# 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_spkb38886 # _entry.id spkb38886 # 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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 ILE 2 1 n LEU 3 1 n GLN 4 1 n ALA 5 1 n ALA 6 1 n LEU 7 1 n PHE 8 1 n LEU 9 1 n ALA 10 1 n GLY 11 1 n LEU 12 1 n THR 13 1 n VAL 14 1 n VAL 15 1 n SER 16 1 n GLY 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 @ 2025-07-09 18:55:56)" _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 94.61 _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 88.25 1 1 A ILE 2 2 93.61 1 2 A LEU 3 2 95.47 1 3 A GLN 4 2 92.49 1 4 A ALA 5 2 97.38 1 5 A ALA 6 2 97.65 1 6 A LEU 7 2 96.05 1 7 A PHE 8 2 95.02 1 8 A LEU 9 2 95.01 1 9 A ALA 10 2 97.67 1 10 A GLY 11 2 98.25 1 11 A LEU 12 2 96.25 1 12 A THR 13 2 96.34 1 13 A VAL 14 2 96.42 1 14 A VAL 15 2 95.72 1 15 A SER 16 2 93.11 1 16 A GLY 17 2 85.90 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 ILE . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n GLN . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n SER . 16 A 16 A 17 1 n GLY . 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 ? -11.173 -7.218 1.785 1.00 93.14 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.515 -5.951 2.140 1.00 93.76 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.634 -5.465 0.992 1.00 94.31 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.405 -5.468 1.079 1.00 92.70 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.667 -6.130 3.397 1.00 89.60 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.507 -6.491 4.602 1.00 84.26 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.513 -6.695 6.087 1.00 83.60 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.791 -7.065 7.270 1.00 74.67 1 A 1 ATOM 9 N N . ILE A 1 2 ? -10.282 -5.058 -0.083 1.00 95.02 2 A 1 ATOM 10 C CA . ILE A 1 2 ? -9.576 -4.590 -1.273 1.00 96.75 2 A 1 ATOM 11 C C . ILE A 1 2 ? -9.098 -3.152 -1.088 1.00 97.51 2 A 1 ATOM 12 O O . ILE A 1 2 ? -8.072 -2.744 -1.639 1.00 96.96 2 A 1 ATOM 13 C CB . ILE A 1 2 ? -10.485 -4.684 -2.509 1.00 95.77 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -11.075 -6.088 -2.650 1.00 92.10 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? -9.700 -4.317 -3.769 1.00 90.49 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -12.195 -6.158 -3.660 1.00 84.31 2 A 1 ATOM 17 N N . LEU A 1 3 ? -9.850 -2.386 -0.295 1.00 97.42 3 A 1 ATOM 18 C CA . LEU A 1 3 ? -9.515 -0.985 -0.042 1.00 97.56 3 A 1 ATOM 19 C C . LEU A 1 3 ? -8.173 -0.864 0.671 1.00 97.77 3 A 1 ATOM 20 O O . LEU A 1 3 ? -7.355 -0.004 0.344 1.00 97.36 3 A 1 ATOM 21 C CB . LEU A 1 3 ? -10.614 -0.336 0.798 1.00 97.25 3 A 1 ATOM 22 C CG . LEU A 1 3 ? -11.928 -0.123 0.055 1.00 94.38 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? -13.046 0.184 1.040 1.00 91.77 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? -11.792 1.005 -0.952 1.00 90.24 3 A 1 ATOM 25 N N . GLN A 1 4 ? -7.951 -1.733 1.644 1.00 96.84 4 A 1 ATOM 26 C CA . GLN A 1 4 ? -6.705 -1.724 