# 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_spkb21888 # _entry.id spkb21888 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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" "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" "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 LYS 2 1 n GLY 3 1 n LEU 4 1 n VAL 5 1 n PHE 6 1 n LEU 7 1 n LEU 8 1 n GLY 9 1 n LEU 10 1 n LEU 11 1 n PRO 12 1 n THR 13 1 n ILE 14 1 n TYR 15 1 n ALA 16 # _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 00:53:41)" _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 88.87 _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 76.79 1 1 A LYS 2 2 80.54 1 2 A GLY 3 2 92.62 1 3 A LEU 4 2 87.36 1 4 A VAL 5 2 93.06 1 5 A PHE 6 2 90.00 1 6 A LEU 7 2 90.99 1 7 A LEU 8 2 90.49 1 8 A GLY 9 2 93.84 1 9 A LEU 10 2 90.87 1 10 A LEU 11 2 90.26 1 11 A PRO 12 2 92.25 1 12 A THR 13 2 91.19 1 13 A ILE 14 2 90.74 1 14 A TYR 15 2 89.10 1 15 A ALA 16 2 87.58 1 16 # _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 GLY . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n GLY . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n ILE . 14 A 14 A 15 1 n TYR . 15 A 15 A 16 1 n ALA . 16 A 16 # _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 ? 0.105 9.224 12.214 1.00 81.27 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.253 8.324 11.981 1.00 83.57 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.319 7.916 10.506 1.00 85.27 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.312 7.907 9.814 1.00 81.80 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.120 7.082 12.855 1.00 76.83 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.896 7.460 14.318 1.00 73.95 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.695 6.340 15.448 1.00 70.05 1 A 1 ATOM 8 C CE . MET A 1 1 ? 1.421 7.189 16.990 1.00 61.61 1 A 1 ATOM 9 N N . LYS A 1 2 ? 2.502 7.584 10.022 1.00 83.68 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 2.689 7.223 8.615 1.00 87.52 2 A 1 ATOM 11 C C . LYS A 1 2 ? 3.123 5.759 8.473 1.00 88.54 2 A 1 ATOM 12 O O . LYS A 1 2 ? 3.884 5.411 7.580 1.00 86.25 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 3.734 8.150 8.000 1.00 83.83 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 3.344 8.627 6.618 1.00 79.11 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 4.294 9.715 6.141 1.00 78.20 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 3.986 10.126 4.717 1.00 72.22 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 4.880 11.243 4.293 1.00 65.47 2 A 1 ATOM 18 N N . GLY A 1 3 ? 2.637 4.909 9.347 1.00 91.12 3 A 1 ATOM 19 C CA . GLY A 1 3 ? 3.018 3.493 9.323 1.00 92.84 3 A 1 ATOM 20 C C . GLY A 1 3 ? 2.121 2.657 8.427 1.00 94.02 3 A 1 ATOM 21 O O . GLY A 1 3 ? 2.461 1.547 8.045 1.00 92.51 3 A 1 ATOM 22 N N . LEU A 1 4 ? 0.958 3.198 8.076 1.00 89.73 4 A 1 ATOM 23 C CA . LEU A 1 4 ? 0.005 2.478 7.231 1.00 90.73 4 A 1 ATOM 24 C C . LEU A 1 4 ? 0.200 2.810 5.756 1.00 92.78 4 A 1 ATOM 25 O O . LEU A 1 4 ? -0.396 2.189 4.888 1.00 91.50 4 A 1 ATOM 26 C CB . LEU A 1 4 ? -1.424 2.834 7.654 1.00 88.67 4 A 1 ATOM 27 C CG . LEU A 1 4 ? -1.654 2.808 9.162 1.00 85.16 4 A 1 ATOM 28 C CD1 . LEU A 1 4 ? -3.072 3.256 9.479 1.00 81.04 4 A 1 ATOM 29 C CD2 . LEU A 1 4 ? -1.409 1.410 9.708 1.00 79.25 4 A 1 ATOM 30 N N . VAL A 1 5 ? 