# 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_spkb29073 # _entry.id spkb29073 # 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" "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" "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" "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 MET 2 1 n LYS 3 1 n LEU 4 1 n VAL 5 1 n ILE 6 1 n ALA 7 1 n LEU 8 1 n CYS 9 1 n LEU 10 1 n ILE 11 1 n GLY 12 1 n ILE 13 1 n SER 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 @ 2025-07-11 23:20:27)" _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 94.34 _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 89.23 1 1 A MET 2 2 92.73 1 2 A LYS 3 2 92.44 1 3 A LEU 4 2 94.41 1 4 A VAL 5 2 97.37 1 5 A ILE 6 2 96.69 1 6 A ALA 7 2 97.82 1 7 A LEU 8 2 95.95 1 8 A CYS 9 2 96.97 1 9 A LEU 10 2 95.77 1 10 A ILE 11 2 96.20 1 11 A GLY 12 2 96.92 1 12 A ILE 13 2 92.41 1 13 A SER 14 2 92.75 1 14 A ALA 15 2 89.85 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 MET . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n CYS . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n ILE . 13 A 13 A 14 1 n SER . 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 ? -4.794 12.313 8.289 1.00 94.49 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.604 11.895 7.525 1.00 95.64 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.526 10.371 7.432 1.00 95.78 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.796 9.736 8.184 1.00 93.67 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.340 12.440 8.188 1.00 92.57 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.283 12.833 7.183 1.00 86.76 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.286 13.217 7.951 1.00 82.52 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.653 14.792 7.210 1.00 72.41 1 A 1 ATOM 9 N N . MET A 1 2 ? -4.287 9.786 6.499 1.00 97.30 2 A 1 ATOM 10 C CA . MET A 1 2 ? -4.332 8.338 6.321 1.00 97.59 2 A 1 ATOM 11 C C . MET A 1 2 ? -3.508 7.891 5.106 1.00 97.91 2 A 1 ATOM 12 O O . MET A 1 2 ? -3.501 6.716 4.748 1.00 97.02 2 A 1 ATOM 13 C CB . MET A 1 2 ? -5.786 7.884 6.172 1.00 96.37 2 A 1 ATOM 14 C CG . MET A 1 2 ? -6.189 6.822 7.180 1.00 92.54 2 A 1 ATOM 15 S SD . MET A 1 2 ? -7.229 7.483 8.476 1.00 87.15 2 A 1 ATOM 16 C CE . MET A 1 2 ? -7.771 5.971 9.268 1.00 75.97 2 A 1 ATOM 17 N N . LYS A 1 3 ? -2.828 8.833 4.477 1.00 97.56 3 A 1 ATOM 18 C CA . LYS A 1 3 ? -2.024 8.558 3.282 1.00 97.90 3 A 1 ATOM 19 C C . LYS A 1 3 ? -0.835 7.650 3.602 1.00 98.20 3 A 1 ATOM 20 O O . LYS A 1 3 ? -0.358 6.916 2.737 1.00 97.89 3 A 1 ATOM 21 C CB . LYS A 1 3 ? -1.540 9.872 2.669 1.00 97.38 3 A 1 ATOM 22 C CG . LYS A 1 3 ? -1.846 9.992 1.189 1.00 93.10 3 A 1 ATOM 23 C CD . LYS A 1 3 ? -0.708 9.487 0.335 1.00 89.50 3 A 1 ATOM 24 C CE . LYS A 1 3 ? -0.974 9.699 -1.145 1.00 83.91 3 A 1 ATOM 25 N NZ . LYS A 1 3 ? 