# 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_spkb14559 # _entry.id spkb14559 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "PEPTIDE LINKING" "C6 H13 N O2" 131.173 ILE y ISOLEUCINE CC[C@H](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" "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 PRO 2 1 n ALA 3 1 n PRO 4 1 n GLY 5 1 n ALA 6 1 n LEU 7 1 n ILE 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n ALA 12 1 n VAL 13 1 n SER 14 1 n ALA 15 1 n SER 16 1 n GLY 17 1 n CYS 18 1 n LEU 19 1 n ALA 20 # _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 06:09:10)" _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 92.14 _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 86.52 1 1 A PRO 2 2 90.70 1 2 A ALA 3 2 94.82 1 3 A PRO 4 2 95.25 1 4 A GLY 5 2 96.25 1 5 A ALA 6 2 96.97 1 6 A LEU 7 2 94.96 1 7 A ILE 8 2 95.26 1 8 A LEU 9 2 94.17 1 9 A LEU 10 2 92.08 1 10 A ALA 11 2 95.54 1 11 A ALA 12 2 95.78 1 12 A VAL 13 2 93.99 1 13 A SER 14 2 93.15 1 14 A ALA 15 2 94.65 1 15 A SER 16 2 93.44 1 16 A GLY 17 2 94.08 1 17 A CYS 18 2 87.56 1 18 A LEU 19 2 83.85 1 19 A ALA 20 2 80.09 1 20 # _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 PRO . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n GLY . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n SER . 16 A 16 A 17 1 n GLY . 17 A 17 A 18 1 n CYS . 18 A 18 A 19 1 n LEU . 19 A 19 A 20 1 n ALA . 20 A 20 # _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 ? -11.488 2.221 11.825 1.00 90.20 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.571 1.255 11.192 1.00 91.39 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.868 1.145 9.699 1.00 92.61 1 A 1 ATOM 4 O O . MET A 1 1 ? -12.031 1.114 9.312 1.00 91.55 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.726 -0.129 11.834 1.00 88.11 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.202 -0.168 13.263 1.00 83.22 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.384 -1.808 13.987 1.00 80.75 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.609 -1.534 15.576 1.00 74.31 1 A 1 ATOM 9 N N . PRO A 1 2 ? -9.834 1.089 8.865 1.00 91.27 2 A 1 ATOM 10 C CA . PRO A 1 2 ? -9.998 0.969 7.413 1.00 92.59 2 A 1 ATOM 11 C C . PRO A 1 2 ? -10.500 -0.415 7.015 1.00 93.90 2 A 1 ATOM 12 O O . PRO A 1 2 ? -10.226 -1.406 7.692 1.00 91.89 2 A 1 ATOM 13 C CB . PRO A 1 2 ? -8.588 1.205 6.871 1.00 89.75 2 A 1 ATOM 14 C CG . PRO A 1 2 ? -7.682 0.806 7.988 1.00 