# 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_spkb13923 # _entry.id spkb13923 # 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" "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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" # _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 THR 2 1 n THR 3 1 n ASP 4 1 n THR 5 1 n ALA 6 1 n ARG 7 1 n ARG 8 1 n HIS 9 1 n THR 10 1 n GLY 11 1 n ALA 12 1 n GLU 13 1 n ARG 14 # _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 22:51:51)" _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 83.31 _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 74.82 1 1 A THR 2 2 79.35 1 2 A THR 3 2 85.06 1 3 A ASP 4 2 88.52 1 4 A THR 5 2 91.07 1 5 A ALA 6 2 93.28 1 6 A ARG 7 2 85.72 1 7 A ARG 8 2 83.74 1 8 A HIS 9 2 85.04 1 9 A THR 10 2 88.93 1 10 A GLY 11 2 89.08 1 11 A ALA 12 2 87.19 1 12 A GLU 13 2 75.94 1 13 A ARG 14 2 72.73 1 14 # _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 THR . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n ASP . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ARG . 7 A 7 A 8 1 n ARG . 8 A 8 A 9 1 n HIS . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n GLU . 13 A 13 A 14 1 n ARG . 14 A 14 # _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 ? -1.821 10.038 -3.283 1.00 73.33 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.197 8.696 -3.767 1.00 80.40 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.587 7.792 -2.602 1.00 84.34 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.780 7.006 -2.117 1.00 79.68 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.029 8.060 -4.533 1.00 74.71 1 A 1 ATOM 6 C CG . MET A 1 1 ? -0.634 8.856 -5.761 1.00 71.85 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.707 8.073 -6.687 1.00 71.19 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.969 9.295 -7.971 1.00 63.05 1 A 1 ATOM 9 N N . THR A 1 2 ? -3.805 7.892 -2.151 1.00 77.48 2 A 1 ATOM 10 C CA . THR A 1 2 ? -4.309 7.082 -1.043 1.00 81.69 2 A 1 ATOM 11 C C . THR A 1 2 ? -4.634 5.659 -1.498 1.00 84.34 2 A 1 ATOM 12 O O . THR A 1 2 ? -5.008 4.809 -0.694 1.00 81.60 2 A 1 ATOM 13 C CB . THR A 1 2 ? -5.573 7.715 -0.444 1.00 79.19 2 A 1 ATOM 14 O OG1 . THR A 1 2 ? -5.431 9.133 -0.385 1.00 75.36 2 A 1 ATOM 15 C CG2 . THR A 1 2 ? -5.832 7.190 0.959 1.00 75.81 2 A 1 ATOM 16 N N . THR A 1 3 ? -4.477 5.385 -2.782 1.00 85.36 3 A 1 ATOM 17 C CA . THR A 1 3 ? -4.762 4.068 -3.349 1.00 86.57 3 A 1 ATOM 18 C C . THR A 1 3 ? -3.773 3.022 -2.837 1.00 88.49 3 A 1 ATOM 19 O O . THR A 1 3 ? -4.015 1.823 -2.934 1.00 86.95 3 A 1 ATOM 20 C CB . THR A 1 3 ? -4.697 4.112 -4.884 1.00 85.10 3 A 1 ATOM 21 O OG1 . THR A 1 3 ? -5.084 2.844 -5.422 1.00 81.75 3 A 1 ATOM 22 C CG2 . THR A 1 3 ? -3.281 4.427 -5.354 1.00 81.17 3 A 1 ATOM 23 N N . ASP A 1 4 ? -2.645 3.469 -2.273 1.00 87.60 4 A 1 ATOM 24 C CA . ASP A 1 4 ? -1.624 2.566 -1.743 1.00 90.09 4 A 1 ATOM 25 C C . ASP A 1 4 ? -2.167 1.758 -0.580 1.00 92.77 4 A 1 ATOM 26 O O . ASP A 1 4 ? -1.665 0.676 -0.283 1.00 91.68 4 A 1 ATOM 27 C CB . ASP A 1 4 ? -0.404 3.369 -1.284 1.00 88.01 4 A 1 ATOM 28 C CG . ASP A 1 4 ? 