# 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_spkb09833 # _entry.id spkb09833 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "C6 H13 N O2" 131.173 ILE y ISOLEUCINE CC[C@H](C)[C@@H](C(=O)O)N ? "L-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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 TYR 2 1 n VAL 3 1 n LEU 4 1 n LEU 5 1 n THR 6 1 n ILE 7 1 n LEU 8 1 n THR 9 1 n SER 10 1 n VAL 11 1 n LEU 12 1 n VAL 13 1 n CYS 14 1 n GLU 15 1 n ALA 16 # _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 @ 2025-07-10 20:40:30)" _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 87.44 _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 80.76 1 1 A TYR 2 2 80.52 1 2 A VAL 3 2 90.69 1 3 A LEU 4 2 86.26 1 4 A LEU 5 2 86.89 1 5 A THR 6 2 91.89 1 6 A ILE 7 2 92.55 1 7 A LEU 8 2 88.27 1 8 A THR 9 2 89.80 1 9 A SER 10 2 90.58 1 10 A VAL 11 2 90.65 1 11 A LEU 12 2 87.24 1 12 A VAL 13 2 92.07 1 13 A CYS 14 2 90.06 1 14 A GLU 15 2 83.18 1 15 A ALA 16 2 84.51 1 16 # _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 TYR . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n THR . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n CYS . 14 A 14 A 15 1 n GLU . 15 A 15 A 16 1 n ALA . 16 A 16 # _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 ? -5.148 11.144 3.005 1.00 85.13 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.789 9.852 2.692 1.00 87.97 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.751 8.875 2.133 1.00 88.79 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.688 8.645 0.928 1.00 87.13 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.918 10.067 1.678 1.00 82.51 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.852 8.872 1.585 1.00 76.05 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.394 9.268 0.743 1.00 72.41 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.858 9.303 -0.962 1.00 66.12 1 A 1 ATOM 9 N N . TYR A 1 2 ? -3.936 8.325 3.019 1.00 81.25 2 A 1 ATOM 10 C CA . TYR A 1 2 ? -2.870 7.403 2.618 1.00 85.41 2 A 1 ATOM 11 C C . TYR A 1 2 ? -3.247 5.944 2.889 1.00 88.24 2 A 1 ATOM 12 O O . TYR A 1 2 ? -2.424 5.046 2.728 1.00 86.89 2 A 1 ATOM 13 C CB . TYR A 1 2 ? -1.588 7.757 3.368 1.00 84.11 2 A 1 ATOM 14 C CG . TYR A 1 2 ? -1.062 9.117 2.968 1.00 79.16 2 A 1 ATOM 15 C CD1 . TYR A 1 2 ? -0.388 9.280 1.760 1.00 78.73 2 A 1 ATOM 16 C CD2 . TYR A 1 2 ? -1.239 10.216 3.796 1.00 77.02 2 A 1 ATOM 17 C CE1 . TYR A 1 2 ? 