# 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_spkb16351 # _entry.id spkb16351 # 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" "C4 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 ALA 3 1 n ARG 4 1 n LEU 5 1 n LEU 6 1 n VAL 7 1 n LEU 8 1 n LEU 9 1 n CYS 10 1 n ALA 11 1 n LEU 12 1 n ALA 13 1 n ALA 14 1 n THR 15 1 n ASP 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 @ 2025-07-03 13:30:01)" _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 90.89 _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 83.02 1 1 A LYS 2 2 86.61 1 2 A ALA 3 2 94.78 1 3 A ARG 4 2 85.53 1 4 A LEU 5 2 91.40 1 5 A LEU 6 2 92.40 1 6 A VAL 7 2 95.72 1 7 A LEU 8 2 93.05 1 8 A LEU 9 2 92.95 1 9 A CYS 10 2 94.62 1 10 A ALA 11 2 96.23 1 11 A LEU 12 2 93.22 1 12 A ALA 13 2 96.34 1 13 A ALA 14 2 96.65 1 14 A THR 15 2 91.72 1 15 A ASP 16 2 84.35 1 16 A ALA 17 2 87.49 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 LYS . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n THR . 15 A 15 A 16 1 n ASP . 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 ? -11.365 1.632 11.391 1.00 87.75 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.084 1.469 10.691 1.00 89.61 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.697 -0.005 10.613 1.00 92.00 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.091 -0.544 11.534 1.00 89.08 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.992 2.249 11.415 1.00 85.32 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.921 1.935 12.905 1.00 80.24 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.786 3.026 13.780 1.00 75.35 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.842 4.422 14.038 1.00 64.77 1 A 1 ATOM 9 N N . LYS A 1 2 ? -10.059 -0.634 9.535 1.00 91.71 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -9.747 -2.051 9.351 1.00 93.03 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.884 -2.266 8.107 1.00 93.63 2 A 1 ATOM 12 O O . LYS A 1 2 ? -7.924 -3.033 8.136 1.00 93.19 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -11.050 -2.845 9.241 1.00 92.19 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -10.801 -4.341 9.226 1.00 85.31 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -12.093 -5.109 9.021 1.00 82.91 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -11.803 -6.591 8.863 1.00 76.95 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -13.060 -7.353 8.650 1.00 70.55 2 A 1 ATOM 18 N N . ALA A 1 3 ? -9.222 -1.573 7.033 1.00 94.58 3 A 1 ATOM 19 C CA . ALA A 1 3 ? -8.480 -1.714 5.783 1.00 95.24 3 A 1 ATOM 20 C C . ALA A 1 3 ? -7.576 -0.506 5.535 1.00 96.03 3 A 1 ATOM 21 O O . ALA A 1 3 ? -7.901 0.371 4.738 1.00 94.38 3 A 1 ATOM 22 C CB . ALA A 1 3 ? -9.459 -1.893 4.634 1.00 93.67 3 A 1 ATOM 23 N N . ARG A 1 4 ? -6.466 -0.456 6.245 1.00 95.31 4 A 1 ATOM 24 C CA . ARG A 1 4 ? -5.507 0.640 6.101 1.00 95.86 4 A 1 ATOM 25 C C . ARG A 1 4 ? -4.111 0.113 5.797 1.00 96.45 4 A 1 ATOM 26 O O . ARG A 1 4 ? -3.352 0.733 5.059 1.00 95.13 4 A 1 ATOM 27 C CB . ARG A 1 4 ? -5.470 1.479 7.380 1.00 95.22 4 A 1 ATOM 28 C CG . ARG A 1 4 ? -6.698 2.367 7.524 1.00 89.85 4 A 1 