# 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_spkb42027 # _entry.id spkb42027 # 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" "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" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])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" "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 LYS 2 1 n PHE 3 1 n ILE 4 1 n ILE 5 1 n LEU 6 1 n THR 7 1 n CYS 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n VAL 12 1 n ALA 13 1 n LEU 14 1 n ALA 15 # _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 @ 2025-07-05 00:35:45)" _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 94.62 _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 89.43 1 1 A LYS 2 2 90.05 1 2 A PHE 3 2 92.18 1 3 A ILE 4 2 96.06 1 4 A ILE 5 2 96.78 1 5 A LEU 6 2 95.35 1 6 A THR 7 2 95.83 1 7 A CYS 8 2 96.83 1 8 A LEU 9 2 96.19 1 9 A LEU 10 2 96.04 1 10 A ALA 11 2 97.72 1 11 A VAL 12 2 96.76 1 12 A ALA 13 2 97.72 1 13 A LEU 14 2 94.36 1 14 A ALA 15 2 92.22 1 15 # _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 LYS . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n THR . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 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 ALA . 15 A 15 # _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 ? 3.610 9.888 -3.198 1.00 94.10 1 A 1 ATOM 2 C CA . MET A 1 1 ? 2.828 8.665 -3.397 1.00 94.76 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.602 7.431 -2.940 1.00 95.28 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.868 6.523 -3.725 1.00 93.40 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.481 8.513 -4.876 1.00 92.30 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.585 9.611 -5.381 1.00 88.10 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.245 9.439 -7.137 1.00 83.64 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.010 10.905 -7.768 1.00 73.86 1 A 1 ATOM 9 N N . LYS A 1 2 ? 3.974 7.435 -1.683 1.00 95.54 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 4.728 6.320 -1.124 1.00 96.10 2 A 1 ATOM 11 C C . LYS A 1 2 ? 3.818 5.410 -0.302 1.00 96.74 2 A 1 ATOM 12 O O . LYS A 1 2 ? 3.960 4.192 -0.312 1.00 96.33 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 5.865 6.861 -0.257 1.00 94.78 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 7.152 6.091 -0.414 1.00 90.26 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 8.268 6.999 -0.916 1.00 86.53 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 9.527 6.222 -1.207 1.00 80.44 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 10.636 7.118 -1.644 1.00 73.71 2 A 1 ATOM 18 N N . PHE A 1 3 ? 2.893 6.026 0.383 1.00 95.70 3 A 1 ATOM 19 C CA . PHE A 1 3 ? 1.946 5.281 1.198 1.00 96.63 3 A 1 ATOM 20 C C . PHE A 1 3 ? 0.927 4.559 0.332 1.00 97.42 3 A 1 ATOM 21 O O . PHE A 1 3 ? 0.364 3.542 0.731 1.00 96.74 3 A 1 ATOM 22 C CB . PHE A 1 3 ? 1.235 6.231 2.161 1.00 95.74 3 A 1 ATOM 23 C CG . PHE A 1 3 ? 