# 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_spkb29609 # _entry.id spkb29609 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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 PRO 3 1 n VAL 4 1 n LEU 5 1 n LEU 6 1 n ALA 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n LEU 12 1 n GLY 13 1 n PRO 14 1 n ALA 15 1 n VAL 16 1 n SER 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 @ 2025-07-13 08:15:01)" _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 93.46 _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 86.74 1 1 A VAL 2 2 93.50 1 2 A PRO 3 2 95.58 1 3 A VAL 4 2 95.68 1 4 A LEU 5 2 93.70 1 5 A LEU 6 2 93.40 1 6 A ALA 7 2 96.55 1 7 A LEU 8 2 93.77 1 8 A LEU 9 2 94.02 1 9 A LEU 10 2 95.56 1 10 A LEU 11 2 95.67 1 11 A LEU 12 2 93.40 1 12 A GLY 13 2 95.52 1 13 A PRO 14 2 95.56 1 14 A ALA 15 2 95.32 1 15 A VAL 16 2 91.81 1 16 A SER 17 2 85.59 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 VAL . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n PRO . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n SER . 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 ? -12.293 -5.690 3.216 1.00 92.53 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.162 -5.114 3.971 1.00 93.38 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.828 -5.490 3.339 1.00 94.18 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.877 -4.716 3.378 1.00 92.56 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.190 -5.584 5.427 1.00 88.59 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.321 -4.929 6.199 1.00 82.15 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.238 -5.285 7.949 1.00 79.34 1 A 1 ATOM 8 C CE . MET A 1 1 ? -13.591 -4.285 8.536 1.00 71.22 1 A 1 ATOM 9 N N . VAL A 1 2 ? -9.792 -6.682 2.775 1.00 94.79 2 A 1 ATOM 10 C CA . VAL A 1 2 ? -8.577 -7.120 2.082 1.00 95.69 2 A 1 ATOM 11 C C . VAL A 1 2 ? -8.177 -6.128 0.993 1.00 96.46 2 A 1 ATOM 12 O O . VAL A 1 2 ? -7.014 -5.710 0.928 1.00 95.81 2 A 1 ATOM 13 C CB . VAL A 1 2 ? -8.762 -8.520 1.480 1.00 94.13 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? -7.501 -8.962 0.760 1.00 88.68 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? -9.130 -9.514 2.568 1.00 88.91 2 A 1 ATOM 16 N N . PRO A 1 3 ? -9.133 -5.758 