# 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_spkb11542 # _entry.id spkb11542 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "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" "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 GLN 2 1 n LEU 3 1 n LEU 4 1 n GLY 5 1 n LEU 6 1 n LEU 7 1 n GLY 8 1 n LEU 9 1 n LEU 10 1 n TRP 11 1 n MET 12 1 n LEU 13 1 n LYS 14 1 n ALA 15 # _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 @ 2025-07-09 12:03:22)" _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 90.70 _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 79.34 1 1 A GLN 2 2 79.37 1 2 A LEU 3 2 93.41 1 3 A LEU 4 2 93.06 1 4 A GLY 5 2 96.45 1 5 A LEU 6 2 95.15 1 6 A LEU 7 2 94.98 1 7 A GLY 8 2 96.78 1 8 A LEU 9 2 94.90 1 9 A LEU 10 2 95.06 1 10 A TRP 11 2 91.72 1 11 A MET 12 2 91.22 1 12 A LEU 13 2 93.74 1 13 A LYS 14 2 86.05 1 14 A ALA 15 2 84.93 1 15 # _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 GLN . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n GLY . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n GLY . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n TRP . 11 A 11 A 12 1 n MET . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LYS . 14 A 14 A 15 1 n ALA . 15 A 15 # _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 ? 11.087 0.859 5.312 1.00 86.47 1 A 1 ATOM 2 C CA . MET A 1 1 ? 10.209 1.603 4.382 1.00 86.39 1 A 1 ATOM 3 C C . MET A 1 1 ? 8.745 1.342 4.738 1.00 86.28 1 A 1 ATOM 4 O O . MET A 1 1 ? 8.154 0.372 4.296 1.00 82.93 1 A 1 ATOM 5 C CB . MET A 1 1 ? 10.483 1.151 2.950 1.00 80.91 1 A 1 ATOM 6 C CG . MET A 1 1 ? 11.865 1.599 2.509 1.00 77.22 1 A 1 ATOM 7 S SD . MET A 1 1 ? 12.198 1.096 0.816 1.00 72.20 1 A 1 ATOM 8 C CE . MET A 1 1 ? 13.834 1.762 0.623 1.00 62.29 1 A 1 ATOM 9 N N . GLN A 1 2 ? 8.201 2.205 5.559 1.00 84.04 2 A 1 ATOM 10 C CA . GLN A 1 2 ? 6.806 2.056 5.992 1.00 86.48 2 A 1 ATOM 11 C C . GLN A 1 2 ? 5.837 2.390 4.855 1.00 88.26 2 A 1 ATOM 12 O O . GLN A 1 2 ? 4.699 1.926 4.853 1.00 83.82 2 A 1 ATOM 13 C CB . GLN A 1 2 ? 6.564 2.977 7.183 1.00 82.46 2 A 1 ATOM 14 C CG . GLN A 1 2 ? 7.414 2.551 8.378 1.00 77.59 2 A 1 ATOM 15 C CD . GLN A 1 2 ? 7.360 3.607 9.466 1.00 76.00 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? 