# 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_spkb23168 # _entry.id spkb23168 # 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 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=O)N ? "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 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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 ASN 2 1 n VAL 3 1 n PHE 4 1 n ILE 5 1 n SER 6 1 n VAL 7 1 n VAL 8 1 n LEU 9 1 n PHE 10 1 n LEU 11 1 n GLY 12 1 n SER 13 1 n ALA 14 1 n ARG 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 @ 2025-07-06 18:30:28)" _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 91.17 _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 80.56 1 1 A ASN 2 2 86.86 1 2 A VAL 3 2 92.90 1 3 A PHE 4 2 90.78 1 4 A ILE 5 2 93.80 1 5 A SER 6 2 95.99 1 6 A VAL 7 2 95.19 1 7 A VAL 8 2 95.79 1 8 A LEU 9 2 94.50 1 9 A PHE 10 2 93.35 1 10 A LEU 11 2 94.21 1 11 A GLY 12 2 96.59 1 12 A SER 13 2 93.31 1 13 A ALA 14 2 95.23 1 14 A ARG 15 2 83.66 1 15 A ALA 16 2 83.45 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 ASN . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ARG . 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 ? -4.941 10.617 -0.320 1.00 86.28 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.117 9.612 -1.002 1.00 88.71 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.731 9.543 -0.366 1.00 90.72 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.742 9.992 -0.936 1.00 87.02 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.985 9.945 -2.490 1.00 81.78 1 A 1 ATOM 6 C CG . MET A 1 1 ? -3.297 8.863 -3.292 1.00 75.17 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.130 9.258 -5.052 1.00 71.60 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.839 9.356 -5.540 1.00 63.17 1 A 1 ATOM 9 N N . ASN A 1 2 ? -2.683 8.994 0.819 1.00 87.58 2 A 1 ATOM 10 C CA . ASN A 1 2 ? -1.432 8.866 1.548 1.00 91.75 2 A 1 ATOM 11 C C . ASN A 1 2 ? -1.334 7.503 2.222 1.00 94.19 2 A 1 ATOM 12 O O . ASN A 1 2 ? -0.511 6.669 1.841 1.00 92.77 2 A 1 ATOM 13 C CB . ASN A 1 2 ? -1.301 9.992 2.576 1.00 87.95 2 A 1 ATOM 14 C CG . ASN A 1 2 ? -2.550 10.162 3.418 1.00 83.30 2 A 1 ATOM 15 O OD1 . ASN A 1 2 ? -2.814 9.379 4.316 1.00 79.24 2 A 1 ATOM 16 N ND2 . ASN A 1 2 ? -3.317 11.197 3.125 