0.144 1.00 95.96 3 A 1 ATOM 17 C CA . PRO A 1 3 ? -8.842 -4.778 -0.911 1.00 96.52 3 A 1 ATOM 18 C C . PRO A 1 3 ? -8.406 -3.449 -0.325 1.00 97.09 3 A 1 ATOM 19 O O . PRO A 1 3 ? -7.585 -2.740 -0.910 1.00 95.92 3 A 1 ATOM 20 C CB . PRO A 1 3 ? -10.176 -4.620 -1.652 1.00 95.05 3 A 1 ATOM 21 C CG . PRO A 1 3 ? -10.964 -5.833 -1.282 1.00 93.50 3 A 1 ATOM 22 C CD . PRO A 1 3 ? -10.502 -6.228 0.094 1.00 95.04 3 A 1 ATOM 23 N N . VAL A 1 4 ? -8.950 -3.124 0.818 1.00 96.72 4 A 1 ATOM 24 C CA . VAL A 1 4 ? -8.598 -1.881 1.504 1.00 96.90 4 A 1 ATOM 25 C C . VAL A 1 4 ? -7.145 -1.930 1.948 1.00 97.13 4 A 1 ATOM 26 O O . VAL A 1 4 ? -6.415 -0.944 1.840 1.00 96.23 4 A 1 ATOM 27 C CB . VAL A 1 4 ? -9.502 -1.651 2.722 1.00 96.33 4 A 1 ATOM 28 C CG1 . VAL A 1 4 ? -9.149 -0.339 3.405 1.00 93.41 4 A 1 ATOM 29 C CG2 . VAL A 1 4 ? -10.963 -1.652 2.302 1.00 93.02 4 A 1 ATOM 30 N N . LEU A 1 5 ? -6.740 -3.093 2.439 1.00 96.56 5 A 1 ATOM 31 C CA . LEU A 1 5 ? -5.362 -3.291 2.871 1.00 96.48 5 A 1 ATOM 32 C C . LEU A 1 5 ? -4.418 -3.147 1.690 1.00 96.80 5 A 1 ATOM 33 O O . LEU A 1 5 ? -3.355 -2.542 1.787 1.00 96.30 5 A 1 ATOM 34 C CB . LEU A 1 5 ? -5.204 -4.676 3.505 1.00 96.20 5 A 1 ATOM 35 C CG . LEU A 1 5 ? -4.819 -4.628 4.977 1.00 90.60 5 A 1 ATOM 36 C CD1 . LEU A 1 5 ? -3.472 -3.956 5.154 1.00 88.50 5 A 1 ATOM 37 C CD2 . LEU A 1 5 ? -5.892 -3.887 5.767 1.00 88.16 5 A 1 ATOM 38 N N . LEU A 1 6 ? -4.832 -3.725 0.570 1.00 96.66 6 A 1 ATOM 39 C CA . LEU A 1 6 ? -4.039 -3.633 -0.651 1.00 96.42 6 A 1 ATOM 40 C C . LEU A 1 6 ? -3.903 -2.183 -1.087 1.00 96.82 6 A 1 ATOM 41 O O . LEU A 1 6 ? -2.828 -1.744 -1.493 1.00 96.62 6 A 1 ATOM 42 C CB . LEU A 1 6 ? -4.700 -4.434 -1.770 1.00 95.80 6 A 1 ATOM 43 C CG . LEU A 1 6 ? -3.800 -4.605 -2.988 1.00 89.18 6 A 1 ATOM 44 C CD1 . LEU A 1 6 ? -2.826 -5.751 -2.767 1.00 87.90 6 A 1 ATOM 45 C CD2 . LEU A 1 6 ? -4.632 -4.850 -4.236 1.00 87.82 6 A 1 ATOM 46 N N . ALA A 1 7 ? -4.998 -1.460 -1.006 1.00 96.65 7 A 1 ATOM 47 C CA . ALA A 1 7 ? -5.002 -0.048 -1.374 1.00 96.73 7 A 1 ATOM 48 C C . ALA A 1 7 ? -4.094 0.744 -0.445 1.00 97.10 7 A 1 ATOM 49 O O . ALA A 1 7 ? -3.362 1.631 -0.882 1.00 95.90 7 A 1 ATOM 50 C CB . ALA A 1 7 ? -6.419 0.500 -1.319 1.00 96.35 7 A 1 ATOM 51 N N . LEU A 1 8 ? -4.148 0.400 