# 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_spkb08362 # _entry.id spkb08362 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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 LEU 2 1 n ALA 3 1 n ARG 4 1 n ALA 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n CYS 9 1 n ALA 10 1 n ALA 11 1 n VAL 12 1 n ALA 13 1 n LEU 14 1 n SER 15 1 n GLY 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 @ 2025-07-07 20:36:31)" _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 95.29 _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 91.28 1 1 A LEU 2 2 94.75 1 2 A ALA 3 2 98.30 1 3 A ARG 4 2 91.31 1 4 A ALA 5 2 98.46 1 5 A LEU 6 2 96.89 1 6 A LEU 7 2 97.26 1 7 A LEU 8 2 96.58 1 8 A CYS 9 2 97.33 1 9 A ALA 10 2 98.39 1 10 A ALA 11 2 98.45 1 11 A VAL 12 2 98.01 1 12 A ALA 13 2 98.41 1 13 A LEU 14 2 96.79 1 14 A SER 15 2 95.18 1 15 A GLY 16 2 93.44 1 16 A ALA 17 2 83.34 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 LEU . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n ARG . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n CYS . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n GLY . 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 ? -10.459 -2.480 7.032 1.00 95.74 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.350 -1.503 7.062 1.00 96.00 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.529 -1.592 5.769 1.00 96.76 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.334 -1.852 5.789 1.00 95.25 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.458 -1.808 8.262 1.00 93.87 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.190 -1.522 9.562 1.00 89.84 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.309 -2.212 10.963 1.00 86.52 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.248 -1.487 12.293 1.00 76.22 1 A 1 ATOM 9 N N . LEU A 1 2 ? -9.181 -1.386 4.656 1.00 97.44 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -8.505 -1.458 3.349 1.00 97.77 2 A 1 ATOM 11 C C . LEU A 1 2 ? -7.657 -0.209 3.107 1.00 98.25 2 A 1 ATOM 12 O O . LEU A 1 2 ? -6.559 -0.291 2.561 1.00 97.96 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -9.578 -1.582 2.266 1.00 97.10 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -10.349 -2.897 2.368 1.00 92.56 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -11.683 -2.778 1.648 1.00 89.17 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -9.527 -4.027 1.746 1.00 87.73 2 A 1 ATOM 17 N N . ALA A 1 3 ? -8.173 0.949 3.507 1.00 98.33 3 A 1 ATOM 18 C CA . ALA A 1 3 ? -7.450 2.214 3.313 1.00 98.41 3 A 1 ATOM 19 C C . ALA A 1 3 ? -6.079 2.175 3.986 1.00 98.52 3 A 1 ATOM 20 O O . ALA A 1 3 ? -5.103 2.712 3.463 1.00 98.21 3 A 1 ATOM 21 C CB . ALA A 1 3 ? -8.292 3.350 3.875 1.00 98.05 3 A 1 ATOM 22 N N . ARG A 1 4 ? -6.015 1.548 5.133 1.00 98.35 4 A 1 ATOM 23 C CA . ARG A 1 4 ? -4.752 1.469 5.890 1.00 98.46 4 A 1 ATOM 24 C C . ARG A 1 4 ? -3.699 0.700 5.073 1.00 98.68 4 A 