ATOM 29 C CD . ARG A 1 4 ? -6.559 3.284 8.719 1.00 85.16 4 A 1 ATOM 30 N NE . ARG A 1 4 ? -7.757 4.106 8.912 1.00 78.16 4 A 1 ATOM 31 C CZ . ARG A 1 4 ? -8.034 5.185 8.189 1.00 74.37 4 A 1 ATOM 32 N NH1 . ARG A 1 4 ? -7.230 5.571 7.214 1.00 68.27 4 A 1 ATOM 33 N NH2 . ARG A 1 4 ? -9.132 5.876 8.441 1.00 67.10 4 A 1 ATOM 34 N N . LEU A 1 5 ? -3.775 -1.026 6.364 1.00 94.62 5 A 1 ATOM 35 C CA . LEU A 1 5 ? -2.474 -1.648 6.129 1.00 95.04 5 A 1 ATOM 36 C C . LEU A 1 5 ? -2.285 -1.978 4.652 1.00 95.74 5 A 1 ATOM 37 O O . LEU A 1 5 ? -1.196 -1.825 4.103 1.00 95.04 5 A 1 ATOM 38 C CB . LEU A 1 5 ? -2.341 -2.918 6.965 1.00 94.86 5 A 1 ATOM 39 C CG . LEU A 1 5 ? -1.547 -2.711 8.247 1.00 86.62 5 A 1 ATOM 40 C CD1 . LEU A 1 5 ? -2.364 -1.911 9.255 1.00 84.56 5 A 1 ATOM 41 C CD2 . LEU A 1 5 ? -1.131 -4.042 8.835 1.00 84.73 5 A 1 ATOM 42 N N . LEU A 1 6 ? -3.351 -2.425 4.026 1.00 95.80 6 A 1 ATOM 43 C CA . LEU A 1 6 ? -3.297 -2.775 2.607 1.00 95.50 6 A 1 ATOM 44 C C . LEU A 1 6 ? -2.957 -1.550 1.765 1.00 95.94 6 A 1 ATOM 45 O O . LEU A 1 6 ? -2.182 -1.633 0.813 1.00 95.53 6 A 1 ATOM 46 C CB . LEU A 1 6 ? -4.647 -3.352 2.170 1.00 95.32 6 A 1 ATOM 47 C CG . LEU A 1 6 ? -4.937 -4.734 2.753 1.00 88.13 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? -6.410 -5.076 2.594 1.00 86.59 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? -4.082 -5.789 2.059 1.00 86.41 6 A 1 ATOM 50 N N . VAL A 1 7 ? -3.543 -0.419 2.133 1.00 96.43 7 A 1 ATOM 51 C CA . VAL A 1 7 ? -3.297 0.830 1.408 1.00 96.65 7 A 1 ATOM 52 C C . VAL A 1 7 ? -1.842 1.260 1.577 1.00 96.80 7 A 1 ATOM 53 O O . VAL A 1 7 ? -1.183 1.664 0.616 1.00 96.29 7 A 1 ATOM 54 C CB . VAL A 1 7 ? -4.236 1.943 1.904 1.00 96.33 7 A 1 ATOM 55 C CG1 . VAL A 1 7 ? -3.981 3.242 1.153 1.00 93.83 7 A 1 ATOM 56 C CG2 . VAL A 1 7 ? -5.688 1.519 1.738 1.00 93.73 7 A 1 ATOM 57 N N . LEU A 1 8 ? -1.355 1.172 2.803 1.00 96.00 8 A 1 ATOM 58 C CA . LEU A 1 8 ? 0.022 1.557 3.100 1.00 95.68 8 A 1 ATOM 59 C C . LEU A 1 8 ? 1.003 0.658 2.355 1.00 95.98 8 A 1 ATOM 60 O O . LEU A 1 8 ? 1.981 1.136 1.773 1.00 95.35 8 A 1 ATOM 61 C CB . LEU A 1 8 ? 0.264 1.466 4.610 1.00 95.57 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -0.456 2.545 5.414 1.00 90.28 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? -0.512 2.163 6.891 1.00 87.70 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? 0.251 3.887 5.259 1.00 87.86 8 A 1 ATOM 65 N N . LEU A 1 9 ? 0.738 -0.630 2.376 1.00 95.77 9 A 1 ATOM 66 C CA . LEU A 1 9 ? 1.595 -1.599 1.704 1.00 95.74 9 A 1 ATOM 67 C C . LEU A 1 9 ? 1.551 -1.397 0.194 1.00 96.25 9 A 1 ATOM 68 O O . LEU A 1 9 ? 2.565 -1.511 -0.492 1.00 95.73 9 A 1 ATOM 69 C CB . LEU A 1 9 ? 1.159 -3.025 2.071 1.00 95.41 9 A 1 ATOM 70 C CG . LEU A 1 9 ? 1.987 -3.651 3.194 1.00 90.18 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? 3.412 -3.898 2.722 1.00 87.34 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? 1.991 -2.769 4.429 1.00 87.20 9 A 1 ATOM 73 N N . CYS A 1 10 ? 0.375 -1.095 -0.309 1.00 95.62 10 A 1 ATOM 74 C CA . CYS A 1 10 ? 0.199 -0.880 -1.743 1.00 95.79 10 A 1 ATOM 75 C C . CYS A 1 10 ? 