1.029 3.794 5.474 1.00 93.77 5 A 1 ATOM 31 C CA . VAL A 1 5 ? 1.285 4.208 4.095 1.00 94.44 5 A 1 ATOM 32 C C . VAL A 1 5 ? 2.112 3.163 3.355 1.00 94.93 5 A 1 ATOM 33 O O . VAL A 1 5 ? 2.068 3.072 2.132 1.00 94.20 5 A 1 ATOM 34 C CB . VAL A 1 5 ? 2.016 5.560 4.061 1.00 93.28 5 A 1 ATOM 35 C CG1 . VAL A 1 5 ? 2.169 6.066 2.641 1.00 90.47 5 A 1 ATOM 36 C CG2 . VAL A 1 5 ? 1.262 6.581 4.900 1.00 90.34 5 A 1 ATOM 37 N N . PHE A 1 6 ? 2.868 2.383 4.107 1.00 93.64 6 A 1 ATOM 38 C CA . PHE A 1 6 ? 3.711 1.354 3.497 1.00 93.25 6 A 1 ATOM 39 C C . PHE A 1 6 ? 2.867 0.211 2.958 1.00 94.24 6 A 1 ATOM 40 O O . PHE A 1 6 ? 3.262 -0.478 2.023 1.00 93.62 6 A 1 ATOM 41 C CB . PHE A 1 6 ? 4.708 0.819 4.525 1.00 92.79 6 A 1 ATOM 42 C CG . PHE A 1 6 ? 6.020 1.561 4.491 1.00 90.16 6 A 1 ATOM 43 C CD1 . PHE A 1 6 ? 6.106 2.859 4.944 1.00 87.03 6 A 1 ATOM 44 C CD2 . PHE A 1 6 ? 7.153 0.943 3.992 1.00 87.22 6 A 1 ATOM 45 C CE1 . PHE A 1 6 ? 7.307 3.550 4.903 1.00 86.49 6 A 1 ATOM 46 C CE2 . PHE A 1 6 ? 8.363 1.622 3.949 1.00 85.78 6 A 1 ATOM 47 C CZ . PHE A 1 6 ? 8.442 2.928 4.405 1.00 85.82 6 A 1 ATOM 48 N N . LEU A 1 7 ? 1.693 0.012 3.528 1.00 93.77 7 A 1 ATOM 49 C CA . LEU A 1 7 ? 0.798 -1.055 3.090 1.00 93.75 7 A 1 ATOM 50 C C . LEU A 1 7 ? -0.217 -0.518 2.084 1.00 94.57 7 A 1 ATOM 51 O O . LEU A 1 7 ? -0.677 -1.242 1.208 1.00 94.38 7 A 1 ATOM 52 C CB . LEU A 1 7 ? 0.061 -1.656 4.292 1.00 93.27 7 A 1 ATOM 53 C CG . LEU A 1 7 ? 0.597 -1.234 5.652 1.00 88.38 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -0.440 -1.523 6.731 1.00 85.07 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? 1.885 -1.981 5.951 1.00 84.72 7 A 1 ATOM 56 N N . LEU A 1 8 ? -0.571 0.756 2.226 1.00 93.50 8 A 1 ATOM 57 C CA . LEU A 1 8 ? -1.542 1.377 1.329 1.00 93.07 8 A 1 ATOM 58 C C . LEU A 1 8 ? -0.854 2.146 0.210 1.00 93.92 8 A 1 ATOM 59 O O . LEU A 1 8 ? -1.474 2.479 -0.801 1.00 92.97 8 A 1 ATOM 60 C CB . LEU A 1 8 ? -2.440 2.324 2.129 1.00 92.23 8 A 1 ATOM 61 C CG . LEU A 1 8 ? -3.855 2.438 1.574 1.00 88.37 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? -4.739 1.351 2.176 1.00 85.11 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? -4.441 3.810 1.876 1.00 84.77 8 A 1 ATOM 64 N N . GLY A 1 9 ? 0.421 2.443 0.402 1.00 93.66 9 A 1 ATOM 65 C CA . GLY A 1 9 ? 1.181 3.193 -0.593 1.00 93.25 9 A 1 ATOM 66 C C . GLY A 1 9 ? 1.703 2.315 -1.710 1.00 94.64 9 A 1 ATOM 67 O O . GLY A 1 9 ? 1.551 2.627 -2.887 1.00 93.82 9 A 1 ATOM 68 N N . LEU A 1 10 ? 2.322 1.199 -1.365 1.00 93.22 10 A 1 ATOM 69 C CA . LEU A 1 10 ? 2.883 0.271 -2.346 1.00 93.32 10 A 1 ATOM 70 C C . LEU A 1 10 ? 1.772 -0.460 -3.092 1.00 94.23 10 A 1 ATOM 71 O O . LEU A 1 10 ? 1.480 -0.145 -4.239 1.00 92.71 10 A 1 ATOM 72 C CB . LEU A 1 10 ? 3.799 -0.730 -1.637 1.00 92.32 10 A 1 ATOM 73 C CG . LEU A 1 10 ? 4.854 -0.070 -0.744 1.00 89.78 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? 5.765 -1.142 -0.151 1.00 86.24 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? 5.667 0.943 -1.526 1.00 85.17 10 A 1 ATOM 76 N N . LEU A 1 11 ? 