# 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_spkb40756 # _entry.id spkb40756 # 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 "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "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" "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 VAL 2 1 n VAL 3 1 n VAL 4 1 n ILE 5 1 n PRO 6 1 n ARG 7 1 n LEU 8 1 n LEU 9 1 n ARG 10 1 n GLY 11 1 n SER 12 1 n LEU 13 1 n GLY 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 @ 2025-07-10 04:07:34)" _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 88.23 _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 83.85 1 1 A VAL 2 2 92.18 1 2 A VAL 3 2 92.93 1 3 A VAL 4 2 91.87 1 4 A ILE 5 2 90.94 1 5 A PRO 6 2 92.84 1 6 A ARG 7 2 87.50 1 7 A LEU 8 2 91.45 1 8 A LEU 9 2 91.23 1 9 A ARG 10 2 83.99 1 10 A GLY 11 2 90.35 1 11 A SER 12 2 88.84 1 12 A LEU 13 2 83.49 1 13 A GLY 14 2 73.35 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 VAL . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n PRO . 6 A 6 A 7 1 n ARG . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ARG . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n GLY . 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 ? -4.518 12.589 1.715 1.00 88.88 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.067 11.714 2.816 1.00 91.42 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.712 12.186 3.340 1.00 91.66 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.803 12.447 2.563 1.00 86.72 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.934 10.276 2.332 1.00 86.08 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.281 9.687 1.939 1.00 78.67 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.133 7.993 1.361 1.00 77.68 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.871 7.627 1.071 1.00 69.67 1 A 1 ATOM 9 N N . VAL A 1 2 ? -2.587 12.302 4.641 1.00 93.08 2 A 1 ATOM 10 C CA . VAL A 1 2 ? -1.340 12.757 5.259 1.00 94.89 2 A 1 ATOM 11 C C . VAL A 1 2 ? -0.483 11.582 5.722 1.00 95.76 2 A 1 ATOM 12 O O . VAL A 1 2 ? 0.739 11.610 5.611 1.00 93.94 2 A 1 ATOM 13 C CB . VAL A 1 2 ? -1.643 13.665 6.462 1.00 93.13 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? -0.351 14.123 7.116 1.00 85.78 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? -2.458 14.866 6.015 1.00 88.66 2 A 1 ATOM 16 N N . VAL A 1 3 ? -1.122 10.542 6.237 1.00 95.05 3 A 1 ATOM 17 C CA . VAL A 1 3 ? -0.406 9.371 6.739 1.00 95.18 3 A 1 ATOM 18 C C . VAL A 1 3 ? -0.212 8.323 5.647 1.00 95.60 3 A 1 ATOM 19 O O . VAL A 1 3 ? 