86.09 2 A 1 ATOM 15 C CD . PRO A 1 2 ? -8.427 1.149 9.262 1.00 89.42 2 A 1 ATOM 16 N N . ALA A 1 3 ? -11.213 -0.480 5.901 1.00 94.02 3 A 1 ATOM 17 C CA . ALA A 1 3 ? -11.745 -1.742 5.397 1.00 95.21 3 A 1 ATOM 18 C C . ALA A 1 3 ? -10.612 -2.605 4.837 1.00 96.14 3 A 1 ATOM 19 O O . ALA A 1 3 ? -9.537 -2.087 4.525 1.00 95.39 3 A 1 ATOM 20 C CB . ALA A 1 3 ? -12.792 -1.460 4.323 1.00 93.36 3 A 1 ATOM 21 N N . PRO A 1 4 ? -10.855 -3.918 4.696 1.00 96.08 4 A 1 ATOM 22 C CA . PRO A 1 4 ? -9.833 -4.818 4.142 1.00 96.49 4 A 1 ATOM 23 C C . PRO A 1 4 ? -9.399 -4.398 2.745 1.00 97.23 4 A 1 ATOM 24 O O . PRO A 1 4 ? -8.217 -4.485 2.394 1.00 96.38 4 A 1 ATOM 25 C CB . PRO A 1 4 ? -10.529 -6.190 4.123 1.00 94.41 4 A 1 ATOM 26 C CG . PRO A 1 4 ? -11.990 -5.885 4.232 1.00 91.97 4 A 1 ATOM 27 C CD . PRO A 1 4 ? -12.090 -4.613 5.031 1.00 94.17 4 A 1 ATOM 28 N N . GLY A 1 5 ? -10.344 -3.931 1.952 1.00 95.45 5 A 1 ATOM 29 C CA . GLY A 1 5 ? -10.029 -3.467 0.601 1.00 95.98 5 A 1 ATOM 30 C C . GLY A 1 5 ? -9.142 -2.239 0.618 1.00 97.00 5 A 1 ATOM 31 O O . GLY A 1 5 ? -8.242 -2.093 -0.209 1.00 96.59 5 A 1 ATOM 32 N N . ALA A 1 6 ? -9.377 -1.354 1.582 1.00 96.87 6 A 1 ATOM 33 C CA . ALA A 1 6 ? -8.580 -0.139 1.732 1.00 97.16 6 A 1 ATOM 34 C C . ALA A 1 6 ? -7.139 -0.478 2.105 1.00 97.54 6 A 1 ATOM 35 O O . ALA A 1 6 ? -6.198 0.143 1.615 1.00 96.74 6 A 1 ATOM 36 C CB . ALA A 1 6 ? -9.200 0.762 2.795 1.00 96.56 6 A 1 ATOM 37 N N . LEU A 1 7 ? -6.975 -1.464 2.975 1.00 96.61 7 A 1 ATOM 38 C CA . LEU A 1 7 ? -5.646 -1.906 3.397 1.00 96.50 7 A 1 ATOM 39 C C . LEU A 1 7 ? -4.869 -2.475 2.217 1.00 96.89 7 A 1 ATOM 40 O O . LEU A 1 7 ? -3.678 -2.211 2.056 1.00 96.58 7 A 1 ATOM 41 C CB . LEU A 1 7 ? -5.778 -2.961 4.496 1.00 96.06 7 A 1 ATOM 42 C CG . LEU A 1 7 ? -6.230 -2.397 5.840 1.00 93.55 7 A 1 ATOM 43 C CD1 . LEU A 1 7 ? -6.593 -3.520 6.793 1.00 92.03 7 A 1 ATOM 44 C CD2 . LEU A 1 7 ? -5.137 -1.527 6.442 1.00 91.45 7 A 1 ATOM 45 N N . ILE A 1 8 ? -5.547 -3.248 1.403 1.00 96.74 8 A 1 ATOM 46 C CA . ILE A 1 8 ? -4.930 -3.844 0.219 1.00 96.49 8 A 1 ATOM 47 C C . ILE A 1 8 ? -4.501 -2.752 -0.755 1.00 96.76 8 A 1 ATOM 48 O O . ILE A 1 8 ? -3.411 -2.806 -1.334 1.00 96.38 8 A 1 ATOM 49 C CB . ILE A 1 8 ? -5.901 -4.820 -0.464 1.00 96.49 8 A 1 ATOM 50 C CG1 . ILE A 1 8 ? -6.180 -6.019 0.446 1.00 95.06 8 A 1 ATOM 51 C CG2 . ILE A 1 8 ? -5.323 -5.299 -1.799 1.00 94.27 8 A 1 ATOM 52 C CD1 . ILE A 1 8 ? -7.349 -6.859 -0.017 