# 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_spkb29338 # _entry.id spkb29338 # 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 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 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" "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 ARG 2 1 n GLY 3 1 n LEU 4 1 n LEU 5 1 n LEU 6 1 n ALA 7 1 n GLY 8 1 n ALA 9 1 n LEU 10 1 n GLY 11 1 n LEU 12 1 n PRO 13 1 n LEU 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 @ 2025-07-02 23:33:23)" _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 86.37 _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 80.44 1 1 A ARG 2 2 80.57 1 2 A GLY 3 2 91.04 1 3 A LEU 4 2 84.54 1 4 A LEU 5 2 85.69 1 5 A LEU 6 2 86.34 1 6 A ALA 7 2 88.70 1 7 A GLY 8 2 89.88 1 8 A ALA 9 2 91.79 1 9 A LEU 10 2 87.38 1 10 A GLY 11 2 91.18 1 11 A LEU 12 2 86.44 1 12 A PRO 13 2 91.82 1 13 A LEU 14 2 87.87 1 14 A ALA 15 2 90.38 1 15 A VAL 16 2 89.82 1 16 A LEU 17 2 84.04 1 17 A ALA 18 2 79.06 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 ARG . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n LEU . 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 GLY . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n PRO . 13 A 13 A 14 1 n LEU . 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 ? -7.556 5.198 11.411 1.00 86.09 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.397 4.287 11.287 1.00 86.32 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.833 4.337 9.867 1.00 87.09 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.549 4.653 8.923 1.00 84.42 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.825 2.859 11.611 1.00 81.66 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.634 2.830 12.916 1.00 77.84 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.784 3.681 14.238 1.00 74.63 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.128 3.863 15.389 1.00 65.43 1 A 1 ATOM 9 N N . ARG A 1 2 ? -4.557 4.034 9.715 1.00 85.34 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -3.901 4.074 8.402 1.00 87.96 2 A 1 ATOM 11 C C . ARG A 1 2 ? -2.984 2.863 8.208 1.00 89.75 2 A 1 ATOM 12 O O . ARG A 1 2 ? -1.819 3.008 7.842 1.00 87.24 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -3.109 5.385 8.281 1.00 84.76 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -2.319 5.650 9.553 1.00 82.21 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -0.829 5.510 9.297 1.00 80.29 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -0.141 4.883 10.410 1.00 75.96 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 1.056 5.252 10.862 1.00 75.08 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 1.691 6.279 10.350 1.00 68.04 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 1.614 4.575 11.842 1.00 69.61 2 A 1 ATOM 20 N N . GLY A 1 3 ? -3.523 1.682 8.459 1.00 89.90 3 A 1 ATOM 21 C CA . GLY A 1 3 ? -2.734 0.455 8.289 1.00 90.52 3 A 1 ATOM 22 C C . GLY A 1 3 ? -2.263 0.274 6.858 1.00 92.48 3 A 1 ATOM 23 O O . GLY A 1 3 ? -1.207 -0.294 6.606 1.00 91.26 3 A 1 ATOM 24 N N . LEU A 1 4 ? -3.058 0.779 5.900 1.00 86.42 4 A 1 ATOM 25 C CA . LEU A 1 4 ? -2.702 0.676 4.479 1.00 86.41 4 A 1 ATOM 26 C C . LEU A 1 4 ? -1.407 1.430 4.197 1.00 88.86 4 A 1 ATOM 27 O O . LEU A 1 4 ? -0.636 1.047 3.323 1.00 86.58 4 A 1 ATOM 28 C CB . LEU A 1 4 ? -3.838 1.255 3.627 1.00 84.67 4 A 1 ATOM 29 C CG . LEU A 1 4 ? -5.184 0.571 3.884 1.00 83.84 4 A 1 ATOM 30 C CD1 . LEU A 1 4 ? -6.267 1.233 3.037 1.00 80.82 4 A 1 ATOM 31 C CD2 . LEU A 1 4 ? -5.088 -0.915 3.529 1.00 78.74 4 A 1 ATOM 32 N N . LEU A 1 5 ? -1.171 2.507 4.942 1.00 86.45 5 A 1 ATOM 33 C CA . LEU A 1 5 ? 