# 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_spkb14358 # _entry.id spkb14358 # 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" "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 ARG 2 1 n LEU 3 1 n THR 4 1 n VAL 5 1 n GLY 6 1 n ALA 7 1 n LEU 8 1 n LEU 9 1 n ALA 10 1 n CYS 11 1 n ALA 12 1 n ALA 13 1 n LEU 14 1 n GLY 15 1 n LEU 16 1 n CYS 17 1 n LEU 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 @ 2025-07-07 12:39:08)" _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 91.55 _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 84.86 1 1 A ARG 2 2 83.91 1 2 A LEU 3 2 91.21 1 3 A THR 4 2 92.46 1 4 A VAL 5 2 94.37 1 5 A GLY 6 2 95.05 1 6 A ALA 7 2 94.91 1 7 A LEU 8 2 93.08 1 8 A LEU 9 2 94.09 1 9 A ALA 10 2 95.34 1 10 A CYS 11 2 94.55 1 11 A ALA 12 2 96.16 1 12 A ALA 13 2 96.10 1 13 A LEU 14 2 94.17 1 14 A GLY 15 2 96.00 1 15 A LEU 16 2 90.03 1 16 A CYS 17 2 91.49 1 17 A LEU 18 2 89.45 1 18 A ALA 19 2 84.70 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 ARG . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n GLY . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n CYS . 17 A 17 A 18 1 n LEU . 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 ? 4.898 -5.904 -7.221 1.00 89.14 1 A 1 ATOM 2 C CA . MET A 1 1 ? 4.740 -7.286 -6.764 1.00 89.67 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.274 -7.569 -6.455 1.00 91.78 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.674 -8.463 -7.035 1.00 88.52 1 A 1 ATOM 5 C CB . MET A 1 1 ? 5.583 -7.522 -5.503 1.00 86.46 1 A 1 ATOM 6 C CG . MET A 1 1 ? 7.062 -7.610 -5.834 1.00 83.68 1 A 1 ATOM 7 S SD . MET A 1 1 ? 7.520 -9.244 -6.381 1.00 80.58 1 A 1 ATOM 8 C CE . MET A 1 1 ? 7.890 -9.986 -4.812 1.00 69.08 1 A 1 ATOM 9 N N . ARG A 1 2 ? 2.692 -6.823 -5.539 1.00 88.73 2 A 1 ATOM 10 C CA . ARG A 1 2 ? 1.279 -7.028 -5.217 1.00 92.22 2 A 1 ATOM 11 C C . ARG A 1 2 ? 0.441 -5.892 -5.779 1.00 94.69 2 A 1 ATOM 12 O O . ARG A 1 2 ? 0.369 -4.808 -5.210 1.00 92.12 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 1.090 -7.124 -3.705 1.00 89.24 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 1.334 -5.786 -2.997 1.00 84.86 2 A 1 ATOM 15 C CD . ARG A 1 2 ? 