0.910 7.993 5.273 1.00 94.05 3 A 1 ATOM 20 C CB . VAL A 1 3 ? -1.164 8.755 7.919 1.00 93.79 3 A 1 ATOM 21 C CG1 . VAL A 1 3 ? -0.377 7.588 8.472 1.00 87.53 3 A 1 ATOM 22 C CG2 . VAL A 1 3 ? -1.385 9.802 8.994 1.00 89.34 3 A 1 ATOM 23 N N . VAL A 1 4 ? -1.319 7.798 5.141 1.00 94.73 4 A 1 ATOM 24 C CA . VAL A 1 4 ? -1.285 6.793 4.074 1.00 93.86 4 A 1 ATOM 25 C C . VAL A 1 4 ? -0.422 5.593 4.466 1.00 94.24 4 A 1 ATOM 26 O O . VAL A 1 4 ? 0.471 5.183 3.726 1.00 92.87 4 A 1 ATOM 27 C CB . VAL A 1 4 ? -0.732 7.404 2.782 1.00 92.00 4 A 1 ATOM 28 C CG1 . VAL A 1 4 ? -1.015 6.471 1.617 1.00 86.94 4 A 1 ATOM 29 C CG2 . VAL A 1 4 ? -1.347 8.759 2.515 1.00 88.45 4 A 1 ATOM 30 N N . ILE A 1 5 ? -0.685 5.037 5.627 1.00 93.71 5 A 1 ATOM 31 C CA . ILE A 1 5 ? 0.071 3.878 6.105 1.00 93.21 5 A 1 ATOM 32 C C . ILE A 1 5 ? -0.043 2.686 5.150 1.00 93.38 5 A 1 ATOM 33 O O . ILE A 1 5 ? 0.954 2.005 4.888 1.00 91.90 5 A 1 ATOM 34 C CB . ILE A 1 5 ? -0.410 3.465 7.502 1.00 92.30 5 A 1 ATOM 35 C CG1 . ILE A 1 5 ? -0.099 4.577 8.506 1.00 88.82 5 A 1 ATOM 36 C CG2 . ILE A 1 5 ? 0.276 2.172 7.925 1.00 88.48 5 A 1 ATOM 37 C CD1 . ILE A 1 5 ? -0.683 4.312 9.875 1.00 85.71 5 A 1 ATOM 38 N N . PRO A 1 6 ? -1.239 2.390 4.630 1.00 94.29 6 A 1 ATOM 39 C CA . PRO A 1 6 ? -1.447 1.246 3.727 1.00 93.48 6 A 1 ATOM 40 C C . PRO A 1 6 ? -0.464 1.204 2.568 1.00 93.45 6 A 1 ATOM 41 O O . PRO A 1 6 ? -0.353 0.193 1.880 1.00 91.57 6 A 1 ATOM 42 C CB . PRO A 1 6 ? -2.875 1.460 3.221 1.00 92.31 6 A 1 ATOM 43 C CG . PRO A 1 6 ? -3.529 2.204 4.331 1.00 91.37 6 A 1 ATOM 44 C CD . PRO A 1 6 ? -2.461 3.087 4.921 1.00 93.38 6 A 1 ATOM 45 N N . ARG A 1 7 ? 0.274 2.281 2.357 1.00 94.18 7 A 1 ATOM 46 C CA . ARG A 1 7 ? 1.260 2.333 1.273 1.00 93.61 7 A 1 ATOM 47 C C . ARG A 1 7 ? 2.260 1.194 1.402 1.00 94.32 7 A 1 ATOM 48 O O . ARG A 1 7 ? 2.759 0.684 0.404 1.00 92.24 7 A 1 ATOM 49 C CB . ARG A 1 7 ? 2.015 3.661 1.312 1.00 92.33 7 A 1 ATOM 50 C CG . ARG A 1 7 ? 1.151 4.795 0.830 1.00 87.57 7 A 1 ATOM 51 C CD . ARG A 1 7 ? 1.971 6.059 0.713 1.00 87.60 7 A 1 ATOM 52 N NE . ARG A 1 7 ? 1.468 6.874 -0.387 1.00 84.15 7 A 1 ATOM 53 C CZ . ARG A 1 7 ? 2.098 7.923 -0.863 1.00 82.37 7 A 1 ATOM 54 N NH1 . ARG A 1 7 ? 3.198 8.373 -0.290 1.00 76.90 7 A 1 ATOM 55 N NH2 . ARG A 1 7 ? 1.631 8.514 -1.938 1.00 77.23 7 A 1 ATOM 56 N N . LEU A 1 8 ? 2.546 0.787 2.608 1.00 94.11 8 A 1 ATOM 57 C CA . LEU A 1 8 ? 3.494 -0.293 2.854 1.00 93.75 8 A 1 ATOM 58 C C . LEU A 1 8 ? 3.004 -1.585 2.216 1.00 94.28 8 A 1 ATOM 59 O O . LEU A 1 8 ? 3.791 -2.344 1.660 1.00 92.20 8 A 1 ATOM 60 C CB . LEU A 1 8 ? 3.672 -0.496 4.358 1.00 93.11 8 A 1 ATOM 61 C CG . LEU A 1 8 ? 4.292 0.718 5.052 1.00 90.38 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? 4.313 0.491 6.556 1.00 87.15 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? 5.703 0.962 4.540 1.00 86.58 8 A 1 ATOM 64 N N . LEU A 1 9 ? 