1.00 89.86 8 A 1 ATOM 53 N N . LEU A 1 9 ? -5.358 -1.758 -0.913 1.00 96.02 9 A 1 ATOM 54 C CA . LEU A 1 9 ? -5.066 -0.639 -1.807 1.00 95.60 9 A 1 ATOM 55 C C . LEU A 1 9 ? -3.841 0.127 -1.318 1.00 96.09 9 A 1 ATOM 56 O O . LEU A 1 9 ? -2.959 0.480 -2.100 1.00 95.77 9 A 1 ATOM 57 C CB . LEU A 1 9 ? -6.276 0.296 -1.878 1.00 95.31 9 A 1 ATOM 58 C CG . LEU A 1 9 ? -6.215 1.297 -3.032 1.00 92.08 9 A 1 ATOM 59 C CD1 . LEU A 1 9 ? -6.549 0.608 -4.350 1.00 91.40 9 A 1 ATOM 60 C CD2 . LEU A 1 9 ? -7.170 2.453 -2.791 1.00 91.13 9 A 1 ATOM 61 N N . LEU A 1 10 ? -3.789 0.367 -0.020 1.00 94.63 10 A 1 ATOM 62 C CA . LEU A 1 10 ? -2.664 1.072 0.590 1.00 93.97 10 A 1 ATOM 63 C C . LEU A 1 10 ? -1.369 0.297 0.388 1.00 94.98 10 A 1 ATOM 64 O O . LEU A 1 10 ? -0.328 0.873 0.059 1.00 94.78 10 A 1 ATOM 65 C CB . LEU A 1 10 ? -2.928 1.260 2.086 1.00 93.20 10 A 1 ATOM 66 C CG . LEU A 1 10 ? -1.959 2.228 2.764 1.00 87.96 10 A 1 ATOM 67 C CD1 . LEU A 1 10 ? -2.293 3.670 2.386 1.00 88.45 10 A 1 ATOM 68 C CD2 . LEU A 1 10 ? -2.005 2.063 4.271 1.00 88.64 10 A 1 ATOM 69 N N . ALA A 1 11 ? -1.436 -1.010 0.585 1.00 95.43 11 A 1 ATOM 70 C CA . ALA A 1 11 ? -0.272 -1.874 0.406 1.00 95.52 11 A 1 ATOM 71 C C . ALA A 1 11 ? 0.201 -1.847 -1.043 1.00 96.16 11 A 1 ATOM 72 O O . ALA A 1 11 ? 1.405 -1.821 -1.310 1.00 95.43 11 A 1 ATOM 73 C CB . ALA A 1 11 ? -0.621 -3.302 0.819 1.00 95.15 11 A 1 ATOM 74 N N . ALA A 1 12 ? -0.738 -1.845 -1.969 1.00 96.13 12 A 1 ATOM 75 C CA . ALA A 1 12 ? -0.416 -1.811 -3.393 1.00 96.01 12 A 1 ATOM 76 C C . ALA A 1 12 ? 0.293 -0.512 -3.758 1.00 96.36 12 A 1 ATOM 77 O O . ALA A 1 12 ? 1.284 -0.521 -4.489 1.00 94.94 12 A 1 ATOM 78 C CB . ALA A 1 12 ? -1.691 -1.970 -4.218 1.00 95.44 12 A 1 ATOM 79 N N . VAL A 1 13 ? -0.204 0.603 -3.239 1.00 95.12 13 A 1 ATOM 80 C CA . VAL A 1 13 ? 0.393 1.915 -3.502 1.00 94.77 13 A 1 ATOM 81 C C . VAL A 1 13 ? 1.798 1.988 -2.918 1.00 95.39 13 A 1 ATOM 82 O O . VAL A 1 13 ? 2.726 2.486 -3.560 1.00 94.64 13 A 1 ATOM 83 C CB . VAL A 1 13 ? -0.481 3.035 -2.919 1.00 93.85 13 A 1 ATOM 84 C CG1 . VAL A 1 13 ? 0.192 4.391 -3.087 1.00 91.91 13 A 1 ATOM 85 C CG2 . VAL A 1 13 ? -1.842 3.052 -3.593 1.00 92.25 13 A 1 ATOM 86 N N . SER A 1 14 ? 1.947 1.491 -1.702 1.00 95.00 14 A 1 ATOM 87 C CA . SER A 1 14 ? 3.239 1.495 -1.022 1.00 94.77 14 A 1 ATOM 88 C C . SER A 1 14 ? 4.255 0.640 -1.768 1.00 95.14 14 A 1 ATOM 89 O O . SER A 1 14 ? 5.412 1.031 -1.927 1.00 94.53 14 A 1 ATOM 90 C CB . SER A 1 14 ? 