# 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_spkb08305 # _entry.id spkb08305 # 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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O3" 105.093 SER y SERINE C([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 GLU 2 1 n PRO 3 1 n LEU 4 1 n ALA 5 1 n ILE 6 1 n LEU 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n SER 11 1 n LEU 12 1 n PRO 13 1 n ILE 14 1 n CYS 15 1 n SER 16 1 n ALA 17 # _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 @ 2025-07-04 07:22:11)" _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 88.92 _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 82.99 1 1 A GLU 2 2 82.11 1 2 A PRO 3 2 91.17 1 3 A LEU 4 2 89.02 1 4 A ALA 5 2 94.09 1 5 A ILE 6 2 91.84 1 6 A LEU 7 2 90.87 1 7 A ALA 8 2 93.94 1 8 A LEU 9 2 91.20 1 9 A LEU 10 2 92.45 1 10 A SER 11 2 92.27 1 11 A LEU 12 2 89.85 1 12 A PRO 13 2 91.90 1 13 A ILE 14 2 86.68 1 14 A CYS 15 2 84.72 1 15 A SER 16 2 86.06 1 16 A ALA 17 2 83.48 1 17 # _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 GLU . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n PRO . 13 A 13 A 14 1 n ILE . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n SER . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? -13.114 -2.234 5.295 1.00 88.31 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.865 -2.763 4.705 1.00 89.77 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.657 -2.408 5.575 1.00 90.38 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.800 -1.984 6.717 1.00 88.77 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.680 -2.175 3.313 1.00 86.36 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.623 -2.816 2.295 1.00 80.20 1 A 1 ATOM 7 S SD . MET A 1 1 ? -11.991 -4.405 1.750 1.00 74.74 1 A 1 ATOM 8 C CE . MET A 1 1 ? -13.189 -4.809 0.484 1.00 65.38 1 A 1 ATOM 9 N N . GLU A 1 2 ? -9.467 -2.556 5.026 1.00 87.72 2 A 1 ATOM 10 C CA . GLU A 1 2 ? -8.231 -2.245 5.744 1.00 90.88 2 A 1 ATOM 11 C C . GLU A 1 2 ? -7.562 -0.998 5.165 1.00 91.86 2 A 1 ATOM 12 O O . GLU A 1 2 ? -6.650 -1.100 4.342 1.00 90.88 2 A 1 ATOM 13 C CB . GLU A 1 2 ? -7.274 -3.430 5.654 1.00 86.58 2 A 1 ATOM 14 C CG . GLU A 1 2 ? -7.754 -4.645 6.435 1.00 75.94 2 A 1 ATOM 15 C CD . GLU A 1 2 ? -7.583 -4.446 7.933 1.00 74.98 2 A 1 ATOM 16 O OE1 . GLU A 1 2 ? -6.662 -3.723 8.320 1.00 67.65 2 A 1 ATOM 17 O OE2 . GLU A 1 2 ? -8.370 -5.023 8.697 1.00 72.52 2 A 1 ATOM 18 N N . PRO A 1 3 ? -8.008 0.174 5.582 1.00 91.18 3 A 1 ATOM 19 C CA . PRO A 1 3 ? -7.431 1.431 5.086 1.00 93.22 3 A 1 ATOM 20 C C . PRO A 1 3 ? -5.957 1.568 5.454 1.00 94.25 3 A 1 ATOM 21 O O . PRO A 1 3 ? -5.194 2.240 4.755 1.00 91.92 3 A 1 ATOM 22 C CB . PRO A 1 3 ? -8.280 2.512 5.768 1.00 90.10 3 A 1 ATOM 23 C CG . PRO A 1 3 ? -8.840 1.840 6.981 1.00 87.60 3 A 1 ATOM 24 C CD . PRO A 1 3 ? -9.053 0.401 6.578 1.00 89.91 3 A 1 ATOM 25 N N . LEU A 1 4 ? -5.559 0.921 6.534 1.00 92.42 4 A 1 ATOM 26 C CA . LEU A 1 4 ? -4.168 0.955 6.978 1.00 92.77 4 A 1 ATOM 27 C C . LEU A 1 4 ? -3.263 0.323 5.924 1.00 94.00 4 A 1 ATOM 28 O O . LEU A 1 4 ? -2.151 0.784 5.673 1.00 92.73 4 A 1 ATOM 29 C CB . LEU A 1 4 ? -4.028 0.209 8.314 1.00 91.32 4 A 1 ATOM 30 C CG . LEU A 1 4 ? -2.999 0.825 9.252 1.00 86.33 4 A 1 ATOM 31 C CD1 . LEU A 1 4 ? -1.619 0.846 8.632 1.00 81.73 4 A 1 ATOM 32 C CD2 . LEU A 1 4 ? -3.447 2.238 9.625 1.00 80.87 4 A 1 ATOM 33 N N . ALA A 1 5 ? -3.757 -0.745 5.309 1.00 93.47 5 A 1 ATOM 34 C CA . ALA A 1 5 ? -2.994 -1.439 4.269 1.00 94.26 5 A 1 ATOM 35 C C . ALA A 1 5 ? -2.765 -0.518 3.075 1.00 95.05 5 A 1 ATOM 36 O O . ALA A 1 5 ? -1.703 -0.537 2.452 1.00 94.21 5 A 1 ATOM 37 C CB . ALA A 1 5 ? -3.736 -2.696 3.831 1.00 93.44 5 A 1 ATOM 38 N N . ILE A 1 6 ? -3.769 0.283 2.766 1.00 93.50 6 A 1 ATOM 39 C CA . ILE A 1 6 ? -3.668 1.227 1.653 1.00 93.44 6 A 1 ATOM 40 C C . ILE A 1 6 ? -2.593 2.268 1.947 1.00 94.14 6 A 1 ATOM 41 O O . ILE A 1 6 ? -1.790 2.616 1.077 1.00 93.25 6 A 1 ATOM 42 C CB . ILE A 1 6 ? -5.019 1.917 1.402 1.00 93.33 6 A 1 ATOM 43 C CG1 . ILE A 1 6 ? -6.091 0.873 1.069 1.00 90.58 6 A 1 ATOM 44 C CG2 . ILE A 1 6 ? -4.888 2.919 0.252 1.00 89.89 6 A 1 ATOM 45 C CD1 . ILE A 1 6 ? -7.490 1.457 1.033 1.00 86.63 6 A 1 ATOM 46 N N . LEU A 1 7 ? -2.574 2.742 3.171 1.00 93.79 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -1.582 3.736 3.578 1.00 93.47 7 A 1 ATOM 48 C C . LEU A 1 7 ? -0.172 3.165 3.454 1.00 94.49 7 A 1 ATOM 49 O O . LEU A 1 7 ? 