2.406 1.00 96.96 4 A 1 ATOM 27 C C . GLN A 1 4 ? -5.526 -2.105 1.517 1.00 97.59 4 A 1 ATOM 28 O O . GLN A 1 4 ? -4.420 -1.588 1.683 1.00 97.16 4 A 1 ATOM 29 C CB . GLN A 1 4 ? -6.804 -2.689 3.582 1.00 95.97 4 A 1 ATOM 30 C CG . GLN A 1 4 ? -5.703 -2.458 4.595 1.00 91.73 4 A 1 ATOM 31 C CD . GLN A 1 4 ? -5.816 -3.376 5.795 1.00 89.75 4 A 1 ATOM 32 O OE1 . GLN A 1 4 ? -6.156 -4.546 5.658 1.00 83.74 4 A 1 ATOM 33 N NE2 . GLN A 1 4 ? -5.531 -2.868 6.977 1.00 82.71 4 A 1 ATOM 34 N N . ALA A 1 5 ? -5.767 -2.998 0.570 1.00 97.32 5 A 1 ATOM 35 C CA . ALA A 1 5 ? -4.728 -3.437 -0.356 1.00 97.52 5 A 1 ATOM 36 C C . ALA A 1 5 ? -4.243 -2.275 -1.213 1.00 97.84 5 A 1 ATOM 37 O O . ALA A 1 5 ? -3.049 -2.151 -1.493 1.00 97.26 5 A 1 ATOM 38 C CB . ALA A 1 5 ? -5.264 -4.560 -1.240 1.00 96.95 5 A 1 ATOM 39 N N . ALA A 1 6 ? -5.180 -1.426 -1.623 1.00 97.79 6 A 1 ATOM 40 C CA . ALA A 1 6 ? -4.854 -0.262 -2.441 1.00 97.74 6 A 1 ATOM 41 C C . ALA A 1 6 ? -4.036 0.745 -1.644 1.00 98.00 6 A 1 ATOM 42 O O . ALA A 1 6 ? -3.112 1.366 -2.171 1.00 97.41 6 A 1 ATOM 43 C CB . ALA A 1 6 ? -6.134 0.385 -2.952 1.00 97.33 6 A 1 ATOM 44 N N . LEU A 1 7 ? -4.384 0.902 -0.365 1.00 97.80 7 A 1 ATOM 45 C CA . LEU A 1 7 ? -3.674 1.823 0.516 1.00 97.80 7 A 1 ATOM 46 C C . LEU A 1 7 ? -2.239 1.362 0.738 1.00 97.99 7 A 1 ATOM 47 O O . LEU A 1 7 ? -1.310 2.170 0.765 1.00 97.74 7 A 1 ATOM 48 C CB . LEU A 1 7 ? -4.397 1.919 1.859 1.00 97.51 7 A 1 ATOM 49 C CG . LEU A 1 7 ? -3.803 2.944 2.815 1.00 94.65 7 A 1 ATOM 50 C CD1 . LEU A 1 7 ? -4.132 4.356 2.352 1.00 92.61 7 A 1 ATOM 51 C CD2 . LEU A 1 7 ? -4.320 2.719 4.229 1.00 92.33 7 A 1 ATOM 52 N N . PHE A 1 8 ? -2.071 0.059 0.906 1.00 97.30 8 A 1 ATOM 53 C CA . PHE A 1 8 ? -0.751 -0.527 1.120 1.00 97.28 8 A 1 ATOM 54 C C . PHE A 1 8 ? 0.150 -0.298 -0.087 1.00 97.65 8 A 1 ATOM 55 O O . PHE A 1 8 ? 1.328 0.036 0.054 1.00 97.35 8 A 1 ATOM 56 C CB . PHE A 1 8 ? -0.898 -2.023 1.389 1.00 97.06 8 A 1 ATOM 57 C CG . PHE A 1 8 ? 0.422 -2.708 1.616 1.00 95.59 8 A 1 ATOM 58 C CD1 . PHE A 1 8 ? 1.120 -2.511 2.793 1.00 92.95 8 A 1 ATOM 59 C CD2 . PHE A 1 8 ? 0.951 -3.548 0.655 1.00 93.20 8 A 1 ATOM 60 C CE1 . PHE A 1 8 ? 2.337 -3.139 3.006 1.00 92.48 8 A 1 ATOM 61 C CE2 . PHE A 1 8 ? 2.172 -4.178 0.862 1.00 91.84 8 A 1 ATOM 62 C CZ . PHE A 1 8 ? 2.865 -3.975 2.039 1.00 92.55 8 A 1 ATOM 63 N N . LEU A 1 9 ? -0.427 -0.474 -1.268 1.00 97.40 9 A 1 ATOM 64 C CA . LEU A 1 9 ? 0.320 -0.285 -2.508 1.00 97.37 9 A 1 ATOM 65 C C . LEU A 1 9 ? 0.734 1.171 -2.679 1.00 97.89 9 A 1 ATOM 66 O O . LEU A 1 9 ? 1.857 1.465 -3.091 1.00 97.78 9 A 1 ATOM 67 C CB . LEU A 1 9 ? -0.523 -0.726 -3.705 1.00 96.75 9 A 1 ATOM 68 C CG . LEU A 1 9 ? 0.196 -1.693 -4.642 1.00 91.53 9 A 1 ATOM 69 C CD1 . LEU A 1 9 ? 0.275 -3.073 -4.018 1.00 90.69 9 A 1 ATOM 70 C CD2 . LEU A 1 9 ? -0.507 -1.754 -5.988 1.00 90.68 9 A 1 ATOM 71 N N . ALA A 1 10 ? -0.186 2.075 -2.352 1.00 97.74 10 A 1 ATOM 72 C CA . ALA A 1 10 ? 0.080 3.506 -2.465 1.00 97.73 10 A 1 ATOM 73 C C . ALA A 1 10 ? 