0.514 3.713 -2.436 1.00 87.91 4 A 1 ATOM 29 O OD1 . ASP A 1 4 ? 0.011 4.178 -3.468 1.00 86.11 4 A 1 ATOM 30 O OD2 . ASP A 1 4 ? 1.734 3.508 -2.302 1.00 84.00 4 A 1 ATOM 31 N N . THR A 1 5 ? -3.188 2.275 0.085 1.00 92.45 5 A 1 ATOM 32 C CA . THR A 1 5 ? -3.805 1.595 1.217 1.00 92.52 5 A 1 ATOM 33 C C . THR A 1 5 ? -4.376 0.242 0.800 1.00 93.68 5 A 1 ATOM 34 O O . THR A 1 5 ? -4.596 -0.631 1.637 1.00 92.89 5 A 1 ATOM 35 C CB . THR A 1 5 ? -4.935 2.448 1.817 1.00 91.03 5 A 1 ATOM 36 O OG1 . THR A 1 5 ? -5.423 1.831 3.005 1.00 87.70 5 A 1 ATOM 37 C CG2 . THR A 1 5 ? -6.087 2.590 0.832 1.00 87.20 5 A 1 ATOM 38 N N . ALA A 1 6 ? -4.607 0.074 -0.486 1.00 93.13 6 A 1 ATOM 39 C CA . ALA A 1 6 ? -5.166 -1.168 -1.006 1.00 93.32 6 A 1 ATOM 40 C C . ALA A 1 6 ? -4.074 -2.111 -1.498 1.00 94.37 6 A 1 ATOM 41 O O . ALA A 1 6 ? -4.189 -3.330 -1.376 1.00 92.99 6 A 1 ATOM 42 C CB . ALA A 1 6 ? -6.149 -0.869 -2.132 1.00 92.57 6 A 1 ATOM 43 N N . ARG A 1 7 ? -3.002 -1.554 -2.046 1.00 91.00 7 A 1 ATOM 44 C CA . ARG A 1 7 ? -1.901 -2.353 -2.584 1.00 91.42 7 A 1 ATOM 45 C C . ARG A 1 7 ? -0.985 -2.870 -1.481 1.00 92.48 7 A 1 ATOM 46 O O . ARG A 1 7 ? -0.628 -4.044 -1.459 1.00 90.81 7 A 1 ATOM 47 C CB . ARG A 1 7 ? -1.092 -1.517 -3.580 1.00 90.17 7 A 1 ATOM 48 C CG . ARG A 1 7 ? -1.919 -1.087 -4.775 1.00 86.43 7 A 1 ATOM 49 C CD . ARG A 1 7 ? -1.096 -0.233 -5.719 1.00 85.93 7 A 1 ATOM 50 N NE . ARG A 1 7 ? -1.896 0.212 -6.863 1.00 82.00 7 A 1 ATOM 51 C CZ . ARG A 1 7 ? -1.433 0.984 -7.838 1.00 81.29 7 A 1 ATOM 52 N NH1 . ARG A 1 7 ? -0.189 1.414 -7.825 1.00 76.19 7 A 1 ATOM 53 N NH2 . ARG A 1 7 ? -2.222 1.337 -8.839 1.00 75.15 7 A 1 ATOM 54 N N . ARG A 1 8 ? -0.598 -2.008 -0.560 1.00 90.08 8 A 1 ATOM 55 C CA . ARG A 1 8 ? 0.281 -2.396 0.540 1.00 89.73 8 A 1 ATOM 56 C C . ARG A 1 8 ? -0.400 -3.371 1.490 1.00 90.85 8 A 1 ATOM 57 O O . ARG A 1 8 ? 0.255 -4.228 2.083 1.00 88.71 8 A 1 ATOM 58 C CB . ARG A 1 8 ? 0.732 -1.154 1.307 1.00 88.45 8 A 1 ATOM 59 C CG . ARG A 1 8 ? -0.409 -0.461 2.026 1.00 84.62 8 A 1 ATOM 60 C CD . ARG A 1 8 ? 0.070 0.822 2.669 1.00 83.82 8 A 1 ATOM 61 N NE . ARG A 1 8 ? -1.002 1.481 3.416 1.00 79.87 8 A 1 ATOM 62 C CZ . ARG A 1 8 ? -0.853 2.625 4.073 1.00 79.43 8 A 1 ATOM 63 N NH1 . ARG A 1 8 ? 