2.769 -5.669 -2.509 1.00 83.15 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 2.961 -4.445 -1.728 1.00 78.11 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 4.075 -4.148 -1.090 1.00 77.85 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 5.099 -4.966 -1.131 1.00 70.20 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 4.162 -3.022 -0.407 1.00 71.86 2 A 1 ATOM 20 N N . LEU A 1 3 ? -0.206 -6.141 -6.906 1.00 91.70 3 A 1 ATOM 21 C CA . LEU A 1 3 ? -1.045 -5.129 -7.553 1.00 93.78 3 A 1 ATOM 22 C C . LEU A 1 3 ? -2.507 -5.368 -7.166 1.00 95.63 3 A 1 ATOM 23 O O . LEU A 1 3 ? -3.316 -5.772 -7.989 1.00 93.68 3 A 1 ATOM 24 C CB . LEU A 1 3 ? -0.874 -5.221 -9.073 1.00 93.34 3 A 1 ATOM 25 C CG . LEU A 1 3 ? -0.388 -6.605 -9.506 1.00 90.46 3 A 1 ATOM 26 C CD1 . LEU A 1 3 ? -0.912 -6.926 -10.890 1.00 86.52 3 A 1 ATOM 27 C CD2 . LEU A 1 3 ? 1.142 -6.609 -9.513 1.00 84.55 3 A 1 ATOM 28 N N . THR A 1 4 ? -2.825 -5.144 -5.927 1.00 94.32 4 A 1 ATOM 29 C CA . THR A 1 4 ? -4.190 -5.347 -5.443 1.00 94.54 4 A 1 ATOM 30 C C . THR A 1 4 ? -4.557 -4.275 -4.422 1.00 95.03 4 A 1 ATOM 31 O O . THR A 1 4 ? -3.785 -3.358 -4.158 1.00 94.32 4 A 1 ATOM 32 C CB . THR A 1 4 ? -4.310 -6.726 -4.779 1.00 93.78 4 A 1 ATOM 33 O OG1 . THR A 1 4 ? -3.467 -6.771 -3.638 1.00 88.37 4 A 1 ATOM 34 C CG2 . THR A 1 4 ? -3.891 -7.817 -5.748 1.00 86.86 4 A 1 ATOM 35 N N . VAL A 1 5 ? -5.733 -4.401 -3.851 1.00 95.67 5 A 1 ATOM 36 C CA . VAL A 1 5 ? -6.187 -3.440 -2.842 1.00 95.78 5 A 1 ATOM 37 C C . VAL A 1 5 ? -5.244 -3.458 -1.646 1.00 95.98 5 A 1 ATOM 38 O O . VAL A 1 5 ? -5.144 -2.484 -0.903 1.00 95.12 5 A 1 ATOM 39 C CB . VAL A 1 5 ? -7.608 -3.783 -2.386 1.00 94.96 5 A 1 ATOM 40 C CG1 . VAL A 1 5 ? -8.106 -2.746 -1.395 1.00 91.43 5 A 1 ATOM 41 C CG2 . VAL A 1 5 ? -8.528 -3.838 -3.597 1.00 91.64 5 A 1 ATOM 42 N N . GLY A 1 6 ? -4.560 -4.574 -1.471 1.00 94.98 6 A 1 ATOM 43 C CA . GLY A 1 6 ? -3.616 -4.691 -0.356 1.00 94.58 6 A 1 ATOM 44 C C . GLY A 1 6 ? -2.577 -3.588 -0.395 1.00 95.42 6 A 1 ATOM 45 O O . GLY A 1 6 ? -2.132 -3.097 0.642 1.00 95.20 6 A 1 ATOM 46 N N . ALA A 1 7 ? -2.187 -3.183 -1.607 1.00 95.03 7 A 1 ATOM 47 C CA . ALA A 1 7 ? -1.203 -2.112 -1.763 1.00 94.84 7 A 1 ATOM 48 C C . ALA A 1 7 ? -1.754 -0.813 -1.184 1.00 95.79 7 A 1 ATOM 49 O O . ALA A 1 7 ? -1.029 -0.043 -0.559 1.00 94.79 7 A 1 ATOM 50 C CB . ALA A 1 7 ? -0.879 -1.928 -3.239 1.00 94.09 7 A 1 ATOM 51 N N . LEU A 1 8 ? -3.039 -0.577 -1.392 1.00 94.05 8 A 1 ATOM 52 C CA . LEU A 1 8 ? -3.676 0.629 -0.866 1.00 94.24 8 A 1 ATOM 53 C C . LEU A 1 8 ? -3.704 0.569 0.654 1.00 95.67 8 A 1 ATOM 54 O O . LEU A 1 8 ? -3.558 1.587 1.326 1.00 95.36 8 A 1 ATOM 55 C CB . LEU A 1 8 ? -5.105 0.732 -1.404 1.00 94.19 8 A 1 ATOM 56 C CG . LEU A 1 8 ? -5.159 0.842 -2.927 1.00 91.45 8 A 1 ATOM 57 C CD1 . LEU A 1 8 ? -6.604 0.821 -3.391 1.00 90.01 8 A 1 ATOM 58 C CD2 . LEU A 1 8 ? -4.479 2.130 -3.386 1.00 89.70 8 A 1 ATOM 59 N N . LEU A 1 9 ? -3.893 -0.628 1.183 1.00 94.61 9 A 1 ATOM 60 C CA . LEU A 1 9 ? -3.922 -0.810 2.633 1.00 95.32 9 A 1 ATOM 61 C C . LEU A 1 9 ? -2.573 -0.436 3.229 1.00 96.60 9 A 1 ATOM 62 O O . LEU A 1 9 ? -2.490 0.268 4.234 1.00 96.65 9 A 1 ATOM 63 C CB . LEU A 1 9 ? -4.251 -2.269 2.967 1.00 95.21 9 A 1 ATOM 64 C CG . LEU A 1 9 ? -5.713 -2.494 3.342 1.00 91.94 9 A 1 ATOM 65 C CD1 . LEU A 1 9 ? -6.041 -1.716 4.594 1.00 91.12 9 A 1 ATOM 66 C CD2 . LEU A 1 9 ? -6.612 -2.060 2.195 1.00 91.25 9 A 1 ATOM 67 N N . ALA A 1 10 ? -1.514 -0.916 2.590 1.00 95.47 10 A 1 ATOM 68 C CA . ALA A 1 10 ? -0.167 -0.609 3.060 1.00 95.22 10 A 1 ATOM 69 C C . ALA A 1 10 ? 0.094 0.890 2.957 1.00 96.31 10 A 1 ATOM 70 O O . ALA A 1 10 ? 0.715 1.486 3.837 1.00 95.46 10 A 1 ATOM 71 C CB . ALA A 1 10 ? 0.849 -1.379 2.223 1.00 94.26 10 A 1 ATOM 72 N N . CYS A 1 11 ? -0.386 1.498 1.880 1.00 95.22 11 A 1 ATOM 73 C CA . CYS A 1 11 ? -0.204 2.933 1.685 1.00 95.27 11 A 1 ATOM 74 C C . CYS A 1 11 ? -0.947 3.714 2.761 1.00 96.13 11 A 1 ATOM 75 O O . CYS A 1 11 ? -0.428 4.674 3.318 1.00 95.06 11 A 1 ATOM 76 C CB . CYS A 1 11 ? -0.720 3.328 0.300 1.00 94.04 11 A 1 ATOM 77 S SG . CYS A 1 11 ? 0.391 2.808 -1.030 1.00 91.57 11 A 1 ATOM 78 N N . ALA A 1 12 ? -2.171 3.296 3.042 1.00 95.82 12 A 1 ATOM 79 C CA . ALA A 1 12 ? -2.969 3.972 4.061 1.00 96.05 12 A 1 ATOM 80 C C . ALA A 1 12 ? -2.332 3.800 5.435 1.00 97.11 12 A 1 ATOM 81 O O . ALA A 1 12 ? -2.343 4.719 6.251 1.00 96.55 12 A 1 ATOM 82 C CB . ALA A 1 12 ? -4.382 3.399 4.064 1.00 95.28 12 A 1 ATOM 83 N N . ALA A 1 13 ? -1.800 2.611 5.691 1.00 95.95 13 A 1 ATOM 84 C CA . ALA A 1 13 ? -1.167 2.332 6.978 1.00 96.18 13 A 1 ATOM 85 C C . ALA A 1 13 ? 0.079 3.193 7.163 1.00 96.97 13 A 1 ATOM 86 O O . ALA A 1 13 ? 0.323 3.722 8.246 1.00 96.06 13 A 1 ATOM 87 C CB . ALA A 1 13 ? -0.798 0.853 7.060 1.00 95.36 13 A 1 ATOM 88 N N . LEU A 1 14 ? 0.865 3.324 6.113 1.00 96.11 14 A 1 ATOM 89 C CA . LEU A 1 14 ? 2.085 4.130 6.169 1.00 96.06 14 A 1 ATOM 90 C C . LEU A 1 14 ? 1.820 5.571 5.758 1.00 96.96 14 A 1 ATOM 91 O O . LEU A 1 14 ? 