1.00 78.11 2 A 1 ATOM 17 N N . VAL A 1 3 ? -2.190 7.275 3.209 1.00 94.03 3 A 1 ATOM 18 C CA . VAL A 1 3 ? -2.224 6.003 3.924 1.00 95.36 3 A 1 ATOM 19 C C . VAL A 1 3 ? -2.751 4.894 3.022 1.00 96.43 3 A 1 ATOM 20 O O . VAL A 1 3 ? -2.286 3.753 3.071 1.00 94.97 3 A 1 ATOM 21 C CB . VAL A 1 3 ? -3.095 6.093 5.189 1.00 93.83 3 A 1 ATOM 22 C CG1 . VAL A 1 3 ? -3.122 4.761 5.918 1.00 87.67 3 A 1 ATOM 23 C CG2 . VAL A 1 3 ? -2.582 7.190 6.105 1.00 88.00 3 A 1 ATOM 24 N N . PHE A 1 4 ? -3.725 5.253 2.171 1.00 93.19 4 A 1 ATOM 25 C CA . PHE A 1 4 ? -4.324 4.306 1.237 1.00 94.14 4 A 1 ATOM 26 C C . PHE A 1 4 ? -3.268 3.690 0.331 1.00 95.70 4 A 1 ATOM 27 O O . PHE A 1 4 ? -3.239 2.475 0.123 1.00 95.04 4 A 1 ATOM 28 C CB . PHE A 1 4 ? -5.390 5.002 0.395 1.00 93.54 4 A 1 ATOM 29 C CG . PHE A 1 4 ? -6.060 4.087 -0.592 1.00 91.22 4 A 1 ATOM 30 C CD1 . PHE A 1 4 ? -7.054 3.219 -0.176 1.00 88.09 4 A 1 ATOM 31 C CD2 . PHE A 1 4 ? -5.693 4.096 -1.925 1.00 87.74 4 A 1 ATOM 32 C CE1 . PHE A 1 4 ? -7.675 2.368 -1.075 1.00 86.55 4 A 1 ATOM 33 C CE2 . PHE A 1 4 ? -6.307 3.242 -2.830 1.00 86.33 4 A 1 ATOM 34 C CZ . PHE A 1 4 ? -7.298 2.379 -2.404 1.00 87.00 4 A 1 ATOM 35 N N . ILE A 1 5 ? -2.397 4.525 -0.203 1.00 95.79 5 A 1 ATOM 36 C CA . ILE A 1 5 ? -1.327 4.064 -1.080 1.00 95.72 5 A 1 ATOM 37 C C . ILE A 1 5 ? -0.355 3.169 -0.322 1.00 96.29 5 A 1 ATOM 38 O O . ILE A 1 5 ? 0.142 2.174 -0.847 1.00 95.65 5 A 1 ATOM 39 C CB . ILE A 1 5 ? -0.569 5.249 -1.696 1.00 95.59 5 A 1 ATOM 40 C CG1 . ILE A 1 5 ? -1.521 6.128 -2.513 1.00 92.73 5 A 1 ATOM 41 C CG2 . ILE A 1 5 ? 0.579 4.756 -2.573 1.00 92.51 5 A 1 ATOM 42 C CD1 . ILE A 1 5 ? -2.207 5.375 -3.645 1.00 86.09 5 A 1 ATOM 43 N N . SER A 1 6 ? -0.087 3.520 0.916 1.00 97.14 6 A 1 ATOM 44 C CA . SER A 1 6 ? 0.810 2.738 1.760 1.00 97.30 6 A 1 ATOM 45 C C . SER A 1 6 ? 0.277 1.320 1.951 1.00 97.69 6 A 1 ATOM 46 O O . SER A 1 6 ? 1.035 0.352 1.932 1.00 96.98 6 A 1 ATOM 47 C CB . SER A 1 6 ? 0.984 3.408 3.117 1.00 96.67 6 A 1 ATOM 48 O OG . SER A 1 6 ? 