1.785 6.145 3.560 1.00 92.76 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? 3.097 6.489 3.826 1.00 89.31 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? 0.980 5.709 4.594 1.00 87.89 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? 3.608 6.399 5.107 1.00 87.39 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? 1.482 5.621 5.881 1.00 87.66 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? 2.799 5.968 6.141 1.00 86.70 3 A 1 ATOM 29 N N . ILE A 1 4 ? 0.697 5.093 -0.848 1.00 97.35 4 A 1 ATOM 30 C CA . ILE A 1 4 ? -0.255 4.511 -1.785 1.00 97.55 4 A 1 ATOM 31 C C . ILE A 1 4 ? 0.179 3.114 -2.202 1.00 97.70 4 A 1 ATOM 32 O O . ILE A 1 4 ? -0.600 2.165 -2.175 1.00 97.30 4 A 1 ATOM 33 C CB . ILE A 1 4 ? -0.401 5.384 -3.043 1.00 97.44 4 A 1 ATOM 34 C CG1 . ILE A 1 4 ? -0.557 6.857 -2.672 1.00 95.54 4 A 1 ATOM 35 C CG2 . ILE A 1 4 ? -1.595 4.902 -3.866 1.00 95.06 4 A 1 ATOM 36 C CD1 . ILE A 1 4 ? -1.817 7.144 -1.898 1.00 90.53 4 A 1 ATOM 37 N N . ILE A 1 5 ? 1.429 3.018 -2.601 1.00 97.73 5 A 1 ATOM 38 C CA . ILE A 1 5 ? 1.978 1.744 -3.043 1.00 97.59 5 A 1 ATOM 39 C C . ILE A 1 5 ? 2.038 0.742 -1.896 1.00 97.50 5 A 1 ATOM 40 O O . ILE A 1 5 ? 1.777 -0.446 -2.078 1.00 97.22 5 A 1 ATOM 41 C CB . ILE A 1 5 ? 3.387 1.939 -3.638 1.00 97.55 5 A 1 ATOM 42 C CG1 . ILE A 1 5 ? 4.303 2.655 -2.655 1.00 96.58 5 A 1 ATOM 43 C CG2 . ILE A 1 5 ? 3.303 2.711 -4.949 1.00 96.42 5 A 1 ATOM 44 C CD1 . ILE A 1 5 ? 5.764 2.402 -2.922 1.00 93.64 5 A 1 ATOM 45 N N . LEU A 1 6 ? 2.390 1.240 -0.739 1.00 97.72 6 A 1 ATOM 46 C CA . LEU A 1 6 ? 2.476 0.398 0.446 1.00 97.67 6 A 1 ATOM 47 C C . LEU A 1 6 ? 1.105 -0.155 0.811 1.00 97.85 6 A 1 ATOM 48 O O . LEU A 1 6 ? 0.961 -1.332 1.139 1.00 97.81 6 A 1 ATOM 49 C CB . LEU A 1 6 ? 3.035 1.200 1.622 1.00 97.43 6 A 1 ATOM 50 C CG . LEU A 1 6 ? 3.614 0.327 2.731 1.00 92.66 6 A 1 ATOM 51 C CD1 . LEU A 1 6 ? 4.985 -0.194 2.324 1.00 90.58 6 A 1 ATOM 52 C CD2 . LEU A 1 6 ? 3.713 1.103 4.034 1.00 91.07 6 A 1 ATOM 53 N N . THR A 1 7 ? 0.118 0.700 0.746 1.00 97.47 7 A 1 ATOM 54 C CA . THR A 1 7 ? -1.254 0.317 1.062 1.00 97.36 7 A 1 ATOM 55 C C . THR A 1 7 ? -1.771 -0.688 0.041 1.00 97.62 7 A 1 ATOM 56 O O . THR A 1 7 ? -2.500 -1.622 0.381 1.00 97.36 7 A 1 ATOM 57 C CB . THR A 1 7 ? -2.170 1.546 1.075 1.00 96.85 7 A 1 ATOM 58 O OG1 . THR A 1 7 ? -1.666 2.513 1.988 1.00 92.73 7 A 1 ATOM 59 C CG2 . THR A 1 7 ? -3.578 1.154 1.506 1.00 91.39 7 A 1 ATOM 60 N N . CYS A 1 8 ? -1.388 -0.484 -1.196 1.00 97.21 8 A 1 ATOM 61 C CA . CYS A 1 8 ? -1.809 -1.361 -2.277 1.00 97.36 8 A 1 ATOM 62 C C . CYS A 1 8 ? -1.295 -2.778 -2.050 1.00 97.54 8 A 1 ATOM 63 O O . CYS A 1 8 ? -2.017 -3.753 -2.241 1.00 96.86 8 A 1 ATOM 64 C CB . CYS A 1 8 ? -1.294 -0.825 -3.611 1.00 97.17 8 A 1 ATOM 65 S SG . CYS A 1 8 ? -1.996 -1.673 -5.032 1.00 94.81 8 A 1 ATOM 66 N N . LEU A 1 9 ? -0.057 -2.866 -1.646 1.00 97.40 9 A 1 ATOM 67 C CA . LEU A 1 9 ? 