A 1 16 ? -3.615 1.176 -10.217 1.00 80.77 16 A 1 ATOM 119 N NH2 . ARG A 1 16 ? -4.942 -0.364 -9.189 1.00 81.99 16 A 1 ATOM 120 N N . ALA A 1 17 ? 0.394 -4.373 -11.976 1.00 95.40 17 A 1 ATOM 121 C CA . ALA A 1 17 ? 1.354 -5.231 -12.660 1.00 93.83 17 A 1 ATOM 122 C C . ALA A 1 17 ? 1.695 -4.647 -14.024 1.00 92.56 17 A 1 ATOM 123 O O . ALA A 1 17 ? 2.880 -4.668 -14.404 1.00 88.33 17 A 1 ATOM 124 C CB . ALA A 1 17 ? 0.790 -6.638 -12.798 1.00 90.16 17 A 1 ATOM 125 O OXT . ALA A 1 17 ? 0.772 -4.165 -14.705 1.00 82.58 17 A 1 #