0.048 3.303 4.762 1.00 86.66 5 A 1 ATOM 34 C C . LEU A 1 5 ? 1.280 2.446 5.054 1.00 89.03 5 A 1 ATOM 35 O O . LEU A 1 5 ? 2.302 2.555 4.379 1.00 87.27 5 A 1 ATOM 36 C CB . LEU A 1 5 ? 0.020 4.506 5.710 1.00 85.68 5 A 1 ATOM 37 C CG . LEU A 1 5 ? 1.014 5.585 5.298 1.00 86.03 5 A 1 ATOM 38 C CD1 . LEU A 1 5 ? 0.418 6.445 4.189 1.00 83.20 5 A 1 ATOM 39 C CD2 . LEU A 1 5 ? 1.360 6.454 6.499 1.00 81.20 5 A 1 ATOM 40 N N . LEU A 1 6 ? 1.170 1.592 6.052 1.00 89.88 6 A 1 ATOM 41 C CA . LEU A 1 6 ? 2.282 0.709 6.423 1.00 88.59 6 A 1 ATOM 42 C C . LEU A 1 6 ? 2.596 -0.244 5.278 1.00 90.53 6 A 1 ATOM 43 O O . LEU A 1 6 ? 3.759 -0.519 4.982 1.00 89.27 6 A 1 ATOM 44 C CB . LEU A 1 6 ? 1.897 -0.079 7.678 1.00 87.02 6 A 1 ATOM 45 C CG . LEU A 1 6 ? 2.845 0.195 8.838 1.00 83.96 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? 2.159 -0.139 10.159 1.00 81.14 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? 4.107 -0.636 8.677 1.00 80.34 6 A 1 ATOM 48 N N . ALA A 1 7 ? 1.545 -0.741 4.627 1.00 89.15 7 A 1 ATOM 49 C CA . ALA A 1 7 ? 1.722 -1.644 3.486 1.00 88.94 7 A 1 ATOM 50 C C . ALA A 1 7 ? 2.482 -0.936 2.367 1.00 90.25 7 A 1 ATOM 51 O O . ALA A 1 7 ? 3.306 -1.540 1.684 1.00 88.04 7 A 1 ATOM 52 C CB . ALA A 1 7 ? 0.355 -2.100 2.990 1.00 87.14 7 A 1 ATOM 53 N N . GLY A 1 8 ? 2.191 0.364 2.191 1.00 89.67 8 A 1 ATOM 54 C CA . GLY A 1 8 ? 2.874 1.149 1.165 1.00 88.66 8 A 1 ATOM 55 C C . GLY A 1 8 ? 4.357 1.241 1.453 1.00 90.94 8 A 1 ATOM 56 O O . GLY A 1 8 ? 5.184 1.226 0.538 1.00 90.25 8 A 1 ATOM 57 N N . ALA A 1 9 ? 4.705 1.335 2.738 1.00 91.72 9 A 1 ATOM 58 C CA . ALA A 1 9 ? 6.109 1.415 3.145 1.00 92.03 9 A 1 ATOM 59 C C . ALA A 1 9 ? 6.844 0.132 2.760 1.00 93.60 9 A 1 ATOM 60 O O . ALA A 1 9 ? 8.036 0.154 2.460 1.00 91.35 9 A 1 ATOM 61 C CB . ALA A 1 9 ? 6.192 1.644 4.654 1.00 90.24 9 A 1 ATOM 62 N N . LEU A 1 10 ? 6.119 -0.983 2.768 1.00 90.50 10 A 1 ATOM 63 C CA . LEU A 1 10 ? 6.703 -2.277 2.408 1.00 90.13 10 A 1 ATOM 64 C C . LEU A 1 10 ? 7.039 -2.318 0.919 1.00 91.50 10 A 1 ATOM 65 O O . LEU A 1 10 ? 7.866 -3.117 0.482 1.00 88.60 10 A 1 ATOM 66 C CB . LEU A 1 10 ? 5.711 -3.395 2.765 1.00 88.55 10 A 1 ATOM 67 C CG . LEU A 1 10 ? 6.052 -4.095 4.079 1.00 86.19 10 A 1 ATOM 68 C CD1 . LEU A 1 10 ? 7.364 -4.833 3.951 1.00 82.66 10 A 1 ATOM 69 C CD2 . LEU A 1 10 ? 6.110 -3.087 5.207 1.00 80.92 10 A 1 ATOM 70 N N . GLY A 1 11 ? 6.395 -1.452 0.138 1.00 90.73 11 A 1 ATOM 71 C CA . GLY A 1 11 ? 6.639 -1.412 -1.307 1.00 90.38 11 A 1 ATOM 72 C C . GLY A 1 11 ? 5.440 -1.897 -2.099 1.00 92.33 11 A 1 ATOM 73 O O . GLY A 1 11 ? 5.582 -2.379 -3.220 1.00 91.29 11 A 1 ATOM 74 N N . LEU A 1 12 ? 4.246 -1.780 -1.516 1.00 89.05 12 A 1 ATOM 75 C CA . LEU A 1 12 ? 