# 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_spkb23705 # _entry.id spkb23705 # 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" "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" "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" "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 THR 2 1 n LYS 3 1 n LEU 4 1 n SER 5 1 n LEU 6 1 n LEU 7 1 n PRO 8 1 n LEU 9 1 n LEU 10 1 n THR 11 1 n LEU 12 1 n ALA 13 1 n SER 14 1 n ALA 15 1 n VAL 16 1 n LEU 17 1 n ALA 18 # _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 @ 2025-07-06 12:41:49)" _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 88.19 _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 74.80 1 1 A THR 2 2 81.95 1 2 A LYS 3 2 76.42 1 3 A LEU 4 2 80.54 1 4 A SER 5 2 87.87 1 5 A LEU 6 2 87.87 1 6 A LEU 7 2 88.73 1 7 A PRO 8 2 93.20 1 8 A LEU 9 2 91.75 1 9 A LEU 10 2 92.16 1 10 A THR 11 2 92.15 1 11 A LEU 12 2 92.12 1 12 A ALA 13 2 95.24 1 13 A SER 14 2 93.47 1 14 A ALA 15 2 96.05 1 15 A VAL 16 2 93.87 1 16 A LEU 17 2 91.03 1 17 A ALA 18 2 87.33 1 18 # _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 THR . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PRO . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n LEU . 17 A 17 A 18 1 n ALA . 18 A 18 # _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 ? -5.107 8.820 14.610 1.00 79.51 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.896 7.526 13.934 1.00 82.18 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.232 7.719 12.572 1.00 83.11 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.774 8.392 11.704 1.00 79.49 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.236 6.816 13.755 1.00 75.49 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.245 7.662 12.997 1.00 72.80 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.865 6.890 12.920 1.00 67.97 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.479 7.322 14.537 1.00 57.88 1 A 1 ATOM 9 N N . THR A 1 2 ? -3.056 7.131 12.396 1.00 84.49 2 A 1 ATOM 10 C CA . THR A 1 2 ? -2.308 7.245 11.143 1.00 85.77 2 A 1 ATOM 11 C C . THR A 1 2 ? -2.087 5.885 10.477 1.00 86.21 2 A 1 ATOM 12 O O . THR A 1 2 ? -1.575 5.818 9.359 1.00 83.07 2 A 1 ATOM 13 C CB . THR A 1 2 ? -0.950 7.892 11.411 1.00 83.06 2 A 1 ATOM 14 O OG1 . THR A 1 2 ? -0.300 7.208 12.473 1.00 76.45 2 A 1 ATOM 15 C CG2 . THR A 1 2 ? -1.118 9.352 11.793 1.00 74.61 2 A 1 ATOM 16 N N . LYS A 1 3 ? -2.463 4.808 11.162 1.00 82.53 3 A 1 ATOM 17 