6.426 3.663 10.245 1.00 69.86 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? 8.339 4.471 9.523 1.00 65.82 2 A 1 ATOM 18 N N . LEU A 1 3 ? 6.291 3.176 3.898 1.00 94.37 3 A 1 ATOM 19 C CA . LEU A 1 3 ? 5.455 3.540 2.748 1.00 95.45 3 A 1 ATOM 20 C C . LEU A 1 3 ? 5.067 2.305 1.946 1.00 96.21 3 A 1 ATOM 21 O O . LEU A 1 3 ? 3.952 2.213 1.436 1.00 95.59 3 A 1 ATOM 22 C CB . LEU A 1 3 ? 6.222 4.528 1.869 1.00 95.23 3 A 1 ATOM 23 C CG . LEU A 1 3 ? 5.779 5.967 2.112 1.00 93.23 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? 6.790 6.918 1.483 1.00 89.10 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? 4.407 6.202 1.508 1.00 88.09 3 A 1 ATOM 26 N N . LEU A 1 4 ? 5.974 1.343 1.858 1.00 95.37 4 A 1 ATOM 27 C CA . LEU A 1 4 ? 5.698 0.110 1.116 1.00 95.35 4 A 1 ATOM 28 C C . LEU A 1 4 ? 4.520 -0.632 1.734 1.00 95.96 4 A 1 ATOM 29 O O . LEU A 1 4 ? 3.736 -1.259 1.028 1.00 95.49 4 A 1 ATOM 30 C CB . LEU A 1 4 ? 6.947 -0.766 1.124 1.00 94.95 4 A 1 ATOM 31 C CG . LEU A 1 4 ? 7.998 -0.289 0.124 1.00 92.48 4 A 1 ATOM 32 C CD1 . LEU A 1 4 ? 9.300 -1.031 0.366 1.00 88.18 4 A 1 ATOM 33 C CD2 . LEU A 1 4 ? 7.521 -0.552 -1.303 1.00 86.74 4 A 1 ATOM 34 N N . GLY A 1 5 ? 4.390 -0.542 3.047 1.00 95.86 5 A 1 ATOM 35 C CA . GLY A 1 5 ? 3.268 -1.182 3.736 1.00 96.35 5 A 1 ATOM 36 C C . GLY A 1 5 ? 1.945 -0.576 3.301 1.00 97.01 5 A 1 ATOM 37 O O . GLY A 1 5 ? 0.967 -1.285 3.077 1.00 96.60 5 A 1 ATOM 38 N N . LEU A 1 6 ? 1.926 0.738 3.173 1.00 96.62 6 A 1 ATOM 39 C CA . LEU A 1 6 ? 0.715 1.437 2.735 1.00 96.95 6 A 1 ATOM 40 C C . LEU A 1 6 ? 0.392 1.080 1.288 1.00 97.23 6 A 1 ATOM 41 O O . LEU A 1 6 ? -0.771 0.881 0.941 1.00 97.06 6 A 1 ATOM 42 C CB . LEU A 1 6 ? 0.932 2.945 2.873 1.00 97.01 6 A 1 ATOM 43 C CG . LEU A 1 6 ? 0.786 3.417 4.318 1.00 94.61 6 A 1 ATOM 44 C CD1 . LEU A 1 6 ? 1.387 4.804 4.471 1.00 90.91 6 A 1 ATOM 45 C CD2 . LEU A 1 6 ? -0.692 3.459 4.705 1.00 90.77 6 A 1 ATOM 46 N N . LEU A 1 7 ? 1.422 0.989 0.476 1.00 97.00 7 A 1 ATOM 47 C CA . LEU A 1 7 ? 1.235 0.639 -0.931 1.00 96.64 7 A 1 ATOM 48 C C . LEU A 1 7 ? 0.674 -0.772 -1.051 1.00 96.75 7 A 1 ATOM 49 O O . LEU A 1 7 ? -0.193 -1.041 -1.875 1.00 96.51 7 A 1 ATOM 50 C CB . LEU A 1 7 ? 2.576 0.759 -1.664 1.00 96.50 7 A 1 ATOM 51 C CG . LEU A 1 7 ? 