0.305 3.244 4.080 1.00 73.25 8 A 1 ATOM 64 N NH2 . ARG A 1 8 ? -1.874 3.146 4.731 1.00 72.37 8 A 1 ATOM 65 N N . HIS A 1 9 ? -1.702 -3.257 1.645 1.00 89.98 9 A 1 ATOM 66 C CA . HIS A 1 9 ? -2.462 -4.129 2.536 1.00 90.14 9 A 1 ATOM 67 C C . HIS A 1 9 ? -2.555 -5.547 1.976 1.00 91.93 9 A 1 ATOM 68 O O . HIS A 1 9 ? -2.441 -6.525 2.710 1.00 89.02 9 A 1 ATOM 69 C CB . HIS A 1 9 ? -3.873 -3.566 2.755 1.00 88.00 9 A 1 ATOM 70 C CG . HIS A 1 9 ? -3.891 -2.410 3.724 1.00 85.98 9 A 1 ATOM 71 N ND1 . HIS A 1 9 ? -2.866 -2.135 4.594 1.00 78.04 9 A 1 ATOM 72 C CD2 . HIS A 1 9 ? -4.850 -1.470 3.952 1.00 77.97 9 A 1 ATOM 73 C CE1 . HIS A 1 9 ? -3.179 -1.074 5.311 1.00 79.47 9 A 1 ATOM 74 N NE2 . HIS A 1 9 ? -4.383 -0.647 4.950 1.00 79.92 9 A 1 ATOM 75 N N . THR A 1 10 ? -2.741 -5.663 0.687 1.00 91.03 10 A 1 ATOM 76 C CA . THR A 1 10 ? -2.878 -6.971 0.047 1.00 90.61 10 A 1 ATOM 77 C C . THR A 1 10 ? -1.597 -7.793 0.168 1.00 90.94 10 A 1 ATOM 78 O O . THR A 1 10 ? -1.647 -9.016 0.299 1.00 87.17 10 A 1 ATOM 79 C CB . THR A 1 10 ? -3.244 -6.818 -1.436 1.00 89.04 10 A 1 ATOM 80 O OG1 . THR A 1 10 ? -2.329 -5.935 -2.068 1.00 87.16 10 A 1 ATOM 81 C CG2 . THR A 1 10 ? -4.653 -6.275 -1.589 1.00 86.58 10 A 1 ATOM 82 N N . GLY A 1 11 ? -0.445 -7.147 0.139 1.00 89.80 11 A 1 ATOM 83 C CA . GLY A 1 11 ? 0.829 -7.843 0.260 1.00 88.70 11 A 1 ATOM 84 C C . GLY A 1 11 ? 2.011 -7.015 -0.192 1.00 90.33 11 A 1 ATOM 85 O O . GLY A 1 11 ? 3.094 -7.547 -0.425 1.00 87.51 11 A 1 ATOM 86 N N . ALA A 1 12 ? 1.821 -5.724 -0.313 1.00 87.89 12 A 1 ATOM 87 C CA . ALA A 1 12 ? 2.876 -4.813 -0.752 1.00 88.02 12 A 1 ATOM 88 C C . ALA A 1 12 ? 3.712 -4.319 0.428 1.00 89.53 12 A 1 ATOM 89 O O . ALA A 1 12 ? 4.069 -3.149 0.505 1.00 85.75 12 A 1 ATOM 90 C CB . ALA A 1 12 ? 2.265 -3.637 -1.500 1.00 84.77 12 A 1 ATOM 91 N N . GLU A 1 13 ? 4.025 -5.230 1.367 1.00 85.16 13 A 1 ATOM 92 C CA . GLU A 1 13 ? 4.812 -4.882 2.554 1.00 83.36 13 A 1 ATOM 93 C C . GLU A 1 13 ? 6.240 -4.499 2.186 1.00 82.44 13 A 1 ATOM 94 O O . GLU A 1 13 ? 6.865 -3.671 2.849 1.00 75.17 13 A 1 ATOM 95 C CB . GLU A 1 13 ? 4.846 -6.067 3.519 1.00 79.54 13 A 1 ATOM 96 C CG . GLU A 1 13 ? 3.477 -6.441 4.049 1.00 74.49 13 A 1 ATOM 97 C CD . GLU A 1 13 ? 3.545 -7.607 5.018 1.00 71.11 13 A 1 ATOM 98 O OE1 . GLU A 1 13 ? 3.989 -7.404 6.153 1.00 65.23 13 A 1 ATOM 99 O OE2 . GLU A 1 13 ? 3.173 -8.721 4.625 1.00 66.95 13 A 1 ATOM 100 N N . ARG A 1 14 ? 6.758 -5.130 1.152 1.00 81.99 14 A 1 ATOM 101 C CA . ARG A 1 14 ? 8.130 -4.863 0.711 1.00 80.46 14 A 1 ATOM 102 C C . ARG A 1 14 ? 8.138 -4.203 -0.655 1.00 75.76 14 A 1 ATOM 103 O O . ARG A 1 14 ? 8.588 -4.827 -1.631 1.00 70.33 14 A 1 ATOM 104 C CB . ARG A 1 14 ? 8.931 -6.156 0.682 1.00 75.39 14 A 1 ATOM 105 C CG . ARG A 1 14 ? 10.366 -5.965 0.277 1.00 74.04 14 A 1 ATOM 106 C CD . ARG A 1 14 ? 11.257 -6.937 0.996 1.00 71.72 14 A 1 ATOM 107 N NE . ARG A 1 14 ? 11.238 -6.676 2.434 1.00 70.50 14 A 1 ATOM 108 C CZ . ARG A 1 14 ? 11.879 -5.694 3.016 1.00 69.17 14 A 1 ATOM 109 N NH1 . ARG A 1 14 ? 12.604 -4.865 2.293 1.00 68.51 14 A 1 ATOM 110 N NH2 . ARG A 1 14 ? 11.801 -5.526 4.313 1.00 63.78 14 A 1 ATOM 111 O OXT . ARG A 1 14 ? 7.734 -3.106 -0.760 1.00 71.06 14 A 1 #