0.250 9.465 -1.960 1.00 76.50 3 A 1 ATOM 26 N N . LEU A 1 4 ? -0.376 7.687 4.840 1.00 97.63 4 A 1 ATOM 27 C CA . LEU A 1 4 ? 0.760 6.877 5.272 1.00 97.83 4 A 1 ATOM 28 C C . LEU A 1 4 ? 0.442 5.388 5.179 1.00 98.15 4 A 1 ATOM 29 O O . LEU A 1 4 ? 1.260 4.593 4.720 1.00 97.85 4 A 1 ATOM 30 C CB . LEU A 1 4 ? 1.158 7.245 6.707 1.00 97.44 4 A 1 ATOM 31 C CG . LEU A 1 4 ? 2.131 8.418 6.847 1.00 90.48 4 A 1 ATOM 32 C CD1 . LEU A 1 4 ? 3.440 8.091 6.159 1.00 87.94 4 A 1 ATOM 33 C CD2 . LEU A 1 4 ? 1.532 9.684 6.271 1.00 87.97 4 A 1 ATOM 34 N N . VAL A 1 5 ? -0.763 5.016 5.609 1.00 98.09 5 A 1 ATOM 35 C CA . VAL A 1 5 ? -1.201 3.620 5.576 1.00 98.16 5 A 1 ATOM 36 C C . VAL A 1 5 ? -1.341 3.134 4.136 1.00 98.24 5 A 1 ATOM 37 O O . VAL A 1 5 ? -0.992 1.997 3.815 1.00 97.91 5 A 1 ATOM 38 C CB . VAL A 1 5 ? -2.539 3.445 6.318 1.00 97.80 5 A 1 ATOM 39 C CG1 . VAL A 1 5 ? -2.935 1.980 6.380 1.00 95.68 5 A 1 ATOM 40 C CG2 . VAL A 1 5 ? -2.460 4.027 7.718 1.00 95.71 5 A 1 ATOM 41 N N . ILE A 1 6 ? -1.863 3.999 3.274 1.00 98.07 6 A 1 ATOM 42 C CA . ILE A 1 6 ? -2.060 3.672 1.864 1.00 97.96 6 A 1 ATOM 43 C C . ILE A 1 6 ? -0.716 3.442 1.181 1.00 97.98 6 A 1 ATOM 44 O O . ILE A 1 6 ? -0.543 2.490 0.424 1.00 97.88 6 A 1 ATOM 45 C CB . ILE A 1 6 ? -2.838 4.784 1.142 1.00 97.87 6 A 1 ATOM 46 C CG1 . ILE A 1 6 ? -4.128 5.119 1.899 1.00 96.10 6 A 1 ATOM 47 C CG2 . ILE A 1 6 ? -3.148 4.363 -0.295 1.00 95.91 6 A 1 ATOM 48 C CD1 . ILE A 1 6 ? -5.050 3.933 2.097 1.00 91.74 6 A 1 ATOM 49 N N . ALA A 1 7 ? 0.235 4.314 1.449 1.00 98.04 7 A 1 ATOM 50 C CA . ALA A 1 7 ? 1.570 4.216 0.867 1.00 97.89 7 A 1 ATOM 51 C C . ALA A 1 7 ? 2.254 2.913 1.275 1.00 97.99 7 A 1 ATOM 52 O O . ALA A 1 7 ? 2.912 2.266 0.462 1.00 97.57 7 A 1 ATOM 53 C CB . ALA A 1 7 ? 2.412 5.408 1.300 1.00 97.63 7 A 1 ATOM 54 N N . LEU A 1 8 ? 2.069 2.521 2.525 1.00 98.04 8 A 1 ATOM 55 C CA . LEU A 1 8 ? 2.652 1.286 3.044 1.00 97.81 8 A 1 ATOM 56 C C . LEU A 1 8 ? 2.047 0.069 2.357 1.00 97.93 8 A 1 ATOM 57 O O . LEU A 1 8 ? 2.751 -0.893 2.051 1.00 97.32 8 A 1 ATOM 58 C CB . LEU A 1 8 ? 2.418 1.202 4.553 1.00 97.43 8 A 1 ATOM 59 C CG . LEU A 1 8 ? 2.992 -0.042 5.226 1.00 94.47 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? 4.511 0.005 5.244 1.00 92.22 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? 2.464 -0.166 6.651 1.00 92.37 8 A 1 ATOM 62 N N . CYS A 1 9 ? 0.744 0.109 2.111 1.00 97.83 9 A 1 ATOM 63 C CA . CYS A 1 9 ? 0.036 -0.988 1.466 1.00 97.82 9 A 1 ATOM 64 C C . CYS A 1 9 ? 0.466 -1.134 0.009 1.00 97.97 9 A 1 ATOM 65 O O . CYS A 1 9 ? 0.561 -2.246 -0.508 1.00 97.25 9 A 1 ATOM 66 C CB . CYS A 1 9 ? -1.474 -0.760 1.553 1.00 97.42 9 A 1 ATOM 67 S SG . CYS A 1 9 ? -2.426 -2.278 1.389 1.00 93.51 9 A 1 ATOM 68 N N . LEU A 1 10 ? 