# 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_spkb16981 # _entry.id spkb16981 # 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" "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" "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 PHE 5 1 n SER 6 1 n ALA 7 1 n ALA 8 1 n ALA 9 1 n LEU 10 1 n SER 11 1 n LEU 12 1 n ALA 13 1 n VAL 14 1 n GLY 15 1 n GLN 16 1 n ALA 17 1 n SER 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 @ 2025-07-06 21:03:16)" _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 87.37 _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 82.71 1 1 A LYS 2 2 81.88 1 2 A GLY 3 2 91.39 1 3 A LEU 4 2 88.88 1 4 A PHE 5 2 84.37 1 5 A SER 6 2 88.11 1 6 A ALA 7 2 91.12 1 7 A ALA 8 2 92.58 1 8 A ALA 9 2 90.43 1 9 A LEU 10 2 86.72 1 10 A SER 11 2 89.19 1 11 A LEU 12 2 88.55 1 12 A ALA 13 2 92.51 1 13 A VAL 14 2 91.09 1 14 A GLY 15 2 91.56 1 15 A GLN 16 2 85.98 1 16 A ALA 17 2 90.71 1 17 A SER 18 2 84.44 1 18 A ALA 19 2 80.23 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 LYS . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n GLY . 15 A 15 A 16 1 n GLN . 16 A 16 A 17 1 n ALA . 17 A 17 A 18 1 n SER . 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 ? -13.010 0.718 6.013 1.00 86.47 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.615 0.695 6.482 1.00 88.27 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.679 0.043 5.464 1.00 89.16 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.473 -0.014 5.672 1.00 85.92 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.534 -0.072 7.803 1.00 83.11 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.170 0.697 8.944 1.00 82.69 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.005 -0.161 10.503 1.00 78.98 1 A 1 ATOM 8 C CE . MET A 1 1 ? -12.590 1.099 11.609 1.00 67.09 1 A 1 ATOM 9 N N . LYS A 1 2 ? -11.236 -0.428 4.380 1.00 87.45 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -10.436 -1.071 3.335 1.00 89.04 2 A 1 ATOM 11 C C . LYS A 1 2 ? -9.473 -0.081 2.684 1.00 89.76 2 A 1 ATOM 12 O O . LYS A 1 2 ? -8.304 -0.389 2.468 1.00 87.42 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -11.358 -1.677 2.273 1.00 85.62 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -11.339 -3.189 2.275 1.00 80.91 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -12.272 -3.757 1.227 1.00 78.87 