# 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_spkb43886 # _entry.id spkb43886 # 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 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" "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 LYS 2 1 n PHE 3 1 n VAL 4 1 n VAL 5 1 n VAL 6 1 n PHE 7 1 n ALA 8 1 n SER 9 1 n CYS 10 1 n VAL 11 1 n LEU 12 1 n ALA 13 1 n VAL 14 1 n SER 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 @ 2025-07-07 05:30:44)" _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 87.65 _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 78.12 1 1 A LYS 2 2 82.78 1 2 A PHE 3 2 83.68 1 3 A VAL 4 2 90.41 1 4 A VAL 5 2 87.36 1 5 A VAL 6 2 90.11 1 6 A PHE 7 2 87.24 1 7 A ALA 8 2 92.95 1 8 A SER 9 2 90.44 1 9 A CYS 10 2 90.96 1 10 A VAL 11 2 90.84 1 11 A LEU 12 2 87.25 1 12 A ALA 13 2 94.37 1 13 A VAL 14 2 89.09 1 14 A SER 15 2 90.38 1 15 A ALA 16 2 86.29 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 LYS . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n SER . 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 ? -8.306 8.891 -2.834 1.00 83.46 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.136 7.451 -2.539 1.00 84.97 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.966 7.239 -1.584 1.00 86.19 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.829 7.521 -1.935 1.00 81.73 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.868 6.685 -3.829 1.00 79.31 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.004 6.837 -4.821 1.00 75.57 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.574 6.146 -6.424 1.00 71.03 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.798 6.932 -7.457 1.00 62.72 1 A 1 ATOM 9 N N . LYS A 1 2 ? -7.269 6.767 -0.385 1.00 90.78 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -6.240 6.544 0.626 1.00 90.71 2 A 1 ATOM 11 C C . LYS A 1 2 ? -5.873 5.068 0.719 1.00 90.85 2 A 1 ATOM 12 O O . LYS A 1 2 ? -4.708 4.720 0.888 1.00 89.58 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -6.754 7.053 1.972 1.00 88.09 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -5.644 7.340 2.957 1.00 81.68 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -5.079 8.738 2.753 1.00 77.62 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -4.015 9.045 3.786 1.00 71.47 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -3.479 10.416 3.612 1.00 64.24 2 A 1 ATOM 18 N N . PHE A 1 3 ? -6.873 4.220 0.608 1.00 86.76 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -6.660 2.780 0.683 1.00 88.14 3 A 1 ATOM 20 C C . PHE A 1 3 ? -5.791 2.285 -0.465 1.00 90.73 3 A 1 ATOM 21 O O . PHE A 1 3 ? -4.980 1.373 -0.303 1.00 88.55 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -8.007 2.057 0.653 1.00 86.31 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -8.414 1.550 2.013 1.00 83.69 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -7.650 0.594 2.658 1.00 80.75 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -9.557 2.025 2.631 1.00 79.88 