0.098 10.528 1.391 1.00 76.03 2 A 1 ATOM 18 C CE2 . TYR A 1 2 ? -0.754 11.468 3.429 1.00 76.69 2 A 1 ATOM 19 C CZ . TYR A 1 2 ? -0.087 11.616 2.227 1.00 77.63 2 A 1 ATOM 20 O OH . TYR A 1 2 ? 0.392 12.845 1.864 1.00 75.10 2 A 1 ATOM 21 N N . VAL A 1 3 ? -4.485 5.706 3.279 1.00 91.72 3 A 1 ATOM 22 C CA . VAL A 1 3 ? -4.962 4.349 3.569 1.00 92.63 3 A 1 ATOM 23 C C . VAL A 1 3 ? -4.908 3.488 2.308 1.00 93.99 3 A 1 ATOM 24 O O . VAL A 1 3 ? -4.477 2.335 2.341 1.00 92.63 3 A 1 ATOM 25 C CB . VAL A 1 3 ? -6.398 4.383 4.128 1.00 91.28 3 A 1 ATOM 26 C CG1 . VAL A 1 3 ? -6.886 2.974 4.427 1.00 86.05 3 A 1 ATOM 27 C CG2 . VAL A 1 3 ? -6.460 5.238 5.383 1.00 86.52 3 A 1 ATOM 28 N N . LEU A 1 4 ? -5.341 4.056 1.196 1.00 88.49 4 A 1 ATOM 29 C CA . LEU A 1 4 ? -5.333 3.340 -0.081 1.00 89.07 4 A 1 ATOM 30 C C . LEU A 1 4 ? -3.907 2.978 -0.490 1.00 90.35 4 A 1 ATOM 31 O O . LEU A 1 4 ? -3.647 1.865 -0.952 1.00 89.79 4 A 1 ATOM 32 C CB . LEU A 1 4 ? -5.987 4.215 -1.159 1.00 88.36 4 A 1 ATOM 33 C CG . LEU A 1 4 ? -7.485 4.437 -0.945 1.00 83.03 4 A 1 ATOM 34 C CD1 . LEU A 1 4 ? -7.969 5.619 -1.774 1.00 80.18 4 A 1 ATOM 35 C CD2 . LEU A 1 4 ? -8.265 3.184 -1.344 1.00 80.84 4 A 1 ATOM 36 N N . LEU A 1 5 ? -2.991 3.908 -0.304 1.00 89.13 5 A 1 ATOM 37 C CA . LEU A 1 5 ? -1.585 3.674 -0.634 1.00 89.70 5 A 1 ATOM 38 C C . LEU A 1 5 ? -0.996 2.585 0.256 1.00 90.95 5 A 1 ATOM 39 O O . LEU A 1 5 ? -0.205 1.762 -0.203 1.00 90.84 5 A 1 ATOM 40 C CB . LEU A 1 5 ? -0.806 4.979 -0.463 1.00 89.23 5 A 1 ATOM 41 C CG . LEU A 1 5 ? -1.098 5.990 -1.575 1.00 83.15 5 A 1 ATOM 42 C CD1 . LEU A 1 5 ? -0.692 7.389 -1.144 1.00 80.62 5 A 1 ATOM 43 C CD2 . LEU A 1 5 ? -0.338 5.604 -2.842 1.00 81.49 5 A 1 ATOM 44 N N . THR A 1 6 ? -1.389 2.575 1.501 1.00 93.09 6 A 1 ATOM 45 C CA . THR A 1 6 ? -0.907 1.580 2.459 1.00 93.63 6 A 1 ATOM 46 C C . THR A 1 6 ? -1.340 0.177 2.034 1.00 94.44 6 A 1 ATOM 47 O O . THR A 1 6 ? -0.562 -0.775 2.113 1.00 93.59 6 A 1 ATOM 48 C CB . THR A 1 6 ? -1.446 1.894 3.857 1.00 92.88 6 A 1 ATOM 49 O OG1 . THR A 1 6 ? -1.057 3.214 4.228 1.00 88.02 6 A 1 ATOM 50 C CG2 . THR A 1 6 ? -0.898 0.911 4.877 1.00 87.59 6 A 1 ATOM 51 N N . ILE A 1 7 ? -2.570 0.056 1.588 1.00 93.61 7 A 1 ATOM 52 C CA . ILE A 