# 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_spkb11493 # _entry.id spkb11493 # 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 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" "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" "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 GLY 2 1 n GLY 3 1 n ALA 4 1 n LEU 5 1 n GLY 6 1 n PRO 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n THR 12 1 n SER 13 1 n LEU 14 1 n LEU 15 1 n GLY 16 1 n ALA 17 1 n TRP 18 1 n ALA 19 # _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 11:36:45)" _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 90.36 _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 71.20 1 1 A GLY 2 2 80.03 1 2 A GLY 3 2 85.58 1 3 A ALA 4 2 88.64 1 4 A LEU 5 2 86.93 1 5 A GLY 6 2 93.45 1 6 A PRO 7 2 93.51 1 7 A ALA 8 2 94.47 1 8 A LEU 9 2 93.67 1 9 A LEU 10 2 93.97 1 10 A LEU 11 2 93.72 1 11 A THR 12 2 93.70 1 12 A SER 13 2 95.53 1 13 A LEU 14 2 95.34 1 14 A LEU 15 2 94.54 1 15 A GLY 16 2 96.41 1 16 A ALA 17 2 96.38 1 17 A TRP 18 2 87.41 1 18 A ALA 19 2 85.74 1 19 # _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 GLY . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n PRO . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n GLY . 16 A 16 A 17 1 n ALA . 17 A 17 A 18 1 n TRP . 18 A 18 A 19 1 n ALA . 19 A 19 # _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 ? -0.133 16.732 7.561 1.00 75.59 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.345 15.475 8.174 1.00 76.39 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.839 14.694 8.729 1.00 77.21 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.782 15.283 9.229 1.00 72.13 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.311 15.791 9.313 1.00 71.92 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.533 16.530 8.808 1.00 69.92 1 A 1 ATOM 7 S SD . MET A 1 1 ? 3.608 17.030 10.157 1.00 67.19 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.818 17.959 9.231 1.00 59.25 1 A 1 ATOM 9 N N . GLY A 1 2 ? -0.780 13.415 8.630 1.00 77.84 2 A 1 ATOM 10 C CA . GLY A 1 2 ? -1.853 12.574 9.128 1.00 80.00 2 A 1 ATOM 11 C C . GLY A 1 2 ? -2.025 11.346 8.255 1.00 83.22 2 A 1 ATOM 12 O O . GLY A 1 2 ? -1.469 11.260 7.159 1.00 79.04 2 A 1 ATOM 13 N N . GLY A 1 3 ? -2.806 10.403 8.732 1.00 81.44 3 A 1 ATOM 14 C CA . GLY A 1 3 ? -3.035 9.176 7.977 1.00 85.24 3 A 1 ATOM 15 C C . GLY A 1 3 ? -1.783 8.323 7.894 1.00 88.89 3 A 1 ATOM 16 O O . GLY A 1 3 ? -1.297 8.032 6.806 1.00 86.74 3 A 1 ATOM 17 N N . ALA A 1 4 ? -1.262 7.929 9.020 1.00 85.18 4 A 1 ATOM 18 C CA . ALA A 1 4 ? -0.076 7.086 9.083 1.00 89.30 4 A 1 ATOM 19 C C . ALA A 1 4 ? -0.472 5.690 9.553 1.00 92.28 4 A 1 ATOM 20 O O . ALA A 1 4 ? -1.542 5.497 10.126 1.00 90.52 4 A 1 ATOM 21 C CB . ALA A 1 4 ? 