1 ATOM 25 O O . ARG A 1 4 ? -2.562 1.132 4.955 1.00 98.55 4 A 1 ATOM 26 C CB . ARG A 1 4 ? -5.058 0.769 7.220 1.00 98.04 4 A 1 ATOM 27 C CG . ARG A 1 4 ? -3.982 0.837 8.261 1.00 92.95 4 A 1 ATOM 28 C CD . ARG A 1 4 ? -3.064 2.017 8.205 1.00 90.62 4 A 1 ATOM 29 N NE . ARG A 1 4 ? -2.769 2.534 9.553 1.00 86.99 4 A 1 ATOM 30 C CZ . ARG A 1 4 ? -2.092 1.839 10.460 1.00 84.62 4 A 1 ATOM 31 N NH1 . ARG A 1 4 ? -1.589 0.655 10.194 1.00 78.57 4 A 1 ATOM 32 N NH2 . ARG A 1 4 ? -1.946 2.343 11.672 1.00 78.62 4 A 1 ATOM 33 N N . ALA A 1 5 ? -4.075 -0.434 4.500 1.00 98.42 5 A 1 ATOM 34 C CA . ALA A 1 5 ? -3.150 -1.242 3.697 1.00 98.48 5 A 1 ATOM 35 C C . ALA A 1 5 ? -2.702 -0.470 2.454 1.00 98.65 5 A 1 ATOM 36 O O . ALA A 1 5 ? -1.531 -0.506 2.076 1.00 98.52 5 A 1 ATOM 37 C CB . ALA A 1 5 ? -3.843 -2.541 3.296 1.00 98.23 5 A 1 ATOM 38 N N . LEU A 1 6 ? -3.638 0.227 1.836 1.00 98.57 6 A 1 ATOM 39 C CA . LEU A 1 6 ? -3.328 1.016 0.637 1.00 98.57 6 A 1 ATOM 40 C C . LEU A 1 6 ? -2.386 2.169 0.976 1.00 98.66 6 A 1 ATOM 41 O O . LEU A 1 6 ? -1.480 2.478 0.202 1.00 98.59 6 A 1 ATOM 42 C CB . LEU A 1 6 ? -4.632 1.555 0.050 1.00 98.42 6 A 1 ATOM 43 C CG . LEU A 1 6 ? -5.467 0.448 -0.597 1.00 95.34 6 A 1 ATOM 44 C CD1 . LEU A 1 6 ? -6.861 0.967 -0.920 1.00 93.58 6 A 1 ATOM 45 C CD2 . LEU A 1 6 ? -4.798 -0.038 -1.884 1.00 93.43 6 A 1 ATOM 46 N N . LEU A 1 7 ? -2.599 2.797 2.120 1.00 98.60 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -1.748 3.913 2.552 1.00 98.60 7 A 1 ATOM 48 C C . LEU A 1 7 ? -0.305 3.452 2.747 1.00 98.68 7 A 1 ATOM 49 O O . LEU A 1 7 ? 0.629 4.109 2.291 1.00 98.61 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -2.304 4.473 3.862 1.00 98.48 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -3.446 5.455 3.617 1.00 95.12 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -4.240 5.671 4.899 1.00 94.80 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -2.885 6.793 3.140 1.00 95.18 7 A 1 ATOM 54 N N . LEU A 1 8 ? -0.129 2.321 3.401 1.00 98.51 8 A 1 ATOM 55 C CA . LEU A 1 8 ? 1.217 1.787 3.644 1.00 98.44 8 A 1 ATOM 56 C C . LEU A 1 8 ? 1.870 1.357 2.333 1.00 98.55 8 A 1 ATOM 57 O O . LEU A 1 8 ? 3.032 1.675 2.076 1.00 98.49 8 A 1 ATOM 58 C CB . LEU A 1 8 ? 1.102 0.594 4.596 1.00 98.23 8 A 1 ATOM 59 C CG . LEU A 1 8 ? 0.895 1.050 6.045 1.00 93.67 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? 0.325 -0.087 6.881 1.00 93.15 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? 2.230 1.499 6.640 1.00 93.57 8 A 1 ATOM 62 N N . CYS A 1 9 ? 1.127 0.650 1.508 1.00 98.49 9 A 1 ATOM 63 C CA . CYS A 1 9 ? 1.657 0.171 0.226 1.00 98.44 9 A 1 ATOM 64 C C . CYS A 1 9 ? 2.009 1.353 -0.678 1.00 98.53 9 A 1 ATOM 65 O O . CYS A 1 9 ? 3.058 1.368 -1.321 1.00 98.32 9 A 1 ATOM 66 C CB . CYS A 1 9 ? 0.607 -0.726 -0.438 1.00 98.06 9 A 1 ATOM 67 S SG . CYS A 1 9 ? 1.383 -1.826 -1.641 1.00 92.16 9 A 1 ATOM 68 N N . ALA A 1 10 ? 1.133 2.338 -0.725 1.00 98.46 10 A 1 ATOM 69 C CA . ALA A 1 10 ? 