1 7 ? -3.103 -1.234 1.150 1.00 93.67 7 A 1 ATOM 53 C C . ILE A 1 7 ? -2.324 -1.736 -0.067 1.00 93.95 7 A 1 ATOM 54 O O . ILE A 1 7 ? -1.934 -2.905 -0.131 1.00 92.53 7 A 1 ATOM 55 C CB . ILE A 1 7 ? -4.607 -1.119 0.820 1.00 93.93 7 A 1 ATOM 56 C CG1 . ILE A 1 7 ? -5.409 -0.799 2.084 1.00 92.39 7 A 1 ATOM 57 C CG2 . ILE A 1 7 ? -5.111 -2.428 0.203 1.00 91.91 7 A 1 ATOM 58 C CD1 . ILE A 1 7 ? -6.786 -0.231 1.785 1.00 88.38 7 A 1 ATOM 59 N N . LEU A 1 8 ? -2.095 -0.853 -1.015 1.00 92.31 8 A 1 ATOM 60 C CA . LEU A 1 8 ? -1.357 -1.210 -2.227 1.00 91.37 8 A 1 ATOM 61 C C . LEU A 1 8 ? 0.065 -1.639 -1.890 1.00 92.05 8 A 1 ATOM 62 O O . LEU A 1 8 ? 0.575 -2.615 -2.445 1.00 91.52 8 A 1 ATOM 63 C CB . LEU A 1 8 ? -1.333 -0.008 -3.175 1.00 90.84 8 A 1 ATOM 64 C CG . LEU A 1 8 ? -2.659 0.214 -3.896 1.00 84.35 8 A 1 ATOM 65 C CD1 . LEU A 1 8 ? -2.758 1.642 -4.416 1.00 81.30 8 A 1 ATOM 66 C CD2 . LEU A 1 8 ? -2.785 -0.763 -5.065 1.00 82.39 8 A 1 ATOM 67 N N . THR A 1 9 ? 0.680 -0.929 -0.980 1.00 91.96 9 A 1 ATOM 68 C CA . THR A 1 9 ? 2.046 -1.236 -0.560 1.00 92.40 9 A 1 ATOM 69 C C . THR A 1 9 ? 2.103 -2.602 0.120 1.00 92.75 9 A 1 ATOM 70 O O . THR A 1 9 ? 3.028 -3.382 -0.114 1.00 90.77 9 A 1 ATOM 71 C CB . THR A 1 9 ? 2.562 -0.151 0.394 1.00 91.25 9 A 1 ATOM 72 O OG1 . THR A 1 9 ? 2.447 1.126 -0.228 1.00 84.31 9 A 1 ATOM 73 C CG2 . THR A 1 9 ? 4.026 -0.390 0.737 1.00 85.14 9 A 1 ATOM 74 N N . SER A 1 10 ? 1.120 -2.886 0.938 1.00 92.05 10 A 1 ATOM 75 C CA . SER A 1 10 ? 1.050 -4.157 1.654 1.00 92.75 10 A 1 ATOM 76 C C . SER A 1 10 ? 0.955 -5.322 0.676 1.00 93.21 10 A 1 ATOM 77 O O . SER A 1 10 ? 1.633 -6.338 0.836 1.00 90.42 10 A 1 ATOM 78 C CB . SER A 1 10 ? -0.151 -4.164 2.595 1.00 91.88 10 A 1 ATOM 79 O OG . SER A 1 10 ? -0.137 -5.318 3.396 1.00 83.14 10 A 1 ATOM 80 N N . VAL A 1 11 ? 0.131 -5.166 -0.341 1.00 93.06 11 A 1 ATOM 81 C CA . VAL A 1 11 ? -0.048 -6.205 -1.359 1.00 93.23 11 A 1 ATOM 82 C C . VAL A 1 11 ? 1.237 -6.386 -2.157 1.00 93.46 11 A 1 ATOM 83 O O . VAL A 1 11 ? 1.624 -7.512 -2.480 1.00 90.88 11 A 1 ATOM 84 C CB . VAL A 1 11 ? -1.215 -5.852 -2.297 1.00 91.78 11 A 1 ATOM 85 C CG1 . VAL A 1 11 ? -1.340 -6.878 -3.415 1.00 85.74 11 A 1 ATOM 86 C CG2 . VAL A 1 11 ? -2.518 -5.790 -1.510 1.00 86.38 11 A 1 ATOM 87 N N . LEU A 1 12 ? 1.888 -5.298 -2.465 1.00 90.51 12 A 1 ATOM 88 C CA . LEU A 1 12 ? 