# 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_spkb25537 # _entry.id spkb25537 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "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" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)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 CYS 2 1 n PRO 3 1 n LEU 4 1 n TRP 5 1 n LEU 6 1 n LEU 7 1 n ALA 8 1 n ALA 9 1 n LEU 10 1 n LEU 11 1 n ALA 12 1 n LEU 13 1 n SER 14 1 n GLN 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 @ 2025-07-08 11:42:33)" _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 94.67 _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 82.95 1 1 A CYS 2 2 92.49 1 2 A PRO 3 2 95.02 1 3 A LEU 4 2 95.35 1 4 A TRP 5 2 95.04 1 5 A LEU 6 2 96.17 1 6 A LEU 7 2 96.35 1 7 A ALA 8 2 97.82 1 8 A ALA 9 2 97.79 1 9 A LEU 10 2 96.62 1 10 A LEU 11 2 96.44 1 11 A ALA 12 2 98.09 1 12 A LEU 13 2 96.42 1 13 A SER 14 2 96.87 1 14 A GLN 15 2 92.63 1 15 A ALA 16 2 91.57 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 CYS . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n TRP . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n GLN . 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 ? -7.198 4.813 15.453 1.00 89.01 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.514 5.382 14.277 1.00 88.61 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.106 4.265 13.322 1.00 89.47 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.247 3.452 13.650 1.00 86.86 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.270 6.153 14.711 1.00 85.16 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.611 7.389 15.526 1.00 79.98 1 A 1 ATOM 7 S SD . MET A 1 1 ? -4.154 8.076 16.319 1.00 76.85 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.884 9.430 17.217 1.00 67.63 1 A 1 ATOM 9 N N . CYS A 1 2 ? -6.731 4.224 12.155 1.00 93.40 2 A 1 ATOM 10 C CA . CYS A 1 2 ? -6.441 3.191 11.169 1.00 94.46 2 A 1 ATOM 11 C C . CYS A 1 2 ? -5.917 3.815 9.875 1.00 95.98 2 A 1 ATOM 12 O O . CYS A 1 2 ? -6.707 4.236 9.028 1.00 94.55 2 A 1 ATOM 13 C CB . CYS A 1 2 ? -7.709 2.393 10.882 1.00 91.34 2 A 1 ATOM 14 S SG . CYS A 1 2 ? -8.396 1.642 12.374 1.00 85.19 2 A 1 ATOM 15 N N . PRO A 1 3 ? -4.592 3.883 9.722 1.00 95.37 3 A 1 ATOM 16 C CA . PRO A 1 3 ? -3.985 4.447 8.517 1.00 96.27 3 A 1 ATOM 17 C C . PRO A 1 3 ? -4.207 3.555 7.299 1.00 97.33 3 A 1 ATOM 18 O O . PRO A 1 3 ? -3.819 2.386 7.301 1.00 96.41 3 A 1 ATOM 19 C CB . PRO A 1 3 ? -2.502 4.529 8.871 1.00 94.30 3 A 1 ATOM 20 C CG . PRO A 1 3 ? -2.290 3.484 9.910 1.00 91.74 3 A 1 ATOM 21 C CD . PRO A 1 3 ? -3.596 3.378 10.668 1.00 93.70 3 A 1 ATOM 22 N N . LEU A 1 4 ? -4.829 4.113 6.289 1.00 96.52 4 A 1 ATOM 23 C CA . LEU A 1 4 ? -5.101 3.367 5.068 1.00 97.21 4 A 1 ATOM 24 C C . LEU A 1 4 ? -3.875 3.331 4.170 1.00 97.85 4 A 1 ATOM 25 O O . LEU A 1 4 ? -3.710 2.410 3.370 1.00 97.73 4 A 1 ATOM 26 C CB . LEU A 1 4 ? -6.279 4.000 4.331 1.00 96.91 4 A 1 ATOM 27 C CG . LEU A 1 4 ? -7.636 3.687 4.948 1.00 94.22 4 A 1 ATOM 28 C CD1 . LEU A 1 4 ? -8.701 4.596 4.364 1.00 91.79 4 A 1 ATOM 29 C CD2 . LEU A 1 4 ? -7.998 2.227 4.708 1.00 90.61 4 A 1 ATOM 30 N N . TRP A 1 5 ? -3.003 4.338 4.315 1.00 97.00 5 A 1 ATOM 31 C CA . TRP A 1 5 ? -1.792 4.403 3.506 1.00 97.08 5 A 1 ATOM 32 C C . TRP A 1 5 ? -0.918 3.180 3.749 1.00 97.61 5 A 1 ATOM 33 O O . TRP A 1 5 ? -0.190 2.739 2.858 1.00 97.51 5 A 1 ATOM 34 C CB . TRP A 1 5 ? -1.015 5.680 3.815 1.00 96.80 5 A 1 ATOM 35 C CG . TRP A 1 5 ? -0.586 5.791 5.243 1.00 95.58 5 A 1 ATOM 36 C CD1 . TRP A 1 5 ? -1.214 6.479 6.225 1.00 94.14 5 A 1 ATOM 37 C CD2 . TRP A 1 5 ? 0.586 5.195 5.838 1.00 95.26 5 A 1 ATOM 38 N NE1 . TRP A 1 5 ? -0.513 6.345 7.404 1.00 93.01 5 A 1 ATOM 39 C CE2 . TRP A 1 5 ? 0.592 5.561 7.191 1.00 94.57 5 A 1 ATOM 40 C CE3 . TRP A 1 5 ? 1.618 4.406 5.343 1.00 93.67 5 A 1 ATOM 41 C CZ2 . TRP A 1 5 ? 1.612 5.147 8.063 1.00 94.02 5 A 1 ATOM 42 C CZ3 . TRP A 1 5 ? 2.631 3.992 6.214 1.00 92.01 5 A 1 ATOM 43 C CH2 . TRP A 1 5 ? 2.612 4.363 7.557 1.00 92.33 5 A 1 ATOM 44 N N . LEU A 1 6 ? -1.011 2.638 4.950 1.00 97.53 6 A 1 ATOM 45 C CA . LEU A 1 6 ? -0.249 1.442 5.296 1.00 97.60 6 A 1 ATOM 46 C C . LEU A 1 6 ? -0.680 0.278 4.413 1.00 97.90 6 A 1 ATOM 47 O O . LEU A 1 6 ? 0.149 -0.477 3.901 1.00 97.98 6 A 1 ATOM 48 C CB . LEU A 1 6 ? -0.458 1.105 6.772 1.00 97.51 6 A 1 ATOM 49 C CG . LEU A 1 6 ? 0.811 1.189 7.616 1.00 94.87 6 A 1 ATOM 50 C CD1 . LEU A 1 6 ? 0.464 1.185 9.102 1.00 93.11 6 A 1 ATOM 51 C CD2 . LEU A 1 6 ? 1.746 0.042 7.291 1.00 92.85 6 A 1 ATOM 52 N N . LEU A 1 7 ? -1.986 0.144 4.236 1.00 97.84 7 A 1 ATOM 53 C CA . LEU A 1 7 ? -2.523 -0.910 3.380 1.00 97.84 7 A 1 ATOM 54 C C . LEU A 1 7 ? -2.139 -0.653 1.930 1.00 98.10 7 A 1 ATOM 55 O O . LEU A 1 7 ? -1.832 -1.584 1.180 1.00 98.12 7 A 1 ATOM 56 C CB . LEU A 1 7 ? -4.045 -0.958 3.521 1.00 97.64 7 A 1 ATOM 57 C CG . LEU A 1 7 ? -4.525 -1.715 4.755 1.00 94.86 7 A 1 ATOM 58 C CD1 . LEU A 1 7 ? -5.934 -1.288 5.125 1.00 93.12 7 A 1 ATOM 59 C CD2 . LEU A 1 7 ? -4.483 -3.216 4.495 1.00 93.27 7 A 1 ATOM 60 N N . ALA A 1 8 ? -2.165 0.612 1.545 1.00 97.89 8 A 1 ATOM 61 C CA . ALA A 1 8 ? -1.794 1.008 0.189 1.00 97.80 8 A 1 ATOM 62 C C . ALA A 1 8 ? -0.335 0.666 -0.081 1.00 98.09 8 A 1 ATOM 63 O O . ALA A 1 8 ? 0.035 0.322 -1.206 1.00 97.94 8 A 1 ATOM 64 C CB . ALA A 1 8 ? -2.018 2.501 0.014 1.00 97.38 8 A 1 ATOM 65 N N . ALA A 1 9 ? 0.493 0.765 0.957 1.00 97.93 9 A 1 ATOM 66 C CA . ALA A 1 9 ? 1.913 0.454 0.839 1.00 97.78 9 A 1 ATOM 67 C C . ALA A 1 9 ? 2.096 -1.011 0.455 1.00 98.05 9 A 1 ATOM 68 O O . ALA A 1 9 ? 2.961 -1.349 -0.355 1.00 97.76 9 A 1 ATOM 69 C CB . ALA A 1 9 ? 2.616 0.753 2.155 1.00 97.44 9 A 1 ATOM 70 N N . LEU A 1 10 ? 1.267 -1.870 1.034 1.00 97.82 10 A 1 ATOM 71 C CA . LEU A 1 10 ? 1.317 -3.297 0.734 1.00 97.73 10 A 1 ATOM 72 C C . LEU A 1 10 ? 0.923 -3.532 -0.719 1.00 97.92 10 A 1 ATOM 73 O O . LEU A 1 10 ? 1.481 -4.395 -1.400 1.00 97.72 10 A 1 ATOM 74 C CB . LEU A 1 10 ? 0.375 -4.061 1.674 1.00 97.62 10 A 1 ATOM 75 C CG . LEU A 1 10 ? 