2.737 2.068 -2.439 1.00 94.45 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? 1.770 2.107 -3.605 1.00 90.99 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? 2.513 3.268 -1.536 1.00 90.98 7 A 1 ATOM 54 N N . GLY A 1 8 ? 1.171 -1.666 -0.215 1.00 96.75 8 A 1 ATOM 55 C CA . GLY A 1 8 ? 0.683 -3.045 -0.222 1.00 96.61 8 A 1 ATOM 56 C C . GLY A 1 8 ? -0.781 -3.108 0.188 1.00 97.03 8 A 1 ATOM 57 O O . GLY A 1 8 ? -1.569 -3.847 -0.399 1.00 96.74 8 A 1 ATOM 58 N N . LEU A 1 9 ? -1.145 -2.324 1.200 1.00 96.63 9 A 1 ATOM 59 C CA . LEU A 1 9 ? -2.536 -2.270 1.654 1.00 96.69 9 A 1 ATOM 60 C C . LEU A 1 9 ? -3.434 -1.731 0.550 1.00 97.07 9 A 1 ATOM 61 O O . LEU A 1 9 ? -4.522 -2.257 0.317 1.00 96.70 9 A 1 ATOM 62 C CB . LEU A 1 9 ? -2.615 -1.374 2.888 1.00 96.64 9 A 1 ATOM 63 C CG . LEU A 1 9 ? -2.666 -2.195 4.172 1.00 94.05 9 A 1 ATOM 64 C CD1 . LEU A 1 9 ? -2.070 -1.404 5.325 1.00 90.55 9 A 1 ATOM 65 C CD2 . LEU A 1 9 ? -4.106 -2.561 4.488 1.00 90.88 9 A 1 ATOM 66 N N . LEU A 1 10 ? -2.970 -0.695 -0.116 1.00 97.23 10 A 1 ATOM 67 C CA . LEU A 1 10 ? -3.724 -0.118 -1.229 1.00 97.04 10 A 1 ATOM 68 C C . LEU A 1 10 ? -3.892 -1.137 -2.340 1.00 96.97 10 A 1 ATOM 69 O O . LEU A 1 10 ? -4.954 -1.226 -2.951 1.00 96.64 10 A 1 ATOM 70 C CB . LEU A 1 10 ? -2.982 1.109 -1.749 1.00 97.10 10 A 1 ATOM 71 C CG . LEU A 1 10 ? -3.569 2.401 -1.196 1.00 94.71 10 A 1 ATOM 72 C CD1 . LEU A 1 10 ? -2.564 3.533 -1.349 1.00 89.95 10 A 1 ATOM 73 C CD2 . LEU A 1 10 ? -4.850 2.750 -1.944 1.00 90.88 10 A 1 ATOM 74 N N . TRP A 1 11 ? -2.850 -1.923 -2.580 1.00 96.66 11 A 1 ATOM 75 C CA . TRP A 1 11 ? -2.894 -2.950 -3.621 1.00 96.06 11 A 1 ATOM 76 C C . TRP A 1 11 ? -3.952 -3.996 -3.278 1.00 96.18 11 A 1 ATOM 77 O O . TRP A 1 11 ? -4.691 -4.446 -4.146 1.00 95.24 11 A 1 ATOM 78 C CB . TRP A 1 11 ? -1.521 -3.596 -3.738 1.00 95.70 11 A 1 ATOM 79 C CG . TRP A 1 11 ? -1.213 -3.962 -5.150 1.00 93.76 11 A 1 ATOM 80 C CD1 . TRP A 1 11 ? -0.731 -3.130 -6.101 1.00 88.86 11 A 1 ATOM 81 C CD2 . TRP A 1 11 ? -1.370 -5.253 -5.781 1.00 91.68 11 A 1 ATOM 82 N NE1 . TRP A 1 11 ? -0.574 -3.822 -7.288 1.00 89.01 11 A 1 ATOM 83 C CE2 . TRP A 1 11 ? -0.957 -5.124 -7.120 1.00 92.00 11 A 1 ATOM 84 C CE3 . TRP A 1 11 ? -1.816 -6.500 -5.328 1.00 89.81 11 A 1 ATOM 85 C CZ2 . TRP A 1 11 ? -0.984 -6.208 -8.006 1.00 89.56 11 A 1 ATOM 86 C CZ3 . TRP A 1 11 ? -1.844 -7.582 -6.216 1.00 84.36 11 A 1 ATOM 87 C CH2 . TRP A 1 11 ? -1.432 -7.426 -7.538 1.00 85.20 11 A 1 ATOM 88 N N . MET A 1 12 ? -4.032 -4.358 -2.012 1.00 96.20 12 A 1 ATOM 89 C CA . MET A 1 12 ? -5.034 -5.331 -1.565 1.00 95.75 12 A 1 ATOM 90 C C . MET A 1 12 ? -6.436 -4.738 -1.642 1.00 95.94 12 A 1 ATOM 91 O O . MET A 1 12 ? -7.372 -5.410 -2.070 1.00 94.08 12 A 1 ATOM 92 C CB . MET A 1 12 ? -4.725 -5.757 -0.135 1.00 94.75 12 A 1 ATOM 93 C CG . MET A 1 12 ? -3.642 -6.810 -0.112 1.00 91.94 12 A 1 ATOM 94 S SD . MET A 1 12 ? -3.351 -7.431 1.553 1.00 84.73 12 A 1 ATOM 95 C CE . MET A 1 12 ? -4.656 -8.634 1.665 1.00 76.35 12 A 1 ATOM 96 N N . LEU A 1 13 ? -6.572 -3.494 -1.211 1.00 95.95 13 A 1 ATOM 97 C CA . LEU A 1 13 ? -7.867 -2.813 -1.265 1.00 96.09 13 A 1 ATOM 98 C C . LEU A 1 13 ? -8.282 -2.565 -2.706 1.00 96.13 13 A 1 ATOM 99 O O . LEU A 1 13 ? -9.437 -2.774 -3.078 1.00 94.88 13 A 1 ATOM 100 C CB . LEU A 1 13 ? -7.771 -1.488 -0.514 1.00 96.04 13 A 1 ATOM 101 C CG . LEU A 1 13 ? -8.738 -1.440 0.664 1.00 93.99 13 A 1 ATOM 102 C CD1 . LEU A 1 13 ? -8.023 -1.833 1.948 1.00 88.96 13 A 1 ATOM 103 C CD2 . LEU A 1 13 ? -9.321 -0.045 0.795 1.00 87.84 13 A 1 ATOM 104 N N . LYS A 1 14 ? -7.332 -2.123 -3.499 1.00 93.93 14 A 1 ATOM 105 C CA . LYS A 1 14 ? -7.584 -1.856 -4.913 1.00 92.66 14 A 1 ATOM 106 C C . LYS A 1 14 ? -7.307 -3.124 -5.711 1.00 91.72 14 A 1 ATOM 107 O O . LYS A 1 14 ? -6.225 -3.298 -6.256 1.00 89.73 14 A 1 ATOM 108 C CB . LYS A 1 14 ? -6.687 -0.711 -5.359 1.00 90.54 14 A 1 ATOM 109 C CG . LYS A 1 14 ? -7.102 -0.163 -6.704 1.00 84.63 14 A 1 ATOM 110 C CD . LYS A 1 14 ? -8.095 0.975 -6.528 1.00 82.91 14 A 1 ATOM 111 C CE . LYS A 1 14 ? -8.491 1.549 -7.870 1.00 77.76 14 A 1 ATOM 112 N NZ . LYS A 1 14 ? -9.389 2.703 -7.698 1.00 70.60 14 A 1 ATOM 113 N N . ALA A 1 15 ? -8.287 -3.999 -5.746 1.00 91.80 15 A 1 ATOM 114 C CA . ALA A 1 15 ? -8.150 -5.260 -6.477 1.00 89.38 15 A 1 ATOM 115 C C . ALA A 1 15 ? -7.710 -5.006 -7.917 1.00 86.40 15 A 1 ATOM 116 O O . ALA A 1 15 ? -6.799 -5.712 -8.387 1.00 83.01 15 A 1 ATOM 117 C CB . ALA A 1 15 ? -9.481 -6.010 -6.445 1.00 84.07 15 A 1 ATOM 118 O OXT . ALA A 1 15 ? -8.238 -4.091 -8.548 1.00 74.91 15 A 1 #