0.949 7.702 10.028 1.00 85.91 4 A 1 ATOM 22 N N . LEU A 1 5 ? 0.409 4.746 9.306 1.00 88.86 5 A 1 ATOM 23 C CA . LEU A 1 5 ? 0.162 3.356 9.718 1.00 89.81 5 A 1 ATOM 24 C C . LEU A 1 5 ? -0.988 2.744 8.931 1.00 91.99 5 A 1 ATOM 25 O O . LEU A 1 5 ? -0.818 1.726 8.270 1.00 90.13 5 A 1 ATOM 26 C CB . LEU A 1 5 ? -0.142 3.313 11.223 1.00 87.70 5 A 1 ATOM 27 C CG . LEU A 1 5 ? 1.023 3.806 12.078 1.00 85.42 5 A 1 ATOM 28 C CD1 . LEU A 1 5 ? 0.523 4.358 13.403 1.00 82.46 5 A 1 ATOM 29 C CD2 . LEU A 1 5 ? 1.999 2.667 12.313 1.00 79.05 5 A 1 ATOM 30 N N . GLY A 1 6 ? -2.151 3.373 9.006 1.00 91.80 6 A 1 ATOM 31 C CA . GLY A 1 6 ? -3.324 2.887 8.285 1.00 92.56 6 A 1 ATOM 32 C C . GLY A 1 6 ? -3.089 2.806 6.789 1.00 94.71 6 A 1 ATOM 33 O O . GLY A 1 6 ? -3.048 1.710 6.214 1.00 94.75 6 A 1 ATOM 34 N N . PRO A 1 7 ? -2.927 3.969 6.132 1.00 93.66 7 A 1 ATOM 35 C CA . PRO A 1 7 ? -2.675 3.991 4.685 1.00 94.64 7 A 1 ATOM 36 C C . PRO A 1 7 ? -1.428 3.206 4.320 1.00 95.67 7 A 1 ATOM 37 O O . PRO A 1 7 ? -1.384 2.560 3.271 1.00 94.71 7 A 1 ATOM 38 C CB . PRO A 1 7 ? -2.488 5.484 4.376 1.00 92.53 7 A 1 ATOM 39 C CG . PRO A 1 7 ? -3.192 6.186 5.489 1.00 90.55 7 A 1 ATOM 40 C CD . PRO A 1 7 ? -3.045 5.290 6.702 1.00 92.79 7 A 1 ATOM 41 N N . ALA A 1 8 ? -0.417 3.254 5.163 1.00 93.93 8 A 1 ATOM 42 C CA . ALA A 1 8 ? 0.823 2.526 4.914 1.00 94.59 8 A 1 ATOM 43 C C . ALA A 1 8 ? 0.544 1.030 4.809 1.00 95.79 8 A 1 ATOM 44 O O . ALA A 1 8 ? 1.072 0.347 3.930 1.00 94.67 8 A 1 ATOM 45 C CB . ALA A 1 8 ? 1.815 2.808 6.034 1.00 93.39 8 A 1 ATOM 46 N N . LEU A 1 9 ? -0.293 0.537 5.692 1.00 95.30 9 A 1 ATOM 47 C CA . LEU A 1 9 ? -0.655 -0.881 5.691 1.00 95.36 9 A 1 ATOM 48 C C . LEU A 1 9 ? -1.456 -1.219 4.440 1.00 96.25 9 A 1 ATOM 49 O O . LEU A 1 9 ? -1.261 -2.272 3.833 1.00 95.85 9 A 1 ATOM 50 C CB . LEU A 1 9 ? -1.474 -1.189 6.943 1.00 94.98 9 A 1 ATOM 51 C CG . LEU A 1 9 ? -0.630 -1.134 8.215 1.00 92.32 9 A 1 ATOM 52 C CD1 . LEU A 1 9 ? -1.528 -1.053 9.439 1.00 89.98 9 A 1 ATOM 53 C CD2 . LEU A 1 9 ? 