1.172 -1.446 -2.457 1.00 93.29 11 A 1 ATOM 77 C CA . LEU A 1 11 ? 0.059 -2.198 -3.046 1.00 93.23 11 A 1 ATOM 78 C C . LEU A 1 11 ? -0.106 -3.553 -2.362 1.00 94.10 11 A 1 ATOM 79 O O . LEU A 1 11 ? 0.349 -4.577 -2.862 1.00 93.31 11 A 1 ATOM 80 C CB . LEU A 1 11 ? 0.291 -2.414 -4.538 1.00 92.08 11 A 1 ATOM 81 C CG . LEU A 1 11 ? -1.006 -2.442 -5.336 1.00 88.06 11 A 1 ATOM 82 C CD1 . LEU A 1 11 ? -0.985 -1.348 -6.398 1.00 84.27 11 A 1 ATOM 83 C CD2 . LEU A 1 11 ? -1.208 -3.797 -5.982 1.00 83.77 11 A 1 ATOM 84 N N . PRO A 1 12 ? -0.770 -3.562 -1.214 1.00 93.53 12 A 1 ATOM 85 C CA . PRO A 1 12 ? -0.973 -4.798 -0.457 1.00 92.96 12 A 1 ATOM 86 C C . PRO A 1 12 ? -1.850 -5.798 -1.207 1.00 93.93 12 A 1 ATOM 87 O O . PRO A 1 12 ? -2.214 -5.582 -2.356 1.00 92.63 12 A 1 ATOM 88 C CB . PRO A 1 12 ? -1.654 -4.324 0.835 1.00 90.60 12 A 1 ATOM 89 C CG . PRO A 1 12 ? -2.021 -2.899 0.651 1.00 89.23 12 A 1 ATOM 90 C CD . PRO A 1 12 ? -1.317 -2.380 -0.575 1.00 92.87 12 A 1 ATOM 91 N N . THR A 1 13 ? -2.193 -6.895 -0.572 1.00 93.64 13 A 1 ATOM 92 C CA . THR A 1 13 ? -3.015 -7.938 -1.184 1.00 93.79 13 A 1 ATOM 93 C C . THR A 1 13 ? -4.507 -7.617 -1.087 1.00 94.55 13 A 1 ATOM 94 O O . THR A 1 13 ? -5.352 -8.503 -1.182 1.00 92.59 13 A 1 ATOM 95 C CB . THR A 1 13 ? -2.738 -9.275 -0.492 1.00 92.07 13 A 1 ATOM 96 O OG1 . THR A 1 13 ? -2.918 -9.131 0.912 1.00 86.59 13 A 1 ATOM 97 C CG2 . THR A 1 13 ? -1.312 -9.717 -0.754 1.00 85.12 13 A 1 ATOM 98 N N . ILE A 1 14 ? -4.821 -6.359 -0.896 1.00 94.22 14 A 1 ATOM 99 C CA . ILE A 1 14 ? -6.215 -5.939 -0.765 1.00 93.47 14 A 1 ATOM 100 C C . ILE A 1 14 ? -6.780 -5.485 -2.107 1.00 94.10 14 A 1 ATOM 101 O O . ILE A 1 14 ? -7.928 -5.759 -2.447 1.00 93.33 14 A 1 ATOM 102 C CB . ILE A 1 14 ? -6.346 -4.797 0.258 1.00 92.23 14 A 1 ATOM 103 C CG1 . ILE A 1 14 ? -5.613 -5.143 1.552 1.00 88.68 14 A 1 ATOM 104 C CG2 . ILE A 1 14 ? -7.821 -4.529 0.546 1.00 86.93 14 A 1 ATOM 105 C CD1 . ILE A 1 14 ? -5.607 -3.990 2.544 1.00 82.98 14 A 1 ATOM 106 N N . TYR A 1 15 ? -5.969 -4.779 -2.870 1.00 94.05 15 A 1 ATOM 107 C CA . TYR A 1 15 ? -6.396 -4.268 -4.174 1.00 93.21 15 A 1 ATOM 108 C C . TYR A 1 15 ? -6.530 -5.399 -5.189 1.00 93.65 15 A 1 ATOM 109 O O . TYR A 1 15 ? -7.536 -5.522 -5.883 1.00 92.81 15 A 1 ATOM 110 C CB . TYR A 1 15 ? -5.383 -3.238 -4.678 1.00 92.05 15 A 1 ATOM 111 C CG . TYR A 1 15 ? -5.096 -2.157 -3.655 1.00 89.10 15 A 1 ATOM 112 C CD1 . TYR A 1 15 ? -4.136 -2.337 -2.674 1.00 86.77 15 A 1 ATOM 113 C CD2 . TYR A 1 15 ? -5.798 -0.959 -3.688 1.00 86.39 15 A 1 ATOM 114 C CE1 . TYR A 1 15 ? -3.873 -1.346 -1.741 1.00 85.49 15 A 1 ATOM 115 C CE2 . TYR A 1 15 ? -5.538 0.042 -2.756 1.00 85.21 15 A 1 ATOM 116 C CZ . TYR A 1 15 ? -4.575 -0.160 -1.786 1.00 86.07 15 A 1 ATOM 117 O OH . TYR A 1 15 ? -4.314 0.821 -0.861 1.00 84.35 15 A 1 ATOM 118 N N . ALA A 1 16 ? -5.523 -6.228 -5.292 1.00 92.75 16 A 1 ATOM 119 C CA . ALA A 1 16 ? -5.539 -7.341 -6.231 1.00 91.13 16 A 1 ATOM 120 C C . ALA A 1 16 ? -4.989 -8.604 -5.584 1.00 89.43 16 A 1 ATOM 121 O O . ALA A 1 16 ? -4.068 -8.498 -4.762 1.00 85.94 16 A 1 ATOM 122 C CB . ALA A 1 16 ? -4.730 -6.985 -7.467 1.00 86.98 16 A 1 ATOM 123 O OXT . ALA A 1 16 ? -5.453 -9.707 -5.900 1.00 79.25 16 A 1 #