1.576 4.689 2.971 1.00 90.15 6 A 1 ATOM 49 N N . VAL A 1 7 ? -1.037 1.203 2.117 1.00 96.05 7 A 1 ATOM 50 C CA . VAL A 1 7 ? -1.684 -0.095 2.285 1.00 96.26 7 A 1 ATOM 51 C C . VAL A 1 7 ? -1.525 -0.938 1.026 1.00 96.59 7 A 1 ATOM 52 O O . VAL A 1 7 ? -1.237 -2.136 1.091 1.00 95.72 7 A 1 ATOM 53 C CB . VAL A 1 7 ? -3.180 0.060 2.612 1.00 95.91 7 A 1 ATOM 54 C CG1 . VAL A 1 7 ? -3.857 -1.302 2.707 1.00 93.04 7 A 1 ATOM 55 C CG2 . VAL A 1 7 ? -3.355 0.833 3.907 1.00 92.74 7 A 1 ATOM 56 N N . VAL A 1 8 ? -1.713 -0.307 -0.125 1.00 96.57 8 A 1 ATOM 57 C CA . VAL A 1 8 ? -1.577 -0.990 -1.408 1.00 96.48 8 A 1 ATOM 58 C C . VAL A 1 8 ? -0.159 -1.518 -1.587 1.00 96.76 8 A 1 ATOM 59 O O . VAL A 1 8 ? 0.050 -2.650 -2.028 1.00 96.38 8 A 1 ATOM 60 C CB . VAL A 1 8 ? -1.927 -0.056 -2.578 1.00 96.03 8 A 1 ATOM 61 C CG1 . VAL A 1 8 ? -1.710 -0.758 -3.911 1.00 94.29 8 A 1 ATOM 62 C CG2 . VAL A 1 8 ? -3.362 0.420 -2.455 1.00 94.00 8 A 1 ATOM 63 N N . LEU A 1 9 ? 0.815 -0.697 -1.233 1.00 96.64 9 A 1 ATOM 64 C CA . LEU A 1 9 ? 2.215 -1.081 -1.343 1.00 96.55 9 A 1 ATOM 65 C C . LEU A 1 9 ? 2.538 -2.231 -0.397 1.00 96.95 9 A 1 ATOM 66 O O . LEU A 1 9 ? 3.317 -3.124 -0.730 1.00 96.75 9 A 1 ATOM 67 C CB . LEU A 1 9 ? 3.117 0.114 -1.029 1.00 96.27 9 A 1 ATOM 68 C CG . LEU A 1 9 ? 3.038 1.254 -2.043 1.00 92.58 9 A 1 ATOM 69 C CD1 . LEU A 1 9 ? 3.866 2.439 -1.567 1.00 90.17 9 A 1 ATOM 70 C CD2 . LEU A 1 9 ? 3.515 0.790 -3.408 1.00 90.09 9 A 1 ATOM 71 N N . PHE A 1 10 ? 1.936 -2.205 0.783 1.00 95.93 10 A 1 ATOM 72 C CA . PHE A 1 10 ? 2.118 -3.253 1.779 1.00 95.59 10 A 1 ATOM 73 C C . PHE A 1 10 ? 1.705 -4.605 1.223 1.00 96.31 10 A 1 ATOM 74 O O . PHE A 1 10 ? 2.449 -5.585 1.317 1.00 95.69 10 A 1 ATOM 75 C CB . PHE A 1 10 ? 1.299 -2.933 3.028 1.00 95.25 10 A 1 ATOM 76 C CG . PHE A 1 10 ? 1.286 -4.054 4.035 1.00 93.66 10 A 1 ATOM 77 C CD1 . PHE A 1 10 ? 2.382 -4.280 4.847 1.00 91.53 10 A 1 ATOM 78 C CD2 . PHE A 1 10 ? 0.179 -4.874 4.160 1.00 91.47 10 A 1 ATOM 79 C CE1 . PHE A 1 10 ? 2.376 -5.313 5.768 1.00 90.63 10 A 1 ATOM 80 C CE2 . PHE A 1 10 ? 0.172 -5.913 5.081 1.00 90.13 10 A 1 ATOM 81 C CZ . PHE A 1 10 ? 1.271 -6.129 5.884 1.00 90.67 10 A 1 ATOM 82 N N . LEU A 1 11 ? 0.517 -4.659 0.635 1.00 96.71 11 A 1 ATOM 83 C CA . LEU A 1 11 ? -0.004 -5.890 0.061 1.00 96.58 11 A 1 ATOM 84 C C . LEU A 1 11 ? 0.785 -6.303 -1.171 1.00 96.63 11 A 1 ATOM 85 O O . LEU A 1 11 ? 1.081 -7.483 -1.364 1.00 95.55 11 A 1 ATOM 86 C CB . LEU A 1 11 ? -1.478 -5.717 -0.306 1.00 96.10 11 A 1 ATOM 87 C CG . LEU A 1 11 ? -2.409 -5.461 0.878 1.00 92.83 11 A 1 ATOM 88 C CD1 . LEU A 1 11 ? -3.815 -5.151 0.387 1.00 89.91 11 A 1 ATOM 89 C CD2 . LEU A 1 11 ? -2.418 -6.660 1.812 1.00 89.37 11 A 1 ATOM 90 N N . GLY A 1 12 ? 