0.262 -2.371 8.307 1.00 89.31 9 A 1 ATOM 54 N N . LEU A 1 10 ? -2.340 -0.316 4.055 1.00 95.29 10 A 1 ATOM 55 C CA . LEU A 1 10 ? -3.151 -0.531 2.856 1.00 95.16 10 A 1 ATOM 56 C C . LEU A 1 10 ? -2.265 -0.553 1.616 1.00 96.00 10 A 1 ATOM 57 O O . LEU A 1 10 ? -2.434 -1.399 0.736 1.00 95.99 10 A 1 ATOM 58 C CB . LEU A 1 10 ? -4.187 0.584 2.746 1.00 95.06 10 A 1 ATOM 59 C CG . LEU A 1 10 ? -5.226 0.524 3.868 1.00 92.81 10 A 1 ATOM 60 C CD1 . LEU A 1 10 ? -6.032 1.812 3.905 1.00 90.92 10 A 1 ATOM 61 C CD2 . LEU A 1 10 ? -6.157 -0.669 3.660 1.00 90.57 10 A 1 ATOM 62 N N . LEU A 1 11 ? -1.319 0.369 1.555 1.00 95.32 11 A 1 ATOM 63 C CA . LEU A 1 11 ? -0.402 0.441 0.419 1.00 95.06 11 A 1 ATOM 64 C C . LEU A 1 11 ? 0.438 -0.822 0.338 1.00 95.86 11 A 1 ATOM 65 O O . LEU A 1 11 ? 0.587 -1.411 -0.735 1.00 95.78 11 A 1 ATOM 66 C CB . LEU A 1 11 ? 0.495 1.669 0.576 1.00 94.61 11 A 1 ATOM 67 C CG . LEU A 1 11 ? -0.251 2.974 0.306 1.00 92.35 11 A 1 ATOM 68 C CD1 . LEU A 1 11 ? 0.560 4.158 0.815 1.00 90.62 11 A 1 ATOM 69 C CD2 . LEU A 1 11 ? -0.506 3.124 -1.192 1.00 90.13 11 A 1 ATOM 70 N N . THR A 1 12 ? 0.979 -1.234 1.452 1.00 95.92 12 A 1 ATOM 71 C CA . THR A 1 12 ? 1.805 -2.437 1.478 1.00 95.34 12 A 1 ATOM 72 C C . THR A 1 12 ? 0.961 -3.657 1.126 1.00 96.09 12 A 1 ATOM 73 O O . THR A 1 12 ? 1.451 -4.604 0.511 1.00 95.09 12 A 1 ATOM 74 C CB . THR A 1 12 ? 2.474 -2.602 2.850 1.00 93.94 12 A 1 ATOM 75 O OG1 . THR A 1 12 ? 3.448 -3.642 2.765 1.00 90.28 12 A 1 ATOM 76 C CG2 . THR A 1 12 ? 1.471 -2.979 3.922 1.00 89.22 12 A 1 ATOM 77 N N . SER A 1 13 ? -0.301 -3.606 1.481 1.00 96.68 13 A 1 ATOM 78 C CA . SER A 1 13 ? -1.223 -4.695 1.175 1.00 96.63 13 A 1 ATOM 79 C C . SER A 1 13 ? -1.383 -4.826 -0.333 1.00 97.22 13 A 1 ATOM 80 O O . SER A 1 13 ? -1.352 -5.932 -0.879 1.00 96.35 13 A 1 ATOM 81 C CB . SER A 1 13 ? -2.581 -4.430 1.823 1.00 95.88 13 A 1 ATOM 82 O OG . SER A 1 13 ? -3.388 -5.572 1.713 1.00 90.40 13 A 1 ATOM 83 N N . LEU A 1 14 ? -1.535 -3.685 -0.997 1.00 96.67 14 A 1 ATOM 84 C CA . LEU A 1 14 ? -1.670 -3.675 -2.455 1.00 96.47 14 A 1 ATOM 85 C C . LEU A 1 14 ? -0.390 -4.191 -3.097 1.00 96.98 14 A 1 ATOM 86 O O . LEU A 1 14 ? -0.435 -5.008 -4.020 1.00 96.62 14 A 1 ATOM 87 C CB . LEU A 1 14 ? -1.961 -2.250 -2.921 1.00 96.18 14 A 1 ATOM 88 C CG . LEU A 1 14 ? -3.355 -1.772 -2.502 1.00 94.84 14 A 1 ATOM 89 C CD1 . LEU A 1 14 ? -3.471 -0.268 -2.658 1.00 92.65 14 A 1 ATOM 90 C CD2 . LEU A 1 14 ? -4.421 -2.470 -3.344 1.00 92.31 14 A 1 ATOM 91 N N . LEU A 1 15 ? 