3.133 -5.325 -3.230 1.00 91.29 12 A 1 ATOM 89 C C . LEU A 1 12 ? 4.206 -6.116 -2.493 1.00 92.10 12 A 1 ATOM 90 O O . LEU A 1 12 ? 4.902 -6.937 -3.089 1.00 90.33 12 A 1 ATOM 91 C CB . LEU A 1 12 ? 3.618 -3.894 -3.472 1.00 90.10 12 A 1 ATOM 92 C CG . LEU A 1 12 ? 4.823 -3.811 -4.404 1.00 83.35 12 A 1 ATOM 93 C CD1 . LEU A 1 12 ? 4.393 -3.986 -5.852 1.00 80.22 12 A 1 ATOM 94 C CD2 . LEU A 1 12 ? 5.528 -2.470 -4.233 1.00 80.03 12 A 1 ATOM 95 N N . VAL A 1 13 ? 4.347 -5.881 -1.212 1.00 94.33 13 A 1 ATOM 96 C CA . VAL A 1 13 ? 5.343 -6.572 -0.390 1.00 94.49 13 A 1 ATOM 97 C C . VAL A 1 13 ? 4.999 -8.051 -0.265 1.00 94.84 13 A 1 ATOM 98 O O . VAL A 1 13 ? 5.886 -8.909 -0.286 1.00 92.95 13 A 1 ATOM 99 C CB . VAL A 1 13 ? 5.442 -5.925 1.000 1.00 92.57 13 A 1 ATOM 100 C CG1 . VAL A 1 13 ? 6.403 -6.697 1.892 1.00 87.65 13 A 1 ATOM 101 C CG2 . VAL A 1 13 ? 5.892 -4.481 0.879 1.00 87.69 13 A 1 ATOM 102 N N . CYS A 1 14 ? 3.731 -8.344 -0.142 1.00 91.38 14 A 1 ATOM 103 C CA . CYS A 1 14 ? 3.271 -9.723 0.007 1.00 92.08 14 A 1 ATOM 104 C C . CYS A 1 14 ? 3.492 -10.525 -1.275 1.00 92.29 14 A 1 ATOM 105 O O . CYS A 1 14 ? 3.928 -11.675 -1.226 1.00 90.20 14 A 1 ATOM 106 C CB . CYS A 1 14 ? 1.790 -9.732 0.384 1.00 89.79 14 A 1 ATOM 107 S SG . CYS A 1 14 ? 1.238 -11.378 0.853 1.00 84.59 14 A 1 ATOM 108 N N . GLU A 1 15 ? 3.177 -9.924 -2.402 1.00 90.17 15 A 1 ATOM 109 C CA . GLU A 1 15 ? 3.320 -10.605 -3.691 1.00 90.36 15 A 1 ATOM 110 C C . GLU A 1 15 ? 4.774 -10.711 -4.114 1.00 90.40 15 A 1 ATOM 111 O O . GLU A 1 15 ? 5.140 -11.643 -4.837 1.00 87.38 15 A 1 ATOM 112 C CB . GLU A 1 15 ? 2.499 -9.872 -4.757 1.00 88.27 15 A 1 ATOM 113 C CG . GLU A 1 15 ? 3.068 -8.524 -5.167 1.00 80.29 15 A 1 ATOM 114 C CD . GLU A 1 15 ? 4.027 -8.648 -6.333 1.00 76.52 15 A 1 ATOM 115 O OE1 . GLU A 1 15 ? 3.981 -9.656 -7.047 1.00 71.98 15 A 1 ATOM 116 O OE2 . GLU A 1 15 ? 4.832 -7.724 -6.520 1.00 73.27 15 A 1 ATOM 117 N N . ALA A 1 16 ? 5.588 -9.774 -3.699 1.00 89.66 16 A 1 ATOM 118 C CA . ALA A 1 16 ? 7.007 -9.752 -4.045 1.00 88.59 16 A 1 ATOM 119 C C . ALA A 1 16 ? 7.722 -10.970 -3.470 1.00 86.28 16 A 1 ATOM 120 O O . ALA A 1 16 ? 8.319 -11.735 -4.247 1.00 81.83 16 A 1 ATOM 121 C CB . ALA A 1 16 ? 7.649 -8.460 -3.539 1.00 84.52 16 A 1 ATOM 122 O OXT . ALA A 1 16 ? 7.696 -11.150 -2.258 1.00 76.19 16 A 1 #