C CA . LYS A 1 3 ? -2.292 3.452 10.626 1.00 83.53 3 A 1 ATOM 18 C C . LYS A 1 3 ? -3.122 3.251 9.365 1.00 84.61 3 A 1 ATOM 19 O O . LYS A 1 3 ? -2.721 2.517 8.462 1.00 85.12 3 A 1 ATOM 20 C CB . LYS A 1 3 ? -2.697 2.427 11.688 1.00 80.51 3 A 1 ATOM 21 C CG . LYS A 1 3 ? -1.609 2.211 12.726 1.00 74.50 3 A 1 ATOM 22 C CD . LYS A 1 3 ? -0.486 1.357 12.166 1.00 71.82 3 A 1 ATOM 23 C CE . LYS A 1 3 ? 0.538 1.025 13.231 1.00 65.90 3 A 1 ATOM 24 N NZ . LYS A 1 3 ? 1.649 0.224 12.671 1.00 59.30 3 A 1 ATOM 25 N N . LEU A 1 4 ? -4.264 3.904 9.287 1.00 84.16 4 A 1 ATOM 26 C CA . LEU A 1 4 ? -5.152 3.794 8.133 1.00 84.59 4 A 1 ATOM 27 C C . LEU A 1 4 ? -4.499 4.380 6.883 1.00 88.03 4 A 1 ATOM 28 O O . LEU A 1 4 ? -4.831 3.993 5.765 1.00 84.81 4 A 1 ATOM 29 C CB . LEU A 1 4 ? -6.468 4.516 8.427 1.00 81.95 4 A 1 ATOM 30 C CG . LEU A 1 4 ? -7.594 4.143 7.470 1.00 77.52 4 A 1 ATOM 31 C CD1 . LEU A 1 4 ? -8.099 2.736 7.789 1.00 72.99 4 A 1 ATOM 32 C CD2 . LEU A 1 4 ? -8.742 5.138 7.591 1.00 70.28 4 A 1 ATOM 33 N N . SER A 1 5 ? -3.569 5.295 7.062 1.00 88.73 5 A 1 ATOM 34 C CA . SER A 1 5 ? -2.874 5.938 5.949 1.00 89.58 5 A 1 ATOM 35 C C . SER A 1 5 ? -1.616 5.166 5.552 1.00 90.86 5 A 1 ATOM 36 O O . SER A 1 5 ? -1.152 5.266 4.421 1.00 90.16 5 A 1 ATOM 37 C CB . SER A 1 5 ? -2.503 7.372 6.324 1.00 88.31 5 A 1 ATOM 38 O OG . SER A 1 5 ? -3.663 8.132 6.595 1.00 79.56 5 A 1 ATOM 39 N N . LEU A 1 6 ? -1.072 4.389 6.480 1.00 90.72 6 A 1 ATOM 40 C CA . LEU A 1 6 ? 0.140 3.616 6.217 1.00 91.65 6 A 1 ATOM 41 C C . LEU A 1 6 ? -0.144 2.423 5.307 1.00 93.42 6 A 1 ATOM 42 O O . LEU A 1 6 ? 0.679 2.076 4.461 1.00 91.65 6 A 1 ATOM 43 C CB . LEU A 1 6 ? 0.737 3.130 7.538 1.00 90.55 6 A 1 ATOM 44 C CG . LEU A 1 6 ? 1.365 4.244 8.374 1.00 84.90 6 A 1 ATOM 45 C CD1 . LEU A 1 6 ? 1.654 3.748 9.782 1.00 80.69 6 A 1 ATOM 46 C CD2 . LEU A 1 6 ? 2.662 4.725 7.725 1.00 79.36 6 A 1 ATOM 47 N N . LEU A 1 7 ? -1.304 1.798 5.483 1.00 92.12 7 A 1 ATOM 48 C CA . LEU A 1 7 ? -1.685 0.640 4.676 1.00 92.29 7 A 1 ATOM 49 C C . LEU A 1 7 ? -1.742 0.974 3.184 1.00 93.85 7 A 1 ATOM 50 O O . LEU A 1 7 ? -1.124 0.279 2.372 1.00 92.68 7 A 1 ATOM 51 C CB . LEU A 1 7 ? -3.034 0.099 5.162 1.00 90.75 7 A 1 ATOM 52 C CG . LEU A 1 7 ? -2.935 -0.706 6.457 1.00 86.20 7 A 1 ATOM 53 C CD1 . LEU A 1 7 ? -4.302 -0.815 7.120 1.00 81.76 7 A 1 ATOM 54 C CD2 . LEU A 1 7 ? -2.388 -2.096 6.162 1.00 80.16 7 A 1 ATOM 55 N N . PRO A 1 8 ? -2.473 2.009 2.785 1.00 93.24 8 A 1 ATOM 56 