3.085 0.979 0.409 1.00 93.58 14 A 1 ATOM 91 O OG . SER A 1 14 ? 4.312 1.059 1.092 1.00 85.89 14 A 1 ATOM 92 N N . ALA A 1 15 ? 3.830 -0.519 -2.226 1.00 95.47 15 A 1 ATOM 93 C CA . ALA A 1 15 ? 4.708 -1.431 -2.959 1.00 94.69 15 A 1 ATOM 94 C C . ALA A 1 15 ? 5.017 -0.908 -4.357 1.00 95.55 15 A 1 ATOM 95 O O . ALA A 1 15 ? 6.091 -1.164 -4.897 1.00 94.21 15 A 1 ATOM 96 C CB . ALA A 1 15 ? 4.064 -2.811 -3.048 1.00 93.31 15 A 1 ATOM 97 N N . SER A 1 16 ? 4.078 -0.174 -4.931 1.00 95.56 16 A 1 ATOM 98 C CA . SER A 1 16 ? 4.235 0.352 -6.286 1.00 95.59 16 A 1 ATOM 99 C C . SER A 1 16 ? 5.162 1.561 -6.328 1.00 96.14 16 A 1 ATOM 100 O O . SER A 1 16 ? 5.913 1.747 -7.287 1.00 93.89 16 A 1 ATOM 101 C CB . SER A 1 16 ? 2.874 0.720 -6.869 1.00 93.56 16 A 1 ATOM 102 O OG . SER A 1 16 ? 3.001 1.132 -8.210 1.00 85.88 16 A 1 ATOM 103 N N . GLY A 1 17 ? 5.122 2.384 -5.285 1.00 94.42 17 A 1 ATOM 104 C CA . GLY A 1 17 ? 5.952 3.588 -5.254 1.00 93.83 17 A 1 ATOM 105 C C . GLY A 1 17 ? 6.469 3.926 -3.868 1.00 94.63 17 A 1 ATOM 106 O O . GLY A 1 17 ? 6.244 5.022 -3.368 1.00 93.46 17 A 1 ATOM 107 N N . CYS A 1 18 ? 7.148 2.981 -3.253 1.00 90.34 18 A 1 ATOM 108 C CA . CYS A 1 18 ? 7.726 3.188 -1.928 1.00 89.84 18 A 1 ATOM 109 C C . CYS A 1 18 ? 9.202 3.573 -2.027 1.00 90.57 18 A 1 ATOM 110 O O . CYS A 1 18 ? 9.691 4.435 -1.293 1.00 87.62 18 A 1 ATOM 111 C CB . CYS A 1 18 ? 7.578 1.917 -1.082 1.00 86.21 18 A 1 ATOM 112 S SG . CYS A 1 18 ? 8.174 2.149 0.605 1.00 80.81 18 A 1 ATOM 113 N N . LEU A 1 19 ? 9.913 2.942 -2.939 1.00 87.71 19 A 1 ATOM 114 C CA . LEU A 1 19 ? 11.342 3.186 -3.123 1.00 88.06 19 A 1 ATOM 115 C C . LEU A 1 19 ? 11.583 4.314 -4.119 1.00 89.69 19 A 1 ATOM 116 O O . LEU A 1 19 ? 11.492 4.117 -5.327 1.00 87.09 19 A 1 ATOM 117 C CB . LEU A 1 19 ? 12.028 1.906 -3.600 1.00 84.59 19 A 1 ATOM 118 C CG . LEU A 1 19 ? 13.546 1.962 -3.524 1.00 81.14 19 A 1 ATOM 119 C CD1 . LEU A 1 19 ? 14.023 1.824 -2.086 1.00 77.65 19 A 1 ATOM 120 C CD2 . LEU A 1 19 ? 14.165 0.864 -4.386 1.00 74.91 19 A 1 ATOM 121 N N . ALA A 1 20 ? 11.908 5.505 -3.563 1.00 85.04 20 A 1 ATOM 122 C CA . ALA A 1 20 ? 12.187 6.672 -4.401 1.00 84.59 20 A 1 ATOM 123 C C . ALA A 1 20 ? 11.031 6.966 -5.367 1.00 82.72 20 A 1 ATOM 124 O O . ALA A 1 20 ? 9.894 6.547 -5.094 1.00 78.03 20 A 1 ATOM 125 C CB . ALA A 1 20 ? 13.503 6.453 -5.157 1.00 77.90 20 A 1 ATOM 126 O OXT . ALA A 1 20 ? 11.246 7.635 -6.379 1.00 72.28 20 A 1 #