0.756 3.857 3.029 1.00 94.00 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -1.845 4.155 5.024 1.00 92.47 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -3.115 4.980 5.198 1.00 87.66 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -3.421 5.161 6.677 1.00 85.33 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -2.957 6.340 4.529 1.00 85.74 7 A 1 ATOM 54 N N . ALA A 1 8 ? -0.024 1.902 3.826 1.00 93.67 8 A 1 ATOM 55 C CA . ALA A 1 8 ? 1.271 1.229 3.742 1.00 93.92 8 A 1 ATOM 56 C C . ALA A 1 8 ? 1.717 1.110 2.286 1.00 94.84 8 A 1 ATOM 57 O O . ALA A 1 8 ? 2.887 1.319 1.964 1.00 93.65 8 A 1 ATOM 58 C CB . ALA A 1 8 ? 1.177 -0.155 4.371 1.00 93.62 8 A 1 ATOM 59 N N . LEU A 1 9 ? 0.771 0.772 1.417 1.00 93.43 9 A 1 ATOM 60 C CA . LEU A 1 9 ? 1.069 0.626 -0.007 1.00 93.35 9 A 1 ATOM 61 C C . LEU A 1 9 ? 1.494 1.963 -0.602 1.00 94.08 9 A 1 ATOM 62 O O . LEU A 1 9 ? 2.372 2.018 -1.465 1.00 92.57 9 A 1 ATOM 63 C CB . LEU A 1 9 ? -0.165 0.093 -0.741 1.00 92.71 9 A 1 ATOM 64 C CG . LEU A 1 9 ? -0.473 -1.375 -0.457 1.00 89.12 9 A 1 ATOM 65 C CD1 . LEU A 1 9 ? -1.844 -1.750 -1.009 1.00 86.98 9 A 1 ATOM 66 C CD2 . LEU A 1 9 ? 0.594 -2.275 -1.071 1.00 87.35 9 A 1 ATOM 67 N N . LEU A 1 10 ? 0.871 3.032 -0.146 1.00 93.98 10 A 1 ATOM 68 C CA . LEU A 1 10 ? 1.202 4.371 -0.624 1.00 93.82 10 A 1 ATOM 69 C C . LEU A 1 10 ? 2.604 4.769 -0.171 1.00 94.93 10 A 1 ATOM 70 O O . LEU A 1 10 ? 3.321 5.485 -0.871 1.00 93.82 10 A 1 ATOM 71 C CB . LEU A 1 10 ? 0.168 5.380 -0.100 1.00 93.47 10 A 1 ATOM 72 C CG . LEU A 1 10 ? -0.880 5.794 -1.127 1.00 91.24 10 A 1 ATOM 73 C CD1 . LEU A 1 10 ? -0.217 6.558 -2.255 1.00 88.91 10 A 1 ATOM 74 C CD2 . LEU A 1 10 ? -1.604 4.577 -1.661 1.00 89.45 10 A 1 ATOM 75 N N . SER A 1 11 ? 2.980 4.299 1.000 1.00 94.27 11 A 1 ATOM 76 C CA . SER A 1 11 ? 4.290 4.611 1.565 1.00 94.48 11 A 1 ATOM 77 C C . SER A 1 11 ? 5.398 3.826 0.874 1.00 94.51 11 A 1 ATOM 78 O O . SER A 1 11 ? 6.552 4.255 0.855 1.00 92.05 11 A 1 ATOM 79 C CB . SER A 1 11 ? 4.303 4.302 3.059 1.00 92.80 11 A 1 ATOM 80 O OG . SER A 1 11 ? 5.564 4.594 3.609 1.00 85.53 11 A 1 ATOM 81 N N . LEU A 1 12 ? 5.047 2.683 0.302 1.00 92.68 12 A 1 ATOM 82 C CA . LEU A 1 12 ? 6.028 1.834 -0.377 1.00 92.22 12 A 1 ATOM 83 C C . LEU A 1 12 ? 6.799 2.609 -1.449 1.00 93.14 12 A 1 ATOM 84 O O . LEU A 1 12 ? 8.031 2.663 -1.408 1.00 91.56 12 A 1 ATOM 85 C CB . LEU A 1 12 ? 5.330 0.618 -1.000 1.00 91.15 12 A 1 ATOM 86 C CG . LEU A 1 12 ? 6.289 -0.372 -1.658 1.00 88.51 12 A 1 ATOM 87 C CD1 . LEU A 1 12 ? 