C CA . PRO A 1 8 ? -2.575 2.380 1.367 1.00 93.83 8 A 1 ATOM 57 C C . PRO A 1 8 ? -1.250 2.870 0.797 1.00 94.97 8 A 1 ATOM 58 O O . PRO A 1 8 ? -0.963 2.671 -0.382 1.00 93.84 8 A 1 ATOM 59 C CB . PRO A 1 8 ? -3.627 3.498 1.361 1.00 92.31 8 A 1 ATOM 60 C CG . PRO A 1 8 ? -3.614 4.041 2.750 1.00 91.34 8 A 1 ATOM 61 C CD . PRO A 1 8 ? -3.283 2.877 3.641 1.00 92.85 8 A 1 ATOM 62 N N . LEU A 1 9 ? -0.430 3.487 1.613 1.00 93.85 9 A 1 ATOM 63 C CA . LEU A 1 9 ? 0.868 3.993 1.173 1.00 94.19 9 A 1 ATOM 64 C C . LEU A 1 9 ? 1.802 2.840 0.816 1.00 95.10 9 A 1 ATOM 65 O O . LEU A 1 9 ? 2.574 2.930 -0.140 1.00 93.74 9 A 1 ATOM 66 C CB . LEU A 1 9 ? 1.489 4.845 2.283 1.00 93.81 9 A 1 ATOM 67 C CG . LEU A 1 9 ? 0.898 6.251 2.387 1.00 90.62 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? 1.349 6.918 3.682 1.00 86.62 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? 1.342 7.098 1.195 1.00 86.08 9 A 1 ATOM 70 N N . LEU A 1 10 ? 1.724 1.756 1.576 1.00 94.70 10 A 1 ATOM 71 C CA . LEU A 1 10 ? 2.556 0.582 1.330 1.00 94.69 10 A 1 ATOM 72 C C . LEU A 1 10 ? 2.195 -0.054 -0.006 1.00 95.65 10 A 1 ATOM 73 O O . LEU A 1 10 ? 3.068 -0.508 -0.746 1.00 94.86 10 A 1 ATOM 74 C CB . LEU A 1 10 ? 2.363 -0.431 2.457 1.00 94.20 10 A 1 ATOM 75 C CG . LEU A 1 10 ? 3.428 -1.526 2.475 1.00 90.65 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? 4.762 -0.964 2.965 1.00 85.79 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? 2.997 -2.674 3.378 1.00 86.72 10 A 1 ATOM 78 N N . THR A 1 11 ? 0.920 -0.091 -0.315 1.00 93.08 11 A 1 ATOM 79 C CA . THR A 1 11 ? 0.437 -0.669 -1.570 1.00 93.55 11 A 1 ATOM 80 C C . THR A 1 11 ? 0.923 0.161 -2.759 1.00 94.56 11 A 1 ATOM 81 O O . THR A 1 11 ? 1.278 -0.382 -3.806 1.00 93.78 11 A 1 ATOM 82 C CB . THR A 1 11 ? -1.093 -0.722 -1.570 1.00 92.73 11 A 1 ATOM 83 O OG1 . THR A 1 11 ? -1.546 -1.395 -0.401 1.00 89.70 11 A 1 ATOM 84 C CG2 . THR A 1 11 ? -1.605 -1.472 -2.795 1.00 87.62 11 A 1 ATOM 85 N N . LEU A 1 12 ? 0.949 1.453 -2.598 1.00 95.52 12 A 1 ATOM 86 C CA . LEU A 1 12 ? 1.394 2.357 -3.657 1.00 95.29 12 A 1 ATOM 87 C C . LEU A 1 12 ? 2.870 2.123 -3.965 1.00 96.07 12 A 1 ATOM 88 O O . LEU A 1 12 ? 3.283 2.123 -5.128 1.00 95.34 12 A 1 ATOM 89 C CB . LEU A 1 12 ? 1.154 3.806 -3.228 1.00 94.50 12 A 1 ATOM 90 C CG . LEU A 1 12 ? 1.039 4.780 -4.402 1.00 88.29 12 A 1 ATOM 91 C CD1 . LEU A 1 12 ? 0.202 5.987 -3.995 1.00 85.15 12 A 1 ATOM 92 C CD2 . LEU A 1 12 ? 2.406 5.244 -4.863 1.00 86.81 12 A 1 ATOM 93 N N . ALA A 1 13 ? 