1.066 -4.650 2.903 1.00 96.18 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? 2.068 -5.709 2.482 1.00 94.05 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? 1.751 -3.560 3.702 1.00 93.92 10 A 1 ATOM 78 N N . LEU A 1 11 ? -0.056 -2.756 -1.170 1.00 98.02 11 A 1 ATOM 79 C CA . LEU A 1 11 ? -0.533 -2.854 -2.547 1.00 97.86 11 A 1 ATOM 80 C C . LEU A 1 11 ? 0.585 -2.463 -3.510 1.00 98.01 11 A 1 ATOM 81 O O . LEU A 1 11 ? 0.795 -3.106 -4.542 1.00 97.90 11 A 1 ATOM 82 C CB . LEU A 1 11 ? -1.751 -1.940 -2.736 1.00 97.61 11 A 1 ATOM 83 C CG . LEU A 1 11 ? -2.672 -2.321 -3.897 1.00 95.23 11 A 1 ATOM 84 C CD1 . LEU A 1 11 ? -2.008 -2.075 -5.233 1.00 93.39 11 A 1 ATOM 85 C CD2 . LEU A 1 11 ? -3.113 -3.769 -3.761 1.00 93.49 11 A 1 ATOM 86 N N . ALA A 1 12 ? 1.297 -1.388 -3.164 1.00 98.26 12 A 1 ATOM 87 C CA . ALA A 1 12 ? 2.400 -0.908 -3.993 1.00 98.13 12 A 1 ATOM 88 C C . ALA A 1 12 ? 3.523 -1.938 -4.034 1.00 98.26 12 A 1 ATOM 89 O O . ALA A 1 12 ? 4.188 -2.105 -5.056 1.00 97.94 12 A 1 ATOM 90 C CB . ALA A 1 12 ? 2.918 0.414 -3.445 1.00 97.85 12 A 1 ATOM 91 N N . LEU A 1 13 ? 3.724 -2.627 -2.910 1.00 98.30 13 A 1 ATOM 92 C CA . LEU A 1 13 ? 4.758 -3.652 -2.822 1.00 98.07 13 A 1 ATOM 93 C C . LEU A 1 13 ? 4.429 -4.818 -3.746 1.00 98.11 13 A 1 ATOM 94 O O . LEU A 1 13 ? 5.323 -5.417 -4.350 1.00 97.58 13 A 1 ATOM 95 C CB . LEU A 1 13 ? 4.876 -4.143 -1.379 1.00 97.68 13 A 1 ATOM 96 C CG . LEU A 1 13 ? 6.254 -4.698 -1.037 1.00 96.39 13 A 1 ATOM 97 C CD1 . LEU A 1 13 ? 7.218 -3.558 -0.733 1.00 93.06 13 A 1 ATOM 98 C CD2 . LEU A 1 13 ? 6.162 -5.648 0.143 1.00 92.17 13 A 1 ATOM 99 N N . SER A 1 14 ? 3.156 -5.122 -3.858 1.00 98.35 14 A 1 ATOM 100 C CA . SER A 1 14 ? 2.690 -6.208 -4.715 1.00 98.12 14 A 1 ATOM 101 C C . SER A 1 14 ? 2.914 -5.880 -6.186 1.00 98.09 14 A 1 ATOM 102 O O . SER A 1 14 ? 3.032 -6.774 -7.030 1.00 96.99 14 A 1 ATOM 103 C CB . SER A 1 14 ? 1.208 -6.469 -4.457 1.00 97.42 14 A 1 ATOM 104 O OG . SER A 1 14 ? 0.718 -7.440 -5.340 1.00 92.27 14 A 1 ATOM 105 N N . GLN A 1 15 ? 2.960 -4.588 -6.484 1.00 97.50 15 A 1 ATOM 106 C CA . GLN A 1 15 ? 3.159 -4.130 -7.855 1.00 96.79 15 A 1 ATOM 107 C C . GLN A 1 15 ? 4.611 -3.718 -8.082 1.00 96.62 15 A 1 ATOM 108 O O . GLN A 1 15 ? 4.905 -2.904 -8.956 1.00 94.70 15 A 1 ATOM 109 C CB . GLN A 1 15 ? 2.233 -2.954 -8.154 1.00 95.66 15 A 1 ATOM 110 C CG . GLN A 1 15 ? 1.657 -3.014 -9.548 1.00 92.91 15 A 1 ATOM 111 C CD . GLN A 1 15 ? 0.855 -1.787 -9.909 1.00 90.42 15 A 1 ATOM 112 O OE1 . GLN A 1 15 ? -0.349 -1.745 -9.711 1.00 84.54 15 A 1 ATOM 113 N NE2 . GLN A 1 15 ? 1.513 -0.778 -10.439 1.00 84.51 15 A 1 ATOM 114 N N . ALA A 1 16 ? 5.520 -4.297 -7.294 1.00 95.81 16 A 1 ATOM 115 C CA . ALA A 1 16 ? 6.941 -3.980 -7.392 1.00 94.30 16 A 1 ATOM 116 C C . ALA A 1 16 ? 7.552 -4.672 -8.604 1.00 93.24 16 A 1 ATOM 117 O O . ALA A 1 16 ? 8.157 -3.980 -9.445 1.00 89.79 16 A 1 ATOM 118 C CB . ALA A 1 16 ? 7.666 -4.387 -6.119 1.00 91.81 16 A 1 ATOM 119 O OXT . ALA A 1 16 ? 7.437 -5.888 -8.706 1.00 84.44 16 A 1 #