0.721 -0.010 -0.645 1.00 97.94 10 A 1 ATOM 69 C CA . LEU A 1 10 ? 1.126 -0.004 -2.049 1.00 97.89 10 A 1 ATOM 70 C C . LEU A 1 10 ? 2.488 -0.661 -2.239 1.00 97.94 10 A 1 ATOM 71 O O . LEU A 1 10 ? 2.667 -1.486 -3.133 1.00 97.27 10 A 1 ATOM 72 C CB . LEU A 1 10 ? 1.162 1.430 -2.578 1.00 97.49 10 A 1 ATOM 73 C CG . LEU A 1 10 ? -0.200 2.108 -2.695 1.00 94.57 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? -0.026 3.574 -3.068 1.00 91.61 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? -1.064 1.402 -3.727 1.00 91.43 10 A 1 ATOM 76 N N . ILE A 1 11 ? 3.448 -0.299 -1.415 1.00 97.99 11 A 1 ATOM 77 C CA . ILE A 1 11 ? 4.786 -0.872 -1.496 1.00 97.69 11 A 1 ATOM 78 C C . ILE A 1 11 ? 4.813 -2.303 -0.979 1.00 97.71 11 A 1 ATOM 79 O O . ILE A 1 11 ? 5.608 -3.121 -1.438 1.00 96.99 11 A 1 ATOM 80 C CB . ILE A 1 11 ? 5.803 -0.019 -0.718 1.00 97.09 11 A 1 ATOM 81 C CG1 . ILE A 1 11 ? 5.324 0.233 0.710 1.00 95.17 11 A 1 ATOM 82 C CG2 . ILE A 1 11 ? 6.050 1.293 -1.454 1.00 95.04 11 A 1 ATOM 83 C CD1 . ILE A 1 11 ? 6.309 1.005 1.554 1.00 91.91 11 A 1 ATOM 84 N N . GLY A 1 12 ? 3.938 -2.599 -0.038 1.00 97.21 12 A 1 ATOM 85 C CA . GLY A 1 12 ? 3.853 -3.934 0.530 1.00 96.98 12 A 1 ATOM 86 C C . GLY A 1 12 ? 3.288 -4.943 -0.444 1.00 97.22 12 A 1 ATOM 87 O O . GLY A 1 12 ? 3.741 -6.084 -0.498 1.00 96.28 12 A 1 ATOM 88 N N . ILE A 1 13 ? 2.284 -4.531 -1.226 1.00 95.62 13 A 1 ATOM 89 C CA . ILE A 1 13 ? 1.657 -5.405 -2.209 1.00 95.53 13 A 1 ATOM 90 C C . ILE A 1 13 ? 2.601 -5.705 -3.366 1.00 96.04 13 A 1 ATOM 91 O O . ILE A 1 13 ? 2.485 -6.743 -4.015 1.00 94.71 13 A 1 ATOM 92 C CB . ILE A 1 13 ? 0.345 -4.774 -2.736 1.00 94.23 13 A 1 ATOM 93 C CG1 . ILE A 1 13 ? -0.625 -5.850 -3.203 1.00 90.52 13 A 1 ATOM 94 C CG2 . ILE A 1 13 ? 0.641 -3.785 -3.859 1.00 88.89 13 A 1 ATOM 95 C CD1 . ILE A 1 13 ? -1.709 -6.149 -2.228 1.00 83.70 13 A 1 ATOM 96 N N . SER A 1 14 ? 3.531 -4.811 -3.626 1.00 95.84 14 A 1 ATOM 97 C CA . SER A 1 14 ? 4.507 -4.966 -4.707 1.00 95.81 14 A 1 ATOM 98 C C . SER A 1 14 ? 5.567 -6.008 -4.371 1.00 95.65 14 A 1 ATOM 99 O O . SER A 1 14 ? 6.362 -6.384 -5.231 1.00 92.91 14 A 1 ATOM 100 C CB . SER A 1 14 ? 5.173 -3.632 -5.020 1.00 93.89 14 A 1 ATOM 101 O OG . SER A 1 14 ? 4.430 -2.908 -5.970 1.00 82.42 14 A 1 ATOM 102 N N . ALA A 1 15 ? 5.570 -6.468 -3.124 1.00 95.01 15 A 1 ATOM 103 C CA . ALA A 1 15 ? 6.520 -7.474 -2.644 1.00 93.52 15 A 1 ATOM 104 C C . ALA A 1 15 ? 7.970 -7.019 -2.807 1.00 92.48 15 A 1 ATOM 105 O O . ALA A 1 15 ? 8.315 -6.479 -3.869 1.00 87.89 15 A 1 ATOM 106 C CB . ALA A 1 15 ? 6.297 -8.807 -3.351 1.00 89.96 15 A 1 ATOM 107 O OXT . ALA A 1 15 ? 8.747 -7.200 -1.861 1.00 80.26 15 A 1 #