# 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_spkb12606 # _entry.id spkb12606 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[C@@H](C(=O)O)N ? "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 GLN 2 1 n PHE 3 1 n SER 4 1 n SER 5 1 n ALA 6 1 n ILE 7 1 n ILE 8 1 n LEU 9 1 n SER 10 1 n ALA 11 1 n VAL 12 1 n ALA 13 1 n GLY 14 1 n SER 15 1 n ALA 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 @ 2025-07-10 00:25:49)" _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 92.18 _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 84.98 1 1 A GLN 2 2 87.44 1 2 A PHE 3 2 89.77 1 3 A SER 4 2 93.08 1 4 A SER 5 2 94.88 1 5 A ALA 6 2 96.47 1 6 A ILE 7 2 94.46 1 7 A ILE 8 2 94.20 1 8 A LEU 9 2 93.34 1 9 A SER 10 2 94.03 1 10 A ALA 11 2 96.87 1 11 A VAL 12 2 96.17 1 12 A ALA 13 2 95.96 1 13 A GLY 14 2 95.45 1 14 A SER 15 2 93.56 1 15 A ALA 16 2 94.32 1 16 A LEU 17 2 89.47 1 17 A ALA 18 2 83.46 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 GLN . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n ALA . 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 ? -0.947 12.252 2.521 1.00 87.42 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.533 11.189 1.687 1.00 90.76 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.260 9.811 2.284 1.00 92.08 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.674 8.942 1.646 1.00 89.49 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.944 11.249 0.282 1.00 86.81 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.301 12.533 -0.422 1.00 83.76 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.581 12.611 -2.069 1.00 80.49 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.517 13.994 -1.860 1.00 69.03 1 A 1 ATOM 9 N N . GLN A 1 2 ? -1.682 9.638 3.509 1.00 91.62 2 A 1 ATOM 10 C CA . GLN A 1 2 ? -1.456 8.379 4.212 1.00 94.45 2 A 1 ATOM 11 C C . GLN A 1 2 ? -2.283 7.250 3.600 1.00 95.81 2 A 1 ATOM 12 O O . GLN A 1 2 ? -1.814 6.118 3.480 1.00 94.24 2 A 1 ATOM 13 C CB . GLN A 1 2 ? -1.806 8.550 5.684 1.00 91.95 2 A 1 ATOM 14 C CG . GLN A 1 2 ? -1.117 7.527 6.551 1.00 84.92 2 A 1 ATOM 15 C CD . GLN A 1 2 ? -1.386 7.746 8.021 1.00 83.41 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? -2.467 7.448 8.501 1.00 76.26 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? -0.421 8.264 8.745 1.00 74.27 2 A 1 ATOM 18 N N . PHE A 1 3 ? -3.507 7.573 3.205 1.00 93.03 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -4.397 6.582 2.602 1.00 93.60 3 A 1 ATOM 20 C C . PHE A 1 3 ? -3.854 6.102 1.265 1.00 95.67 3 A 1 ATOM 21 O O . PHE A 1 3 ? -3.838 4.906 0.983 1.00 94.96 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -5.789 7.178 2.419 1.00 92.00 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -6.624 7.072 3.668 1.00 88.97 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -6.442 7.961 4.706 1.00 86.49 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -7.575 6.075 3.792 1.00 86.47 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -7.198 7.863 5.866 1.00 86.13 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -8.338 5.966 4.943 1.00 85.41 