3.025 -2.228 -2.186 1.00 89.23 12 A 1 ATOM 76 C C . LEU A 1 12 ? 2.133 -1.039 -2.528 1.00 90.93 12 A 1 ATOM 77 O O . LEU A 1 12 ? 1.599 -0.392 -1.630 1.00 89.03 12 A 1 ATOM 78 C CB . LEU A 1 12 ? 2.282 -3.201 -1.272 1.00 87.91 12 A 1 ATOM 79 C CG . LEU A 1 12 ? 3.102 -4.455 -0.957 1.00 83.90 12 A 1 ATOM 80 C CD1 . LEU A 1 12 ? 2.429 -5.249 0.154 1.00 81.62 12 A 1 ATOM 81 C CD2 . LEU A 1 12 ? 3.226 -5.315 -2.211 1.00 79.88 12 A 1 ATOM 82 N N . PRO A 1 13 ? 1.969 -0.733 -3.813 1.00 92.65 13 A 1 ATOM 83 C CA . PRO A 1 13 ? 1.128 0.386 -4.260 1.00 92.23 13 A 1 ATOM 84 C C . PRO A 1 13 ? -0.328 0.202 -3.840 1.00 93.42 13 A 1 ATOM 85 O O . PRO A 1 13 ? -0.766 -0.914 -3.554 1.00 91.73 13 A 1 ATOM 86 C CB . PRO A 1 13 ? 1.253 0.347 -5.791 1.00 90.35 13 A 1 ATOM 87 C CG . PRO A 1 13 ? 2.527 -0.402 -6.048 1.00 89.60 13 A 1 ATOM 88 C CD . PRO A 1 13 ? 2.657 -1.389 -4.907 1.00 92.78 13 A 1 ATOM 89 N N . LEU A 1 14 ? -1.072 1.305 -3.802 1.00 90.66 14 A 1 ATOM 90 C CA . LEU A 1 14 ? -2.484 1.261 -3.420 1.00 90.30 14 A 1 ATOM 91 C C . LEU A 1 14 ? -3.271 0.381 -4.388 1.00 92.04 14 A 1 ATOM 92 O O . LEU A 1 14 ? -4.219 -0.299 -4.003 1.00 90.69 14 A 1 ATOM 93 C CB . LEU A 1 14 ? -3.046 2.689 -3.417 1.00 88.72 14 A 1 ATOM 94 C CG . LEU A 1 14 ? -3.514 3.130 -2.039 1.00 85.39 14 A 1 ATOM 95 C CD1 . LEU A 1 14 ? -4.650 2.260 -1.549 1.00 83.05 14 A 1 ATOM 96 C CD2 . LEU A 1 14 ? -2.348 3.097 -1.069 1.00 82.13 14 A 1 ATOM 97 N N . ALA A 1 15 ? -2.874 0.408 -5.664 1.00 90.05 15 A 1 ATOM 98 C CA . ALA A 1 15 ? -3.550 -0.383 -6.698 1.00 90.54 15 A 1 ATOM 99 C C . ALA A 1 15 ? -3.487 -1.873 -6.372 1.00 91.82 15 A 1 ATOM 100 O O . ALA A 1 15 ? -4.436 -2.615 -6.615 1.00 89.53 15 A 1 ATOM 101 C CB . ALA A 1 15 ? -2.896 -0.117 -8.046 1.00 89.98 15 A 1 ATOM 102 N N . VAL A 1 16 ? -2.367 -2.311 -5.822 1.00 92.07 16 A 1 ATOM 103 C CA . VAL A 1 16 ? -2.195 -3.722 -5.464 1.00 91.61 16 A 1 ATOM 104 C C . VAL A 1 16 ? -3.047 -4.069 -4.250 1.00 92.18 16 A 1 ATOM 105 O O . VAL A 1 16 ? -3.621 -5.155 -4.167 1.00 90.23 16 A 1 ATOM 106 C CB . VAL A 1 16 ? -0.717 -4.023 -5.158 1.00 90.44 16 A 1 ATOM 107 C CG1 . VAL A 1 16 ? -0.542 -5.492 -4.787 1.00 86.20 16 A 1 ATOM 108 C CG2 . VAL A 1 16 ? 0.146 -3.685 -6.364 1.00 85.98 16 A 1 ATOM 109 N N . LEU A 1 17 ? -3.123 -3.134 -3.302 1.00 87.07 17 A 1 ATOM 110 C CA . LEU A 1 17 ? -3.912 -3.353 -2.092 1.00 86.98 17 A 1 ATOM 111 C C . LEU A 1 17 ? -5.401 -3.361 -2.412 1.00 88.33 17 A 1 ATOM 112 O O . LEU A 1 17 ? -6.178 -4.090 -1.793 1.00 86.11 17 A 1 ATOM 113 C CB . LEU A 1 17 ? -3.602 -2.245 -1.072 1.00 85.08 17 A 1 ATOM 114 C CG . LEU A 1 17 ? -2.673 -2.705 0.048 1.00 82.44 17 A 1 ATOM 115 C CD1 . LEU A 1 17 ? -3.323 -3.832 0.831 1.00 79.60 17 A 1 ATOM 116 C CD2 . LEU A 1 17 ? -1.348 -3.169 -0.533 1.00 76.68 17 A 1 ATOM 117 N N . ALA A 1 18 ? -5.795 -2.537 -3.380 1.00 84.68 18 A 1 ATOM 118 C CA . ALA A 1 18 ? -7.203 -2.429 -3.769 1.00 82.60 18 A 1 ATOM 119 C C . ALA A 1 18 ? -7.542 -3.479 -4.822 1.00 80.00 18 A 1 ATOM 120 O O . ALA A 1 18 ? -8.308 -4.414 -4.505 1.00 77.90 18 A 1 ATOM 121 C CB . ALA A 1 18 ? -7.484 -1.025 -4.290 1.00 76.83 18 A 1 ATOM 122 O OXT . ALA A 1 18 ? -7.021 -3.359 -5.942 1.00 72.33 18 A 1 #