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -11.928 -5.200 0.923 1.00 72.25 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -12.866 -5.775 -0.077 1.00 65.58 2 A 1 ATOM 18 N N . GLY A 1 3 ? -9.966 1.110 2.376 1.00 89.43 3 A 1 ATOM 19 C CA . GLY A 1 3 ? -9.139 2.133 1.741 1.00 91.14 3 A 1 ATOM 20 C C . GLY A 1 3 ? -8.007 2.608 2.636 1.00 93.42 3 A 1 ATOM 21 O O . GLY A 1 3 ? -6.961 3.036 2.154 1.00 91.58 3 A 1 ATOM 22 N N . LEU A 1 4 ? -8.205 2.531 3.940 1.00 90.21 4 A 1 ATOM 23 C CA . LEU A 1 4 ? -7.192 2.949 4.909 1.00 91.85 4 A 1 ATOM 24 C C . LEU A 1 4 ? -5.935 2.087 4.786 1.00 93.43 4 A 1 ATOM 25 O O . LEU A 1 4 ? -4.813 2.589 4.775 1.00 91.47 4 A 1 ATOM 26 C CB . LEU A 1 4 ? -7.754 2.851 6.336 1.00 90.27 4 A 1 ATOM 27 C CG . LEU A 1 4 ? -7.212 3.897 7.304 1.00 87.26 4 A 1 ATOM 28 C CD1 . LEU A 1 4 ? -5.697 3.823 7.401 1.00 84.61 4 A 1 ATOM 29 C CD2 . LEU A 1 4 ? -7.655 5.285 6.878 1.00 81.96 4 A 1 ATOM 30 N N . PHE A 1 5 ? -6.132 0.778 4.687 1.00 85.65 5 A 1 ATOM 31 C CA . PHE A 1 5 ? -5.016 -0.162 4.570 1.00 86.40 5 A 1 ATOM 32 C C . PHE A 1 5 ? -4.280 0.036 3.250 1.00 88.92 5 A 1 ATOM 33 O O . PHE A 1 5 ? -3.046 0.024 3.203 1.00 86.78 5 A 1 ATOM 34 C CB . PHE A 1 5 ? -5.531 -1.598 4.657 1.00 85.16 5 A 1 ATOM 35 C CG . PHE A 1 5 ? -6.232 -1.887 5.958 1.00 85.32 5 A 1 ATOM 36 C CD1 . PHE A 1 5 ? -7.560 -1.543 6.132 1.00 82.55 5 A 1 ATOM 37 C CD2 . PHE A 1 5 ? -5.552 -2.503 6.998 1.00 82.58 5 A 1 ATOM 38 C CE1 . PHE A 1 5 ? -8.204 -1.799 7.334 1.00 81.73 5 A 1 ATOM 39 C CE2 . PHE A 1 5 ? -6.193 -2.767 8.199 1.00 81.60 5 A 1 ATOM 40 C CZ . PHE A 1 5 ? -7.522 -2.413 8.366 1.00 81.40 5 A 1 ATOM 41 N N . SER A 1 6 ? -5.025 0.224 2.181 1.00 89.64 6 A 1 ATOM 42 C CA . SER A 1 6 ? -4.445 0.434 0.854 1.00 90.45 6 A 1 ATOM 43 C C . SER A 1 6 ? -3.658 1.741 0.792 1.00 91.92 6 A 1 ATOM 44 O O . SER A 1 6 ? -2.565 1.793 0.227 1.00 90.38 6 A 1 ATOM 45 C CB . SER A 1 6 ? -5.545 0.445 -0.203 1.00 88.00 6 A 1 ATOM 46 O OG . SER A 1 6 ? -6.159 -0.824 -0.290 1.00 78.26 6 A 1 ATOM 47 N N . ALA A 1 7 ? -4.205 2.796 1.373 1.00 90.44 7 A 1 ATOM 48 C CA . ALA A 1 7 ? -3.553 4.105 1.381 1.00 91.55 7 A 1 ATOM 49 C C . ALA A 1 7 ? -2.217 4.058 2.121 1.00 93.07 7 A 1 ATOM 50 O O . ALA A 1 7 ? -1.216 4.594 1.646 1.00 91.11 7 A 1 ATOM 51 C CB . ALA A 1 7 ? -4.476 5.133 2.025 1.00 89.45 7 A 1 ATOM 52 N N . ALA A 1 8 ? -2.204 3.411 3.270 1.00 92.32 8 A 1 ATOM 53 C CA . ALA A 1 8 ? -0.987 3.294 4.071 1.00 92.54 8 A 1 ATOM 54 C C . ALA A 1 8 ? 