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -8.150 6.863 5.986 1.00 84.78 3 A 1 ATOM 29 N N . SER A 1 4 ? -3.398 7.036 0.444 1.00 94.00 4 A 1 ATOM 30 C CA . SER A 1 4 ? -2.822 6.702 -0.854 1.00 94.66 4 A 1 ATOM 31 C C . SER A 1 4 ? -1.626 5.776 -0.681 1.00 96.05 4 A 1 ATOM 32 O O . SER A 1 4 ? -1.473 4.785 -1.394 1.00 95.23 4 A 1 ATOM 33 C CB . SER A 1 4 ? -2.396 7.970 -1.583 1.00 92.83 4 A 1 ATOM 34 O OG . SER A 1 4 ? -3.480 8.529 -2.294 1.00 85.71 4 A 1 ATOM 35 N N . SER A 1 5 ? -0.787 6.110 0.284 1.00 95.43 5 A 1 ATOM 36 C CA . SER A 1 5 ? 0.396 5.311 0.582 1.00 96.39 5 A 1 ATOM 37 C C . SER A 1 5 ? -0.006 3.923 1.066 1.00 97.08 5 A 1 ATOM 38 O O . SER A 1 5 ? 0.633 2.924 0.732 1.00 96.45 5 A 1 ATOM 39 C CB . SER A 1 5 ? 1.243 6.007 1.643 1.00 95.32 5 A 1 ATOM 40 O OG . SER A 1 5 ? 2.476 5.360 1.802 1.00 88.62 5 A 1 ATOM 41 N N . ALA A 1 6 ? -1.069 3.873 1.845 1.00 95.92 6 A 1 ATOM 42 C CA . ALA A 1 6 ? -1.569 2.611 2.377 1.00 96.59 6 A 1 ATOM 43 C C . ALA A 1 6 ? -2.003 1.683 1.250 1.00 97.30 6 A 1 ATOM 44 O O . ALA A 1 6 ? -1.776 0.474 1.306 1.00 96.73 6 A 1 ATOM 45 C CB . ALA A 1 6 ? -2.731 2.877 3.320 1.00 95.83 6 A 1 ATOM 46 N N . ILE A 1 7 ? -2.627 2.254 0.231 1.00 96.56 7 A 1 ATOM 47 C CA . ILE A 1 7 ? -3.081 1.479 -0.917 1.00 96.51 7 A 1 ATOM 48 C C . ILE A 1 7 ? -1.901 0.832 -1.621 1.00 96.98 7 A 1 ATOM 49 O O . ILE A 1 7 ? -1.928 -0.348 -1.975 1.00 96.66 7 A 1 ATOM 50 C CB . ILE A 1 7 ? -3.846 2.367 -1.906 1.00 96.20 7 A 1 ATOM 51 C CG1 . ILE A 1 7 ? -5.050 3.015 -1.213 1.00 93.71 7 A 1 ATOM 52 C CG2 . ILE A 1 7 ? -4.313 1.530 -3.100 1.00 92.58 7 A 1 ATOM 53 C CD1 . ILE A 1 7 ? -6.016 1.991 -0.645 1.00 86.51 7 A 1 ATOM 54 N N . ILE A 1 8 ? -0.877 1.622 -1.825 1.00 95.83 8 A 1 ATOM 55 C CA . ILE A 1 8 ? 0.327 1.136 -2.491 1.00 95.63 8 A 1 ATOM 56 C C . ILE A 1 8 ? 0.990 0.051 -1.655 1.00 96.04 8 A 1 ATOM 57 O O . ILE A 1 8 ? 1.424 -0.982 -2.172 1.00 95.66 8 A 1 ATOM 58 C CB . ILE A 1 8 ? 1.312 2.291 -2.730 1.00 95.62 8 A 1 ATOM 59 C CG1 . ILE A 1 8 ? 0.683 3.341 -3.646 1.00 93.97 8 A 1 ATOM 60 C CG2 . ILE A 1 8 ? 2.607 1.757 -3.353 1.00 93.21 8 A 1 ATOM 61 C CD1 . ILE A 1 8 ? 1.477 4.627 -3.695 1.00 87.66 8 A 1 ATOM 62 N N . LEU A 1 9 ? 1.057 0.296 -0.364 1.00 95.79 9 A 1 ATOM 63 C CA . LEU A 1 9 ? 1.663 -0.661 0.553 1.00 95.34 9 A 1 ATOM 64 C C . LEU A 1 9 ? 0.905 -1.985 0.520 1.00 96.02 9 A 1 ATOM 65 O O . LEU A 1 9 ? 1.505 -3.062 0.500 1.00 95.82 9 A 1 ATOM 66 C CB . LEU A 1 9 ? 1.661 -0.090 1.970 1.00 94.76 9 A 1 ATOM 67 C CG . LEU A 1 9 ? 2.913 -0.448 2.770 1.00 90.44 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? 4.116 0.305 2.233 1.00 89.35 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? 2.700 -0.137 4.245 1.00 89.17 9 A 1 ATOM 70 N N . SER A 1 10 ? -0.406 -1.891 0.511 1.00 95.99 10 A 1 ATOM 71 C CA . SER A 1 10 ? -1.260 -3.072 0.459 1.00 95.87 10 A 1 ATOM 72 C C . SER A 1 10 ? -1.027 -3.842 -0.832 1.00 96.41 10 A 1 ATOM 73 O O . SER A 1 10 ? -0.985 -5.072 -0.840 1.00 95.28 10 A 1 ATOM 74 C CB . SER A 1 10 ? -2.723 -2.667 0.568 1.00 94.80 10 A 1 ATOM 75 O OG . SER A 1 10 ? -3.041 -2.324 1.901 1.00 85.81 10 A 1 ATOM 76 N N . ALA A 1 11 ? -0.873 -3.102 -1.918 1.00 96.77 11 A 1 ATOM 77 C CA . ALA A 1 11 ? -0.632 -3.712 -3.222 1.00 97.02 11 A 1 ATOM 78 C C . ALA A 1 11 ? 