1.175 3.935 -1.497 1.00 98.07 10 A 1 ATOM 74 O O . ALA A 1 10 ? 1.945 4.850 -1.780 1.00 97.52 10 A 1 ATOM 75 C CB . ALA A 1 10 ? -1.197 4.288 -2.196 1.00 97.28 10 A 1 ATOM 76 N N . GLY A 1 11 ? 1.233 3.271 -0.352 1.00 98.20 11 A 1 ATOM 77 C CA . GLY A 1 11 ? 2.236 3.596 0.652 1.00 98.26 11 A 1 ATOM 78 C C . GLY A 1 11 ? 3.634 3.207 0.225 1.00 98.44 11 A 1 ATOM 79 O O . GLY A 1 11 ? 4.584 3.960 0.430 1.00 98.12 11 A 1 ATOM 80 N N . LEU A 1 12 ? 3.772 2.031 -0.370 1.00 98.06 12 A 1 ATOM 81 C CA . LEU A 1 12 ? 5.083 1.549 -0.798 1.00 97.90 12 A 1 ATOM 82 C C . LEU A 1 12 ? 5.633 2.384 -1.950 1.00 98.03 12 A 1 ATOM 83 O O . LEU A 1 12 ? 6.847 2.561 -2.069 1.00 97.32 12 A 1 ATOM 84 C CB . LEU A 1 12 ? 4.994 0.066 -1.196 1.00 97.42 12 A 1 ATOM 85 C CG . LEU A 1 12 ? 4.264 -0.210 -2.512 1.00 95.58 12 A 1 ATOM 86 C CD1 . LEU A 1 12 ? 5.214 -0.142 -3.691 1.00 93.34 12 A 1 ATOM 87 C CD2 . LEU A 1 12 ? 3.608 -1.581 -2.457 1.00 92.37 12 A 1 ATOM 88 N N . THR A 1 13 ? 4.749 2.893 -2.797 1.00 97.80 13 A 1 ATOM 89 C CA . THR A 1 13 ? 5.179 3.703 -3.934 1.00 97.76 13 A 1 ATOM 90 C C . THR A 1 13 ? 5.725 5.045 -3.464 1.00 97.92 13 A 1 ATOM 91 O O . THR A 1 13 ? 6.662 5.584 -4.051 1.00 96.98 13 A 1 ATOM 92 C CB . THR A 1 13 ? 4.027 3.920 -4.933 1.00 97.03 13 A 1 ATOM 93 O OG1 . THR A 1 13 ? 4.556 4.494 -6.130 1.00 93.71 13 A 1 ATOM 94 C CG2 . THR A 1 13 ? 2.967 4.842 -4.383 1.00 93.19 13 A 1 ATOM 95 N N . VAL A 1 14 ? 5.155 5.573 -2.385 1.00 97.80 14 A 1 ATOM 96 C CA . VAL A 1 14 ? 5.604 6.840 -1.814 1.00 97.78 14 A 1 ATOM 97 C C . VAL A 1 14 ? 6.987 6.681 -1.196 1.00 97.92 14 A 1 ATOM 98 O O . VAL A 1 14 ? 7.835 7.569 -1.305 1.00 97.10 14 A 1 ATOM 99 C CB . VAL A 1 14 ? 4.619 7.347 -0.753 1.00 96.94 14 A 1 ATOM 100 C CG1 . VAL A 1 14 ? 5.154 8.606 -0.084 1.00 93.59 14 A 1 ATOM 101 C CG2 . VAL A 1 14 ? 3.263 7.619 -1.377 1.00 93.79 14 A 1 ATOM 102 N N . VAL A 1 15 ? 7.213 5.559 -0.535 1.00 97.64 15 A 1 ATOM 103 C CA . VAL A 1 15 ? 8.506 5.276 0.089 1.00 97.45 15 A 1 ATOM 104 C C . VAL A 1 15 ? 9.588 5.107 -0.971 1.00 97.48 15 A 1 ATOM 105 O O . VAL A 1 15 ? 10.730 5.535 -0.780 1.00 96.26 15 A 1 ATOM 106 C CB . VAL A 1 15 ? 8.427 4.010 0.956 1.00 96.33 15 A 1 ATOM 107 C CG1 . VAL A 1 15 ? 9.792 3.685 1.547 1.00 92.05 15 A 1 ATOM 108 C CG2 . VAL A 1 15 ? 7.401 4.183 2.061 1.00 92.82 15 A 1 ATOM 109 N N . SER A 1 16 ? 9.225 4.493 -2.080 1.00 96.49 16 A 1 ATOM 110 C CA . SER A 1 16 ? 10.161 4.264 -3.182 1.00 95.92 16 A 1 ATOM 111 C C . SER A 1 16 ? 10.575 5.581 -3.834 1.00 95.67 16 A 1 ATOM 112 O O . SER A 1 16 ? 11.702 5.719 -4.311 1.00 91.86 16 A 1 ATOM 113 C CB . SER A 1 16 ? 9.538 3.343 -4.230 1.00 93.71 16 A 1 ATOM 114 O OG . SER A 1 16 ? 10.515 2.943 -5.165 1.00 84.99 16 A 1 ATOM 115 N N . GLY A 1 17 ? 9.659 6.541 -3.829 1.00 92.61 17 A 1 ATOM 116 C CA . GLY A 1 17 ? 9.915 7.863 -4.423 1.00 88.74 17 A 1 ATOM 117 C C . GLY A 1 17 ? 8.716 8.345 -5.192 1.00 85.73 17 A 1 ATOM 118 O O . GLY A 1 17 ? 8.014 9.239 -4.692 1.00 79.12 17 A 1 ATOM 119 O OXT . GLY A 1 17 ? 8.480 7.825 -6.275 1.00 83.29 17 A 1 #