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -8.012 0.118 3.907 1.00 78.41 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -9.928 1.555 3.882 1.00 79.24 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -9.156 0.600 4.521 1.00 78.01 3 A 1 ATOM 29 N N . VAL A 1 4 ? -5.973 2.876 -1.628 1.00 91.69 4 A 1 ATOM 30 C CA . VAL A 1 4 ? -5.203 2.489 -2.810 1.00 92.42 4 A 1 ATOM 31 C C . VAL A 1 4 ? -3.710 2.647 -2.552 1.00 93.51 4 A 1 ATOM 32 O O . VAL A 1 4 ? -2.906 1.776 -2.895 1.00 91.96 4 A 1 ATOM 33 C CB . VAL A 1 4 ? -5.605 3.334 -4.031 1.00 90.82 4 A 1 ATOM 34 C CG1 . VAL A 1 4 ? -4.814 2.907 -5.260 1.00 85.96 4 A 1 ATOM 35 C CG2 . VAL A 1 4 ? -7.098 3.202 -4.296 1.00 86.54 4 A 1 ATOM 36 N N . VAL A 1 5 ? -3.355 3.759 -1.953 1.00 89.22 5 A 1 ATOM 37 C CA . VAL A 1 5 ? -1.954 4.045 -1.656 1.00 89.20 5 A 1 ATOM 38 C C . VAL A 1 5 ? -1.418 3.061 -0.624 1.00 90.77 5 A 1 ATOM 39 O O . VAL A 1 5 ? -0.313 2.535 -0.761 1.00 89.42 5 A 1 ATOM 40 C CB . VAL A 1 5 ? -1.785 5.483 -1.137 1.00 87.25 5 A 1 ATOM 41 C CG1 . VAL A 1 5 ? -0.320 5.779 -0.851 1.00 81.91 5 A 1 ATOM 42 C CG2 . VAL A 1 5 ? -2.331 6.478 -2.154 1.00 83.78 5 A 1 ATOM 43 N N . VAL A 1 6 ? -2.204 2.829 0.399 1.00 91.51 6 A 1 ATOM 44 C CA . VAL A 1 6 ? -1.815 1.908 1.464 1.00 91.67 6 A 1 ATOM 45 C C . VAL A 1 6 ? -1.686 0.489 0.921 1.00 92.75 6 A 1 ATOM 46 O O . VAL A 1 6 ? -0.801 -0.268 1.319 1.00 91.90 6 A 1 ATOM 47 C CB . VAL A 1 6 ? -2.843 1.927 2.601 1.00 90.12 6 A 1 ATOM 48 C CG1 . VAL A 1 6 ? -2.438 0.961 3.701 1.00 85.77 6 A 1 ATOM 49 C CG2 . VAL A 1 6 ? -2.981 3.334 3.159 1.00 87.04 6 A 1 ATOM 50 N N . PHE A 1 7 ? -2.577 0.148 0.017 1.00 88.81 7 A 1 ATOM 51 C CA . PHE A 1 7 ? -2.572 -1.179 -0.590 1.00 89.11 7 A 1 ATOM 52 C C . PHE A 1 7 ? -1.267 -1.429 -1.328 1.00 91.17 7 A 1 ATOM 53 O O . PHE A 1 7 ? -0.632 -2.471 -1.168 1.00 90.57 7 A 1 ATOM 54 C CB . PHE A 1 7 ? -3.751 -1.307 -1.553 1.00 89.08 7 A 1 ATOM 55 C CG . PHE A 1 7 ? -3.910 -2.709 -2.084 1.00 87.33 7 A 1 ATOM 56 C CD1 . PHE A 1 7 ? -4.297 -3.736 -1.242 1.00 85.11 7 A 1 ATOM 57 C CD2 . PHE A 1 7 ? -3.670 -2.986 -3.419 1.00 85.54 7 A 1 ATOM 58 C CE1 . PHE A 1 7 ? -4.444 -5.030 -1.719 1.00 83.99 7 A 1 ATOM 59 C CE2 . PHE A 1 7 ? -3.813 -4.281 -3.905 1.00 84.40 7 A 1 ATOM 60 C CZ . PHE A 1 7 ? -4.199 -5.302 -3.054 1.00 84.52 7 A 1 ATOM 61 N N . ALA A 1 8 ? -0.874 -0.472 -2.130 1.00 92.98 8 A 1 ATOM 62 C CA . ALA A 1 8 ? 0.362 -0.589 -2.896 1.00 93.11 8 A 1 ATOM 63 C C . ALA A 1 8 ? 1.570 -0.694 -1.971 1.00 94.04 8 A 1 ATOM 64 O O . ALA A 1 8 ? 2.478 -1.492 -2.202 1.00 92.28 8 A 1 ATOM 65 C CB . ALA A 1 8 ? 0.509 0.617 -3.815 1.00 92.34 8 A 1 ATOM 66 N N . SER A 1 9 ? 1.560 0.105 -0.929 1.00 92.99 9 A 1 ATOM 67 C CA . SER A 1 9 ? 2.653 0.116 0.038 1.00 92.70 9 A 1 ATOM 68 C C . SER A 1 9 ? 2.698 -1.194 0.818 1.00 93.35 9 A 1 ATOM 69 O O . SER A 1 9 ? 3.771 -1.732 1.090 1.00 91.57 9 A 1 ATOM 70 C CB . SER A 1 9 ? 2.488 1.289 1.000 1.00 91.12 9 A 1 ATOM 71 O OG . SER A 1 9 ? 