0.992 0.345 -2.200 1.00 96.17 10 A 1 ATOM 76 O O . CYS A 1 10 ? 1.641 0.328 -3.244 1.00 94.89 10 A 1 ATOM 77 C CB . CYS A 1 10 ? -1.285 -0.691 -2.065 1.00 95.12 10 A 1 ATOM 78 S SG . CYS A 1 10 ? -1.616 -0.829 -3.828 1.00 90.11 10 A 1 ATOM 79 N N . ALA A 1 11 ? 0.931 1.398 -1.405 1.00 96.33 11 A 1 ATOM 80 C CA . ALA A 1 11 ? 1.648 2.629 -1.733 1.00 96.43 11 A 1 ATOM 81 C C . ALA A 1 11 ? 3.158 2.397 -1.709 1.00 96.93 11 A 1 ATOM 82 O O . ALA A 1 11 ? 3.882 2.881 -2.580 1.00 95.57 11 A 1 ATOM 83 C CB . ALA A 1 11 ? 1.264 3.725 -0.746 1.00 95.89 11 A 1 ATOM 84 N N . LEU A 1 12 ? 3.621 1.650 -0.725 1.00 96.20 12 A 1 ATOM 85 C CA . LEU A 1 12 ? 5.044 1.350 -0.598 1.00 96.09 12 A 1 ATOM 86 C C . LEU A 1 12 ? 5.508 0.450 -1.731 1.00 96.71 12 A 1 ATOM 87 O O . LEU A 1 12 ? 6.596 0.633 -2.277 1.00 95.62 12 A 1 ATOM 88 C CB . LEU A 1 12 ? 5.307 0.688 0.758 1.00 95.31 12 A 1 ATOM 89 C CG . LEU A 1 12 ? 6.210 1.520 1.664 1.00 91.04 12 A 1 ATOM 90 C CD1 . LEU A 1 12 ? 5.988 1.174 3.122 1.00 87.33 12 A 1 ATOM 91 C CD2 . LEU A 1 12 ? 7.665 1.322 1.281 1.00 87.44 12 A 1 ATOM 92 N N . ALA A 1 13 ? 4.687 -0.515 -2.077 1.00 96.62 13 A 1 ATOM 93 C CA . ALA A 1 13 ? 5.015 -1.448 -3.153 1.00 96.62 13 A 1 ATOM 94 C C . ALA A 1 13 ? 5.159 -0.717 -4.480 1.00 96.92 13 A 1 ATOM 95 O O . ALA A 1 13 ? 6.059 -1.006 -5.267 1.00 95.77 13 A 1 ATOM 96 C CB . ALA A 1 13 ? 3.929 -2.511 -3.256 1.00 95.78 13 A 1 ATOM 97 N N . ALA A 1 14 ? 4.273 0.226 -4.729 1.00 97.25 14 A 1 ATOM 98 C CA . ALA A 1 14 ? 4.303 0.993 -5.971 1.00 97.11 14 A 1 ATOM 99 C C . ALA A 1 14 ? 5.515 1.916 -6.009 1.00 97.15 14 A 1 ATOM 100 O O . ALA A 1 14 ? 6.134 2.098 -7.058 1.00 95.53 14 A 1 ATOM 101 C CB . ALA A 1 14 ? 3.023 1.806 -6.108 1.00 96.21 14 A 1 ATOM 102 N N . THR A 1 15 ? 5.844 2.501 -4.875 1.00 95.59 15 A 1 ATOM 103 C CA . THR A 1 15 ? 6.986 3.410 -4.780 1.00 95.08 15 A 1 ATOM 104 C C . THR A 1 15 ? 8.303 2.645 -4.781 1.00 94.87 15 A 1 ATOM 105 O O . THR A 1 15 ? 9.294 3.106 -5.345 1.00 91.86 15 A 1 ATOM 106 C CB . THR A 1 15 ? 6.893 4.257 -3.509 1.00 93.31 15 A 1 ATOM 107 O OG1 . THR A 1 15 ? 5.645 4.947 -3.485 1.00 87.02 15 A 1 ATOM 108 C CG2 . THR A 1 15 ? 8.013 5.282 -3.459 1.00 84.30 15 A 1 ATOM 109 N N . ASP A 1 16 ? 8.310 1.502 -4.148 1.00 89.03 16 A 1 ATOM 110 C CA . ASP A 1 16 ? 9.513 0.672 -4.058 1.00 89.43 16 A 1 ATOM 111 C C . ASP A 1 16 ? 9.939 0.172 -5.433 1.00 90.66 16 A 1 ATOM 112 O O . ASP A 1 16 ? 11.128 0.145 -5.755 1.00 87.30 16 A 1 ATOM 113 C CB . ASP A 1 16 ? 9.264 -0.524 -3.146 1.00 85.60 16 A 1 ATOM 114 C CG . ASP A 1 16 ? 10.567 -1.115 -2.670 1.00 79.79 16 A 1 ATOM 115 O OD1 . ASP A 1 16 ? 11.165 -0.541 -1.747 1.00 75.65 16 A 1 ATOM 116 O OD2 . ASP A 1 16 ? 10.987 -2.147 -3.214 1.00 77.31 16 A 1 ATOM 117 N N . ALA A 1 17 ? 8.981 -0.219 -6.231 1.00 93.01 17 A 1 ATOM 118 C CA . ALA A 1 17 ? 9.252 -0.741 -7.565 1.00 91.83 17 A 1 ATOM 119 C C . ALA A 1 17 ? 9.820 0.348 -8.473 1.00 89.88 17 A 1 ATOM 120 O O . ALA A 1 17 ? 9.296 1.470 -8.451 1.00 83.20 17 A 1 ATOM 121 C CB . ALA A 1 17 ? 7.987 -1.331 -8.163 1.00 88.54 17 A 1 ATOM 122 O OXT . ALA A 1 17 ? 10.772 0.071 -9.220 1.00 78.48 17 A 1 #