0.689 -4.473 -3.220 1.00 97.41 11 A 1 ATOM 79 O O . ALA A 1 11 ? 0.784 -5.572 -3.768 1.00 96.53 11 A 1 ATOM 80 C CB . ALA A 1 11 ? -0.617 -2.635 -4.298 1.00 96.61 11 A 1 ATOM 81 N N . VAL A 1 12 ? 1.690 -3.882 -2.604 1.00 96.98 12 A 1 ATOM 82 C CA . VAL A 1 12 ? 3.009 -4.510 -2.522 1.00 96.83 12 A 1 ATOM 83 C C . VAL A 1 12 ? 2.924 -5.815 -1.747 1.00 97.10 12 A 1 ATOM 84 O O . VAL A 1 12 ? 3.472 -6.839 -2.163 1.00 96.50 12 A 1 ATOM 85 C CB . VAL A 1 12 ? 4.020 -3.570 -1.846 1.00 96.09 12 A 1 ATOM 86 C CG1 . VAL A 1 12 ? 5.361 -4.272 -1.667 1.00 94.53 12 A 1 ATOM 87 C CG2 . VAL A 1 12 ? 4.204 -2.308 -2.676 1.00 95.13 12 A 1 ATOM 88 N N . ALA A 1 13 ? 2.241 -5.760 -0.623 1.00 96.44 13 A 1 ATOM 89 C CA . ALA A 1 13 ? 2.081 -6.941 0.215 1.00 96.29 13 A 1 ATOM 90 C C . ALA A 1 13 ? 1.322 -8.032 -0.530 1.00 96.59 13 A 1 ATOM 91 O O . ALA A 1 13 ? 1.665 -9.213 -0.448 1.00 95.27 13 A 1 ATOM 92 C CB . ALA A 1 13 ? 1.352 -6.566 1.496 1.00 95.20 13 A 1 ATOM 93 N N . GLY A 1 14 ? 0.294 -7.624 -1.251 1.00 95.58 14 A 1 ATOM 94 C CA . GLY A 1 14 ? -0.496 -8.575 -2.024 1.00 94.92 14 A 1 ATOM 95 C C . GLY A 1 14 ? 0.310 -9.196 -3.143 1.00 95.94 14 A 1 ATOM 96 O O . GLY A 1 14 ? 0.204 -10.393 -3.414 1.00 95.36 14 A 1 ATOM 97 N N . SER A 1 15 ? 1.127 -8.383 -3.787 1.00 96.13 15 A 1 ATOM 98 C CA . SER A 1 15 ? 1.983 -8.852 -4.873 1.00 95.89 15 A 1 ATOM 99 C C . SER A 1 15 ? 2.981 -9.881 -4.362 1.00 96.12 15 A 1 ATOM 100 O O . SER A 1 15 ? 3.273 -10.874 -5.026 1.00 93.74 15 A 1 ATOM 101 C CB . SER A 1 15 ? 2.733 -7.678 -5.497 1.00 94.30 15 A 1 ATOM 102 O OG . SER A 1 15 ? 2.349 -7.489 -6.837 1.00 85.21 15 A 1 ATOM 103 N N . ALA A 1 16 ? 3.503 -9.630 -3.172 1.00 94.72 16 A 1 ATOM 104 C CA . ALA A 1 16 ? 4.462 -10.541 -2.555 1.00 94.52 16 A 1 ATOM 105 C C . ALA A 1 16 ? 3.819 -11.898 -2.288 1.00 95.41 16 A 1 ATOM 106 O O . ALA A 1 16 ? 4.472 -12.938 -2.402 1.00 93.75 16 A 1 ATOM 107 C CB . ALA A 1 16 ? 4.987 -9.941 -1.258 1.00 93.20 16 A 1 ATOM 108 N N . LEU A 1 17 ? 2.552 -11.869 -1.923 1.00 93.05 17 A 1 ATOM 109 C CA . LEU A 1 17 ? 1.810 -13.095 -1.650 1.00 93.01 17 A 1 ATOM 110 C C . LEU A 1 17 ? 1.522 -13.858 -2.934 1.00 94.27 17 A 1 ATOM 111 O O . LEU A 1 17 ? 1.401 -15.087 -2.934 1.00 92.57 17 A 1 ATOM 112 C CB . LEU A 1 17 ? 0.500 -12.769 -0.926 1.00 90.49 17 A 1 ATOM 113 C CG . LEU A 1 17 ? 0.453 -13.205 0.537 1.00 86.40 17 A 1 ATOM 114 C CD1 . LEU A 1 17 ? 0.653 -14.709 0.640 1.00 84.24 17 A 1 ATOM 115 C CD2 . LEU A 1 17 ? 1.521 -12.474 1.332 1.00 81.69 17 A 1 ATOM 116 N N . ALA A 1 18 ? 1.398 -13.112 -4.021 1.00 87.55 18 A 1 ATOM 117 C CA . ALA A 1 18 ? 1.094 -13.701 -5.317 1.00 87.38 18 A 1 ATOM 118 C C . ALA A 1 18 ? 2.250 -14.560 -5.833 1.00 85.96 18 A 1 ATOM 119 O O . ALA A 1 18 ? 3.378 -14.444 -5.325 1.00 81.57 18 A 1 ATOM 120 C CB . ALA A 1 18 ? 0.756 -12.600 -6.309 1.00 82.37 18 A 1 ATOM 121 O OXT . ALA A 1 18 ? 2.043 -15.351 -6.763 1.00 75.96 18 A 1 #