0.067 2.453 3.361 1.00 93.83 8 A 1 ATOM 55 O O . ALA A 1 8 ? 1.249 2.802 3.351 1.00 92.55 8 A 1 ATOM 56 C CB . ALA A 1 8 ? -1.322 2.674 5.423 1.00 91.66 8 A 1 ATOM 57 N N . ALA A 1 9 ? -0.357 1.348 2.760 1.00 90.43 9 A 1 ATOM 58 C CA . ALA A 1 9 ? 0.548 0.452 2.047 1.00 90.44 9 A 1 ATOM 59 C C . ALA A 1 9 ? 1.163 1.131 0.827 1.00 92.09 9 A 1 ATOM 60 O O . ALA A 1 9 ? 2.356 0.986 0.565 1.00 90.03 9 A 1 ATOM 61 C CB . ALA A 1 9 ? -0.201 -0.805 1.621 1.00 89.16 9 A 1 ATOM 62 N N . LEU A 1 10 ? 0.352 1.871 0.080 1.00 89.64 10 A 1 ATOM 63 C CA . LEU A 1 10 ? 0.820 2.569 -1.118 1.00 89.28 10 A 1 ATOM 64 C C . LEU A 1 10 ? 1.852 3.635 -0.772 1.00 91.89 10 A 1 ATOM 65 O O . LEU A 1 10 ? 2.905 3.721 -1.405 1.00 89.95 10 A 1 ATOM 66 C CB . LEU A 1 10 ? -0.365 3.214 -1.836 1.00 88.21 10 A 1 ATOM 67 C CG . LEU A 1 10 ? -1.230 2.240 -2.628 1.00 83.23 10 A 1 ATOM 68 C CD1 . LEU A 1 10 ? -2.561 2.887 -2.985 1.00 81.11 10 A 1 ATOM 69 C CD2 . LEU A 1 10 ? -0.510 1.791 -3.888 1.00 80.41 10 A 1 ATOM 70 N N . SER A 1 11 ? 1.558 4.445 0.219 1.00 90.83 11 A 1 ATOM 71 C CA . SER A 1 11 ? 2.458 5.515 0.646 1.00 90.39 11 A 1 ATOM 72 C C . SER A 1 11 ? 3.788 4.959 1.150 1.00 92.24 11 A 1 ATOM 73 O O . SER A 1 11 ? 4.854 5.471 0.808 1.00 91.36 11 A 1 ATOM 74 C CB . SER A 1 11 ? 1.804 6.351 1.743 1.00 89.30 11 A 1 ATOM 75 O OG . SER A 1 11 ? 2.605 7.465 2.054 1.00 81.00 11 A 1 ATOM 76 N N . LEU A 1 12 ? 3.719 3.909 1.937 1.00 91.87 12 A 1 ATOM 77 C CA . LEU A 1 12 ? 4.924 3.285 2.487 1.00 91.81 12 A 1 ATOM 78 C C . LEU A 1 12 ? 5.748 2.607 1.400 1.00 93.88 12 A 1 ATOM 79 O O . LEU A 1 12 ? 6.972 2.739 1.367 1.00 93.06 12 A 1 ATOM 80 C CB . LEU A 1 12 ? 4.535 2.255 3.545 1.00 90.99 12 A 1 ATOM 81 C CG . LEU A 1 12 ? 5.722 1.725 4.344 1.00 83.92 12 A 1 ATOM 82 C CD1 . LEU A 1 12 ? 6.207 2.775 5.331 1.00 81.33 12 A 1 ATOM 83 C CD2 . LEU A 1 12 ? 5.333 0.450 5.074 1.00 81.51 12 A 1 ATOM 84 N N . ALA A 1 13 ? 5.084 1.880 0.510 1.00 92.57 13 A 1 ATOM 85 C CA . ALA A 1 13 ? 5.756 1.169 -0.574 1.00 92.34 13 A 1 ATOM 86 C C . ALA A 1 13 ? 6.490 2.129 -1.504 1.00 93.92 13 A 1 ATOM 87 O O . ALA A 1 13 ? 7.644 1.895 -1.861 1.00 92.43 13 A 1 ATOM 88 C CB . ALA A 1 13 ? 4.740 0.351 -1.365 1.00 91.31 13 A 1 ATOM 89 N N . VAL A 1 14 ? 5.830 3.211 -1.901 1.00 92.93 14 A 1 ATOM 90 C CA . VAL A 1 14 ? 