1.703 -1.838 2.290 1.00 94.01 9 A 1 ATOM 65 C CA . LEU A 1 9 ? 1.119 -3.045 1.714 1.00 93.07 9 A 1 ATOM 66 C C . LEU A 1 9 ? 1.213 -3.007 0.199 1.00 93.30 9 A 1 ATOM 67 O O . LEU A 1 9 ? 1.487 -4.017 -0.439 1.00 91.70 9 A 1 ATOM 68 C CB . LEU A 1 9 ? -0.343 -3.161 2.137 1.00 92.27 9 A 1 ATOM 69 C CG . LEU A 1 9 ? -0.521 -3.313 3.642 1.00 90.64 9 A 1 ATOM 70 C CD1 . LEU A 1 9 ? -1.997 -3.271 3.993 1.00 88.29 9 A 1 ATOM 71 C CD2 . LEU A 1 9 ? 0.087 -4.626 4.113 1.00 86.58 9 A 1 ATOM 72 N N . ARG A 1 10 ? 0.982 -1.851 -0.360 1.00 93.89 10 A 1 ATOM 73 C CA . ARG A 1 10 ? 1.035 -1.678 -1.812 1.00 93.41 10 A 1 ATOM 74 C C . ARG A 1 10 ? 2.440 -1.914 -2.344 1.00 93.21 10 A 1 ATOM 75 O O . ARG A 1 10 ? 2.622 -2.618 -3.331 1.00 89.60 10 A 1 ATOM 76 C CB . ARG A 1 10 ? 0.579 -0.268 -2.175 1.00 90.87 10 A 1 ATOM 77 C CG . ARG A 1 10 ? 0.533 -0.081 -3.676 1.00 83.11 10 A 1 ATOM 78 C CD . ARG A 1 10 ? 0.073 1.314 -4.017 1.00 83.83 10 A 1 ATOM 79 N NE . ARG A 1 10 ? 0.070 1.511 -5.468 1.00 79.25 10 A 1 ATOM 80 C CZ . ARG A 1 10 ? -0.259 2.652 -6.047 1.00 76.24 10 A 1 ATOM 81 N NH1 . ARG A 1 10 ? -0.616 3.694 -5.325 1.00 70.09 10 A 1 ATOM 82 N NH2 . ARG A 1 10 ? -0.228 2.754 -7.359 1.00 70.38 10 A 1 ATOM 83 N N . GLY A 1 11 ? 3.438 -1.329 -1.725 1.00 91.44 11 A 1 ATOM 84 C CA . GLY A 1 11 ? 4.822 -1.495 -2.164 1.00 90.06 11 A 1 ATOM 85 C C . GLY A 1 11 ? 5.389 -2.845 -1.790 1.00 91.50 11 A 1 ATOM 86 O O . GLY A 1 11 ? 6.220 -3.399 -2.502 1.00 88.40 11 A 1 ATOM 87 N N . SER A 1 12 ? 4.946 -3.391 -0.665 1.00 91.68 12 A 1 ATOM 88 C CA . SER A 1 12 ? 5.430 -4.686 -0.191 1.00 91.97 12 A 1 ATOM 89 C C . SER A 1 12 ? 4.956 -5.819 -1.091 1.00 92.55 12 A 1 ATOM 90 O O . SER A 1 12 ? 5.763 -6.573 -1.624 1.00 88.86 12 A 1 ATOM 91 C CB . SER A 1 12 ? 4.951 -4.950 1.231 1.00 88.85 12 A 1 ATOM 92 O OG . SER A 1 12 ? 5.447 -6.196 1.673 1.00 79.14 12 A 1 ATOM 93 N N . LEU A 1 13 ? 3.644 -5.948 -1.256 1.00 88.76 13 A 1 ATOM 94 C CA . LEU A 1 13 ? 3.068 -7.003 -2.089 1.00 88.08 13 A 1 ATOM 95 C C . LEU A 1 13 ? 3.382 -6.776 -3.558 1.00 89.50 13 A 1 ATOM 96 O O . LEU A 1 13 ? 3.790 -7.691 -4.259 1.00 83.52 13 A 1 ATOM 97 C CB . LEU A 1 13 ? 1.557 -7.050 -1.876 1.00 85.49 13 A 1 ATOM 98 C CG . LEU A 1 13 ? 1.183 -7.443 -0.452 1.00 81.54 13 A 1 ATOM 99 C CD1 . LEU A 1 13 ? -0.317 -7.339 -0.268 1.00 77.54 13 A 1 ATOM 100 C CD2 . LEU A 1 13 ? 1.650 -8.863 -0.161 1.00 73.48 13 A 1 ATOM 101 N N . GLY A 1 14 ? 3.211 -5.561 -4.019 1.00 81.56 14 A 1 ATOM 102 C CA . GLY A 1 14 ? 3.480 -5.215 -5.419 1.00 76.69 14 A 1 ATOM 103 C C . GLY A 1 14 ? 2.581 -4.098 -5.894 1.00 73.46 14 A 1 ATOM 104 O O . GLY A 1 14 ? 2.424 -3.109 -5.169 1.00 66.88 14 A 1 ATOM 105 O OXT . GLY A 1 14 ? 2.034 -4.186 -7.007 1.00 68.16 14 A 1 #