1.364 3.527 -1.554 1.00 98.42 10 A 1 ATOM 70 C C . ALA A 1 10 ? 2.581 4.303 -1.054 1.00 98.55 10 A 1 ATOM 71 O O . ALA A 1 10 ? 3.378 4.796 -1.851 1.00 98.37 10 A 1 ATOM 72 C CB . ALA A 1 10 ? 0.123 4.412 -1.516 1.00 98.13 10 A 1 ATOM 73 N N . ALA A 1 11 ? 2.724 4.415 0.252 1.00 98.58 11 A 1 ATOM 74 C CA . ALA A 1 11 ? 3.860 5.135 0.837 1.00 98.51 11 A 1 ATOM 75 C C . ALA A 1 11 ? 5.174 4.454 0.467 1.00 98.60 11 A 1 ATOM 76 O O . ALA A 1 11 ? 6.147 5.118 0.112 1.00 98.35 11 A 1 ATOM 77 C CB . ALA A 1 11 ? 3.699 5.180 2.352 1.00 98.20 11 A 1 ATOM 78 N N . VAL A 1 12 ? 5.206 3.135 0.530 1.00 98.69 12 A 1 ATOM 79 C CA . VAL A 1 12 ? 6.416 2.377 0.185 1.00 98.60 12 A 1 ATOM 80 C C . VAL A 1 12 ? 6.731 2.539 -1.298 1.00 98.66 12 A 1 ATOM 81 O O . VAL A 1 12 ? 7.884 2.747 -1.679 1.00 98.46 12 A 1 ATOM 82 C CB . VAL A 1 12 ? 6.223 0.896 0.527 1.00 98.24 12 A 1 ATOM 83 C CG1 . VAL A 1 12 ? 7.407 0.068 0.039 1.00 96.46 12 A 1 ATOM 84 C CG2 . VAL A 1 12 ? 6.080 0.740 2.034 1.00 96.99 12 A 1 ATOM 85 N N . ALA A 1 13 ? 5.719 2.442 -2.131 1.00 98.64 13 A 1 ATOM 86 C CA . ALA A 1 13 ? 5.905 2.583 -3.578 1.00 98.53 13 A 1 ATOM 87 C C . ALA A 1 13 ? 6.430 3.978 -3.922 1.00 98.57 13 A 1 ATOM 88 O O . ALA A 1 13 ? 7.324 4.125 -4.755 1.00 98.13 13 A 1 ATOM 89 C CB . ALA A 1 13 ? 4.576 2.332 -4.282 1.00 98.18 13 A 1 ATOM 90 N N . LEU A 1 14 ? 5.874 4.993 -3.278 1.00 98.51 14 A 1 ATOM 91 C CA . LEU A 1 14 ? 6.301 6.376 -3.518 1.00 98.29 14 A 1 ATOM 92 C C . LEU A 1 14 ? 7.677 6.631 -2.923 1.00 98.30 14 A 1 ATOM 93 O O . LEU A 1 14 ? 8.455 7.411 -3.472 1.00 97.59 14 A 1 ATOM 94 C CB . LEU A 1 14 ? 5.279 7.321 -2.885 1.00 97.81 14 A 1 ATOM 95 C CG . LEU A 1 14 ? 3.966 7.352 -3.664 1.00 96.45 14 A 1 ATOM 96 C CD1 . LEU A 1 14 ? 2.869 7.961 -2.816 1.00 94.13 14 A 1 ATOM 97 C CD2 . LEU A 1 14 ? 4.143 8.163 -4.949 1.00 93.26 14 A 1 ATOM 98 N N . SER A 1 15 ? 7.981 5.979 -1.826 1.00 98.00 15 A 1 ATOM 99 C CA . SER A 1 15 ? 9.275 6.148 -1.153 1.00 97.56 15 A 1 ATOM 100 C C . SER A 1 15 ? 10.415 5.822 -2.100 1.00 97.44 15 A 1 ATOM 101 O O . SER A 1 15 ? 11.418 6.530 -2.151 1.00 94.81 15 A 1 ATOM 102 C CB . SER A 1 15 ? 9.333 5.243 0.071 1.00 96.02 15 A 1 ATOM 103 O OG . SER A 1 15 ? 10.382 5.657 0.913 1.00 87.24 15 A 1 ATOM 104 N N . GLY A 1 16 ? 10.266 4.768 -2.879 1.00 95.75 16 A 1 ATOM 105 C CA . GLY A 1 16 ? 11.290 4.360 -3.844 1.00 94.04 16 A 1 ATOM 106 C C . GLY A 1 16 ? 12.670 4.376 -3.209 1.00 93.72 16 A 1 ATOM 107 O O . GLY A 1 16 ? 13.426 5.325 -3.380 1.00 90.26 16 A 1 ATOM 108 N N . ALA A 1 17 ? 12.991 3.336 -2.478 1.00 92.25 17 A 1 ATOM 109 C CA . ALA A 1 17 ? 14.275 3.272 -1.778 1.00 88.17 17 A 1 ATOM 110 C C . ALA A 1 17 ? 15.451 3.438 -2.738 1.00 85.38 17 A 1 ATOM 111 O O . ALA A 1 17 ? 15.339 3.051 -3.913 1.00 77.79 17 A 1 ATOM 112 C CB . ALA A 1 17 ? 14.379 1.951 -1.030 1.00 82.48 17 A 1 ATOM 113 O OXT . ALA A 1 17 ? 16.514 3.928 -2.317 1.00 73.99 17 A 1 #