# 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_spkb11247 # _entry.id spkb11247 # 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" "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" "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 TRP 2 1 n GLN 3 1 n LEU 4 1 n LEU 5 1 n PRO 6 1 n PRO 7 1 n ALA 8 1 n ALA 9 1 n LEU 10 1 n LEU 11 1 n LEU 12 1 n LEU 13 1 n VAL 14 1 n SER 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 @ 2025-07-07 18:56:05)" _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 92.39 _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 84.57 1 1 A TRP 2 2 86.15 1 2 A GLN 3 2 88.91 1 3 A LEU 4 2 92.78 1 4 A LEU 5 2 92.88 1 5 A PRO 6 2 95.32 1 6 A PRO 7 2 95.48 1 7 A ALA 8 2 96.72 1 8 A ALA 9 2 96.35 1 9 A LEU 10 2 94.26 1 10 A LEU 11 2 95.56 1 11 A LEU 12 2 95.78 1 12 A LEU 13 2 94.41 1 13 A VAL 14 2 94.97 1 14 A SER 15 2 94.87 1 15 A ALA 16 2 88.14 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 TRP . 2 A 2 A 3 1 n GLN . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n PRO . 6 A 6 A 7 1 n PRO . 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 LEU . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n SER . 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 ? -11.742 -0.583 -0.246 1.00 89.78 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.631 -0.933 0.651 1.00 90.11 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.235 0.283 1.484 1.00 90.76 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.872 1.322 0.947 1.00 90.27 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.424 -1.394 -0.154 1.00 86.57 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.911 -0.314 -1.086 1.00 81.15 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.437 -0.827 -1.958 1.00 78.15 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.285 0.544 -3.101 1.00 69.79 1 A 1 ATOM 9 N N . TRP A 1 2 ? -10.333 0.164 2.791 1.00 90.93 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -10.012 1.281 3.679 1.00 92.03 2 A 1 ATOM 11 C C . TRP A 1 2 ? -9.611 0.749 5.046 1.00 93.16 2 A 1 ATOM 12 O O . TRP A 1 2 ? -10.234 -0.166 5.565 1.00 91.03 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -11.222 2.215 3.800 1.00 90.20 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -12.317 1.861 2.851 1.00 87.04 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -13.348 1.013 3.095 1.00 84.30 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? -12.474 2.324 1.492 1.00 86.34 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? -14.149 0.914 1.972 1.00 83.14 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? -13.629 1.714 0.973 1.00 85.19 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? -11.745 3.189 0.679 1.00 82.47 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? -14.074 1.947 -0.335 1.00 83.37 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? -12.184 3.423 -0.619 1.00 78.38 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? -13.333 2.810 -1.117 1.00 78.46 2 A 1 ATOM 23 N N . GLN A 1 3 ? -8.560 1.338 5.610 1.00 94.49 3 A 1 ATOM 24 C CA . GLN A 1 3 ? -8.094 0.941 6.945 1.00 94.85 3 A 1 ATOM 25 C C . GLN A 1 3 ? -7.698 -0.534 6.980 1.00 95.65 3 A 1 ATOM 26 O O . GLN A 1 3 ? -7.808 -1.187 8.015 1.00 94.20 3 A 1 ATOM 27 C CB . GLN A 1 3 ? -9.195 1.205 7.974 1.00 93.72 3 A 1 ATOM 28 C CG . GLN A 1 3 ? -9.633 2.662 7.966 1.00 88.46 3 A 1 ATOM 29 C CD . GLN A 1 3 ? -10.813 2.886 8.887 1.00 84.04 3 A 1 ATOM 30 O OE1 . GLN A 1 3 ? -11.216 1.996 9.626 1.00 78.15 3 A 1 ATOM 31 N NE2 . GLN A 1 3 ? -11.388 4.070 8.859 1.00 76.60 3 A 1 ATOM 32 N N . LEU A 1 4 ? -7.238 -1.055 5.845 1.00 94.69 4 A 1 ATOM 33 C CA . LEU A 1 4 ? -6.833 -2.460 5.769 1.00 94.88 4 A 1 ATOM 34 C C . LEU A 1 4 ? -5.350 -2.601 5.448 1.00 95.56 4 A 1 ATOM 35 O O . LEU A 1 4 ? -4.811 -3.705 5.466 1.00 94.43 4 A 1 ATOM 36 C CB . LEU A 1 4 ? -7.666 -3.168 4.697 1.00 94.45 4 A 1 ATOM 37 C CG . LEU A 1 4 ? -9.140 -3.278 5.065 1.00 92.04 4 A 1 ATOM 38 C CD1 . LEU A 1 4 ? -9.913 -3.882 3.894 1.00 88.54 4 A 1 ATOM 39 C CD2 . LEU A 1 4 ? -9.321 -4.155 6.297 1.00 87.65 4 A 1 ATOM 40 N N . LEU A 1 5 ? -4.666 -1.513 5.141 1.00 95.14 5 A 1 ATOM 41 C CA . LEU A 1 5 ? -3.240 -1.541 4.830 1.00 95.00 5 A 1 ATOM 42 C C . LEU A 1 5 ? -2.498 -0.424 5.554 1.00 95.53 5 A 1 ATOM 43 O O . LEU A 1 5 ? -2.816 0.746 5.380 1.00 95.22 5 A 1 ATOM 44 C CB . LEU A 1 5 ? -3.027 -1.410 3.319 1.00 94.39 5 A 1 ATOM 45 C CG . LEU A 1 5 ? -3.587 -0.117 2.727 1.00 91.91 5 A 1 ATOM 46 C CD1 . LEU A 1 5 ? -2.690 0.351 1.585 1.00 88.61 5 A 1 ATOM 47 C CD2 . LEU A 1 5 ? -4.997 -0.342 2.207 1.00 87.21 5 A 1 ATOM 48 N N . PRO A 1 6 ? -1.496 -0.760 6.357 1.00 96.02 6 A 1 ATOM 49 C CA . PRO A 1 6 ? -0.713 0.223 7.107 1.00 95.93 6 A 1 ATOM 50 C C . PRO A 1 6 ? 0.219 1.016 6.190 1.00 96.64 6 A 1 ATOM 51 O O . PRO A 1 6 ? 0.512 0.592 5.069 1.00 96.55 6 A 1 ATOM 52 C CB . PRO A 1 6 ? 0.077 -0.639 8.098 1.00 94.26 6 A 1 ATOM 53 C CG . PRO A 1 6 ? 0.200 -1.960 7.417 1.00 92.82 6 A 1 ATOM 54 C CD . PRO A 1 6 ? -1.087 -2.128 6.639 1.00 95.02 6 A 1 ATOM 55 N N . PRO A 1 7 ? 0.705 2.169 6.640 1.00 95.89 7 A 1 ATOM 56 C CA . PRO A 1 7 ? 1.605 3.012 5.838 1.00 96.09 7 A 1 ATOM 57 C C . PRO A 1 7 ? 2.916 2.308 5.504 1.00 96.74 7 A 1 ATOM 58 O O . PRO A 1 7 ? 3.474 2.500 4.422 1.00 96.28 7 A 1 ATOM 59 C CB . PRO A 1 7 ? 1.836 4.234 6.733 1.00 94.70 7 A 1 ATOM 60 C CG . PRO A 1 7 ? 1.543 3.749 8.115 1.00 93.39 7 A 1 ATOM 61 C CD . PRO A 1 7 ? 0.453 2.720 7.961 1.00 95.28 7 A 1 ATOM 62 N N . ALA A 1 8 ? 3.416 1.494 6.425 1.00 96.61 8 A 1 ATOM 63 C CA . ALA A 1 8 ? 4.671 0.771 6.208 1.00 96.83 8 A 1 ATOM 64 C C . ALA A 1 8 ? 4.539 -0.207 5.043 1.00 97.38 8 A 1 ATOM 65 O O . ALA A 1 8 ? 5.434 -0.321 4.206 1.00 96.75 8 A 1 ATOM 66 C CB . ALA A 1 8 ? 5.050 0.026 7.481 1.00 96.04 8 A 1 ATOM 67 N N . ALA A 1 9 ? 3.431 -0.909 4.980 1.00 96.31 9 A 1 ATOM 68 C CA . ALA A 1 9 ? 3.200 -1.879 3.909 1.00 96.31 9 A 1 ATOM 69 C C . ALA A 1 9 ? 3.104 -1.171 2.559 1.00 97.04 9 A 1 ATOM 70 O O . ALA A 1 9 ? 3.613 -1.658 1.553 1.00 96.51 9 A 1 ATOM 71 C CB . ALA A 1 9 ? 1.920 -2.654 4.195 1.00 95.57 9 A 1 ATOM 72 N N . LEU A 1 10 ? 2.464 -0.024 2.531 1.00 96.37 10 A 1 ATOM 73 C CA . LEU A 1 10 ? 2.317 0.748 1.298 1.00 96.45 10 A 1 ATOM 74 C C . LEU A 1 10 ? 3.682 1.173 0.763 1.00 97.28 10 A 1 ATOM 75 O O . LEU A 1 10 ? 