# 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_spkb16652 # _entry.id spkb16652 # 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 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" "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 ALA 2 1 n VAL 3 1 n ALA 4 1 n ALA 5 1 n LEU 6 1 n ALA 7 1 n LEU 8 1 n LEU 9 1 n ALA 10 1 n LEU 11 1 n LEU 12 1 n PRO 13 1 n GLN 14 1 n ALA 15 1 n LEU 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 @ 2025-07-02 12:42:24)" _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 95.51 _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 86.48 1 1 A ALA 2 2 95.84 1 2 A VAL 3 2 97.14 1 3 A ALA 4 2 97.86 1 4 A ALA 5 2 98.14 1 5 A LEU 6 2 96.20 1 6 A ALA 7 2 97.99 1 7 A LEU 8 2 96.55 1 8 A LEU 9 2 96.19 1 9 A ALA 10 2 98.16 1 10 A LEU 11 2 97.51 1 11 A LEU 12 2 96.13 1 12 A PRO 13 2 97.46 1 13 A GLN 14 2 94.78 1 14 A ALA 15 2 96.68 1 15 A LEU 16 2 94.13 1 16 A GLY 17 2 88.86 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 ALA . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n PRO . 13 A 13 A 14 1 n GLN . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n LEU . 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 ? -3.487 1.107 14.022 1.00 92.84 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.156 1.419 13.463 1.00 92.00 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.801 0.445 12.342 1.00 92.65 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.188 0.826 11.350 1.00 90.80 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.098 1.353 14.564 1.00 88.28 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.321 2.454 15.600 1.00 82.86 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.121 2.392 16.933 1.00 81.54 1 A 1 ATOM 8 C CE . MET A 1 1 ? -0.748 3.722 17.957 1.00 70.84 1 A 1 ATOM 9 N N . ALA A 1 2 ? -2.210 -0.799 12.510 1.00 93.36 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -1.959 -1.803 11.476 1.00 96.28 2 A 1 ATOM 11 C C . ALA A 1 2 ? -2.761 -1.496 10.215 1.00 97.51 2 A 1 ATOM 12 O O . ALA A 1 2 ? -2.348 -1.820 9.102 1.00 96.82 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -2.306 -3.187 12.009 1.00 95.21 2 A 1 ATOM 14 N N . VAL A 1 3 ? -3.898 -0.855 10.390 1.00 97.99 3 A 1 ATOM 15 C CA . VAL A 1 3 ? -4.756 -0.470 9.265 1.00 98.18 3 A 1 ATOM 16 C C . VAL A 1 3 ? -4.038 0.522 8.359 1.00 98.40 3 A 1 ATOM 17 O O . VAL A 1 3 ? -4.182 0.482 7.133 1.00 98.07 3 A 1 ATOM 18 C CB . VAL A 1 3 ? -6.071 0.138 9.782 1.00 97.61 3 A 1 ATOM 19 C CG1 . VAL A 1 3 ? -6.971 0.537 8.622 1.00 94.69 3 A 1 ATOM 20 C CG2 . VAL A 1 3 ? -6.794 -0.854 10.683 1.00 95.04 3 A 1 ATOM 21 N N . ALA A 1 4 ? -3.254 1.401 8.965 1.00 97.50 4 A 1 ATOM 22 C CA . ALA A 1 4 ? -2.495 2.396 8.207 1.00 97.93 4 A 1 ATOM 23 C C . ALA A 1 4 ? -1.460 1.711 7.320 1.00 98.32 4 A 1 ATOM 24 O O . ALA A 1 4 ? -1.214 2.143 6.193 1.00 98.04 4 A 1 ATOM 25 C CB . ALA A 1 4 ? -1.814 3.365 9.166 1.00 97.52 4 A 1 ATOM 26 N N . ALA A 1 5 ? -0.862 0.641 7.832 1.00 98.16 5 A 1 ATOM 27 C CA . ALA A 1 5 ? 