2.527 6.486 6.176 1.00 95.90 14 A 1 ATOM 92 C CB . LEU A 1 14 ? 3.137 3.509 5.244 1.00 95.33 14 A 1 ATOM 93 C CG . LEU A 1 14 ? 3.543 2.098 5.663 1.00 92.72 14 A 1 ATOM 94 C CD1 . LEU A 1 14 ? 4.437 1.482 4.594 1.00 90.71 14 A 1 ATOM 95 C CD2 . LEU A 1 14 ? 4.279 2.145 6.996 1.00 89.54 14 A 1 ATOM 96 N N . GLY A 1 15 ? 0.804 5.768 4.947 1.00 95.69 15 A 1 ATOM 97 C CA . GLY A 1 15 ? 0.480 7.111 4.484 1.00 95.63 15 A 1 ATOM 98 C C . GLY A 1 15 ? 1.433 7.560 3.393 1.00 96.60 15 A 1 ATOM 99 O O . GLY A 1 15 ? 1.665 8.752 3.214 1.00 96.08 15 A 1 ATOM 100 N N . LEU A 1 16 ? 1.974 6.600 2.659 1.00 92.35 16 A 1 ATOM 101 C CA . LEU A 1 16 ? 2.910 6.907 1.580 1.00 92.37 16 A 1 ATOM 102 C C . LEU A 1 16 ? 2.170 7.299 0.309 1.00 94.05 16 A 1 ATOM 103 O O . LEU A 1 16 ? 2.480 8.312 -0.314 1.00 91.70 16 A 1 ATOM 104 C CB . LEU A 1 16 ? 3.796 5.685 1.312 1.00 91.67 16 A 1 ATOM 105 C CG . LEU A 1 16 ? 4.632 5.277 2.526 1.00 89.00 16 A 1 ATOM 106 C CD1 . LEU A 1 16 ? 5.423 4.019 2.198 1.00 85.69 16 A 1 ATOM 107 C CD2 . LEU A 1 16 ? 5.577 6.408 2.917 1.00 83.37 16 A 1 ATOM 108 N N . CYS A 1 17 ? 1.195 6.493 -0.078 1.00 92.23 17 A 1 ATOM 109 C CA . CYS A 1 17 ? 0.418 6.801 -1.273 1.00 92.72 17 A 1 ATOM 110 C C . CYS A 1 17 ? -0.328 8.126 -1.113 1.00 93.70 17 A 1 ATOM 111 O O . CYS A 1 17 ? -0.314 8.738 -0.053 1.00 91.62 17 A 1 ATOM 112 C CB . CYS A 1 17 ? -0.570 5.660 -1.537 1.00 90.87 17 A 1 ATOM 113 S SG . CYS A 1 17 ? 0.180 4.272 -2.416 1.00 87.82 17 A 1 ATOM 114 N N . LEU A 1 18 ? -0.986 8.554 -2.173 1.00 91.86 18 A 1 ATOM 115 C CA . LEU A 1 18 ? -1.708 9.831 -2.171 1.00 92.01 18 A 1 ATOM 116 C C . LEU A 1 18 ? -0.728 10.990 -2.271 1.00 93.27 18 A 1 ATOM 117 O O . LEU A 1 18 ? -1.114 12.128 -2.527 1.00 91.21 18 A 1 ATOM 118 C CB . LEU A 1 18 ? -2.543 9.964 -0.888 1.00 90.49 18 A 1 ATOM 119 C CG . LEU A 1 18 ? -4.032 9.771 -1.102 1.00 88.86 18 A 1 ATOM 120 C CD1 . LEU A 1 18 ? -4.541 10.820 -2.066 1.00 85.52 18 A 1 ATOM 121 C CD2 . LEU A 1 18 ? -4.283 8.380 -1.630 1.00 82.36 18 A 1 ATOM 122 N N . ALA A 1 19 ? 0.540 10.718 -2.054 1.00 90.33 19 A 1 ATOM 123 C CA . ALA A 1 19 ? 1.566 11.753 -2.110 1.00 88.50 19 A 1 ATOM 124 C C . ALA A 1 19 ? 2.250 11.783 -3.474 1.00 86.82 19 A 1 ATOM 125 O O . ALA A 1 19 ? 2.072 10.835 -4.260 1.00 82.00 19 A 1 ATOM 126 C CB . ALA A 1 19 ? 2.594 11.517 -1.006 1.00 83.77 19 A 1 ATOM 127 O OXT . ALA A 1 19 ? 2.972 12.746 -3.767 1.00 76.77 19 A 1 #