7.081 -1.116 -0.592 1.00 85.09 12 A 1 ATOM 88 C CD2 . LEU A 1 12 ? 5.512 -1.356 -2.522 1.00 84.43 12 A 1 ATOM 89 N N . PRO A 1 13 ? 6.095 3.197 -2.427 1.00 92.68 13 A 1 ATOM 90 C CA . PRO A 1 13 ? 6.771 3.953 -3.486 1.00 92.73 13 A 1 ATOM 91 C C . PRO A 1 13 ? 7.489 5.182 -2.950 1.00 93.06 13 A 1 ATOM 92 O O . PRO A 1 13 ? 8.531 5.577 -3.471 1.00 90.28 13 A 1 ATOM 93 C CB . PRO A 1 13 ? 5.632 4.350 -4.433 1.00 91.11 13 A 1 ATOM 94 C CG . PRO A 1 13 ? 4.412 4.317 -3.577 1.00 90.47 13 A 1 ATOM 95 C CD . PRO A 1 13 ? 4.647 3.203 -2.588 1.00 92.97 13 A 1 ATOM 96 N N . ILE A 1 14 ? 6.949 5.780 -1.918 1.00 89.96 14 A 1 ATOM 97 C CA . ILE A 1 14 ? 7.553 6.961 -1.311 1.00 89.69 14 A 1 ATOM 98 C C . ILE A 1 14 ? 8.882 6.606 -0.653 1.00 90.10 14 A 1 ATOM 99 O O . ILE A 1 14 ? 9.875 7.320 -0.805 1.00 87.94 14 A 1 ATOM 100 C CB . ILE A 1 14 ? 6.607 7.578 -0.268 1.00 88.87 14 A 1 ATOM 101 C CG1 . ILE A 1 14 ? 5.293 7.995 -0.925 1.00 85.62 14 A 1 ATOM 102 C CG2 . ILE A 1 14 ? 7.281 8.785 0.384 1.00 83.83 14 A 1 ATOM 103 C CD1 . ILE A 1 14 ? 4.240 8.392 0.090 1.00 77.45 14 A 1 ATOM 104 N N . CYS A 1 15 ? 8.895 5.497 0.078 1.00 86.36 15 A 1 ATOM 105 C CA . CYS A 1 15 ? 10.112 5.044 0.747 1.00 86.54 15 A 1 ATOM 106 C C . CYS A 1 15 ? 11.152 4.585 -0.269 1.00 87.46 15 A 1 ATOM 107 O O . CYS A 1 15 ? 12.348 4.769 -0.071 1.00 85.46 15 A 1 ATOM 108 C CB . CYS A 1 15 ? 9.786 3.898 1.709 1.00 83.81 15 A 1 ATOM 109 S SG . CYS A 1 15 ? 8.836 4.439 3.145 1.00 78.69 15 A 1 ATOM 110 N N . SER A 1 16 ? 10.681 3.968 -1.342 1.00 88.36 16 A 1 ATOM 111 C CA . SER A 1 16 ? 11.567 3.477 -2.392 1.00 88.51 16 A 1 ATOM 112 C C . SER A 1 16 ? 12.205 4.632 -3.152 1.00 88.76 16 A 1 ATOM 113 O O . SER A 1 16 ? 13.350 4.536 -3.600 1.00 86.81 16 A 1 ATOM 114 C CB . SER A 1 16 ? 10.791 2.587 -3.360 1.00 86.51 16 A 1 ATOM 115 O OG . SER A 1 16 ? 11.639 2.108 -4.372 1.00 77.42 16 A 1 ATOM 116 N N . ALA A 1 17 ? 11.477 5.715 -3.306 1.00 90.23 17 A 1 ATOM 117 C CA . ALA A 1 17 ? 11.954 6.891 -4.027 1.00 87.79 17 A 1 ATOM 118 C C . ALA A 1 17 ? 13.155 7.504 -3.311 1.00 84.76 17 A 1 ATOM 119 O O . ALA A 1 17 ? 14.168 7.773 -3.978 1.00 80.90 17 A 1 ATOM 120 C CB . ALA A 1 17 ? 10.830 7.909 -4.160 1.00 82.64 17 A 1 ATOM 121 O OXT . ALA A 1 17 ? 13.056 7.737 -2.102 1.00 74.53 17 A 1 #