0.824 1.00 96.36 8 A 1 ATOM 52 C CA . LEU A 1 8 ? -3.314 1.067 1.817 1.00 95.94 8 A 1 ATOM 53 C C . LEU A 1 8 ? -1.847 0.793 1.529 1.00 96.55 8 A 1 ATOM 54 O O . LEU A 1 8 ? -1.002 1.684 1.617 1.00 95.80 8 A 1 ATOM 55 C CB . LEU A 1 8 ? -3.684 0.579 3.212 1.00 95.37 8 A 1 ATOM 56 C CG . LEU A 1 8 ? -3.459 1.627 4.297 1.00 90.98 8 A 1 ATOM 57 C CD1 . LEU A 1 8 ? -4.344 1.343 5.496 1.00 89.77 8 A 1 ATOM 58 C CD2 . LEU A 1 8 ? -2.005 1.659 4.724 1.00 89.38 8 A 1 ATOM 59 N N . LEU A 1 9 ? -1.556 -0.455 1.175 1.00 96.04 9 A 1 ATOM 60 C CA . LEU A 1 9 ? -0.192 -0.844 0.841 1.00 95.84 9 A 1 ATOM 61 C C . LEU A 1 9 ? 0.263 -0.116 -0.413 1.00 96.57 9 A 1 ATOM 62 O O . LEU A 1 9 ? 1.401 0.352 -0.503 1.00 95.97 9 A 1 ATOM 63 C CB . LEU A 1 9 ? -0.122 -2.354 0.625 1.00 95.28 9 A 1 ATOM 64 C CG . LEU A 1 9 ? 1.163 -3.004 1.138 1.00 92.07 9 A 1 ATOM 65 C CD1 . LEU A 1 9 ? 1.199 -4.468 0.764 1.00 90.49 9 A 1 ATOM 66 C CD2 . LEU A 1 9 ? 2.398 -2.298 0.614 1.00 89.92 9 A 1 ATOM 67 N N . LEU A 1 10 ? -0.641 -0.024 -1.382 1.00 96.93 10 A 1 ATOM 68 C CA . LEU A 1 10 ? -0.348 0.677 -2.625 1.00 96.84 10 A 1 ATOM 69 C C . LEU A 1 10 ? -0.035 2.138 -2.358 1.00 97.30 10 A 1 ATOM 70 O O . LEU A 1 10 ? 0.686 2.775 -3.126 1.00 96.31 10 A 1 ATOM 71 C CB . LEU A 1 10 ? -1.536 0.566 -3.575 1.00 96.49 10 A 1 ATOM 72 C CG . LEU A 1 10 ? -1.562 -0.745 -4.361 1.00 94.75 10 A 1 ATOM 73 C CD1 . LEU A 1 10 ? -2.917 -0.945 -5.016 1.00 93.02 10 A 1 ATOM 74 C CD2 . LEU A 1 10 ? -0.465 -0.746 -5.412 1.00 92.82 10 A 1 ATOM 75 N N . LEU A 1 11 ? -0.585 2.648 -1.285 1.00 97.35 11 A 1 ATOM 76 C CA . LEU A 1 11 ? -0.329 4.027 -0.903 1.00 97.26 11 A 1 ATOM 77 C C . LEU A 1 11 ? 0.935 4.120 -0.060 1.00 97.39 11 A 1 ATOM 78 O O . LEU A 1 11 ? 1.657 5.115 -0.116 1.00 96.09 11 A 1 ATOM 79 C CB . LEU A 1 11 ? -1.524 4.570 -0.125 1.00 96.93 11 A 1 ATOM 80 C CG . LEU A 1 11 ? -2.762 4.814 -0.989 1.00 95.03 11 A 1 ATOM 81 C CD1 . LEU A 1 11 ? -4.005 4.934 -0.128 1.00 92.93 11 A 1 ATOM 82 C CD2 . LEU A 1 11 ? -2.577 6.077 -1.822 1.00 92.36 11 A 1 ATOM 83 N N . LEU A 1 12 ? 1.183 3.070 0.709 1.00 96.56 12 A 1 ATOM 84 C CA . LEU A 1 12 ? 2.349 3.022 1.577 1.00 96.23 12 A 1 ATOM 85 C C . LEU A 1 12 ? 3.617 2.793 0.774 1.00 96.49 12 A 1 ATOM 86 O O . LEU A 1 12 ? 