0.134 -0.113 7.076 1.00 98.20 5 A 1 ATOM 28 C C . ALA A 1 5 ? -0.514 -0.792 5.872 1.00 98.38 5 A 1 ATOM 29 O O . ALA A 1 5 ? 0.059 -0.819 4.783 1.00 97.99 5 A 1 ATOM 30 C CB . ALA A 1 5 ? 0.799 -1.143 7.981 1.00 97.96 5 A 1 ATOM 31 N N . LEU A 1 6 ? -1.717 -1.317 6.067 1.00 98.11 6 A 1 ATOM 32 C CA . LEU A 1 6 ? -2.448 -1.978 4.990 1.00 97.86 6 A 1 ATOM 33 C C . LEU A 1 6 ? -2.889 -0.963 3.941 1.00 98.09 6 A 1 ATOM 34 O O . LEU A 1 6 ? -2.875 -1.252 2.746 1.00 97.72 6 A 1 ATOM 35 C CB . LEU A 1 6 ? -3.661 -2.702 5.570 1.00 97.41 6 A 1 ATOM 36 C CG . LEU A 1 6 ? -3.299 -3.999 6.281 1.00 94.27 6 A 1 ATOM 37 C CD1 . LEU A 1 6 ? -4.462 -4.470 7.138 1.00 93.17 6 A 1 ATOM 38 C CD2 . LEU A 1 6 ? -2.938 -5.073 5.259 1.00 93.01 6 A 1 ATOM 39 N N . ALA A 1 7 ? -3.260 0.211 4.392 1.00 97.97 7 A 1 ATOM 40 C CA . ALA A 1 7 ? -3.685 1.281 3.492 1.00 98.01 7 A 1 ATOM 41 C C . ALA A 1 7 ? -2.528 1.722 2.600 1.00 98.24 7 A 1 ATOM 42 O O . ALA A 1 7 ? -2.710 1.964 1.406 1.00 97.89 7 A 1 ATOM 43 C CB . ALA A 1 7 ? -4.202 2.462 4.303 1.00 97.85 7 A 1 ATOM 44 N N . LEU A 1 8 ? -1.350 1.818 3.197 1.00 97.86 8 A 1 ATOM 45 C CA . LEU A 1 8 ? -0.158 2.211 2.454 1.00 97.61 8 A 1 ATOM 46 C C . LEU A 1 8 ? 0.271 1.095 1.510 1.00 97.87 8 A 1 ATOM 47 O O . LEU A 1 8 ? 0.720 1.352 0.393 1.00 97.43 8 A 1 ATOM 48 C CB . LEU A 1 8 ? 0.969 2.535 3.437 1.00 97.32 8 A 1 ATOM 49 C CG . LEU A 1 8 ? 0.796 3.896 4.119 1.00 95.67 8 A 1 ATOM 50 C CD1 . LEU A 1 8 ? 1.678 3.987 5.358 1.00 94.46 8 A 1 ATOM 51 C CD2 . LEU A 1 8 ? 1.157 5.021 3.153 1.00 94.16 8 A 1 ATOM 52 N N . LEU A 1 9 ? 0.123 -0.138 1.959 1.00 97.69 9 A 1 ATOM 53 C CA . LEU A 1 9 ? 0.484 -1.301 1.153 1.00 97.51 9 A 1 ATOM 54 C C . LEU A 1 9 ? -0.425 -1.410 -0.067 1.00 97.96 9 A 1 ATOM 55 O O . LEU A 1 9 ? 0.004 -1.865 -1.126 1.00 97.66 9 A 1 ATOM 56 C CB . LEU A 1 9 ? 0.370 -2.562 2.009 1.00 97.16 9 A 1 ATOM 57 C CG . LEU A 1 9 ? 0.910 -3.814 1.333 1.00 94.91 9 A 1 ATOM 58 C CD1 . LEU A 1 9 ? 2.433 -3.781 1.270 1.00 93.27 9 A 1 ATOM 59 C CD2 . LEU A 1 9 ? 0.445 -5.055 2.076 1.00 93.36 9 A 1 ATOM 60 N N . ALA A 1 10 ? -1.656 -0.989 0.080 1.00 98.21 10 A 1 ATOM 61 C CA . ALA A 1 10 ? -2.636 -1.042 -0.999 1.00 98.22 10 A 1 ATOM 62 C C . ALA A 1 10 ? -2.319 -0.036 -2.103 1.00 98.41 10 A 1 ATOM 63 O O . ALA A 1 10 ? -2.818 -0.161 -3.221 1.00 97.95 10 A 1 ATOM 64 C CB . ALA A 1 10 ? -4.026 -0.780 -0.436 1.00 98.01 10 A 1 ATOM 65 N N . LEU A 1 11 ? -1.492 0.940 -1.793 1.00 98.35 11 A 1 ATOM 66 C CA . LEU A 1 11 ? -1.117 1.961 -2.770 1.00 98.24 11 A 1 ATOM 67 C C . LEU A 1 11 ? -0.181 1.391 -3.826 1.00 98.33 11 A 1 ATOM 68 O O . LEU A 1 11 ? -0.154 1.869 -4.958 1.00 97.85 11 A 1 ATOM 69 C CB . LEU A 1 11 ? -0.440 3.135 -2.058 1.00 98.16 11 A 1 ATOM 70 C CG . LEU A 1 11 ? -1.387 3.933 -1.159 1.00 97.44 11 A 1 ATOM 71 C CD1 . LEU A 1 11 ? -0.601 4.886 -0.276 1.00 95.92 11 A 1 ATOM 72 C CD2 . LEU A 1 11 ? -2.379 4.726 -2.007 1.00 95.80 11 A 1 ATOM 73 N N . LEU A 1 12 ? 