3.667 1.467 1.749 1.00 80.89 9 A 1 ATOM 72 N N . CYS A 1 10 ? 1.528 -1.702 1.159 1.00 92.79 10 A 1 ATOM 73 C CA . CYS A 1 10 ? 1.425 -2.948 1.914 1.00 93.21 10 A 1 ATOM 74 C C . CYS A 1 10 ? 1.970 -4.116 1.099 1.00 94.30 10 A 1 ATOM 75 O O . CYS A 1 10 ? 2.700 -4.962 1.608 1.00 91.69 10 A 1 ATOM 76 C CB . CYS A 1 10 ? -0.033 -3.205 2.291 1.00 91.09 10 A 1 ATOM 77 S SG . CYS A 1 10 ? -0.184 -4.339 3.682 1.00 82.70 10 A 1 ATOM 78 N N . VAL A 1 11 ? 1.603 -4.153 -0.161 1.00 92.19 11 A 1 ATOM 79 C CA . VAL A 1 11 ? 2.061 -5.214 -1.056 1.00 92.65 11 A 1 ATOM 80 C C . VAL A 1 11 ? 3.574 -5.167 -1.202 1.00 93.70 11 A 1 ATOM 81 O O . VAL A 1 11 ? 4.243 -6.201 -1.265 1.00 92.47 11 A 1 ATOM 82 C CB . VAL A 1 11 ? 1.406 -5.076 -2.435 1.00 91.00 11 A 1 ATOM 83 C CG1 . VAL A 1 11 ? 1.963 -6.113 -3.396 1.00 86.19 11 A 1 ATOM 84 C CG2 . VAL A 1 11 ? -0.100 -5.221 -2.314 1.00 87.68 11 A 1 ATOM 85 N N . LEU A 1 12 ? 4.095 -3.973 -1.260 1.00 91.41 12 A 1 ATOM 86 C CA . LEU A 1 12 ? 5.537 -3.784 -1.399 1.00 91.11 12 A 1 ATOM 87 C C . LEU A 1 12 ? 6.269 -4.351 -0.190 1.00 92.81 12 A 1 ATOM 88 O O . LEU A 1 12 ? 7.311 -4.992 -0.324 1.00 90.67 12 A 1 ATOM 89 C CB . LEU A 1 12 ? 5.858 -2.294 -1.540 1.00 89.89 12 A 1 ATOM 90 C CG . LEU A 1 12 ? 7.245 -2.031 -2.125 1.00 83.58 12 A 1 ATOM 91 C CD1 . LEU A 1 12 ? 7.210 -2.096 -3.639 1.00 78.76 12 A 1 ATOM 92 C CD2 . LEU A 1 12 ? 7.768 -0.679 -1.663 1.00 79.76 12 A 1 ATOM 93 N N . ALA A 1 13 ? 5.724 -4.113 0.983 1.00 95.15 13 A 1 ATOM 94 C CA . ALA A 1 13 ? 6.316 -4.595 2.227 1.00 94.94 13 A 1 ATOM 95 C C . ALA A 1 13 ? 6.320 -6.120 2.269 1.00 95.58 13 A 1 ATOM 96 O O . ALA A 1 13 ? 7.297 -6.739 2.690 1.00 92.77 13 A 1 ATOM 97 C CB . ALA A 1 13 ? 5.549 -4.034 3.417 1.00 93.43 13 A 1 ATOM 98 N N . VAL A 1 14 ? 5.228 -6.717 1.834 1.00 92.56 14 A 1 ATOM 99 C CA . VAL A 1 14 ? 5.108 -8.173 1.813 1.00 91.82 14 A 1 ATOM 100 C C . VAL A 1 14 ? 6.054 -8.774 0.783 1.00 92.77 14 A 1 ATOM 101 O O . VAL A 1 14 ? 6.649 -9.832 1.005 1.00 90.05 14 A 1 ATOM 102 C CB . VAL A 1 14 ? 3.666 -8.593 1.500 1.00 89.31 14 A 1 ATOM 103 C CG1 . VAL A 1 14 ? 3.559 -10.109 1.442 1.00 82.96 14 A 1 ATOM 104 C CG2 . VAL A 1 14 ? 2.719 -8.035 2.549 1.00 84.14 14 A 1 ATOM 105 N N . SER A 1 15 ? 6.178 -8.106 -0.337 1.00 92.81 15 A 1 ATOM 106 C CA . SER A 1 15 ? 7.055 -8.557 -1.415 1.00 93.07 15 A 1 ATOM 107 C C . SER A 1 15 ? 8.511 -8.560 -0.972 1.00 93.12 15 A 1 ATOM 108 O O . SER A 1 15 ? 9.309 -9.391 -1.408 1.00 90.87 15 A 1 ATOM 109 C CB . SER A 1 15 ? 6.893 -7.653 -2.634 1.00 91.09 15 A 1 ATOM 110 O OG . SER A 1 15 ? 7.620 -8.169 -3.724 1.00 81.34 15 A 1 ATOM 111 N N . ALA A 1 16 ? 8.850 -7.626 -0.112 1.00 92.63 16 A 1 ATOM 112 C CA . ALA A 1 16 ? 10.209 -7.506 0.389 1.00 90.08 16 A 1 ATOM 113 C C . ALA A 1 16 ? 10.583 -8.672 1.306 1.00 89.22 16 A 1 ATOM 114 O O . ALA A 1 16 ? 9.723 -9.522 1.605 1.00 84.64 16 A 1 ATOM 115 C CB . ALA A 1 16 ? 10.359 -6.177 1.127 1.00 84.82 16 A 1 ATOM 116 O OXT . ALA A 1 16 ? 11.749 -8.735 1.752 1.00 76.36 16 A 1 #