0.738 -3.715 -2.609 1.00 96.66 15 A 1 ATOM 92 C CA . LEU A 1 15 ? 2.029 -4.155 -3.132 1.00 96.21 15 A 1 ATOM 93 C C . LEU A 1 15 ? 2.186 -5.657 -2.944 1.00 96.57 15 A 1 ATOM 94 O O . LEU A 1 15 ? 2.645 -6.359 -3.846 1.00 95.92 15 A 1 ATOM 95 C CB . LEU A 1 15 ? 3.142 -3.404 -2.405 1.00 95.56 15 A 1 ATOM 96 C CG . LEU A 1 15 ? 3.274 -1.958 -2.882 1.00 93.74 15 A 1 ATOM 97 C CD1 . LEU A 1 15 ? 4.064 -1.132 -1.876 1.00 91.14 15 A 1 ATOM 98 C CD2 . LEU A 1 15 ? 3.956 -1.924 -4.244 1.00 90.55 15 A 1 ATOM 99 N N . GLY A 1 16 ? 1.793 -6.143 -1.794 1.00 96.70 16 A 1 ATOM 100 C CA . GLY A 1 16 ? 1.875 -7.571 -1.515 1.00 96.16 16 A 1 ATOM 101 C C . GLY A 1 16 ? 0.985 -8.365 -2.444 1.00 96.82 16 A 1 ATOM 102 O O . GLY A 1 16 ? 1.339 -9.463 -2.878 1.00 95.95 16 A 1 ATOM 103 N N . ALA A 1 17 ? -0.166 -7.798 -2.769 1.00 96.68 17 A 1 ATOM 104 C CA . ALA A 1 17 ? -1.105 -8.448 -3.682 1.00 96.63 17 A 1 ATOM 105 C C . ALA A 1 17 ? -0.481 -8.599 -5.068 1.00 97.18 17 A 1 ATOM 106 O O . ALA A 1 17 ? -0.668 -9.620 -5.734 1.00 95.86 17 A 1 ATOM 107 C CB . ALA A 1 17 ? -2.393 -7.633 -3.758 1.00 95.54 17 A 1 ATOM 108 N N . TRP A 1 18 ? 0.241 -7.556 -5.498 1.00 93.52 18 A 1 ATOM 109 C CA . TRP A 1 18 ? 0.906 -7.591 -6.807 1.00 92.08 18 A 1 ATOM 110 C C . TRP A 1 18 ? 2.216 -8.362 -6.720 1.00 92.59 18 A 1 ATOM 111 O O . TRP A 1 18 ? 2.649 -8.958 -7.703 1.00 91.41 18 A 1 ATOM 112 C CB . TRP A 1 18 ? 1.170 -6.163 -7.299 1.00 89.82 18 A 1 ATOM 113 C CG . TRP A 1 18 ? -0.008 -5.253 -7.100 1.00 87.89 18 A 1 ATOM 114 C CD1 . TRP A 1 18 ? -0.000 -4.022 -6.525 1.00 86.12 18 A 1 ATOM 115 C CD2 . TRP A 1 18 ? -1.380 -5.498 -7.471 1.00 87.93 18 A 1 ATOM 116 N NE1 . TRP A 1 18 ? -1.262 -3.488 -6.512 1.00 84.33 18 A 1 ATOM 117 C CE2 . TRP A 1 18 ? -2.140 -4.375 -7.083 1.00 86.06 18 A 1 ATOM 118 C CE3 . TRP A 1 18 ? -2.040 -6.569 -8.095 1.00 84.73 18 A 1 ATOM 119 C CZ2 . TRP A 1 18 ? -3.515 -4.295 -7.295 1.00 84.60 18 A 1 ATOM 120 C CZ3 . TRP A 1 18 ? -3.407 -6.488 -8.305 1.00 81.05 18 A 1 ATOM 121 C CH2 . TRP A 1 18 ? -4.136 -5.364 -7.909 1.00 81.66 18 A 1 ATOM 122 N N . ALA A 1 19 ? 2.836 -8.336 -5.576 1.00 92.97 19 A 1 ATOM 123 C CA . ALA A 1 19 ? 4.123 -8.992 -5.364 1.00 90.38 19 A 1 ATOM 124 C C . ALA A 1 19 ? 3.971 -10.517 -5.349 1.00 87.36 19 A 1 ATOM 125 O O . ALA A 1 19 ? 2.891 -11.040 -5.654 1.00 82.65 19 A 1 ATOM 126 C CB . ALA A 1 19 ? 4.733 -8.499 -4.060 1.00 84.76 19 A 1 ATOM 127 O OXT . ALA A 1 19 ? 4.950 -11.215 -5.039 1.00 76.31 19 A 1 #