0.589 0.372 -3.458 1.00 97.95 12 A 1 ATOM 74 C CA . LEU A 1 12 ? 1.528 -0.261 -4.383 1.00 97.80 12 A 1 ATOM 75 C C . LEU A 1 12 ? 0.796 -0.877 -5.582 1.00 97.98 12 A 1 ATOM 76 O O . LEU A 1 12 ? 1.095 -0.528 -6.726 1.00 97.44 12 A 1 ATOM 77 C CB . LEU A 1 12 ? 2.360 -1.312 -3.642 1.00 97.49 12 A 1 ATOM 78 C CG . LEU A 1 12 ? 3.672 -1.652 -4.339 1.00 95.65 12 A 1 ATOM 79 C CD1 . LEU A 1 12 ? 4.710 -0.567 -4.098 1.00 92.57 12 A 1 ATOM 80 C CD2 . LEU A 1 12 ? 4.187 -2.995 -3.841 1.00 92.19 12 A 1 ATOM 81 N N . PRO A 1 13 ? -0.155 -1.783 -5.356 1.00 98.02 13 A 1 ATOM 82 C CA . PRO A 1 13 ? -0.901 -2.385 -6.465 1.00 97.79 13 A 1 ATOM 83 C C . PRO A 1 13 ? -1.957 -1.449 -7.034 1.00 97.93 13 A 1 ATOM 84 O O . PRO A 1 13 ? -2.389 -1.619 -8.175 1.00 97.15 13 A 1 ATOM 85 C CB . PRO A 1 13 ? -1.556 -3.613 -5.828 1.00 97.08 13 A 1 ATOM 86 C CG . PRO A 1 13 ? -1.694 -3.248 -4.392 1.00 96.69 13 A 1 ATOM 87 C CD . PRO A 1 13 ? -0.511 -2.350 -4.076 1.00 97.55 13 A 1 ATOM 88 N N . GLN A 1 14 ? -2.370 -0.472 -6.274 1.00 97.57 14 A 1 ATOM 89 C CA . GLN A 1 14 ? -3.374 0.494 -6.708 1.00 97.51 14 A 1 ATOM 90 C C . GLN A 1 14 ? -2.872 1.288 -7.907 1.00 97.83 14 A 1 ATOM 91 O O . GLN A 1 14 ? -3.638 1.618 -8.814 1.00 96.77 14 A 1 ATOM 92 C CB . GLN A 1 14 ? -3.705 1.437 -5.557 1.00 96.85 14 A 1 ATOM 93 C CG . GLN A 1 14 ? -4.921 2.280 -5.843 1.00 95.12 14 A 1 ATOM 94 C CD . GLN A 1 14 ? -5.222 3.232 -4.706 1.00 93.31 14 A 1 ATOM 95 O OE1 . GLN A 1 14 ? -5.547 2.823 -3.600 1.00 89.34 14 A 1 ATOM 96 N NE2 . GLN A 1 14 ? -5.103 4.516 -4.956 1.00 88.68 14 A 1 ATOM 97 N N . ALA A 1 15 ? -1.572 1.602 -7.920 1.00 97.21 15 A 1 ATOM 98 C CA . ALA A 1 15 ? -0.967 2.354 -9.016 1.00 96.88 15 A 1 ATOM 99 C C . ALA A 1 15 ? -0.842 1.489 -10.265 1.00 97.23 15 A 1 ATOM 100 O O . ALA A 1 15 ? -0.918 1.994 -11.386 1.00 95.98 15 A 1 ATOM 101 C CB . ALA A 1 15 ? 0.406 2.874 -8.591 1.00 96.12 15 A 1 ATOM 102 N N . LEU A 1 16 ? -0.643 0.186 -10.069 1.00 96.63 16 A 1 ATOM 103 C CA . LEU A 1 16 ? -0.490 -0.757 -11.172 1.00 96.33 16 A 1 ATOM 104 C C . LEU A 1 16 ? -1.832 -1.300 -11.639 1.00 96.47 16 A 1 ATOM 105 O O . LEU A 1 16 ? -1.911 -1.936 -12.690 1.00 94.73 16 A 1 ATOM 106 C CB . LEU A 1 16 ? 0.427 -1.905 -10.736 1.00 95.60 16 A 1 ATOM 107 C CG . LEU A 1 16 ? 1.873 -1.477 -10.493 1.00 94.17 16 A 1 ATOM 108 C CD1 . LEU A 1 16 ? 2.636 -2.562 -9.752 1.00 90.69 16 A 1 ATOM 109 C CD2 . LEU A 1 16 ? 2.561 -1.174 -11.821 1.00 88.46 16 A 1 ATOM 110 N N . GLY A 1 17 ? -2.862 -1.047 -10.878 1.00 94.37 17 A 1 ATOM 111 C CA . GLY A 1 17 ? -4.191 -1.537 -11.213 1.00 91.09 17 A 1 ATOM 112 C C . GLY A 1 17 ? -5.077 -0.473 -11.818 1.00 88.40 17 A 1 ATOM 113 O O . GLY A 1 17 ? -4.624 0.658 -12.031 1.00 83.63 17 A 1 ATOM 114 O OXT . GLY A 1 17 ? -6.276 -0.774 -12.060 1.00 86.82 17 A 1 #