0.562 -4.160 -1.391 1.00 97.43 9 A 1 ATOM 68 C C . LEU A 1 9 ? -0.134 -4.876 -0.241 1.00 97.75 9 A 1 ATOM 69 O O . LEU A 1 9 ? -0.345 -6.089 -0.284 1.00 97.56 9 A 1 ATOM 70 C CB . LEU A 1 9 ? 2.045 -3.964 -1.068 1.00 97.28 9 A 1 ATOM 71 C CG . LEU A 1 9 ? 2.897 -5.210 -1.266 1.00 95.52 9 A 1 ATOM 72 C CD1 . LEU A 1 9 ? 4.260 -4.832 -1.831 1.00 93.32 9 A 1 ATOM 73 C CD2 . LEU A 1 9 ? 3.069 -5.959 0.037 1.00 93.23 9 A 1 ATOM 74 N N . LEU A 1 10 ? -0.470 -4.119 0.769 1.00 97.64 10 A 1 ATOM 75 C CA . LEU A 1 10 ? -1.151 -4.670 1.933 1.00 97.58 10 A 1 ATOM 76 C C . LEU A 1 10 ? -2.552 -5.133 1.566 1.00 97.98 10 A 1 ATOM 77 O O . LEU A 1 10 ? -3.025 -6.166 2.044 1.00 97.83 10 A 1 ATOM 78 C CB . LEU A 1 10 ? -1.213 -3.612 3.036 1.00 97.10 10 A 1 ATOM 79 C CG . LEU A 1 10 ? -1.058 -4.177 4.443 1.00 94.64 10 A 1 ATOM 80 C CD1 . LEU A 1 10 ? -0.538 -3.108 5.388 1.00 92.49 10 A 1 ATOM 81 C CD2 . LEU A 1 10 ? -2.377 -4.727 4.945 1.00 93.06 10 A 1 ATOM 82 N N . ALA A 1 11 ? -3.206 -4.358 0.726 1.00 97.82 11 A 1 ATOM 83 C CA . ALA A 1 11 ? -4.555 -4.683 0.284 1.00 97.85 11 A 1 ATOM 84 C C . ALA A 1 11 ? -4.559 -5.929 -0.588 1.00 98.07 11 A 1 ATOM 85 O O . ALA A 1 11 ? -5.444 -6.775 -0.473 1.00 97.50 11 A 1 ATOM 86 C CB . ALA A 1 11 ? -5.144 -3.507 -0.479 1.00 97.34 11 A 1 ATOM 87 N N . VAL A 1 12 ? -3.575 -6.039 -1.449 1.00 97.85 12 A 1 ATOM 88 C CA . VAL A 1 12 ? -3.458 -7.185 -2.344 1.00 97.70 12 A 1 ATOM 89 C C . VAL A 1 12 ? -3.218 -8.459 -1.553 1.00 97.95 12 A 1 ATOM 90 O O . VAL A 1 12 ? -3.774 -9.517 -1.858 1.00 97.48 12 A 1 ATOM 91 C CB . VAL A 1 12 ? -2.315 -6.981 -3.348 1.00 96.95 12 A 1 ATOM 92 C CG1 . VAL A 1 12 ? -2.087 -8.240 -4.168 1.00 94.70 12 A 1 ATOM 93 C CG2 . VAL A 1 12 ? -2.621 -5.810 -4.260 1.00 94.70 12 A 1 ATOM 94 N N . ALA A 1 13 ? -2.385 -8.353 -0.550 1.00 97.87 13 A 1 ATOM 95 C CA . ALA A 1 13 ? -2.064 -9.496 0.296 1.00 97.90 13 A 1 ATOM 96 C C . ALA A 1 13 ? -3.271 -9.918 1.126 1.00 98.11 13 A 1 ATOM 97 O O . ALA A 1 13 ? -3.442 -11.096 1.437 1.00 97.43 13 A 1 ATOM 98 C CB . ALA A 1 13 ? -0.896 -9.155 1.213 1.00 97.31 13 A 1 ATOM 99 N N . LEU A 1 14 ? -4.075 -8.948 1.488 1.00 97.41 14 A 1 ATOM 100 C CA . LEU A 1 14 ? -5.264 -9.197 2.288 1.00 97.23 14 A 1 ATOM 101 C C . LEU A 1 14 ? -6.342 -9.875 1.461 1.00 97.32 14 A 1 ATOM 102 O O . LEU A 1 14 ? -6.994 -10.824 1.913 1.00 96.10 14 A 1 ATOM 103 C CB . LEU A 1 14 ? -5.784 -7.880 2.871 1.00 96.30 14 A 1 ATOM 104 C CG . LEU A 1 14 ? -6.494 -8.020 4.216 1.00 93.03 14 A 1 ATOM 105 C CD1 . LEU A 1 14 ? -6.580 -6.669 4.907 1.00 89.27 14 A 1 ATOM 106 C CD2 . LEU A 1 14 ? -7.879 -8.608 4.042 1.00 88.25 14 A 1 ATOM 107 N N . ALA A 1 15 ? -6.540 -9.382 0.259 1.00 95.93 15 A 1 ATOM 108 C CA . ALA A 1 15 ? -7.551 -9.922 -0.640 1.00 95.18 15 A 1 ATOM 109 C C . ALA A 1 15 ? -7.019 -11.143 -1.373 1.00 94.72 15 A 1 ATOM 110 O O . ALA A 1 15 ? -7.234 -12.278 -0.888 1.00 90.81 15 A 1 ATOM 111 C CB . ALA A 1 15 ? -7.998 -8.853 -1.629 1.00 92.47 15 A 1 ATOM 112 O OXT . ALA A 1 15 ? -6.378 -10.973 -2.402 1.00 84.23 15 A 1 #