3.933 1.115 -0.440 1.00 97.15 10 A 1 ATOM 76 C CB . LEU A 1 10 ? 1.454 1.978 1.571 1.00 95.98 10 A 1 ATOM 77 C CG . LEU A 1 10 ? 1.157 2.780 0.314 1.00 91.89 10 A 1 ATOM 78 C CD1 . LEU A 1 10 ? 0.271 1.980 -0.629 1.00 89.46 10 A 1 ATOM 79 C CD2 . LEU A 1 10 ? 0.474 4.087 0.684 1.00 89.52 10 A 1 ATOM 80 N N . LEU A 1 11 ? 4.564 1.594 1.644 1.00 96.82 11 A 1 ATOM 81 C CA . LEU A 1 11 ? 5.910 2.022 1.255 1.00 97.09 11 A 1 ATOM 82 C C . LEU A 1 11 ? 6.679 0.865 0.616 1.00 97.63 11 A 1 ATOM 83 O O . LEU A 1 11 ? 7.368 1.042 -0.388 1.00 97.51 11 A 1 ATOM 84 C CB . LEU A 1 11 ? 6.659 2.528 2.489 1.00 96.97 11 A 1 ATOM 85 C CG . LEU A 1 11 ? 8.017 3.130 2.151 1.00 93.89 11 A 1 ATOM 86 C CD1 . LEU A 1 11 ? 7.853 4.420 1.359 1.00 92.13 11 A 1 ATOM 87 C CD2 . LEU A 1 11 ? 8.795 3.414 3.430 1.00 92.41 11 A 1 ATOM 88 N N . LEU A 1 12 ? 6.572 -0.320 1.192 1.00 96.82 12 A 1 ATOM 89 C CA . LEU A 1 12 ? 7.270 -1.501 0.678 1.00 97.07 12 A 1 ATOM 90 C C . LEU A 1 12 ? 6.758 -1.870 -0.714 1.00 97.55 12 A 1 ATOM 91 O O . LEU A 1 12 ? 7.535 -2.228 -1.595 1.00 97.12 12 A 1 ATOM 92 C CB . LEU A 1 12 ? 7.062 -2.668 1.647 1.00 97.04 12 A 1 ATOM 93 C CG . LEU A 1 12 ? 7.813 -2.489 2.972 1.00 94.79 12 A 1 ATOM 94 C CD1 . LEU A 1 12 ? 7.367 -3.554 3.966 1.00 92.77 12 A 1 ATOM 95 C CD2 . LEU A 1 12 ? 9.315 -2.589 2.749 1.00 93.12 12 A 1 ATOM 96 N N . LEU A 1 13 ? 5.463 -1.777 -0.920 1.00 96.87 13 A 1 ATOM 97 C CA . LEU A 1 13 ? 4.856 -2.115 -2.208 1.00 96.65 13 A 1 ATOM 98 C C . LEU A 1 13 ? 5.364 -1.186 -3.306 1.00 96.97 13 A 1 ATOM 99 O O . LEU A 1 13 ? 5.663 -1.632 -4.413 1.00 96.31 13 A 1 ATOM 100 C CB . LEU A 1 13 ? 3.332 -2.004 -2.086 1.00 96.28 13 A 1 ATOM 101 C CG . LEU A 1 13 ? 2.715 -3.124 -1.248 1.00 92.25 13 A 1 ATOM 102 C CD1 . LEU A 1 13 ? 1.254 -2.804 -0.953 1.00 90.03 13 A 1 ATOM 103 C CD2 . LEU A 1 13 ? 2.809 -4.453 -1.989 1.00 89.92 13 A 1 ATOM 104 N N . VAL A 1 14 ? 5.467 0.093 -3.014 1.00 97.03 14 A 1 ATOM 105 C CA . VAL A 1 14 ? 5.944 1.075 -3.992 1.00 96.66 14 A 1 ATOM 106 C C . VAL A 1 14 ? 7.435 0.885 -4.267 1.00 97.04 14 A 1 ATOM 107 O O . VAL A 1 14 ? 7.904 1.132 -5.382 1.00 96.04 14 A 1 ATOM 108 C CB . VAL A 1 14 ? 5.678 2.498 -3.479 1.00 95.48 14 A 1 ATOM 109 C CG1 . VAL A 1 14 ? 6.236 3.531 -4.443 1.00 91.08 14 A 1 ATOM 110 C CG2 . VAL A 1 14 ? 4.182 2.710 -3.305 1.00 91.48 14 A 1 ATOM 111 N N . SER A 1 15 ? 8.191 0.456 -3.275 1.00 96.68 15 A 1 ATOM 112 C CA . SER A 1 15 ? 9.637 0.255 -3.404 1.00 96.49 15 A 1 ATOM 113 C C . SER A 1 15 ? 9.974 -1.038 -4.144 1.00 96.50 15 A 1 ATOM 114 O O . SER A 1 15 ? 11.142 -1.312 -4.408 1.00 94.97 15 A 1 ATOM 115 C CB . SER A 1 15 ? 10.278 0.226 -2.013 1.00 95.33 15 A 1 ATOM 116 O OG . SER A 1 15 ? 10.071 1.459 -1.351 1.00 89.23 15 A 1 ATOM 117 N N . ALA A 1 16 ? 8.982 -1.844 -4.498 1.00 94.03 16 A 1 ATOM 118 C CA . ALA A 1 16 ? 9.191 -3.116 -5.188 1.00 91.31 16 A 1 ATOM 119 C C . ALA A 1 16 ? 9.926 -2.907 -6.514 1.00 89.10 16 A 1 ATOM 120 O O . ALA A 1 16 ? 9.726 -1.871 -7.168 1.00 86.88 16 A 1 ATOM 121 C CB . ALA A 1 16 ? 7.851 -3.803 -5.424 1.00 87.84 16 A 1 ATOM 122 O OXT . ALA A 1 16 ? 10.696 -3.800 -6.910 1.00 79.66 16 A 1 #