4.641 3.429 1.005 1.00 94.53 12 A 1 ATOM 87 C CB . LEU A 1 12 ? 2.179 1.910 2.613 1.00 95.14 12 A 1 ATOM 88 C CG . LEU A 1 12 ? 2.614 2.288 4.023 1.00 92.26 12 A 1 ATOM 89 C CD1 . LEU A 1 12 ? 4.044 2.777 4.040 1.00 88.84 12 A 1 ATOM 90 C CD2 . LEU A 1 12 ? 1.673 3.346 4.581 1.00 87.13 12 A 1 ATOM 91 N N . GLY A 1 13 ? 3.533 1.862 -0.190 1.00 95.84 13 A 1 ATOM 92 C CA . GLY A 1 13 ? 4.676 1.559 -1.039 1.00 95.33 13 A 1 ATOM 93 C C . GLY A 1 13 ? 5.240 2.789 -1.714 1.00 95.94 13 A 1 ATOM 94 O O . GLY A 1 13 ? 6.398 3.153 -1.494 1.00 94.96 13 A 1 ATOM 95 N N . PRO A 1 14 ? 4.432 3.429 -2.543 1.00 96.92 14 A 1 ATOM 96 C CA . PRO A 1 14 ? 4.866 4.645 -3.230 1.00 96.54 14 A 1 ATOM 97 C C . PRO A 1 14 ? 5.195 5.756 -2.257 1.00 96.68 14 A 1 ATOM 98 O O . PRO A 1 14 ? 6.078 6.573 -2.527 1.00 94.59 14 A 1 ATOM 99 C CB . PRO A 1 14 ? 3.657 5.029 -4.087 1.00 94.85 14 A 1 ATOM 100 C CG . PRO A 1 14 ? 2.870 3.769 -4.216 1.00 93.47 14 A 1 ATOM 101 C CD . PRO A 1 14 ? 3.123 2.984 -2.953 1.00 95.84 14 A 1 ATOM 102 N N . ALA A 1 15 ? 4.499 5.785 -1.139 1.00 96.10 15 A 1 ATOM 103 C CA . ALA A 1 15 ? 4.730 6.803 -0.124 1.00 95.96 15 A 1 ATOM 104 C C . ALA A 1 15 ? 6.126 6.666 0.462 1.00 95.78 15 A 1 ATOM 105 O O . ALA A 1 15 ? 6.779 7.657 0.774 1.00 94.07 15 A 1 ATOM 106 C CB . ALA A 1 15 ? 3.689 6.694 0.980 1.00 94.69 15 A 1 ATOM 107 N N . VAL A 1 16 ? 6.569 5.422 0.621 1.00 95.89 16 A 1 ATOM 108 C CA . VAL A 1 16 ? 7.898 5.158 1.154 1.00 94.63 16 A 1 ATOM 109 C C . VAL A 1 16 ? 8.967 5.486 0.124 1.00 94.01 16 A 1 ATOM 110 O O . VAL A 1 16 ? 10.069 5.918 0.471 1.00 90.96 16 A 1 ATOM 111 C CB . VAL A 1 16 ? 8.034 3.695 1.582 1.00 92.67 16 A 1 ATOM 112 C CG1 . VAL A 1 16 ? 9.453 3.405 2.046 1.00 87.17 16 A 1 ATOM 113 C CG2 . VAL A 1 16 ? 7.046 3.380 2.681 1.00 87.37 16 A 1 ATOM 114 N N . SER A 1 17 ? 8.631 5.277 -1.132 1.00 92.85 17 A 1 ATOM 115 C CA . SER A 1 17 ? 9.550 5.550 -2.230 1.00 91.03 17 A 1 ATOM 116 C C . SER A 1 17 ? 9.672 7.049 -2.463 1.00 87.10 17 A 1 ATOM 117 O O . SER A 1 17 ? 10.794 7.525 -2.691 1.00 81.46 17 A 1 ATOM 118 C CB . SER A 1 17 ? 9.079 4.871 -3.510 1.00 86.71 17 A 1 ATOM 119 O OG . SER A 1 17 ? 9.346 3.498 -3.468 1.00 79.58 17 A 1 ATOM 120 O OXT . SER A 1 17 ? 8.639 7.733 -2.433 1.00 80.38 17 A 1 #