1.119 -5.330 -2.005 1.00 96.87 12 A 1 ATOM 91 C CA . GLY A 1 12 ? 1.883 -5.592 -3.215 1.00 96.53 12 A 1 ATOM 92 C C . GLY A 1 12 ? 3.253 -6.160 -2.924 1.00 96.96 12 A 1 ATOM 93 O O . GLY A 1 12 ? 3.708 -7.091 -3.588 1.00 95.99 12 A 1 ATOM 94 N N . SER A 1 13 ? 3.920 -5.613 -1.917 1.00 96.38 13 A 1 ATOM 95 C CA . SER A 1 13 ? 5.248 -6.063 -1.524 1.00 96.18 13 A 1 ATOM 96 C C . SER A 1 13 ? 5.202 -7.459 -0.921 1.00 95.92 13 A 1 ATOM 97 O O . SER A 1 13 ? 6.090 -8.277 -1.161 1.00 93.09 13 A 1 ATOM 98 C CB . SER A 1 13 ? 5.866 -5.096 -0.515 1.00 94.54 13 A 1 ATOM 99 O OG . SER A 1 13 ? 7.159 -5.509 -0.147 1.00 83.76 13 A 1 ATOM 100 N N . ALA A 1 14 ? 4.165 -7.737 -0.144 1.00 96.21 14 A 1 ATOM 101 C CA . ALA A 1 14 ? 4.006 -9.025 0.515 1.00 95.79 14 A 1 ATOM 102 C C . ALA A 1 14 ? 3.618 -10.130 -0.458 1.00 95.98 14 A 1 ATOM 103 O O . ALA A 1 14 ? 4.114 -11.251 -0.363 1.00 93.83 14 A 1 ATOM 104 C CB . ALA A 1 14 ? 2.964 -8.927 1.623 1.00 94.32 14 A 1 ATOM 105 N N . ARG A 1 15 ? 2.731 -9.816 -1.393 1.00 93.64 15 A 1 ATOM 106 C CA . ARG A 1 15 ? 2.248 -10.796 -2.360 1.00 92.62 15 A 1 ATOM 107 C C . ARG A 1 15 ? 3.284 -11.084 -3.433 1.00 91.42 15 A 1 ATOM 108 O O . ARG A 1 15 ? 3.978 -12.099 -3.376 1.00 86.99 15 A 1 ATOM 109 C CB . ARG A 1 15 ? 0.937 -10.320 -2.998 1.00 89.27 15 A 1 ATOM 110 C CG . ARG A 1 15 ? 1.060 -9.005 -3.719 1.00 83.76 15 A 1 ATOM 111 C CD . ARG A 1 15 ? -0.152 -8.720 -4.588 1.00 82.89 15 A 1 ATOM 112 N NE . ARG A 1 15 ? -1.394 -8.690 -3.814 1.00 79.00 15 A 1 ATOM 113 C CZ . ARG A 1 15 ? -2.574 -8.423 -4.349 1.00 77.14 15 A 1 ATOM 114 N NH1 . ARG A 1 15 ? -2.682 -8.162 -5.647 1.00 71.83 15 A 1 ATOM 115 N NH2 . ARG A 1 15 ? -3.659 -8.417 -3.588 1.00 71.74 15 A 1 ATOM 116 N N . ALA A 1 16 ? 3.362 -10.191 -4.404 1.00 89.57 16 A 1 ATOM 117 C CA . ALA A 1 16 ? 4.308 -10.295 -5.519 1.00 88.14 16 A 1 ATOM 118 C C . ALA A 1 16 ? 3.910 -9.351 -6.650 1.00 86.55 16 A 1 ATOM 119 O O . ALA A 1 16 ? 3.611 -9.814 -7.757 1.00 81.12 16 A 1 ATOM 120 C CB . ALA A 1 16 ? 4.368 -11.719 -6.047 1.00 81.38 16 A 1 ATOM 121 O OXT . ALA A 1 16 ? 3.868 -8.117 -6.409 1.00 73.93 16 A 1 #