3.660 1.909 -2.929 1.00 95.38 13 A 1 ATOM 94 C CA . ALA A 1 13 ? 5.092 1.661 -3.092 1.00 95.18 13 A 1 ATOM 95 C C . ALA A 1 13 ? 5.334 0.366 -3.861 1.00 96.16 13 A 1 ATOM 96 O O . ALA A 1 13 ? 6.268 0.273 -4.658 1.00 95.23 13 A 1 ATOM 97 C CB . ALA A 1 13 ? 5.756 1.595 -1.721 1.00 94.25 13 A 1 ATOM 98 N N . SER A 1 14 ? 4.492 -0.634 -3.629 1.00 95.62 14 A 1 ATOM 99 C CA . SER A 1 14 ? 4.605 -1.924 -4.307 1.00 95.49 14 A 1 ATOM 100 C C . SER A 1 14 ? 4.335 -1.777 -5.800 1.00 95.95 14 A 1 ATOM 101 O O . SER A 1 14 ? 4.988 -2.416 -6.625 1.00 94.55 14 A 1 ATOM 102 C CB . SER A 1 14 ? 3.616 -2.914 -3.698 1.00 94.01 14 A 1 ATOM 103 O OG . SER A 1 14 ? 3.823 -4.193 -4.233 1.00 85.19 14 A 1 ATOM 104 N N . ALA A 1 15 ? 3.380 -0.944 -6.151 1.00 96.35 15 A 1 ATOM 105 C CA . ALA A 1 15 ? 3.023 -0.702 -7.550 1.00 96.32 15 A 1 ATOM 106 C C . ALA A 1 15 ? 4.146 0.033 -8.283 1.00 97.02 15 A 1 ATOM 107 O O . ALA A 1 15 ? 4.377 -0.189 -9.470 1.00 95.41 15 A 1 ATOM 108 C CB . ALA A 1 15 ? 1.732 0.108 -7.613 1.00 95.17 15 A 1 ATOM 109 N N . VAL A 1 16 ? 4.838 0.900 -7.588 1.00 96.05 16 A 1 ATOM 110 C CA . VAL A 1 16 ? 5.939 1.672 -8.174 1.00 95.79 16 A 1 ATOM 111 C C . VAL A 1 16 ? 7.139 0.776 -8.468 1.00 96.15 16 A 1 ATOM 112 O O . VAL A 1 16 ? 7.901 1.024 -9.407 1.00 94.98 16 A 1 ATOM 113 C CB . VAL A 1 16 ? 6.356 2.816 -7.232 1.00 94.15 16 A 1 ATOM 114 C CG1 . VAL A 1 16 ? 7.561 3.569 -7.785 1.00 89.88 16 A 1 ATOM 115 C CG2 . VAL A 1 16 ? 5.200 3.780 -7.032 1.00 90.06 16 A 1 ATOM 116 N N . LEU A 1 17 ? 7.305 -0.275 -7.672 1.00 95.50 17 A 1 ATOM 117 C CA . LEU A 1 17 ? 8.420 -1.207 -7.846 1.00 94.99 17 A 1 ATOM 118 C C . LEU A 1 17 ? 8.340 -1.919 -9.193 1.00 95.28 17 A 1 ATOM 119 O O . LEU A 1 17 ? 9.362 -2.186 -9.828 1.00 94.02 17 A 1 ATOM 120 C CB . LEU A 1 17 ? 8.412 -2.227 -6.706 1.00 93.41 17 A 1 ATOM 121 C CG . LEU A 1 17 ? 8.966 -1.677 -5.387 1.00 88.30 17 A 1 ATOM 122 C CD1 . LEU A 1 17 ? 8.641 -2.622 -4.240 1.00 83.71 17 A 1 ATOM 123 C CD2 . LEU A 1 17 ? 10.478 -1.495 -5.492 1.00 83.07 17 A 1 ATOM 124 N N . ALA A 1 18 ? 7.131 -2.242 -9.623 1.00 92.99 18 A 1 ATOM 125 C CA . ALA A 1 18 ? 6.917 -2.931 -10.890 1.00 90.64 18 A 1 ATOM 126 C C . ALA A 1 18 ? 6.416 -1.973 -11.972 1.00 88.99 18 A 1 ATOM 127 O O . ALA A 1 18 ? 5.890 -0.903 -11.638 1.00 85.91 18 A 1 ATOM 128 C CB . ALA A 1 18 ? 5.938 -4.086 -10.693 1.00 86.68 18 A 1 ATOM 129 O OXT . ALA A 1 18 ? 6.534 -2.303 -13.168 1.00 78.80 18 A 1 #