6.423 4.204 -2.800 1.00 93.01 14 A 1 ATOM 91 C C . VAL A 1 14 ? 7.597 4.916 -2.136 1.00 94.13 14 A 1 ATOM 92 O O . VAL A 1 14 ? 8.647 5.113 -2.753 1.00 93.02 14 A 1 ATOM 93 C CB . VAL A 1 14 ? 5.370 5.231 -3.241 1.00 91.64 14 A 1 ATOM 94 C CG1 . VAL A 1 14 ? 6.011 6.323 -4.090 1.00 85.60 14 A 1 ATOM 95 C CG2 . VAL A 1 14 ? 4.259 4.549 -4.023 1.00 87.29 14 A 1 ATOM 96 N N . GLY A 1 15 ? 7.420 5.302 -0.891 1.00 91.74 15 A 1 ATOM 97 C CA . GLY A 1 15 ? 8.467 5.998 -0.152 1.00 90.77 15 A 1 ATOM 98 C C . GLY A 1 15 ? 9.696 5.140 0.083 1.00 92.40 15 A 1 ATOM 99 O O . GLY A 1 15 ? 10.826 5.582 -0.122 1.00 91.32 15 A 1 ATOM 100 N N . GLN A 1 16 ? 9.489 3.909 0.484 1.00 92.18 16 A 1 ATOM 101 C CA . GLN A 1 16 ? 10.596 2.989 0.761 1.00 92.03 16 A 1 ATOM 102 C C . GLN A 1 16 ? 11.270 2.514 -0.522 1.00 92.62 16 A 1 ATOM 103 O O . GLN A 1 16 ? 12.494 2.390 -0.575 1.00 90.44 16 A 1 ATOM 104 C CB . GLN A 1 16 ? 10.090 1.784 1.554 1.00 90.50 16 A 1 ATOM 105 C CG . GLN A 1 16 ? 9.798 2.127 3.001 1.00 84.45 16 A 1 ATOM 106 C CD . GLN A 1 16 ? 9.901 0.916 3.902 1.00 81.06 16 A 1 ATOM 107 O OE1 . GLN A 1 16 ? 10.981 0.497 4.284 1.00 76.18 16 A 1 ATOM 108 N NE2 . GLN A 1 16 ? 8.775 0.311 4.234 1.00 74.38 16 A 1 ATOM 109 N N . ALA A 1 17 ? 10.491 2.257 -1.557 1.00 92.18 17 A 1 ATOM 110 C CA . ALA A 1 17 ? 11.029 1.798 -2.836 1.00 91.10 17 A 1 ATOM 111 C C . ALA A 1 17 ? 11.908 2.860 -3.491 1.00 92.17 17 A 1 ATOM 112 O O . ALA A 1 17 ? 12.905 2.535 -4.138 1.00 89.39 17 A 1 ATOM 113 C CB . ALA A 1 17 ? 9.890 1.412 -3.773 1.00 88.71 17 A 1 ATOM 114 N N . SER A 1 18 ? 11.541 4.129 -3.336 1.00 89.47 18 A 1 ATOM 115 C CA . SER A 1 18 ? 12.290 5.244 -3.920 1.00 87.85 18 A 1 ATOM 116 C C . SER A 1 18 ? 13.430 5.715 -3.021 1.00 87.53 18 A 1 ATOM 117 O O . SER A 1 18 ? 14.414 6.283 -3.496 1.00 82.89 18 A 1 ATOM 118 C CB . SER A 1 18 ? 11.352 6.416 -4.203 1.00 84.69 18 A 1 ATOM 119 O OG . SER A 1 18 ? 10.451 6.102 -5.243 1.00 74.20 18 A 1 ATOM 120 N N . ALA A 1 19 ? 13.289 5.499 -1.730 1.00 86.70 19 A 1 ATOM 121 C CA . ALA A 1 19 ? 14.293 5.931 -0.768 1.00 84.63 19 A 1 ATOM 122 C C . ALA A 1 19 ? 15.373 4.871 -0.558 1.00 82.60 19 A 1 ATOM 123 O O . ALA A 1 19 ? 15.256 3.763 -1.098 1.00 77.50 19 A 1 ATOM 124 C CB . ALA A 1 19 ? 13.622 6.278 0.557 1.00 78.41 19 A 1 ATOM 125 O OXT . ALA A 1 19 ? 16.328 5.157 0.178 1.00 71.53 19 A 1 #